Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 8 of 33
Found at i:1002722 original size:2 final size:2
Alignment explanation
Indices: 1002715--1002741 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1002705 AACATCCATT
1002715 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
1002742 GTAGATCATT
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:1005859 original size:22 final size:23
Alignment explanation
Indices: 1005808--1005866 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
1005798 AGCACCCTTC
*
1005808 AAAATTTTATA-T-ATGAAATTT
1 AAAATTTTAAATTCATGAAATTT
*
1005829 ATAATTTTTAAATTCATG-AATTT
1 A-AAATTTTAAATTCATGAAATTT
*
1005852 AAAATTTTTAATTCA
1 AAAATTTTAAATTCA
1005867 GATAATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 20 0.65
23 7 0.23
24 3 0.10
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
AAAATTTTAAATTCATGAAATTT
Found at i:1005873 original size:23 final size:23
Alignment explanation
Indices: 1005824--1005866 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1005814 TTATATATGA
*
1005824 AATTTATAATTTTTAAATTCATG
1 AATTTAAAATTTTTAAATTCATG
1005847 AATTTAAAATTTTT-AATTCA
1 AATTTAAAATTTTTAAATTCA
1005867 GATAATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTTAAAATTTTTAAATTCATG
Found at i:1005875 original size:22 final size:23
Alignment explanation
Indices: 1005820--1005880 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
1005810 AATTTTATAT
*
1005820 ATGAAATTTATAATTTTTAAATTC
1 ATGAAA-TTAAAATTTTTAAATTC
*
1005844 ATGAATTTAAAATTTTT-AATTC
1 ATGAAATTAAAATTTTTAAATTC
*
1005866 A-GATAATTAAGATTT
1 ATGA-AATTAAAATTT
1005881 GGATTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 15 0.47
23 10 0.31
24 5 0.16
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (23 bp):
ATGAAATTAAAATTTTTAAATTC
Found at i:1007081 original size:39 final size:39
Alignment explanation
Indices: 1006973--1007084 Score: 100
Period size: 39 Copynumber: 2.8 Consensus size: 39
1006963 CAATGCATTT
* * * * *
1006973 TATTAGTGCAAATGCTATATATACGAGTAACTACCTACCTTA
1 TATTATTGCAAATGCTATATTTACAAGTAA--A-TTACCCTA
* * * * *
1007015 TATT-TTGTAAATGCAACAGTTATAAGTAAATTACCCTA
1 TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
1007053 TATTATTGCAAATGCTATATTTACAAGTAAAT
1 TATTATTGCAAATGCTATATTTACAAGTAAAT
1007085 AAATATATAA
Statistics
Matches: 54, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
38 10 0.19
39 23 0.43
41 17 0.31
42 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (39 bp):
TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
Found at i:1007609 original size:22 final size:23
Alignment explanation
Indices: 1007571--1007615 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1007561 ATAATATAAA
1007571 AAATAAATAATTATTTTA-AATT
1 AAATAAATAATTATTTTATAATT
*
1007593 AAATAAAATGATT-TTTTATAATT
1 AAAT-AAATAATTATTTTATAATT
1007616 TTATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAATAAATAATTATTTTATAATT
Found at i:1012040 original size:16 final size:17
Alignment explanation
Indices: 1012019--1012051 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1012009 TTGATAGATA
1012019 TTAAAAAATTA-ATTTT
1 TTAAAAAATTATATTTT
1012035 TTAAAAAATTATATTTT
1 TTAAAAAATTATATTTT
1012052 AAATTTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAAAAATTATATTTT
Found at i:1012080 original size:53 final size:53
Alignment explanation
Indices: 1012023--1012126 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 53
1012013 TAGATATTAA
1012023 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
1 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
* *
1012076 AAAATTAATTTTTTTAAAAATTATGTTTTAAATTTTACCACGAAATCACTT
1 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTT
1012127 TTAACCATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (53 bp):
AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
Found at i:1012312 original size:52 final size:52
Alignment explanation
Indices: 1012234--1012338 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
1012224 TTTATTGGTG
*
1012234 GGATTTGACAAGACCATGCTTTGGTGTAACACCTCAAGAACCCCAATAGCAA
1 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
*
1012286 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACTCCAATAGCAA
1 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
1012338 G
1 G
1012339 CTACTATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (52 bp):
GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
Found at i:1013379 original size:14 final size:14
Alignment explanation
Indices: 1013360--1013387 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1013350 TATATTAGTA
1013360 TTTTCTATTCTATT
1 TTTTCTATTCTATT
1013374 TTTTCTATTCTATT
1 TTTTCTATTCTATT
1013388 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:1013395 original size:6 final size:6
Alignment explanation
Indices: 1013384--1013434 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
1013374 TTTTCTATTC
* *
1013384 TATTAG TATTAG -ATTAG TATTA- TATT-C TATTGG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1013428 TATTAG T
1 TATTAG T
1013435 TAATAATCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 18 0.46
6 21 0.54
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:1013409 original size:27 final size:27
Alignment explanation
Indices: 1013379--1013432 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1013369 CTATTTTTTC
1013379 TATTCTATTAGTATTAGATTAGTATTA
1 TATTCTATTAGTATTAGATTAGTATTA
*
1013406 TATTCTATTGGTATTAGATTAGTATTA
1 TATTCTATTAGTATTAGATTAGTATTA
1013433 GTTAATAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (27 bp):
TATTCTATTAGTATTAGATTAGTATTA
Found at i:1015729 original size:51 final size:51
Alignment explanation
Indices: 1015653--1015755 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
1015643 GACATAAAAG
*
1015653 GACCACATAAAACTATTTTAAATTTACAACGAATCAGGCTTTTATTGGTGA
1 GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
* *
1015704 GACCACATAAAACTATTTTAAATTTATAACAAATTAGGCTTTTATTGGTGA
1 GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
1015755 G
1 G
1015756 GTGTGCCAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (51 bp):
GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
Found at i:1017152 original size:77 final size:77
Alignment explanation
Indices: 1017023--1017177 Score: 283
Period size: 77 Copynumber: 2.0 Consensus size: 77
1017013 CATGTTGAAA
*
1017023 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCTAATTACATTAC
1 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
1017088 CCCAAGCTTTAC
66 CCCAAGCTTTAC
* *
1017100 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCTATTTCTTTTTTTCCAATTACATTAC
1 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
1017165 CCCAAGCTTTAC
66 CCCAAGCTTTAC
1017177 T
1 T
1017178 TCGCTATTTC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.22, C:0.25, G:0.07, T:0.46
Consensus pattern (77 bp):
TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
CCCAAGCTTTAC
Found at i:1017436 original size:77 final size:77
Alignment explanation
Indices: 1017347--1017503 Score: 271
Period size: 77 Copynumber: 2.0 Consensus size: 77
1017337 TCTACATATT
*
1017347 ATGGGATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATT-GATGAG
1 ATGGGACGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGA-GAG
1017411 GTGCACCAAATCC
65 GTGCACCAAATCC
*
1017424 ATGGGACGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGGGG
1 ATGGGACGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGG
*
1017489 TGCGCCAAATCC
66 TGCACCAAATCC
1017501 ATG
1 ATG
1017504 CAGTAGTGCA
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
77 74 0.97
78 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (77 bp):
ATGGGACGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGG
TGCACCAAATCC
Found at i:1019964 original size:13 final size:13
Alignment explanation
Indices: 1019946--1019980 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1019936 AAGAAATCAA
*
1019946 AAAAATCAAAAAG
1 AAAAATAAAAAAG
*
1019959 AAAAATAAAAAAT
1 AAAAATAAAAAAG
1019972 AAAAATAAA
1 AAAAATAAA
1019981 TAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAATAAAAAAG
Found at i:1019970 original size:8 final size:8
Alignment explanation
Indices: 1019910--1019995 Score: 50
Period size: 8 Copynumber: 10.1 Consensus size: 8
1019900 AAGACATTTT
1019910 AAAAAATA
1 AAAAAATA
*
1019918 AAAATTATTA
1 AAAA--AATA
*
1019928 AAAAAATC
1 AAAAAATA
*
1019936 AAGAAATCA
1 AAAAAAT-A
1019945 AAAAAATCA
1 AAAAAAT-A
1019954 AAAAGAA-A
1 AAAA-AATA
1019962 AATAAAA-A
1 AA-AAAATA
1019970 ATAAAAATA
1 A-AAAAATA
*
1019979 AATAAATA
1 AAAAAATA
*
1019987 AATAAATA
1 AAAAAATA
1019995 A
1 A
1019996 TACAAATAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
8 38 0.59
9 17 0.27
10 9 0.14
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAAATA
Found at i:1019983 original size:17 final size:17
Alignment explanation
Indices: 1019909--1019997 Score: 58
Period size: 18 Copynumber: 4.9 Consensus size: 17
1019899 CAAGACATTT
* *
1019909 TAAAAAATAAAAATTAT
1 TAAAAAATAAAAATAAA
1019926 TAAAAAAATCAAGAAATCAAA
1 T-AAAAAAT-AA-AAAT-AAA
1019947 -AAAATCAA-AAAGAA-AAA
1 TAAAA--AATAAA-AATAAA
1019964 TAAAAAATAAAAATAAA
1 TAAAAAATAAAAATAAA
1019981 TAAATAAATAAATAATA
1 TAAA-AAATAAA-AATA
1019998 CAAATAATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
16 4 0.07
17 14 0.24
18 19 0.33
19 14 0.24
20 4 0.07
21 3 0.05
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.19
Consensus pattern (17 bp):
TAAAAAATAAAAATAAA
Found at i:1022115 original size:19 final size:20
Alignment explanation
Indices: 1022093--1022135 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1022083 AGATGACAGA
*
1022093 TATTTTATTCATATAT-TTT
1 TATTTTATTCAAATATATTT
*
1022112 TATTTTTTTCAAATATATTT
1 TATTTTATTCAAATATATTT
1022132 TATT
1 TATT
1022136 GGGCAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTATTCAAATATATTT
Found at i:1026080 original size:2 final size:2
Alignment explanation
Indices: 1026075--1026106 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1026065 TGTGCGTGTG
1026075 TA TA TA TA TA TA TA TA T- TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1026107 GCTTTAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1027967 original size:21 final size:22
Alignment explanation
Indices: 1027924--1027969 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1027914 TGTTCAGACA
* * *
1027924 AGTAGTACTCCACAGCAGGTGG
1 AGTAGTACTCCAAAACAGATGG
1027946 AGTA-TACTCCAAAACAGATGG
1 AGTAGTACTCCAAAACAGATGG
1027967 AGT
1 AGT
1027970 TTTAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGATGG
Found at i:1028883 original size:10 final size:10
Alignment explanation
Indices: 1028868--1028892 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1028858 TTCTCGGTAT
1028868 AGAGATAAAC
1 AGAGATAAAC
1028878 AGAGATAAAC
1 AGAGATAAAC
1028888 AGAGA
1 AGAGA
1028893 GGCAAGCTTT
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:0.60, C:0.08, G:0.24, T:0.08
Consensus pattern (10 bp):
AGAGATAAAC
Found at i:1029891 original size:28 final size:27
Alignment explanation
Indices: 1029825--1029903 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
1029815 CAAAAGCCAC
* *
1029825 CTTTGTGTTTGTCAAAAATGGTGGTTA
1 CTTTGTGTTTGTCAAAAATGATGGATA
* *
1029852 CTTTGTATTTGTCAAAAATGATGGATC
1 CTTTGTGTTTGTCAAAAATGATGGATA
* *
1029879 CTTTTTTGTTTGTCAAAAATTATGG
1 C-TTTGTGTTTGTCAAAAATGATGG
1029904 CTTGTTGTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.25, C:0.09, G:0.20, T:0.46
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGATGGATA
Found at i:1029914 original size:28 final size:28
Alignment explanation
Indices: 1029830--1029920 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 28
1029820 GCCACCTTTG
* * * *
1029830 TGTTTGTCAAAAATGGTGGTTACTT-TG
1 TGTTTGTCAAAAATGATGGATCCTTGTT
* *
1029857 TATTTGTCAAAAATGATGGATCCTTTTT
1 TGTTTGTCAAAAATGATGGATCCTTGTT
*
1029885 TGTTTGTCAAAAATTATGG---CTTG-T
1 TGTTTGTCAAAAATGATGGATCCTTGTT
1029909 TGTTTGTCAAAA
1 TGTTTGTCAAAA
1029921 TTGGTGATTA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
24 13 0.24
25 3 0.05
27 21 0.38
28 18 0.33
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (28 bp):
TGTTTGTCAAAAATGATGGATCCTTGTT
Found at i:1030684 original size:21 final size:21
Alignment explanation
Indices: 1030658--1030700 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1030648 CAGTCTGAGA
1030658 ACCTTCCTCTACTACTTCAGT
1 ACCTTCCTCTACTACTTCAGT
*
1030679 ACCTTCCTCTACTATTTCAGT
1 ACCTTCCTCTACTACTTCAGT
1030700 A
1 A
1030701 GGGGCTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.35, G:0.05, T:0.40
Consensus pattern (21 bp):
ACCTTCCTCTACTACTTCAGT
Found at i:1031350 original size:2 final size:2
Alignment explanation
Indices: 1031343--1031376 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1031333 TGTTATTTTA
1031343 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
1031377 GAAAAGGAGT
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:1033802 original size:32 final size:32
Alignment explanation
Indices: 1033764--1033831 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
1033754 TGATGAATTG
*
1033764 TTGATATTATCCTGATGAATCATATAAACATC
1 TTGATATTATCCTGATAAATCATATAAACATC
* * * *
1033796 TTGATATTATCTTGATAAATTATATAATCATG
1 TTGATATTATCCTGATAAATCATATAAACATC
1033828 TTGA
1 TTGA
1033832 GTCAACTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (32 bp):
TTGATATTATCCTGATAAATCATATAAACATC
Found at i:1033973 original size:20 final size:21
Alignment explanation
Indices: 1033935--1033973 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1033925 GACCTAATTT
1033935 TTATTATTAGATAAAATTTTG
1 TTATTATTAGATAAAATTTTG
1033956 TTATT-TTA-ATACAAATTT
1 TTATTATTAGATA-AAATTT
1033974 AAAAAATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 9 0.53
21 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (21 bp):
TTATTATTAGATAAAATTTTG
Found at i:1034707 original size:15 final size:15
Alignment explanation
Indices: 1034687--1034718 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1034677 GAATTCCTGC
*
1034687 ATTTTGATTAAAATA
1 ATTTTGACTAAAATA
1034702 ATTTTGACTAAAATA
1 ATTTTGACTAAAATA
1034717 AT
1 AT
1034719 AAAAAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTTTGACTAAAATA
Found at i:1035437 original size:2 final size:2
Alignment explanation
Indices: 1035425--1035458 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1035415 CAACATATCA
*
1035425 AT AT A- AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1035459 ATACTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1041235 original size:27 final size:27
Alignment explanation
Indices: 1041203--1041292 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 27
1041193 CACCCATTTG
1041203 TTTGTCAAAAATGAGGGTTATTTTGTA
1 TTTGTCAAAAATGAGGGTTATTTTGTA
1041230 TTTGTCAAAAATG-GTGGTT-TCCTTTGTA
1 TTTGTCAAAAATGAG-GGTTAT--TTTGTA
* *
1041258 TTTGTCAAATATGGAGGCTTA--TT-TA
1 TTTGTCAAAAAT-GAGGGTTATTTTGTA
1041283 TTTGTCAAAA
1 TTTGTCAAAA
1041293 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
25 11 0.20
26 4 0.07
27 17 0.31
28 17 0.31
29 4 0.07
30 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (27 bp):
TTTGTCAAAAATGAGGGTTATTTTGTA
Found at i:1041256 original size:28 final size:26
Alignment explanation
Indices: 1041203--1041292 Score: 89
Period size: 28 Copynumber: 3.4 Consensus size: 26
1041193 CACCCATTTG
1041203 TTTGTCAAAAATGAGGGTTATTTTGTA
1 TTTGTCAAAAATG-GGGTTATTTTGTA
1041230 TTTGTCAAAAATGGTGGTT-TCCTTTGTA
1 TTTGTCAAAAATGG-GGTTAT--TTTGTA
*
1041258 TTTGTCAAATATGGAGGCTTA--TT-TA
1 TTTGTCAAAAATGG-GG-TTATTTTGTA
1041283 TTTGTCAAAA
1 TTTGTCAAAA
1041293 TTTGTGGCTA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
25 11 0.20
26 4 0.07
27 17 0.31
28 21 0.38
29 2 0.04
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (26 bp):
TTTGTCAAAAATGGGGTTATTTTGTA
Found at i:1044464 original size:28 final size:28
Alignment explanation
Indices: 1044405--1044469 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
1044395 CCACCTATTT
1044405 ATTTGTCAAAAATGGTGGTTATTTTGTG
1 ATTTGTCAAAAATGGTGGTTATTTTGTG
1044433 -TTTGTCAAAAATGGTGGTT-TCCTTTG-G
1 ATTTGTCAAAAATGGTGGTTAT--TTTGTG
1044460 ATTTGTCAAA
1 ATTTGTCAAA
1044470 TATAGAGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 1 0.03
27 20 0.59
28 13 0.38
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.45
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGGTTATTTTGTG
Found at i:1046766 original size:39 final size:39
Alignment explanation
Indices: 1046661--1046768 Score: 103
Period size: 39 Copynumber: 2.8 Consensus size: 39
1046651 CAATGCATTT
* * * * *
1046661 TATTAGTGCAAATGCTATATATACGAGT-AACTACCTTA
1 TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
* * * * *
1046699 TATT-TTGTAAATGCAACAGTTATAAGTAAATTACCCTA
1 TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
*
1046737 TATTATTGCAAAGGCTATATTTACAAGTAAAT
1 TATTATTGCAAATGCTATATTTACAAGTAAAT
1046769 AAATGGACAA
Statistics
Matches: 52, Mismatches: 16, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
37 15 0.29
38 16 0.31
39 21 0.40
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (39 bp):
TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
Found at i:1052144 original size:23 final size:23
Alignment explanation
Indices: 1052114--1052162 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1052104 CCTTAAGTCC
*
1052114 ATTTTTAAAGTATAAAAACAAAA
1 ATTTTTAAAGTACAAAAACAAAA
1052137 ATTTTTAAAGTACAAAAACAAAA
1 ATTTTTAAAGTACAAAAACAAAA
1052160 ATT
1 ATT
1052163 ACTAACCGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (23 bp):
ATTTTTAAAGTACAAAAACAAAA
Found at i:1052226 original size:18 final size:17
Alignment explanation
Indices: 1052191--1052223 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1052181 ATGGGTAGCT
1052191 AAAAAGCCATTTTTTTA
1 AAAAAGCCATTTTTTTA
*
1052208 AAAAAGTCATTTTTTT
1 AAAAAGCCATTTTTTT
1052224 TAATTTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
AAAAAGCCATTTTTTTA
Found at i:1053043 original size:55 final size:55
Alignment explanation
Indices: 1052959--1053112 Score: 245
Period size: 55 Copynumber: 2.8 Consensus size: 55
1052949 TCGTTGCCAC
* * * *
1052959 AAATTATTACGTAGGCTCCCCTACGTGAGGAGACCTTGCAACAATACCTCCCCAA
1 AAATTATGACATAGGGTCCCCTACGTGAGGAGACCTTGTAACAATACCTCCCCAA
*
1053014 AAATTATGACATTGGGTCCCCTACGTGAGGAGACCTTGTAACAATACCTCCCCAA
1 AAATTATGACATAGGGTCCCCTACGTGAGGAGACCTTGTAACAATACCTCCCCAA
* *
1053069 AAATTATGACATAGGGTCCCCTACTTGAGCAGACCTTGTAACAA
1 AAATTATGACATAGGGTCCCCTACGTGAGGAGACCTTGTAACAA
1053113 CACCCGAAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (55 bp):
AAATTATGACATAGGGTCCCCTACGTGAGGAGACCTTGTAACAATACCTCCCCAA
Found at i:1053201 original size:81 final size:81
Alignment explanation
Indices: 1053066--1053229 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
1053056 AATACCTCCC
1053066 CAAAAATTATGACATAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAAATGACAAAG
1 CAAAAATTATGACATAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAAATGACAAAG
1053131 GGGTCCCCTACTTGAG
66 GGGTCCCCTACTTGAG
1053147 CAAAAATTATGACATAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAAATGACAAAG
1 CAAAAATTATGACATAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAAATGACAAAG
1053212 GGGTCCCCTACTTGAG
66 GGGTCCCCTACTTGAG
1053228 CA
1 CA
1053230 GACCTTGTAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (81 bp):
CAAAAATTATGACATAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAAATGACAAAG
GGGTCCCCTACTTGAG
Found at i:1053251 original size:130 final size:134
Alignment explanation
Indices: 1053011--1053275 Score: 407
Period size: 130 Copynumber: 2.0 Consensus size: 134
1053001 AATACCTCCC
* * *
1053011 CAAAAATTATGACATTGGGTCCCCTACGTGAGGAGACCTTGTAACAATACCTCCCCAAAAATTAT
1 CAAAAATTATGACATAGGGTCCCCTACGTGAGCAGACCTTGTAACAATACCTACCCAAAAA-TAT
*
1053076 GACATAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAAATGACAAAGGGGTCCCCTA
65 GACAAAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAAATGACAAA-GGGTCCCCTA
1053141 CTTGAG
129 CTTGAG
* *
1053147 CAAAAATTATGACATAGGGTCCCCTACTTGAGCAGACCTTGTAAC-A-A-C-ACCC-GAAA-ATG
1 CAAAAATTATGACATAGGGTCCCCTACGTGAGCAGACCTTGTAACAATACCTACCCAAAAATATG
1053206 ACAAAGGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAAATGACAAAGGGTCCCCTAC
66 ACAAA-GGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAAATGACAAAGGGTCCCCTAC
1053271 TTGAG
130 TTGAG
1053276 GAGACCTTGT
Statistics
Matches: 122, Mismatches: 6, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
129 23 0.19
130 48 0.39
131 3 0.02
132 3 0.02
133 1 0.01
134 1 0.01
135 1 0.01
136 42 0.34
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (134 bp):
CAAAAATTATGACATAGGGTCCCCTACGTGAGCAGACCTTGTAACAATACCTACCCAAAAATATG
ACAAAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAAATGACAAAGGGTCCCCTACT
TGAG
Found at i:1053283 original size:48 final size:48
Alignment explanation
Indices: 1053155--1053301 Score: 258
Period size: 49 Copynumber: 3.0 Consensus size: 48
1053145 AGCAAAAATT
*
1053155 ATGACATAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAA
1 ATGACAAAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAA
1053203 ATGACAAAGGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAA
1 ATGACAAA-GGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAA
* *
1053252 ATGACAAAGGGTCCCCTACTTGAGGAGACCTTGTAACAACACCCAAAA
1 ATGACAAAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAA
1053300 AT
1 AT
1053302 TATAACATAG
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
48 47 0.49
49 48 0.51
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (48 bp):
ATGACAAAGGGTCCCCTACTTGAGCAGACCTTGTAACAACACCCGAAA
Found at i:1053356 original size:12 final size:12
Alignment explanation
Indices: 1053339--1053364 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1053329 ACACCTCTCC
1053339 TAAAAATTGACA
1 TAAAAATTGACA
1053351 TAAAAATTGACA
1 TAAAAATTGACA
1053363 TA
1 TA
1053365 TTATCCCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (12 bp):
TAAAAATTGACA
Found at i:1054823 original size:61 final size:61
Alignment explanation
Indices: 1054730--1054851 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 61
1054720 CAATAAATAT
* *
1054730 ATATATATATATACATTTTAATTGAAAGGAAGCTATTACTTTTTTAATTTTATTTTTTAAA
1 ATATATATATATACATTTTAATTGAAAGGAAGCTATCACTTTTTTAATTTTATTCTTTAAA
* *
1054791 ATATATATATATACATTTTAATTTAATGGAAGCTATCACTTTTTTAATTTTATTCTTTAAA
1 ATATATATATATACATTTTAATTGAAAGGAAGCTATCACTTTTTTAATTTTATTCTTTAAA
1054852 GCTCATAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.51
Consensus pattern (61 bp):
ATATATATATATACATTTTAATTGAAAGGAAGCTATCACTTTTTTAATTTTATTCTTTAAA
Found at i:1060289 original size:28 final size:28
Alignment explanation
Indices: 1060234--1060289 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1060224 GCATCTAAGG
* * ***
1060234 AATTTTAAAAAATAAAAATAATTTAAAA
1 AATTTAAAAAAATAAAAAAAAGGAAAAA
1060262 AATTTAAAAAAATAAAAAAAAGGAAAAA
1 AATTTAAAAAAATAAAAAAAAGGAAAAA
1060290 TTAGGAAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (28 bp):
AATTTAAAAAAATAAAAAAAAGGAAAAA
Found at i:1065750 original size:50 final size:50
Alignment explanation
Indices: 1065682--1065940 Score: 416
Period size: 50 Copynumber: 5.2 Consensus size: 50
1065672 AGTTGTTGTC
*
1065682 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
1065732 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGTCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
*
1065782 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
1065832 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
*
1065882 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1065932 ATTGTTGAC
1 ATTGTTGAC
1065941 TCTAAGTATA
Statistics
Matches: 195, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
49 1 0.01
50 192 0.98
51 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:1065855 original size:100 final size:100
Alignment explanation
Indices: 1065682--1065940 Score: 475
Period size: 100 Copynumber: 2.6 Consensus size: 100
1065672 AGTTGTTGTC
* *
1065682 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTC
*
1065746 TTCACCAACCTTTGACAATAGAAGGAGGTGGTCATA
65 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1065782 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
1065847 TCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
66 TCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1065882 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1065941 TCTAAGTATA
Statistics
Matches: 155, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
100 153 0.99
101 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (100 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
TCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
Found at i:1070402 original size:50 final size:50
Alignment explanation
Indices: 1070334--1070592 Score: 407
Period size: 50 Copynumber: 5.2 Consensus size: 50
1070324 AGTTGTTGTC
*
1070334 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * *
1070384 ATTGTTAACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGTCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
*
1070434 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1070484 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
1070534 ATTGTTGACAATTCTTCACCAACTTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1070584 ATTGTTGAC
1 ATTGTTGAC
1070593 TCTAAGTATA
Statistics
Matches: 194, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
49 1 0.01
50 191 0.98
51 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:1070507 original size:100 final size:100
Alignment explanation
Indices: 1070334--1070592 Score: 448
Period size: 100 Copynumber: 2.6 Consensus size: 100
1070324 AGTTGTTGTC
* * * *
1070334 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTAACGATTC
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACAATTC
*
1070398 TTCACCAACCTTTGACAATAGAAGGAGGTGGTCATA
65 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1070434 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACAATTCT
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACAATTCT
1070499 TCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
66 TCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
*
1070534 ATTGTTGACAATTCTTCACCAACTTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1070593 TCTAAGTATA
Statistics
Matches: 152, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
100 150 0.99
101 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (100 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACAATTCT
TCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
Found at i:1072087 original size:2 final size:2
Alignment explanation
Indices: 1072031--1072068 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1072021 TGTTATTTTA
*
1072031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1072069 TACGAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1072168 original size:33 final size:31
Alignment explanation
Indices: 1072114--1072175 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
1072104 TGAATTCGAG
* * *
1072114 TAAGTTATCATTTTGAGTTTGAGATTTTTTA
1 TAAGTTATCATTTAGAATTTGAAATTTTTTA
1072145 TAAGTTAAGTCATTTAGAATTTGAAATTTTT
1 TAAGTT-A-TCATTTAGAATTTGAAATTTTT
1072176 GGGTTCAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 6 0.23
32 1 0.04
33 19 0.73
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.52
Consensus pattern (31 bp):
TAAGTTATCATTTAGAATTTGAAATTTTTTA
Found at i:1072425 original size:23 final size:25
Alignment explanation
Indices: 1072385--1072430 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1072375 TTAAATAATT
1072385 AATCATAAAAAATATGAT-ATATTA
1 AATCATAAAAAATATGATGATATTA
1072409 AATC-TAATAAAAT-TGATGATAT
1 AATCATAA-AAAATATGATGATAT
1072431 GACAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (25 bp):
AATCATAAAAAATATGATGATATTA
Found at i:1080589 original size:7 final size:7
Alignment explanation
Indices: 1080577--1080601 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1080567 AATGTTAATA
1080577 TAATATT
1 TAATATT
1080584 TAATATT
1 TAATATT
1080591 TAATATT
1 TAATATT
1080598 TAAT
1 TAAT
1080602 GTGATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TAATATT
Found at i:1081216 original size:18 final size:17
Alignment explanation
Indices: 1081195--1081234 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
1081185 TATTCTCTTC
1081195 AAAAATTATCACTTT-TT
1 AAAAATTATCA-TTTATT
1081212 AAAAATTATCATTTCATT
1 AAAAATTATCATTT-ATT
1081230 AAAAA
1 AAAAA
1081235 ACTATTACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.14
17 11 0.52
18 7 0.33
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAAATTATCATTTATT
Found at i:1082669 original size:21 final size:19
Alignment explanation
Indices: 1082637--1082678 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 19
1082627 TAATTTATTT
1082637 AAAATTTGAAATTTAATTAAA
1 AAAATTTGAAA-TT-ATTAAA
1082658 AAAATATT-AAATTATTAAA
1 AAAAT-TTGAAATTATTAAA
1082677 AA
1 AA
1082679 TTAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.40
20 2 0.10
21 8 0.40
22 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATTTGAAATTATTAAA
Found at i:1082712 original size:16 final size:16
Alignment explanation
Indices: 1082656--1082713 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
1082646 AATTTAATTA
*
1082656 AAAAAATATTAAATTATT
1 AAAAAATA-TATATT-TT
* *
1082674 AAAAATTA-ATTTTTT
1 AAAAAATATATATTTT
1082689 AAAAAATATATATTTT
1 AAAAAATATATATTTT
1082705 AAAAAATAT
1 AAAAAATAT
1082714 GAATCAACCT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 9 0.26
16 18 0.53
18 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAAATATATATTTT
Found at i:1087653 original size:76 final size:76
Alignment explanation
Indices: 1087527--1087688 Score: 315
Period size: 76 Copynumber: 2.1 Consensus size: 76
1087517 TACCAAACAA
1087527 TTAGGCTAGGCTATGTGACAAGATCATGCTTTAGTGCAACACATGGATGACACTCAAGACATGGA
1 TTAGGCTAGGCTATGTGACAAGATCATGCTTTAGTGCAACACATGGATGACACTCAAGACATGGA
1087592 TTAGGCTAGGC
66 TTAGGCTAGGC
*
1087603 TTAGGCTAGGCTATGTGACAAGATGATGCTTTAGTGCAACACATGGATGACACTCAAGACATGGA
1 TTAGGCTAGGCTATGTGACAAGATCATGCTTTAGTGCAACACATGGATGACACTCAAGACATGGA
1087668 TTAGGCTAGGC
66 TTAGGCTAGGC
1087679 TTAGGCTAGG
1 TTAGGCTAGG
1087689 TGACAAGATC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 85 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (76 bp):
TTAGGCTAGGCTATGTGACAAGATCATGCTTTAGTGCAACACATGGATGACACTCAAGACATGGA
TTAGGCTAGGC
Found at i:1087724 original size:48 final size:48
Alignment explanation
Indices: 1087653--1087748 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1087643 ACATGGATGA
1087653 CACTCAAGACATGGATTAGGCTAGGCTTAGGCTAGGTGACAAGATCAT
1 CACTCAAGACATGGATTAGGCTAGGCTTAGGCTAGGTGACAAGATCAT
1087701 CACTCAAGACATGGATTAGGCTAGGCTTAGGCTAGGTGACAAGATCAT
1 CACTCAAGACATGGATTAGGCTAGGCTTAGGCTAGGTGACAAGATCAT
1087749 GCTTTAGTGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (48 bp):
CACTCAAGACATGGATTAGGCTAGGCTTAGGCTAGGTGACAAGATCAT
Found at i:1087890 original size:62 final size:62
Alignment explanation
Indices: 1087812--1087998 Score: 163
Period size: 62 Copynumber: 3.0 Consensus size: 62
1087802 AGAACAACAA
1087812 TTAGGATATTATTGGTGGGATGTGATAAGACCATGCTATAGTGTGACACCTCGAGATTAGGC
1 TTAGGATATTATTGGTGGGATGTGATAAGACCATGCTATAGTGTGACACCTCGAGATTAGGC
* ** ** * * * **
1087874 TTAGGCTATTATTGGTGATCATGCTTTTAGTGCAACA--C-AT-G-GATGACA-CTCAAGAACA-
1 TTAGGATATTATTGGTG-GGATG-TGATA-AG-ACCATGCTATAGTG-TGACACCTCGAGATTAG
*
1087932 AC
61 GC
1087934 AATTAGGATATTATTGGTGGGATGTGATAAGACCATGCTATAGTGTGACACCTCGAGATTAGGC
1 --TTAGGATATTATTGGTGGGATGTGATAAGACCATGCTATAGTGTGACACCTCGAGATTAGGC
1087998 T
1 T
1087999 ATTATTGGTG
Statistics
Matches: 89, Mismatches: 22, Indels: 28
0.64 0.16 0.20
Matches are distributed among these distances:
58 3 0.03
59 1 0.01
60 5 0.06
61 13 0.15
62 45 0.51
63 13 0.15
64 5 0.06
65 1 0.01
66 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.30
Consensus pattern (62 bp):
TTAGGATATTATTGGTGGGATGTGATAAGACCATGCTATAGTGTGACACCTCGAGATTAGGC
Found at i:1087986 original size:124 final size:124
Alignment explanation
Indices: 1087766--1087998 Score: 466
Period size: 124 Copynumber: 1.9 Consensus size: 124
1087756 TGCGTTACAA
1087766 GATCATGCTTTTAGTGCAACACATGGATGACACTCAAGAACAACAATTAGGATATTATTGGTGGG
1 GATCATGCTTTTAGTGCAACACATGGATGACACTCAAGAACAACAATTAGGATATTATTGGTGGG
1087831 ATGTGATAAGACCATGCTATAGTGTGACACCTCGAGATTAGGCTTAGGCTATTATTGGT
66 ATGTGATAAGACCATGCTATAGTGTGACACCTCGAGATTAGGCTTAGGCTATTATTGGT
1087890 GATCATGCTTTTAGTGCAACACATGGATGACACTCAAGAACAACAATTAGGATATTATTGGTGGG
1 GATCATGCTTTTAGTGCAACACATGGATGACACTCAAGAACAACAATTAGGATATTATTGGTGGG
1087955 ATGTGATAAGACCATGCTATAGTGTGACACCTCGAGATTAGGCT
66 ATGTGATAAGACCATGCTATAGTGTGACACCTCGAGATTAGGCT
1087999 ATTATTGGTG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 109 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (124 bp):
GATCATGCTTTTAGTGCAACACATGGATGACACTCAAGAACAACAATTAGGATATTATTGGTGGG
ATGTGATAAGACCATGCTATAGTGTGACACCTCGAGATTAGGCTTAGGCTATTATTGGT
Found at i:1089125 original size:27 final size:27
Alignment explanation
Indices: 1089095--1089148 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1089085 CTATTTTTTC
*
1089095 TATTCTATTAGTATTAGATTAGTATTA
1 TATTCTATTAGTATTAGATTAATATTA
*
1089122 TATTCTATTGGTATTAGATTAATATTA
1 TATTCTATTAGTATTAGATTAATATTA
1089149 ATTAGTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (27 bp):
TATTCTATTAGTATTAGATTAATATTA
Found at i:1092502 original size:51 final size:51
Alignment explanation
Indices: 1092426--1092528 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
1092416 AATAGGAAAG
* * *
1092426 GATCACATAGAACTATTTCAAATTTACAACGAATCAGGTTTTTATTGGTGA
1 GATCACATAGAACTATTTCAAATTTACAACAAATCAAGCTTTTATTGGTGA
* *
1092477 GATCACATAGAACTATTTTAAATTTACAACAAATTAAGCTTTTATTGGTGA
1 GATCACATAGAACTATTTCAAATTTACAACAAATCAAGCTTTTATTGGTGA
1092528 G
1 G
1092529 GTGTGCCAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (51 bp):
GATCACATAGAACTATTTCAAATTTACAACAAATCAAGCTTTTATTGGTGA
Found at i:1093891 original size:77 final size:77
Alignment explanation
Indices: 1093762--1093916 Score: 283
Period size: 77 Copynumber: 2.0 Consensus size: 77
1093752 CATTAGCCAT
1093762 TATCTGTTTCTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCTAATTACAATAC
1 TATCTGTTTCTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCTAATTACAATAC
1093827 CCCAAGCTTTAC
66 CCCAAGCTTTAC
* * *
1093839 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTTTTTTCTAATTACATTAC
1 TATCTGTTTCTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCTAATTACAATAC
1093904 CCCAAGCTTTAC
66 CCCAAGCTTTAC
1093916 T
1 T
1093917 TCGCTATTTC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (77 bp):
TATCTGTTTCTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCTAATTACAATAC
CCCAAGCTTTAC
Found at i:1094174 original size:77 final size:77
Alignment explanation
Indices: 1094086--1094242 Score: 280
Period size: 77 Copynumber: 2.0 Consensus size: 77
1094076 TCTACATATT
1094086 ATGGGATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATT-GATGAG
1 ATGGGATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGA-GAG
1094150 GTGCACCAAATCC
65 GTGCACCAAATCC
*
1094163 ATGGGATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGGGG
1 ATGGGATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGG
*
1094228 TGCGCCAAATCC
66 TGCACCAAATCC
1094240 ATG
1 ATG
1094243 CAGTAGTGCA
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
77 75 0.97
78 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (77 bp):
ATGGGATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGG
TGCACCAAATCC
Found at i:1096812 original size:14 final size:14
Alignment explanation
Indices: 1096795--1096821 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1096785 ATTAAAAAGA
1096795 AAAATAAATAAATT
1 AAAATAAATAAATT
1096809 AAAATAAATAAAT
1 AAAATAAATAAAT
1096822 AATACAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAAATAAATT
Found at i:1097094 original size:2 final size:2
Alignment explanation
Indices: 1097087--1097117 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1097077 AACATCCAGT
*
1097087 TA TA TA TA TA TA TA GA 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
1097118 TATTAAATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1098604 original size:50 final size:50
Alignment explanation
Indices: 1098545--1098803 Score: 439
Period size: 50 Copynumber: 5.2 Consensus size: 50
1098535 TATACTTAGA
* *
1098545 GTCAACAATTATGGCCACCTCCCTCTATTGTCATAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1098595 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1098645 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1098695 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
1098745 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATC
1098795 GTCAACAAT
1 GTCAACAAT
1098804 GCCAACAACT
Statistics
Matches: 198, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
50 197 0.99
51 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1103995 original size:21 final size:21
Alignment explanation
Indices: 1103970--1104025 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1103960 AGGCAATAAT
1103970 AGATGATGAAGGTGATTCAGA
1 AGATGATGAAGGTGATTCAGA
1103991 AGATGATGAAGGTGATTCAGA
1 AGATGATGAAGGTGATTCAGA
*
1104012 AGATGATGATGGTG
1 AGATGATGAAGGTG
1104026 CTAATATCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.04, G:0.36, T:0.25
Consensus pattern (21 bp):
AGATGATGAAGGTGATTCAGA
Found at i:1106973 original size:2 final size:2
Alignment explanation
Indices: 1106966--1106994 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1106956 ATCCTTACTT
1106966 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1106995 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1107834 original size:18 final size:17
Alignment explanation
Indices: 1107811--1107871 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 17
1107801 TTATAAGATA
1107811 AATATTAATATAATATTT
1 AATATTAAT-TAATATTT
* *
1107829 AATATT-GTTAA-A-TA
1 AATATTAATTAATATTT
1107843 AATATTAATGTAATATTT
1 AATATTAAT-TAATATTT
1107861 AATATT-ATTAA
1 AATATTAATTAA
1107872 ATATCATGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 7 0.20
15 2 0.06
16 9 0.26
17 4 0.11
18 13 0.37
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
AATATTAATTAATATTT
Found at i:1107844 original size:32 final size:32
Alignment explanation
Indices: 1107798--1107874 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
1107788 TTTTGTGTTT
1107798 ATATTA-TAAGATAAATATTAATATAATATTTA
1 ATATTATTAA-ATAAATATTAATATAATATTTA
* *
1107830 ATATTGTTAAATAAATATTAATGTAATATTTA
1 ATATTATTAAATAAATATTAATATAATATTTA
1107862 ATATTATTAAATA
1 ATATTATTAAATA
1107875 TCATGTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 38 0.93
33 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (32 bp):
ATATTATTAAATAAATATTAATATAATATTTA
Found at i:1108414 original size:20 final size:21
Alignment explanation
Indices: 1108391--1108443 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
1108381 ACCACTTTTT
*
1108391 AAAAAAATTATCA-TTTGTTA
1 AAAAAAATTATCATTTTATTA
* *
1108411 AAAAAAACTATTATTTTATTA
1 AAAAAAATTATCATTTTATTA
1108432 AATAAAAATTAT
1 AA-AAAAATTAT
1108444 TCTATTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
22 8 0.30
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAAAATTATCATTTTATTA
Found at i:1108444 original size:19 final size:19
Alignment explanation
Indices: 1108420--1108458 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1108410 AAAAAAAACT
*
1108420 ATTATTTTATTAAATAAAA
1 ATTATTCTATTAAATAAAA
*
1108439 ATTATTCTATTGAATAAAA
1 ATTATTCTATTAAATAAAA
1108458 A
1 A
1108459 CCACTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
ATTATTCTATTAAATAAAA
Found at i:1108900 original size:17 final size:18
Alignment explanation
Indices: 1108878--1108913 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1108868 AACTTATTGA
*
1108878 TTATTTATT-TTGATAAT
1 TTATTTATTAATGATAAT
1108895 TTATTTATTAATGATAAT
1 TTATTTATTAATGATAAT
1108913 T
1 T
1108914 AGATTAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
TTATTTATTAATGATAAT
Found at i:1109471 original size:21 final size:24
Alignment explanation
Indices: 1109447--1109493 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 24
1109437 TTTTTTAATT
1109447 TTTTCTTTCTT-TTTTT-TT-TTG
1 TTTTCTTTCTTATTTTTCTTCTTG
*
1109468 TTTTTTTTCTTATTTTTCTTCTTG
1 TTTTCTTTCTTATTTTTCTTCTTG
1109492 TT
1 TT
1109494 CCCTTTCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 5 0.23
23 2 0.09
24 5 0.23
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.83
Consensus pattern (24 bp):
TTTTCTTTCTTATTTTTCTTCTTG
Found at i:1109483 original size:24 final size:25
Alignment explanation
Indices: 1109445--1109493 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1109435 TTTTTTTTAA
* * *
1109445 TTTTTTCTTTCTTTTTTTTTTTGTT
1 TTTTTTCTTTATTTTTCTTCTTGTT
1109470 TTTTTTC-TTATTTTTCTTCTTGTT
1 TTTTTTCTTTATTTTTCTTCTTGTT
1109494 CCCTTTCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.84
Consensus pattern (25 bp):
TTTTTTCTTTATTTTTCTTCTTGTT
Found at i:1111794 original size:34 final size:33
Alignment explanation
Indices: 1111726--1111848 Score: 158
Period size: 34 Copynumber: 3.7 Consensus size: 33
1111716 AAATTAATGT
1111726 TTGTTGATTAAATGGTGATTTGATAGTTTACCA
1 TTGTTGATTAAATGGTGATTTGATAGTTTACCA
* *
1111759 TTGTTGATTAAATAGGTGATTTGGT-GATTTGCCA
1 TTGTTGATTAAAT-GGTGATTTGATAG-TTTACCA
* * * *
1111793 TTATTGACTAAATGGGAGATTTGATAGCTTACCA
1 TTGTTGATTAAAT-GGTGATTTGATAGTTTACCA
1111827 TTGTTGATTAAATGGTGATTTG
1 TTGTTGATTAAATGGTGATTTG
1111849 GTGGCTTATC
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
33 22 0.29
34 52 0.69
35 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.43
Consensus pattern (33 bp):
TTGTTGATTAAATGGTGATTTGATAGTTTACCA
Found at i:1111862 original size:67 final size:67
Alignment explanation
Indices: 1111729--1111863 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 67
1111719 TTAATGTTTG
* * * * *
1111729 TTGATTAAATGGTGATTTGATAGTTTACCATTGTTGATTAAATAGGTGATTTGGTGATTTGCCAT
1 TTGACTAAATGGAGATTTGATAGCTTACCATTGTTGATTAAATAGGTGATTTGGTGACTTACCAT
1111794 TA
66 TA
* *
1111796 TTGACTAAATGGGAGATTTGATAGCTTACCATTGTTGATTAAAT-GGTGATTTGGTGGCTTATCA
1 TTGACTAAAT-GGAGATTTGATAGCTTACCATTGTTGATTAAATAGGTGATTTGGTGACTTACCA
1111860 TTA
65 TTA
1111863 T
1 T
1111864 GGTAGATTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 29 0.48
68 31 0.52
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (67 bp):
TTGACTAAATGGAGATTTGATAGCTTACCATTGTTGATTAAATAGGTGATTTGGTGACTTACCAT
TA
Found at i:1116366 original size:34 final size:34
Alignment explanation
Indices: 1116308--1116492 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
1116298 AAGTGGGAGA
* *
1116308 ATTGTTGATTAAAT-AGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1116341 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1116375 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
*
1116409 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1116443 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1116477 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1116493 TTGTTTTTAC
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
33 17 0.13
34 115 0.86
35 1 0.01
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1116408 original size:68 final size:68
Alignment explanation
Indices: 1116308--1116492 Score: 282
Period size: 68 Copynumber: 2.7 Consensus size: 68
1116298 AAGTGGGAGA
* * * * *
1116308 ATTGTTGATTAAAT-AGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
*
1116372 GCC
66 ACC
1116375 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1116440 ACC
66 ACC
* * *
1116443 ATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCATTGTTGATTAAATGG
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGG
1116493 TTGTTTTTAC
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
67 13 0.12
68 95 0.88
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (68 bp):
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
ACC
Found at i:1116448 original size:102 final size:101
Alignment explanation
Indices: 1116308--1116492 Score: 284
Period size: 102 Copynumber: 1.8 Consensus size: 101
1116298 AAGTGGGAGA
* *
1116308 ATTGTTGATTAAATAGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGT-GATTTGGT-GGTT
1 ATTGTTGATTAAATAGTGATTTGGTAGCTTACCATTGTTGACTAAAT-GGTAGATTTGGTAGG-T
1116371 TGCCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
64 TGCCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
* *
1116409 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGTAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-AGTGATTTGGTAGCTTACCATTGTTGACTAAATGGTAGATTTGGTAGGTT
*
1116474 GCCATTGTTGATTAAATGG
65 GCCATTGTTGACTAAATGG
1116493 TTGTTTTTAC
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
101 17 0.22
102 57 0.75
103 2 0.03
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATAGTGATTTGGTAGCTTACCATTGTTGACTAAATGGTAGATTTGGTAGGTTG
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1118806 original size:45 final size:45
Alignment explanation
Indices: 1118756--1118846 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
1118746 CACCAATTTA
1118756 TCTGATTGAATTAAAATTGGTGGGATGCACAGTGCAACATGTTGG
1 TCTGATTGAATTAAAATTGGTGGGATGCACAGTGCAACATGTTGG
1118801 TCTGATTGAATTAAAATTGGTGGGATGCACAGTGCAACATGTTGG
1 TCTGATTGAATTAAAATTGGTGGGATGCACAGTGCAACATGTTGG
1118846 T
1 T
1118847 GATGTTCCAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (45 bp):
TCTGATTGAATTAAAATTGGTGGGATGCACAGTGCAACATGTTGG
Found at i:1121102 original size:22 final size:22
Alignment explanation
Indices: 1121077--1121120 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1121067 GTGATTTAAA
1121077 TAATTAAACTATTATAGGTGGG
1 TAATTAAACTATTATAGGTGGG
1121099 TAATTAAACTATTATAGGTGGG
1 TAATTAAACTATTATAGGTGGG
1121121 CTGTGCCAAG
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:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (22 bp):
TAATTAAACTATTATAGGTGGG
Found at i:1122413 original size:20 final size:20
Alignment explanation
Indices: 1122396--1122448 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
1122386 TATATTAAGT
*
1122396 TAATTTTATTTTTTTTAAAA
1 TAATTATATTTTTTTTAAAA
**
1122416 TAATTATATTTTAATT-AAA
1 TAATTATATTTTTTTTAAAA
*
1122435 TTATTAT-TTTTTTT
1 TAATTATATTTTTTT
1122449 GGCCAGAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 5 0.19
19 9 0.33
20 13 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TAATTATATTTTTTTTAAAA
Found at i:1122446 original size:19 final size:18
Alignment explanation
Indices: 1122397--1122448 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
1122387 ATATTAAGTT
1122397 AATT-TTATTTTTTTTAA
1 AATTATTATTTTTTTTAA
* *
1122414 AATAATTATATTTTAATT-A
1 AATTATTAT-TTTT-TTTAA
1122433 AATTATTATTTTTTTT
1 AATTATTATTTTTTTT
1122449 GGCCAGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 5 0.18
18 8 0.29
19 13 0.46
20 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
AATTATTATTTTTTTTAA
Found at i:1123807 original size:28 final size:27
Alignment explanation
Indices: 1123748--1123807 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1123738 AAAAATCACC
* *
1123748 TTTGTTTGTCAAAAATGATAATTCTTT
1 TTTGTTTGTCAAAAATGATAATTATTG
* *
1123775 TTTGTTTGTCAAAAATTATGACTTATTG
1 TTTGTTTGTCAAAAATGAT-AATTATTG
1123803 TTTGT
1 TTTGT
1123808 AAAAATTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (27 bp):
TTTGTTTGTCAAAAATGATAATTATTG
Found at i:1128181 original size:27 final size:26
Alignment explanation
Indices: 1128148--1128220 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 26
1128138 AAAAACCACC
*
1128148 CTTTGTATTTGTCAACAATGGTGGTT
1 CTTTGTATTTGTCAAAAATGGTGGTT
1128174 ACTTTGTATTTGTCAAAAATGGTGGTT
1 -CTTTGTATTTGTCAAAAATGGTGGTT
* *
1128201 CTTTTTTGTTTGTCAAAAAT
1 C-TTTGTATTTGTCAAAAAT
1128221 TATGACTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (26 bp):
CTTTGTATTTGTCAAAAATGGTGGTT
Found at i:1131437 original size:40 final size:44
Alignment explanation
Indices: 1131332--1131452 Score: 119
Period size: 40 Copynumber: 2.8 Consensus size: 44
1131322 AGTATCTATT
*
1131332 TATATTATAATTTAAATTAATATTATTAATATTTAATAAAATTATGA
1 TATATTATAATTT-AATTAA-ATTATT-ATATTTAATAAAATTATCA
* *
1131379 TATATAATAA-ATATATTAAATTATTAT-TTT-A-AAAA-TATCA
1 TATATTATAATTTA-ATTAAATTATTATATTTAATAAAATTATCA
* *
1131419 TATATTATAATTTAATT-AATTATTAAATATAATA
1 TATATTATAATTTAATTAAATTATTATATTTAATA
1131453 TCAATATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
39 8 0.13
40 18 0.29
41 7 0.11
42 2 0.03
43 3 0.05
44 2 0.03
45 7 0.11
46 6 0.10
47 9 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (44 bp):
TATATTATAATTTAATTAAATTATTATATTTAATAAAATTATCA
Found at i:1132156 original size:23 final size:20
Alignment explanation
Indices: 1132113--1132170 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
1132103 TAATTAAAAT
1132113 ATTTATATAAATTTTTGTAA
1 ATTTATATAAATTTTTGTAA
*
1132133 ATTTATATTATAATTTTATTTAA
1 ATTTATA-TA-AATTTT-TGTAA
1132156 A--TATATAAATATTTT
1 ATTTATATAAAT-TTTT
1132171 ATATTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 4 0.12
20 12 0.36
21 6 0.18
22 6 0.18
23 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTATATAAATTTTTGTAA
Found at i:1132179 original size:21 final size:23
Alignment explanation
Indices: 1132145--1132189 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
1132135 TTATATTATA
1132145 ATTTTATTTAAATA-TA-TAAAT
1 ATTTTATTTAAATATTATTAAAT
1132166 ATTTTATATT-AATATTATTAAAT
1 ATTTTAT-TTAAATATTATTAAAT
1132189 A
1 A
1132190 AATATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 11 0.52
22 4 0.19
23 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTTATTTAAATATTATTAAAT
Found at i:1132218 original size:29 final size:30
Alignment explanation
Indices: 1132149--1132220 Score: 76
Period size: 33 Copynumber: 2.4 Consensus size: 30
1132139 ATTATAATTT
* **
1132149 TATTTAA-ATATATAAATATTTTATATTAA
1 TATTTAATAAATATAAATATAGTATATTAA
1132178 TATTATTAAATAAATATAAATATAGTAT-TTAA
1 TA-T-TT-AATAAATATAAATATAGTATATTAA
1132210 TATTTAATAAA
1 TATTTAATAAA
1132221 ATTATGATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 8 0.22
30 3 0.08
31 3 0.08
32 8 0.22
33 14 0.39
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (30 bp):
TATTTAATAAATATAAATATAGTATATTAA
Found at i:1132230 original size:18 final size:18
Alignment explanation
Indices: 1132209--1132249 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1132199 ATAGTATTTA
*
1132209 ATATTTAATAAAATTATG
1 ATATTTAATAAAAATATG
*
1132227 ATATGTAATAAAAATATG
1 ATATTTAATAAAAATATG
1132245 ATATT
1 ATATT
1132250 ATTATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (18 bp):
ATATTTAATAAAAATATG
Found at i:1133983 original size:6 final size:6
Alignment explanation
Indices: 1133964--1133998 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
1133954 CACCATTTTC
1133964 TCCTCT TACCTCT TCCTCT TCCTCT TCCTCT TCCT
1 TCCTCT T-CCTCT TCCTCT TCCTCT TCCTCT TCCT
1133999 TTCGCCATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (6 bp):
TCCTCT
Found at i:1135431 original size:2 final size:2
Alignment explanation
Indices: 1135424--1135474 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1135414 ATTGATAGCG
1135424 TA TA TA TA 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 TA
1135466 TA TA TA TA T
1 TA TA TA TA T
1135475 GCATACTGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1138151 original size:217 final size:217
Alignment explanation
Indices: 1137776--1138214 Score: 788
Period size: 217 Copynumber: 2.0 Consensus size: 217
1137766 TACGTCCTAC
*
1137776 TAAAATTGGGAGAAATGAAAGAGATTAATCATCATCAATTCTAGTCAACATTCGTGAATCCTTTG
1 TAAAATTGGGAGAAATGAAAGAGATTAATCATCATCAATTCTAGTCAACATTCCTGAATCCTTTG
* *
1137841 CCATATTGAAATGCAAATGCCTAGCATCAAACATGCATTTCTTAGATGAAAGTTCAACTGTTAAA
66 CAATATTGAAATGCAAATGCCTAGCATCAAACATGCATTCCTTAGATGAAAGTTCAACTGTTAAA
*
1137906 ATGAAGTAATTTAAGCCTAACCTTTTGGTTCAAGAATGAATAAATCGCGTCTGACATCAGGCTTA
131 ATGAAGTAATTTAAGCCTAACCTTTTGGTTCAAGAATGAATAAATCGCGTCTGACATCAGGCTCA
1137971 TGATCTCTGGTTATAGATTCAG
196 TGATCTCTGGTTATAGATTCAG
* * *
1137993 TAAAATTGGGAGCAATGAAAGAGATTAATCATCATTAATTCTAGTCAACATTCCTGAATGCTTTG
1 TAAAATTGGGAGAAATGAAAGAGATTAATCATCATCAATTCTAGTCAACATTCCTGAATCCTTTG
**
1138058 CAATATTGAAATGCAAATGCCTAGCATCAATTATGCATTCCTTAGATGAAAGTTCAACTGTTAAA
66 CAATATTGAAATGCAAATGCCTAGCATCAAACATGCATTCCTTAGATGAAAGTTCAACTGTTAAA
*
1138123 ATGAAGTAATTTAAGCCTAACCTTTTGGTTCAAGAATGAATATATCGCGTCTGACATCAGGCTCA
131 ATGAAGTAATTTAAGCCTAACCTTTTGGTTCAAGAATGAATAAATCGCGTCTGACATCAGGCTCA
1138188 TGATCTCTGGTTATAGATTCAG
196 TGATCTCTGGTTATAGATTCAG
1138210 TAAAA
1 TAAAA
1138215 CTAATGCCGG
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 212 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (217 bp):
TAAAATTGGGAGAAATGAAAGAGATTAATCATCATCAATTCTAGTCAACATTCCTGAATCCTTTG
CAATATTGAAATGCAAATGCCTAGCATCAAACATGCATTCCTTAGATGAAAGTTCAACTGTTAAA
ATGAAGTAATTTAAGCCTAACCTTTTGGTTCAAGAATGAATAAATCGCGTCTGACATCAGGCTCA
TGATCTCTGGTTATAGATTCAG
Found at i:1141011 original size:13 final size:14
Alignment explanation
Indices: 1140995--1141055 Score: 72
Period size: 13 Copynumber: 4.4 Consensus size: 14
1140985 AATTTTATTT
1140995 TTTAT-TATTAATA
1 TTTATATATTAATA
1141008 TTTATA-ATTAATA
1 TTTATATATTAATA
*
1141021 TTTATCATAATAATA
1 TTTAT-ATATTAATA
*
1141036 TTTATATATTTATA
1 TTTATATATTAATA
*
1141050 ATTATA
1 TTTATA
1141056 ATAAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
13 17 0.41
14 13 0.32
15 11 0.27
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTATATATTAATA
Found at i:1141036 original size:15 final size:13
Alignment explanation
Indices: 1141003--1141041 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
1140993 TTTTTATTAT
*
1141003 TAATATTTATAAT
1 TAATATTTATAAA
1141016 TAATATTTATCATAA
1 TAATATTTAT-A-AA
1141031 TAATATTTATA
1 TAATATTTATA
1141042 TATTTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 10 0.43
14 2 0.09
15 11 0.48
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATATTTATAAA
Found at i:1141064 original size:23 final size:23
Alignment explanation
Indices: 1141018--1141064 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1141008 TTTATAATTA
* **
1141018 ATATTTATCATAATAATATTTAT
1 ATATTTATAATAATAATAAATAT
*
1141041 ATATTTATAATTATAATAAATAT
1 ATATTTATAATAATAATAAATAT
1141064 A
1 A
1141065 ATAAGATTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTTATAATAATAATAAATAT
Found at i:1142150 original size:14 final size:13
Alignment explanation
Indices: 1142119--1142149 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1142109 TTTATTTTTA
1142119 TTTTTAAAATAAT
1 TTTTTAAAATAAT
1142132 TTTTTAAAATAAT
1 TTTTTAAAATAAT
1142145 TTTTT
1 TTTTT
1142150 TTATAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTTAAAATAAT
Found at i:1143308 original size:23 final size:22
Alignment explanation
Indices: 1143282--1143337 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
1143272 AATTCATTTG
1143282 ATTTAAAATAAAAAAAATTAATA
1 ATTTAAAATAAAAAAAATT-ATA
* * * *
1143305 ATTTAAATTTAAAATAATTTTA
1 ATTTAAAATAAAAAAAATTATA
*
1143327 ATTTTAAATAA
1 ATTTAAAATAA
1143338 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTTAAAATAAAAAAAATTATA
Found at i:1143322 original size:16 final size:16
Alignment explanation
Indices: 1143301--1143356 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
1143291 AAAAAAAATT
1143301 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
* *
1143317 AATAATTTTAATTTTA
1 AATAATTTAAATTTAA
1143333 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
1143349 AATAATTT
1 AATAATTT
1143357 TAAAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:1143354 original size:26 final size:26
Alignment explanation
Indices: 1143325--1143377 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1143315 AAAATAATTT
*
1143325 TAATTTTAAATAATTTAAATTTAAAA
1 TAATTTTAAAAAATTTAAATTTAAAA
*
1143351 TAATTTTAAAAAATTTAAATTTTAAA
1 TAATTTTAAAAAATTTAAATTTAAAA
1143377 T
1 T
1143378 TAACCTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TAATTTTAAAAAATTTAAATTTAAAA
Found at i:1143371 original size:16 final size:16
Alignment explanation
Indices: 1143304--1143376 Score: 70
Period size: 16 Copynumber: 4.9 Consensus size: 16
1143294 AAAAATTAAT
1143304 AATTTAAA-TTTAAAA
1 AATTTAAATTTTAAAA
* *
1143319 TAATTTTAATTTTAAAT
1 -AATTTAAATTTTAAAA
1143336 AATTTAAA-TTT--AA
1 AATTTAAATTTTAAAA
1143349 AA--T-AATTTTAAAA
1 AATTTAAATTTTAAAA
1143362 AATTTAAATTTTAAA
1 AATTTAAATTTTAAA
1143377 TTAACCTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 2 0.04
11 4 0.09
13 7 0.15
15 4 0.09
16 23 0.50
17 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAAATTTTAAAA
Found at i:1143386 original size:26 final size:26
Alignment explanation
Indices: 1143331--1143386 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
1143321 ATTTTAATTT
* **
1143331 TAAATAATTTAAATTTAAAATAATTT
1 TAAAAAATTTAAATTTAAAATAATCC
*
1143357 TAAAAAATTTAAATTTTAAATTAA-CC
1 TAAAAAATTTAAA-TTTAAAATAATCC
1143383 TAAA
1 TAAA
1143387 TTAATCTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAAAAATTTAAATTTAAAATAATCC
Found at i:1144204 original size:3 final size:3
Alignment explanation
Indices: 1144196--1144285 Score: 144
Period size: 3 Copynumber: 29.7 Consensus size: 3
1144186 AAGCCAGAAA
* * *
1144196 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATT CAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
1144242 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1144286 ATATTCATTT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
3 77 0.96
4 3 0.04
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1150800 original size:6 final size:6
Alignment explanation
Indices: 1150789--1150818 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1150779 GTATATCTTT
1150789 ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA
1150819 CTGAAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:1151365 original size:4 final size:4
Alignment explanation
Indices: 1151356--1151381 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1151346 GTCTCTTATT
1151356 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
1151382 GGTGTTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:1156119 original size:18 final size:18
Alignment explanation
Indices: 1156096--1156130 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1156086 ACATAACCTT
*
1156096 AGCATAACTAAAAAAAAC
1 AGCATAACGAAAAAAAAC
*
1156114 AGCATAAGGAAAAAAAA
1 AGCATAACGAAAAAAAA
1156131 GACTCATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.11, G:0.11, T:0.09
Consensus pattern (18 bp):
AGCATAACGAAAAAAAAC
Found at i:1157438 original size:15 final size:15
Alignment explanation
Indices: 1157414--1157455 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1157404 ATAATAAAAA
*
1157414 ATTA-TAAATTTTAT
1 ATTATTAAATTTAAT
1157428 ATTATTAAATTTAAT
1 ATTATTAAATTTAAT
1157443 ATT-TTAATATTTA
1 ATTATTAA-ATTTA
1157456 TAATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTAAATTTAAT
Found at i:1157694 original size:29 final size:29
Alignment explanation
Indices: 1157661--1157716 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1157651 TTTATTTCTT
1157661 ATTTAAAAATAAAAAAATAAAAATATTAA
1 ATTTAAAAATAAAAAAATAAAAATATTAA
* * *
1157690 ATTTAATAATATAAAAATTAAAATATT
1 ATTTAAAAATAAAAAAATAAAAATATT
1157717 TTACTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (29 bp):
ATTTAAAAATAAAAAAATAAAAATATTAA
Found at i:1157700 original size:15 final size:14
Alignment explanation
Indices: 1157674--1157716 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1157664 TAAAAATAAA
*
1157674 AAAATAAAAATATT
1 AAAATTAAAATATT
* *
1157688 AAATTTAATAATATA
1 AAAATTAA-AATATT
1157703 AAAATTAAAATATT
1 AAAATTAAAATATT
1157717 TTACTATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATTAAAATATT
Found at i:1158827 original size:22 final size:21
Alignment explanation
Indices: 1158777--1158827 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
1158767 TCTTCATTTG
1158777 AAAAAAATACTAATTTTTTAA
1 AAAAAAATACTAATTTTTTAA
* * *
1158798 ATTTAAATATA-TTATTTTTTAA
1 A--AAAAAATACTAATTTTTTAA
1158820 AAAAAAAT
1 AAAAAAAT
1158828 TAAAAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 5
0.70 0.15 0.15
Matches are distributed among these distances:
20 5 0.22
21 1 0.04
22 11 0.48
23 6 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAAAAATACTAATTTTTTAA
Found at i:1165766 original size:16 final size:16
Alignment explanation
Indices: 1165742--1165775 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1165732 TTGTAATTGT
*
1165742 ATTTGGGTTAGAAAAA
1 ATTTGGGTTAAAAAAA
*
1165758 ATTTTGGTTAAAAAAA
1 ATTTGGGTTAAAAAAA
1165774 AT
1 AT
1165776 GTAGTTTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (16 bp):
ATTTGGGTTAAAAAAA
Found at i:1165852 original size:16 final size:18
Alignment explanation
Indices: 1165819--1165863 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
1165809 GTTAAATGTA
1165819 AAAAAAATAAATATGTTT
1 AAAAAAATAAATATGTTT
*
1165837 AAAATAATAAA-A-GTTT
1 AAAAAAATAAATATGTTT
*
1165853 AAAAATATAAA
1 AAAAAAATAAA
1165864 AATAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 1 0.04
18 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAAAAATAAATATGTTT
Found at i:1166756 original size:2 final size:2
Alignment explanation
Indices: 1166737--1166794 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
1166727 GTTACTAGTT
* * * *
1166737 TA TA TC TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TG TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1166779 TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA
1166795 AAGGAGGCTA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1168313 original size:20 final size:21
Alignment explanation
Indices: 1168269--1168320 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
1168259 TACATTATTT
1168269 AATTTAATA-T-ATTTTTATTA
1 AATTTAATATTAATTTTTA-TA
*
1168289 TATTTAATATTAATTTTTA-A
1 AATTTAATATTAATTTTTATA
1168309 AATTTAAT-TTAA
1 AATTTAATATTAA
1168321 ATTCAACCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 1 0.04
22 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTTAATATTAATTTTTATA
Found at i:1177417 original size:1 final size:1
Alignment explanation
Indices: 1177413--1177438 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1177403 AACGTGGATG
1177413 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1177439 CTAGGAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1180072 original size:11 final size:11
Alignment explanation
Indices: 1180056--1180080 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1180046 TCAATATAGA
1180056 AATAAAATATC
1 AATAAAATATC
1180067 AATAAAATATC
1 AATAAAATATC
1180078 AAT
1 AAT
1180081 TTGAATAACT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAAATATC
Found at i:1184909 original size:16 final size:16
Alignment explanation
Indices: 1184888--1184919 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1184878 AAAATAAATT
1184888 TAAATATTAAATAAAA
1 TAAATATTAAATAAAA
*
1184904 TAAATATTTAATAAAA
1 TAAATATTAAATAAAA
1184920 ATATATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAATATTAAATAAAA
Found at i:1184920 original size:17 final size:17
Alignment explanation
Indices: 1184888--1184951 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
1184878 AAAATAAATT
*
1184888 TAAATATTAAAT-AAAA
1 TAAATATTTAATAAAAA
1184904 TAAATATTTAATAAAAA
1 TAAATATTTAATAAAAA
* * *
1184921 TATATTTTTAATTAAATATT
1 TAAATATTTAA-TAAA-A-A
1184941 TAAATATTTAA
1 TAAATATTTAA
1184952 ATCTAATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
16 11 0.29
17 13 0.34
18 4 0.11
19 1 0.03
20 9 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATATTTAATAAAAA
Found at i:1184921 original size:22 final size:22
Alignment explanation
Indices: 1184877--1184922 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1184867 TTGATTCAAT
*
1184877 TAAAATAAATTTAAATATTAAA
1 TAAAATAAATTTAAATATAAAA
*
1184899 TAAAATAAATATTTAATA-AAAA
1 TAAAATAAAT-TTAAATATAAAA
1184921 TA
1 TA
1184923 TATTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATTTAAATATAAAA
Found at i:1185756 original size:39 final size:40
Alignment explanation
Indices: 1185713--1185795 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
1185703 TCTAAATAGA
*
1185713 TTTTAT-ATAT-TAATATATTTATGTCATATTTATAA-TATT
1 TTTTATAATATATAATAT-TTTATATCATATTT-TAATTATT
* *
1185752 TTTTATAATATATCATATTTTATATTATATTTTAATTATT
1 TTTTATAATATATAATATTTTATATCATATTTTAATTATT
1185792 TTTT
1 TTTT
1185796 TGTATTACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
39 9 0.24
40 24 0.63
41 5 0.13
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (40 bp):
TTTTATAATATATAATATTTTATATCATATTTTAATTATT
Done.