Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 13 of 235
Found at i:3553704 original size:28 final size:28
Alignment explanation
Indices: 3553662--3553773 Score: 125
Period size: 28 Copynumber: 4.0 Consensus size: 28
3553652 GGCTATGTAC
*
3553662 GGCACTTAGTGTGCGAGATATCAAGTAT
1 GGCACTTAGTGTGCGAGATATCGAGTAT
* * *
3553690 GGCACTTAGTATGCGAGATATCGACTGT
1 GGCACTTAGTGTGCGAGATATCGAGTAT
* * * *
3553718 GGCATTTAGTGTACGAAATATTGAGTAT
1 GGCACTTAGTGTGCGAGATATCGAGTAT
* * *
3553746 GACACTTAGTGTGCGAGACATTGAGTAT
1 GGCACTTAGTGTGCGAGATATCGAGTAT
3553774 TCAACTGCAT
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (28 bp):
GGCACTTAGTGTGCGAGATATCGAGTAT
Found at i:3560003 original size:46 final size:46
Alignment explanation
Indices: 3559927--3560286 Score: 542
Period size: 46 Copynumber: 7.8 Consensus size: 46
3559917 TGATGTCATA
* * * * *
3559927 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCAGGTTGCCATG
* *** *
3559973 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGTTGCCATG
*
3560020 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
3560066 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
3560112 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
3560158 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
3560204 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
3560250 GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
3560287 AGAGCACACT
Statistics
Matches: 297, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
46 258 0.87
47 39 0.13
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
Found at i:3562245 original size:20 final size:21
Alignment explanation
Indices: 3562216--3562256 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3562206 ACATCTTCGA
3562216 TTTTCCCTTTTT-TTTCTTTC
1 TTTTCCCTTTTTCTTTCTTTC
*
3562236 TTTTCTCTTTTTCTTTCTTTC
1 TTTTCCCTTTTTCTTTCTTTC
3562257 CTTCCCCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCCCTTTTTCTTTCTTTC
Found at i:3566955 original size:40 final size:40
Alignment explanation
Indices: 3566900--3566992 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
3566890 CAGCTATTGG
3566900 TGGCACTTAGTGTGCGAATCGACATAGCTTCGACTATATA
1 TGGCACTTAGTGTGCGAATCGACATAGCTTCGACTATATA
* * * * *
3566940 TGGCACTTAGTGTGCGATTTGAGATAGCTTCGGCTATGTA
1 TGGCACTTAGTGTGCGAATCGACATAGCTTCGACTATATA
* *
3566980 CGACACTTAGTGT
1 TGGCACTTAGTGT
3566993 ACGAGATATC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGAATCGACATAGCTTCGACTATATA
Found at i:3567900 original size:15 final size:15
Alignment explanation
Indices: 3567882--3567910 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3567872 CACACTATCA
3567882 TGTTACACGGTCGTG
1 TGTTACACGGTCGTG
3567897 TGTTACACGGTCGT
1 TGTTACACGGTCGT
3567911 ATGTCCCCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.31, T:0.34
Consensus pattern (15 bp):
TGTTACACGGTCGTG
Found at i:3569907 original size:22 final size:22
Alignment explanation
Indices: 3569882--3569928 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3569872 AAAACATGTT
* *
3569882 AATTTATACTTATTGCATGAAA
1 AATTTAAACTTAATGCATGAAA
*
3569904 AATTTAAACTTAATGCATTAAA
1 AATTTAAACTTAATGCATGAAA
3569926 AAT
1 AAT
3569929 GTCATTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (22 bp):
AATTTAAACTTAATGCATGAAA
Found at i:3575529 original size:14 final size:14
Alignment explanation
Indices: 3575510--3575540 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3575500 GTGATCTCAC
3575510 TCTTAATACATTGG
1 TCTTAATACATTGG
3575524 TCTTAATACATTGG
1 TCTTAATACATTGG
3575538 TCT
1 TCT
3575541 CTATGATGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (14 bp):
TCTTAATACATTGG
Found at i:3581745 original size:8 final size:8
Alignment explanation
Indices: 3581728--3581767 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
3581718 ATAAACAAGC
3581728 ATAGAGAG
1 ATAGAGAG
*
3581736 ATAGATAG
1 ATAGAGAG
3581744 ATAGAGAG
1 ATAGAGAG
*
3581752 AGAGAGAG
1 ATAGAGAG
*
3581760 AGAGAGAG
1 ATAGAGAG
3581768 TGATAATGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.40, T:0.10
Consensus pattern (8 bp):
ATAGAGAG
Found at i:3585803 original size:24 final size:25
Alignment explanation
Indices: 3585765--3585813 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3585755 TAATTTTTTT
3585765 AAAAATTTATTTTTAA-ATTGTTAG
1 AAAAATTTATTTTTAATATTGTTAG
*
3585789 AAAACATTTA-TTTTAATATTTTTAG
1 AAAA-ATTTATTTTTAATATTGTTAG
3585814 TGTATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (25 bp):
AAAAATTTATTTTTAATATTGTTAG
Found at i:3587254 original size:18 final size:18
Alignment explanation
Indices: 3587233--3587269 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3587223 TAAATTTTTG
3587233 AATTCAAATAACTCAAAT
1 AATTCAAATAACTCAAAT
* *
3587251 AATTCGAATAAGTCAAAT
1 AATTCAAATAACTCAAAT
3587269 A
1 A
3587270 TTAAATCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (18 bp):
AATTCAAATAACTCAAAT
Found at i:3587456 original size:53 final size:53
Alignment explanation
Indices: 3587388--3587523 Score: 127
Period size: 53 Copynumber: 2.6 Consensus size: 53
3587378 TCCCCGAAAT
* **
3587388 TTTTA-TTCCCCAAACCCTTAAAAATATTTTTCTTTTATTTTTTTCT-C-AAAAC
1 TTTTACTTCTCCAAACCC-TAAAAATATTTTTCTTTT-TTGCTTTCTCCTAAAAC
* ** *
3587440 TTTTACTTCTCCAAACCCTCAATTTTTTTTTCTTTTTTGCTTTCTCCTAAAAC
1 TTTTACTTCTCCAAACCCTAAAAATATTTTTCTTTTTTGCTTTCTCCTAAAAC
* * *
3587493 TTTTACCTCTCCCAAA-CCTCAAAATTTTTTT
1 TTTTACTTCT-CCAAACCCTAAAAATATTTTT
3587524 TGAACTTATG
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
51 7 0.10
52 20 0.29
53 38 0.54
54 5 0.07
ACGTcount: A:0.24, C:0.25, G:0.01, T:0.50
Consensus pattern (53 bp):
TTTTACTTCTCCAAACCCTAAAAATATTTTTCTTTTTTGCTTTCTCCTAAAAC
Found at i:3590536 original size:21 final size:21
Alignment explanation
Indices: 3590510--3590552 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3590500 GGTTCGTTGT
*
3590510 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
3590531 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
3590552 A
1 A
3590553 ATAGAGGTGT
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:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:3590552 original size:16 final size:16
Alignment explanation
Indices: 3590533--3590565 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3590523 TGTATTGGAT
*
3590533 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
3590549 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
3590565 T
1 T
3590566 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:3590610 original size:45 final size:44
Alignment explanation
Indices: 3590544--3590638 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
3590534 GGATTAGAGG
* *
3590544 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
3590589 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
3590633 TGTAAT
1 TGTAAT
3590639 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:3590821 original size:18 final size:17
Alignment explanation
Indices: 3590800--3590834 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3590790 TTATTATTTA
*
3590800 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3590818 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3590835 TCTTAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3590828 original size:28 final size:27
Alignment explanation
Indices: 3590758--3590830 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
3590748 TTTATTATCA
*
3590758 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
3590786 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
3590813 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
3590831 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:3590947 original size:144 final size:147
Alignment explanation
Indices: 3590719--3590990 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
3590709 ATGATTATTG
3590719 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
3590784 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
3590849 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
3590868 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
3590930 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
3590991 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:3590965 original size:18 final size:17
Alignment explanation
Indices: 3590944--3590978 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3590934 TTATTATTAA
*
3590944 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3590962 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3590979 TCTTAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3605646 original size:27 final size:27
Alignment explanation
Indices: 3605610--3605662 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
3605600 TACATATAAG
3605610 TTGTCATGCTAATATCGTTAAAAAAAA
1 TTGTCATGCTAATATCGTTAAAAAAAA
3605637 TTGTCATGCTAATATCGTTAAAAAAA
1 TTGTCATGCTAATATCGTTAAAAAAA
3605663 TTAACTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (27 bp):
TTGTCATGCTAATATCGTTAAAAAAAA
Found at i:3607095 original size:56 final size:56
Alignment explanation
Indices: 3607006--3607115 Score: 193
Period size: 56 Copynumber: 2.0 Consensus size: 56
3606996 ATTGAGTTGA
*
3607006 TGACCAATCAAATTAAGAGTGACACTACCTTAATAAATTCTTAAATATATATATGT
1 TGACCAATCAAATTAAGAGTGACACCACCTTAATAAATTCTTAAATATATATATGT
* *
3607062 TGACCAATCAAATTAAGAGTGACACCACTTTAATAAATTCTTGAATATATATAT
1 TGACCAATCAAATTAAGAGTGACACCACCTTAATAAATTCTTAAATATATATAT
3607116 ATATATATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (56 bp):
TGACCAATCAAATTAAGAGTGACACCACCTTAATAAATTCTTAAATATATATATGT
Found at i:3611693 original size:20 final size:18
Alignment explanation
Indices: 3611646--3611694 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
3611636 CAAGCTAAAC
3611646 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
3611663 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
3611683 ATTAAATTAATA
1 ATTAAATTAATA
3611695 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:3615124 original size:16 final size:16
Alignment explanation
Indices: 3615074--3615125 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
3615064 TCAAACTTGA
*
3615074 GTATTCGGTTACATGT
1 GTATTTGGTTACATGT
* *
3615090 GAATTTATGTTGAACATGT
1 GTATTT-GGTT--ACATGT
3615109 GTATTTGGTTACATGT
1 GTATTTGGTTACATGT
3615125 G
1 G
3615126 AGTTTATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 3 0.11
19 11 0.39
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (16 bp):
GTATTTGGTTACATGT
Found at i:3620497 original size:14 final size:13
Alignment explanation
Indices: 3620473--3620502 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3620463 GGTTGTTTAT
3620473 TAAACTAATTAAC
1 TAAACTAATTAAC
3620486 TAAACTTAATTAAC
1 TAAAC-TAATTAAC
3620500 TAA
1 TAA
3620503 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:3623042 original size:30 final size:30
Alignment explanation
Indices: 3623008--3623067 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3622998 CTTTAATACG
3623008 AACTTTGGAAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGAAAAATTACAC-TTTTGCCCCTA
* * *
3623038 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
3623068 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:3625143 original size:15 final size:15
Alignment explanation
Indices: 3625114--3625152 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
3625104 AACAGAGAAG
3625114 CCAAGAATAAAGAAAT
1 CCAAG-ATAAAGAAAT
3625130 CCAAGATAAAGAAAT
1 CCAAGATAAAGAAAT
*
3625145 CCATGATA
1 CCAAGATA
3625153 CGAGAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (15 bp):
CCAAGATAAAGAAAT
Found at i:3632626 original size:38 final size:38
Alignment explanation
Indices: 3632575--3632651 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
3632565 CTCTAGTGAA
* *
3632575 TGGTCAGGGTGGTTCGAGGAGCTCGTATTCCTCATTCC
1 TGGTCAGGGTGGTTCGAGGAGCTCATACTCCTCATTCC
* * *
3632613 TGGTCATGGTGGTTCGAGGAGTTTATACTCCTCATTCC
1 TGGTCAGGGTGGTTCGAGGAGCTCATACTCCTCATTCC
3632651 T
1 T
3632652 ACTATCAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.14, C:0.22, G:0.29, T:0.35
Consensus pattern (38 bp):
TGGTCAGGGTGGTTCGAGGAGCTCATACTCCTCATTCC
Found at i:3634225 original size:32 final size:32
Alignment explanation
Indices: 3634187--3634250 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
3634177 GGTTATTTTG
*
3634187 AGATCTAAAGTTATTGTTACCCATATAGTTAA
1 AGATCTAAACTTATTGTTACCCATATAGTTAA
3634219 AGATCTAAACTTATTGTTACCCATATAGTTAA
1 AGATCTAAACTTATTGTTACCCATATAGTTAA
3634251 CTTGTTCCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (32 bp):
AGATCTAAACTTATTGTTACCCATATAGTTAA
Found at i:3635642 original size:14 final size:13
Alignment explanation
Indices: 3635618--3635647 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3635608 GGTTGTTTAT
3635618 TAAACTAATTAAC
1 TAAACTAATTAAC
3635631 TAAACTTAATTAAC
1 TAAAC-TAATTAAC
3635645 TAA
1 TAA
3635648 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:3636095 original size:14 final size:14
Alignment explanation
Indices: 3636076--3636102 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3636066 TAATTCAAGC
3636076 ATTAAGAACAAATA
1 ATTAAGAACAAATA
3636090 ATTAAGAACAAAT
1 ATTAAGAACAAAT
3636103 CAAGTATTTA
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:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (14 bp):
ATTAAGAACAAATA
Found at i:3639414 original size:35 final size:35
Alignment explanation
Indices: 3639375--3639450 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
3639365 ACAAGTAAGC
*
3639375 TTATATCAAACTTGAGAATTCGGTTACATGTGAAT
1 TTATATCAAACATGAGAATTCGGTTACATGTGAAT
** * * * *
3639410 TTATATTGAACATGTGTATTTGGTTACATGTGAGT
1 TTATATCAAACATGAGAATTCGGTTACATGTGAAT
3639445 TTATAT
1 TTATAT
3639451 TGAGCTTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.43
Consensus pattern (35 bp):
TTATATCAAACATGAGAATTCGGTTACATGTGAAT
Found at i:3640172 original size:16 final size:16
Alignment explanation
Indices: 3640151--3640187 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3640141 TTTATCTTTG
*
3640151 AACTTTTGGCATGTAT
1 AACTTTTAGCATGTAT
3640167 AAC-TTTAGCATGTAT
1 AACTTTTAGCATGTAT
3640182 AACTTT
1 AACTTT
3640188 AGCCATGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (16 bp):
AACTTTTAGCATGTAT
Found at i:3640179 original size:15 final size:15
Alignment explanation
Indices: 3640159--3640190 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3640149 TGAACTTTTG
3640159 GCATGTATAACTTTA
1 GCATGTATAACTTTA
3640174 GCATGTATAACTTTA
1 GCATGTATAACTTTA
3640189 GC
1 GC
3640191 CATGCGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (15 bp):
GCATGTATAACTTTA
Found at i:3641961 original size:19 final size:21
Alignment explanation
Indices: 3641930--3641975 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3641920 TAAGATAACT
*
3641930 TAATT-AAACAAAATT-AAGA
1 TAATTGAAACAAAATTAAAAA
3641949 TAATTGAAA-AAAATTAAAAA
1 TAATTGAAACAAAATTAAAAA
3641969 TAATTGA
1 TAATTGA
3641976 GGTTGTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (21 bp):
TAATTGAAACAAAATTAAAAA
Found at i:3648717 original size:38 final size:38
Alignment explanation
Indices: 3648675--3648864 Score: 166
Period size: 38 Copynumber: 5.2 Consensus size: 38
3648665 ATAGAAATGT
* *
3648675 GGTGATATTCGGGCTATATGCCTAGCAGGCTTTGTGTC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGCC
* * *
3648713 GGTGATATTCGGGCTACGTGTCTAGCAAG---T-T---
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGCC
* * *
3648744 GGT-ATTATTCGAGCTCTGTGCCTAGCAGGCTTTGTGCT
1 GGTGA-TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCC
* * *
3648782 GATGATATTCGGGCTATGTGCCTAGCAAGCTTTGTACC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGCC
* * * *
3648820 AGTGTTATTCGGGCTTTGTGCCTAGTAGGC-TTGTGCC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGCC
3648857 GGTG-TATT
1 GGTGATATT
3648865 GAAAATTTAC
Statistics
Matches: 120, Mismatches: 23, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
30 1 0.01
31 22 0.18
34 2 0.02
35 2 0.02
36 4 0.03
37 9 0.08
38 79 0.66
39 1 0.01
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.35
Consensus pattern (38 bp):
GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGCC
Found at i:3651412 original size:43 final size:43
Alignment explanation
Indices: 3651354--3651588 Score: 189
Period size: 43 Copynumber: 5.5 Consensus size: 43
3651344 CAATGCCGAC
* * *
3651354 GTCCCGGACATGGTCTTACATGTAATTCAATATCGATGCCTCT
1 GTCCCAGACATGGTCTTACACGTAATTCAATATCGATGCCTAT
* * *
3651397 GTCCCAGACAGGGTCTTACACG-AAATCAGATA-CGATGCCGAT
1 GTCCCAGACATGGTCTTACACGTAATTCA-ATATCGATGCCTAT
* * *
3651439 GTCCCAGACATGGTCTTATACGTAAATCTC-A-ATCGAGGCCTGT
1 GTCCCAGACATGGTCTTACACGT-AAT-TCAATATCGATGCCTAT
** * * * *
3651482 GTCCCAGACACAGTCTTACATG-AAATCAGATA-CAATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAATTCA-ATATCGATGCCTAT
* * *
3651524 GTCCCAGACATGGTCTTATACGTAAATCTC-A-ATCGAGGCCTGT
1 GTCCCAGACATGGTCTTACACGT-AAT-TCAATATCGATGCCTAT
*
3651567 GTCCCAGACACGGTCTTACACG
1 GTCCCAGACATGGTCTTACACG
3651589 ATGTCTCAGA
Statistics
Matches: 148, Mismatches: 32, Indels: 24
0.73 0.16 0.12
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 60 0.41
43 76 0.51
44 4 0.03
45 4 0.03
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAATTCAATATCGATGCCTAT
Found at i:3651489 original size:85 final size:85
Alignment explanation
Indices: 3651342--3651589 Score: 365
Period size: 85 Copynumber: 2.9 Consensus size: 85
3651332 CATAAACAAG
* * * * * *
3651342 TACAATGCCGACGTCCCGGACATGGTCTTACATGT-AAT-TCAATATCGATGCCTCTGTCCCAGA
1 TACAATGCCGATGTCCCAGACATGGTCTTATACGTAAATCTC-A-ATCGAGGCCTGTGTCCCAGA
*
3651405 CAGGGTCTTACACGAAATCAGA
64 CACGGTCTTACACGAAATCAGA
*
3651427 TACGATGCCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACA
1 TACAATGCCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACA
* *
3651492 CAGTCTTACATGAAATCAGA
66 CGGTCTTACACGAAATCAGA
*
3651512 TACAATGCCAATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACA
1 TACAATGCCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACA
3651577 CGGTCTTACACGA
66 CGGTCTTACACGA
3651590 TGTCTCAGAC
Statistics
Matches: 147, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
85 141 0.96
86 4 0.03
87 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.25
Consensus pattern (85 bp):
TACAATGCCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACA
CGGTCTTACACGAAATCAGA
Found at i:3652747 original size:16 final size:17
Alignment explanation
Indices: 3652716--3652748 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3652706 TTTATAAGTA
3652716 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
3652733 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
3652749 GTTTCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:3653303 original size:46 final size:46
Alignment explanation
Indices: 3653034--3653307 Score: 379
Period size: 46 Copynumber: 6.0 Consensus size: 46
3653024 TTTGACATGA
* * * * *
3653034 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT
* * *
3653080 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* * *** *
3653126 TGCCACGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
3653172 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
3653218 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
3653264 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
3653308 AGAGCACACT
Statistics
Matches: 211, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 4 0.02
46 207 0.98
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
Found at i:3662494 original size:42 final size:42
Alignment explanation
Indices: 3662386--3662626 Score: 161
Period size: 43 Copynumber: 5.7 Consensus size: 42
3662376 AACAAGTACA
* * * * *
3662386 ATGCCGACGTCTCGGACGTGGTCTTACATGTAATTCAATATCG
1 ATGCCGATGTCCCAGACATGGTCTTACATGTAAATCAATA-CG
** * *
3662429 ATGCCTCTGTCCCAGATAGGGTCTTACATG-AAATCAGATACG
1 ATGCCGATGTCCCAGACATGGTCTTACATGTAAATCA-ATACG
* * *
3662471 ATGCCGATATCCTAGACATGGTCTTATATGTAAATCTCAAT-CG
1 ATGCCGATGTCCCAGACATGGTCTTACATGTAAA--TCAATACG
* * * * * *
3662514 AGGCATG-TGTCCCAAACACGGTCTTACACG-AAATCGATTACG
1 ATGC-CGATGTCCCAGACATGGTCTTACATGTAAATC-AATACG
* * *
3662556 ATGCCGATGTCCCAGACATGGTCTTATACGTAAATCTCAAT-TG
1 ATGCCGATGTCCCAGACATGGTCTTACATGTAAA--TCAATACG
*
3662599 AGGCCTG-TGTCCCAGACATGGTCTTACA
1 ATGCC-GATGTCCCAGACATGGTCTTACA
3662627 CGATGTCTCA
Statistics
Matches: 152, Mismatches: 34, Indels: 24
0.72 0.16 0.11
Matches are distributed among these distances:
40 2 0.01
41 3 0.02
42 58 0.38
43 78 0.51
44 6 0.04
45 5 0.03
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (42 bp):
ATGCCGATGTCCCAGACATGGTCTTACATGTAAATCAATACG
Found at i:3662537 original size:85 final size:85
Alignment explanation
Indices: 3662448--3662629 Score: 276
Period size: 85 Copynumber: 2.1 Consensus size: 85
3662438 TCCCAGATAG
* * *
3662448 GGTCTTACATGAAATCAGA-TACGATGCCGATATCCTAGACATGGTCTTATATGTAAATCTCAAT
1 GGTCTTACACGAAATC-GATTACGATGCCGATATCCCAGACATGGTCTTATACGTAAATCTCAAT
3662512 CGAGGCATGTGTCCCAAACAC
65 CGAGGCATGTGTCCCAAACAC
* *
3662533 GGTCTTACACGAAATCGATTACGATGCCGATGTCCCAGACATGGTCTTATACGTAAATCTCAATT
1 GGTCTTACACGAAATCGATTACGATGCCGATATCCCAGACATGGTCTTATACGTAAATCTCAATC
* * *
3662598 GAGGCCTGTGTCCCAGACAT
66 GAGGCATGTGTCCCAAACAC
3662618 GGTCTTACACGA
1 GGTCTTACACGA
3662630 TGTCTCAGAC
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 2 0.02
85 86 0.98
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (85 bp):
GGTCTTACACGAAATCGATTACGATGCCGATATCCCAGACATGGTCTTATACGTAAATCTCAATC
GAGGCATGTGTCCCAAACAC
Found at i:3665480 original size:46 final size:47
Alignment explanation
Indices: 3665204--3665480 Score: 217
Period size: 49 Copynumber: 5.9 Consensus size: 47
3665194 CATGGGTAAG
* * * *
3665204 GTGCCGATGCCATGTCCTAGACATGGTCTTACAATGGCTATCATCTTC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATC-TC
* * *
3665252 GAGGCCGATGTCATGTCCCGGACATGGTCTTACACTAGCTCTCA-CATAACC
1 G-TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATC-T---C
* * * *
3665303 GTGTCGATTCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTC
** * * **
3665348 ACAGCCGATG-CATGTCCCAAACAT-GTCTTACACTAGCACTTGTCTC
1 -GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTC
* * * * * *
3665394 GATGCTGATGCCACGTCCCAGACAAGATCTTACACTAGCTCTCATATT
1 G-TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTC
3665442 GTGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTC
1 GT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC
3665481 ACACAAGTGA
Statistics
Matches: 178, Mismatches: 39, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
44 10 0.06
45 15 0.08
46 31 0.17
47 24 0.13
48 30 0.17
49 37 0.21
50 29 0.16
51 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTC
Found at i:3665841 original size:30 final size:30
Alignment explanation
Indices: 3665800--3665857 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
3665790 AAATTTACAC
*
3665800 CTTTGGTAAAATGACCATTTTGCCCCTAGA
1 CTTTGGCAAAATGACCATTTTGCCCCTAGA
3665830 CTTTGGCAAAATGACCATTTTGCCCCTA
1 CTTTGGCAAAATGACCATTTTGCCCCTA
3665858 TGCTTGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTGCCCCTAGA
Found at i:3682946 original size:55 final size:55
Alignment explanation
Indices: 3682877--3683003 Score: 166
Period size: 55 Copynumber: 2.3 Consensus size: 55
3682867 CCTTATGTAT
* * *
3682877 GCAATACTGACTTTAAAACACGGCCATGACACACACCCGTGTGGCTTGCCCGTGTA
1 GCAAAACTGACTTTAAAACACGACCATGACACACACCCGTGTGGCCTGCCCGTG-A
* * ** *
3682933 -CAACACTGACTTTAAAACACGACCATTACACACGTCCGTGTGGCCTGTCCGTGA
1 GCAAAACTGACTTTAAAACACGACCATGACACACACCCGTGTGGCCTGCCCGTGA
3682987 GCAAAACTGACTTTAAA
1 GCAAAACTGACTTTAAA
3683004 TTTTAAGTGC
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
54 1 0.02
55 61 0.98
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (55 bp):
GCAAAACTGACTTTAAAACACGACCATGACACACACCCGTGTGGCCTGCCCGTGA
Found at i:3686667 original size:44 final size:47
Alignment explanation
Indices: 3686509--3686729 Score: 155
Period size: 49 Copynumber: 4.7 Consensus size: 47
3686499 GGGATATGTT
* * * * * *
3686509 GCCGATGCCATGTCTCAGACATGGTCTTAGAGTGGCTATCATCATCGAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTATCACCCTCGAG
* * * ** **
3686558 GCTGATGCCATGTCCCAGACATGGTCTTATACTAGCTCTC-GTCTATATG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTATCACCCTCGA-G
* *
3686607 TGCTGATGCATGTCCCAGACATGTCTTACACTAGC-A-CAACCCT-TA-
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGCTATC-ACCCTCGAG
* ** * * *
3686652 GCCGATGCGTGTCCCAGACACATCTTACACTGGCTATCATCGTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTATCACCCTCGAG
3686699 GCCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
3686730 GGTACACAAG
Statistics
Matches: 138, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
44 29 0.21
45 4 0.03
46 3 0.02
47 30 0.22
48 16 0.12
49 49 0.36
50 7 0.05
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTATCACCCTCGAG
Found at i:3689247 original size:18 final size:18
Alignment explanation
Indices: 3689195--3689238 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3689185 TTTGTCATTA
* *
3689195 TTATTATCATCGTTATTG
1 TTATTATTATCATTATTG
*
3689213 TTATTATTATCATTATTT
1 TTATTATTATCATTATTG
3689231 TTATTATT
1 TTATTATT
3689239 TATTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (18 bp):
TTATTATTATCATTATTG
Found at i:3689555 original size:19 final size:21
Alignment explanation
Indices: 3689509--3689555 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
3689499 AATTTCACAT
*
3689509 ATGTTTTTTAAGAAAAAGGGA
1 ATGTTTTTTAAGAAAAAGGCA
* *
3689530 AT-TTTTTTTA-AAATAGGCA
1 ATGTTTTTTAAGAAAAAGGCA
3689549 ATGTTTT
1 ATGTTTT
3689556 GTATTTGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 9 0.41
20 11 0.50
21 2 0.09
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (21 bp):
ATGTTTTTTAAGAAAAAGGCA
Found at i:3691603 original size:38 final size:38
Alignment explanation
Indices: 3691556--3691652 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 38
3691546 AATAGAAATG
* * *
3691556 CGGTGATATTTGGGCTATGTGTCTAGTAGGCTTTGTGC
1 CGGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* *
3691594 CGGTAATATTCGGGCTATGTGCCTAGCAGGCTTTGTGT
1 CGGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* *
3691632 CGGTGATATTCAGGCTTTGTG
1 CGGTGATATTCGGGCTATGTG
3691653 TCGGTGTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.14, C:0.15, G:0.33, T:0.37
Consensus pattern (38 bp):
CGGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
Found at i:3691648 original size:22 final size:22
Alignment explanation
Indices: 3691620--3691669 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
3691610 ATGTGCCTAG
3691620 CAGGCTTTGTGTCGGTGATATT
1 CAGGCTTTGTGTCGGTGATATT
*
3691642 CAGGCTTTGTGTCGGTGTTATT
1 CAGGCTTTGTGTCGGTGATATT
*
3691664 CGGGCT
1 CAGGCT
3691670 CTGTACCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.10, C:0.16, G:0.34, T:0.40
Consensus pattern (22 bp):
CAGGCTTTGTGTCGGTGATATT
Found at i:3696109 original size:44 final size:41
Alignment explanation
Indices: 3695960--3696122 Score: 155
Period size: 43 Copynumber: 3.8 Consensus size: 41
3695950 AGCTCATACA
* * * * * *
3695960 ATGCCAAAGTCCCAAACGTTGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATC-AA-ATCG
* * *
3696003 ATGCCATTGTCTCAGACAGGGTCTTACACGAAATCAAATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAAT-CG
* * * *
3696045 ATACCGATGTCCCAGGCATGGTCTTACACATAAATCATAAGTCG
1 ATGCCAATGTCCCAGACATGGTCTTACAC-GAAATCA-AA-TCG
3696089 ATGCCAATGTCCCAGACATGGTCTTACACGAAAT
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAAT
3696123 TACATATCGA
Statistics
Matches: 96, Mismatches: 20, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
41 2 0.02
42 27 0.28
43 36 0.38
44 30 0.31
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATCG
Found at i:3702231 original size:2 final size:2
Alignment explanation
Indices: 3702224--3702262 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3702214 ATTACTGGTT
3702224 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3702263 CTTCATTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:3702494 original size:36 final size:36
Alignment explanation
Indices: 3702448--3702525 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
3702438 ATCTAATTTA
*
3702448 ATTTGATTTTAAAATATTAAATATTTAAATTTTATT
1 ATTTCATTTTAAAATATTAAATATTTAAATTTTATT
3702484 ATTTCATTTTAAAATATTAAATATTTAAATTTTATT
1 ATTTCATTTTAAAATATTAAATATTTAAATTTTATT
3702520 ATTTCA
1 ATTTCA
3702526 AATTTGAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (36 bp):
ATTTCATTTTAAAATATTAAATATTTAAATTTTATT
Found at i:3705526 original size:31 final size:31
Alignment explanation
Indices: 3705491--3705551 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3705481 ATAGTCACTA
* * *
3705491 AATTATTTGAAAGTTTTTATTTCAGTCATTG
1 AATTATTCGAAAATTTTTATTTAAGTCATTG
3705522 AATTATTCGAAAATTTTTATTTAAGTCATT
1 AATTATTCGAAAATTTTTATTTAAGTCATT
3705552 TGGCTCCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.51
Consensus pattern (31 bp):
AATTATTCGAAAATTTTTATTTAAGTCATTG
Found at i:3707437 original size:15 final size:15
Alignment explanation
Indices: 3707417--3707446 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3707407 CTAAGGAAAT
*
3707417 CCAAGCCGCTGCTTC
1 CCAAGCAGCTGCTTC
3707432 CCAAGCAGCTGCTTC
1 CCAAGCAGCTGCTTC
3707447 AACATATCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.43, G:0.20, T:0.20
Consensus pattern (15 bp):
CCAAGCAGCTGCTTC
Found at i:3708065 original size:6 final size:6
Alignment explanation
Indices: 3708030--3708057 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3708020 TATAGCTTGG
3708030 AAAAGA AAAAGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAA
3708058 AAGTAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:3709354 original size:40 final size:40
Alignment explanation
Indices: 3709309--3709397 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
3709299 CCAAATATAC
* *
3709309 TTATAAAAT-GTTATAAGAATTAAAA-AAATGTCATAAAATT
1 TTATAAAATATTTAT-A-AATTAAAATAAAGGTCATAAAATT
* *
3709349 TTATAAAATATTTATAAATTAAAATATAGGTTATAAAATT
1 TTATAAAATATTTATAAATTAAAATAAAGGTCATAAAATT
*
3709389 TTATGAAAT
1 TTATAAAAT
3709398 TAAGAACTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 8 0.19
40 30 0.71
41 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (40 bp):
TTATAAAATATTTATAAATTAAAATAAAGGTCATAAAATT
Found at i:3709356 original size:20 final size:20
Alignment explanation
Indices: 3709309--3709357 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
3709299 CCAAATATAC
*
3709309 TTATAAAATGTTATAAGAAT
1 TTATAAAATGTCATAAGAAT
* *
3709329 TAAAAAAATGTCATAA-AATT
1 TTATAAAATGTCATAAGAA-T
3709349 TTATAAAAT
1 TTATAAAAT
3709358 ATTTATAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (20 bp):
TTATAAAATGTCATAAGAAT
Found at i:3711368 original size:20 final size:21
Alignment explanation
Indices: 3711329--3711368 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3711319 TTGGGTGTCT
**
3711329 TAGTATCGTGATACCCATTAC
1 TAGTATCGCAATACCCATTAC
3711350 TAGTATCGCAATA-CCATTA
1 TAGTATCGCAATACCCATTA
3711369 TAGATAGCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (21 bp):
TAGTATCGCAATACCCATTAC
Found at i:3714166 original size:46 final size:46
Alignment explanation
Indices: 3714116--3714291 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
3714106 TGGTTGAGCA
3714116 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3714162 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
3714207 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
3714255 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3714292 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3714272 original size:93 final size:93
Alignment explanation
Indices: 3714113--3714283 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
3714103 GGATGGTTGA
* *
3714113 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3714178 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
3714206 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3714271 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3714284 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3717251 original size:15 final size:15
Alignment explanation
Indices: 3717231--3717299 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
3717221 GTATCTTGGG
3717231 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
3717246 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
3717261 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
3717276 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
3717291 TTTCTTTAT
1 TTTCTTTAT
3717300 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:3717300 original size:30 final size:30
Alignment explanation
Indices: 3717222--3717309 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
3717212 CATAGTATCG
* * * *
3717222 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
3717252 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
3717282 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
3717310 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:3719746 original size:46 final size:45
Alignment explanation
Indices: 3719696--3719871 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
3719686 TGTTTGGGCA
3719696 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
3719742 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
3719789 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
3719835 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3719872 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:3719851 original size:93 final size:93
Alignment explanation
Indices: 3719692--3719863 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
3719682 AGGATGTTTG
* *
3719692 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3719757 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
3719785 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3719850 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
3719864 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:3722505 original size:57 final size:58
Alignment explanation
Indices: 3722416--3722534 Score: 186
Period size: 57 Copynumber: 2.1 Consensus size: 58
3722406 TAGTTTACTC
* * * *
3722416 TAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATCTAT
1 TAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTAAATATTAAATATAT
*
3722474 TAAATTAATAGAATAC-TATCAAGATAAATATTAAATTAAATTAAATATTTAATATAT
1 TAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTAAATATTAAATATAT
3722531 TAAA
1 TAAA
3722535 ATAACATTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 41 0.73
58 15 0.27
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (58 bp):
TAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTAAATATTAAATATAT
Found at i:3727429 original size:46 final size:46
Alignment explanation
Indices: 3727377--3727635 Score: 349
Period size: 46 Copynumber: 5.6 Consensus size: 46
3727367 TGCTATAGTG
* * * * *
3727377 TCTTTCAACTATGGTCTTACTCATTTCCTGTCATGTTGCAATGATA
1 TCTTTCAACCATGGTCTTACACATTTCATGTCATGTTGCCATGGTA
** *
3727423 TCTTTCAACCATGGTCTTATTCATTTC-TCGTCATGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCAT-GTCATGTTGCCATGGTA
* *** * *
3727469 TCTTTCAACCATGGTGTTGTTCATTTCATGCCAAGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATGTCATGTTGCCATGGTA
* *
3727515 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATA
1 TCTTTCAACCATGGTCTTACACATTTCATGTCATGTTGCCATGGTA
*
3727561 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATGTCATGTTGCCATGGTA
3727607 TCTTTCAACCATGGTCTTACACATTTCAT
1 TCTTTCAACCATGGTCTTACACATTTCAT
3727636 TTTAGAAAGC
Statistics
Matches: 192, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 190 0.99
47 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATGTCATGTTGCCATGGTA
Found at i:3727587 original size:21 final size:21
Alignment explanation
Indices: 3727517--3727588 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
3727507 CCATGGTATC
3727517 TTTCAACCATGGTCTTACACA
1 TTTCAACCATGGTCTTACACA
* * * *
3727538 TTTCATATCATGTTGCCATGATATC-
1 TTTCA-ACCATG--GTC-TTACA-CA
3727563 TTTCAACCATGGTCTTACACA
1 TTTCAACCATGGTCTTACACA
3727584 TTTCA
1 TTTCA
3727589 TATCATGTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 1 0.03
21 13 0.35
22 7 0.19
24 7 0.19
25 8 0.22
26 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.39
Consensus pattern (21 bp):
TTTCAACCATGGTCTTACACA
Found at i:3727632 original size:138 final size:138
Alignment explanation
Indices: 3727377--3727635 Score: 385
Period size: 138 Copynumber: 1.9 Consensus size: 138
3727367 TGCTATAGTG
* * * *
3727377 TCTTTCAACTATGGTCTTACTCATTTCCTGTCATGTTGCAATGATATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCAATGATATCTTTCAACCATGGTCTTA
** * * ***
3727442 TTCATTTCTCGTCATGCTGCCATGGTATCTTTCAACCATGGTGTTGTTCATTTCATGCCAAGTTG
66 CACATTTCTCATCATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGCCAAGTTG
3727507 CCATGGTA
131 CCATGGTA
*
3727515 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCAATGATATCTTTCAACCATGGTCTTA
*
3727580 CACATTTCAT-ATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
66 CACATTTC-TCATCATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
3727636 TTTAGAAAGC
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
138 106 0.99
139 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (138 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCAATGATATCTTTCAACCATGGTCTTA
CACATTTCTCATCATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGCCAAGTTG
CCATGGTA
Found at i:3734271 original size:42 final size:42
Alignment explanation
Indices: 3734212--3734295 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
3734202 ATATTGACAT
*
3734212 AACTCAAAATTCCCCTTTTCTTCACTTTATTTCCTTATTTTA
1 AACTCAAAATTCCCCTTTTCTTCACTTTAATTCCTTATTTTA
3734254 AACTCAAAATTCCCCTTTTCTTCACTTTAATTCCTTATTTTA
1 AACTCAAAATTCCCCTTTTCTTCACTTTAATTCCTTATTTTA
3734296 CTATATCAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.26, G:0.00, T:0.49
Consensus pattern (42 bp):
AACTCAAAATTCCCCTTTTCTTCACTTTAATTCCTTATTTTA
Found at i:3734285 original size:21 final size:21
Alignment explanation
Indices: 3734219--3734287 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 21
3734209 CATAACTCAA
3734219 AATTCCCCTTTTCTTCACTTT
1 AATTCCCCTTTTCTTCACTTT
* * **
3734240 -ATT-TCCTTATT-TTAAACTCAA
1 AATTCCCCTT-TTCTT-CACT-TT
3734261 AATTCCCCTTTTCTTCACTTT
1 AATTCCCCTTTTCTTCACTTT
3734282 AATTCC
1 AATTCC
3734288 TTATTTTACT
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 6 0.18
20 8 0.24
21 6 0.18
22 8 0.24
23 6 0.18
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTCCCCTTTTCTTCACTTT
Found at i:3734518 original size:13 final size:14
Alignment explanation
Indices: 3734488--3734524 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3734478 CTATCCTTTC
*
3734488 ATTTCACATTTTAT
1 ATTTCACATTTAAT
3734502 -TTTCA-ATTTAAT
1 ATTTCACATTTAAT
3734514 ATTTCACATTT
1 ATTTCACATTT
3734525 GTCTCTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 6 0.30
13 10 0.50
14 4 0.20
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTCACATTTAAT
Found at i:3736894 original size:46 final size:46
Alignment explanation
Indices: 3736824--3737034 Score: 255
Period size: 46 Copynumber: 4.6 Consensus size: 46
3736814 TGCCATAGTG
* * * * * *
3736824 TCTTTCAACTATTGTTTTACTCATTTCCTGTCATGTTTCTATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCCTATCATGTTGCTATGGTA
** ** *
3736870 TCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCTATAGTA
1 TCTTTCAACCATGGTCTTACACATTTCCTATCATGTTGCTATGGTA
* * *
3736916 TCTTTCAACCATGGTCTTACACACTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCCTATCATGTTGCTATGGTA
*
3736962 TCTTTCAACCACGGTCTTACACATTTCAC-ATCATGTTGCCT-TGGTA
1 TCTTTCAACCATGGTCTTACACATTTC-CTATCATGTTG-CTATGGTA
3737008 TCTTTCAACCATGGTCTTACACATTTC
1 TCTTTCAACCATGGTCTTACACATTTC
3737035 ATTTCAGAAA
Statistics
Matches: 143, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
46 142 0.99
47 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCCTATCATGTTGCTATGGTA
Found at i:3752289 original size:39 final size:40
Alignment explanation
Indices: 3752241--3752648 Score: 126
Period size: 39 Copynumber: 10.1 Consensus size: 40
3752231 AACTTAATAC
3752241 TTATCTTAATAATATT-ATATTAATTTAATATTAAAATGA
1 TTATCTTAATAATATTAATATTAATTTAATATTAAAATGA
* * * *
3752280 TTATCTTAAT-AT-TTATTGTTTATCGTGT-ATA-TAAATATTCTA
1 TTATCTTAATAATATTAATATTAAT--T-TAATATTAAA-A-T-GA
* * * *
3752322 TTATTTTAATAAGATTTAATATTAAATTTAAT-CTAATAT--
1 TTATCTTAATAATA-TTAATATT-AATTTAATATTAAAATGA
*
3752361 TTATCTTGATAAATATTAATATTAATTTAATATTAAAATGA
1 TTATCTTAAT-AATATTAATATTAATTTAATATTAAAATGA
* * * * *
3752402 CTATCTTAA-CAT-TT-ATCGTTTATCGTGT-ATA-TAAATATTCTA
1 TTATCTTAATAATATTAAT-ATTAAT--T-TAATATTAAA-A-T-GA
* * * *
3752444 TTATTTTAATAAGATTTAATATTAAATTTAAT-CTAATAT--
1 TTATCTTAATAATA-TTAATATT-AATTTAATATTAAAATGA
*
3752483 TTATCTTGATAAATATTAATATTAATTTAATATTAAAATGA
1 TTATCTTAAT-AATATTAATATTAATTTAATATTAAAATGA
* * * * *
3752524 CTATCTTAA-CAT-TT-ATCGTTTATCGTGT-ATA-TAAATATTCTA
1 TTATCTTAATAATATTAAT-ATTAAT--T-TAATATTAAA-A-T-GA
* * * *
3752566 TTATTTTAATAAGATTTAATATTAAATTTAAT-CTAATAT--
1 TTATCTTAATAATA-TTAATATT-AATTTAATATTAAAATGA
*
3752605 TTATCTTGATAAATATTAATATTAATTTAATATTAAAATGA
1 TTATCTTAAT-AATATTAATATTAATTTAATATTAAAATGA
3752646 TTA
1 TTA
3752649 AGTTTAACCA
Statistics
Matches: 265, Mismatches: 51, Indels: 104
0.63 0.12 0.25
Matches are distributed among these distances:
37 6 0.02
38 43 0.16
39 89 0.34
40 24 0.09
41 23 0.09
42 29 0.11
43 9 0.03
44 18 0.07
45 14 0.05
46 10 0.04
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (40 bp):
TTATCTTAATAATATTAATATTAATTTAATATTAAAATGA
Found at i:3752407 original size:122 final size:122
Alignment explanation
Indices: 3752202--3752645 Score: 790
Period size: 122 Copynumber: 3.7 Consensus size: 122
3752192 TCAAAAATAA
* * *
3752202 TATTATTTTAAT-AG-TTTAATATTAATTTTAA-CTTAATACTTATCTTAAT-AATATT-ATATT
1 TATTATTTTAATAAGATTTAATATTAAATTTAATC-TAATATTTATCTTGATAAATATTAATATT
* * *
3752262 AATTTAATATTAAAATGATTATCTTAATATTTATTGTTTATCGTGTATATAAATATTC
65 AATTTAATATTAAAATGACTATCTTAACATTTATCGTTTATCGTGTATATAAATATTC
3752320 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTAATATTA
1 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTAATATTA
3752385 ATTTAATATTAAAATGACTATCTTAACATTTATCGTTTATCGTGTATATAAATATTC
66 ATTTAATATTAAAATGACTATCTTAACATTTATCGTTTATCGTGTATATAAATATTC
3752442 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTAATATTA
1 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTAATATTA
3752507 ATTTAATATTAAAATGACTATCTTAACATTTATCGTTTATCGTGTATATAAATATTC
66 ATTTAATATTAAAATGACTATCTTAACATTTATCGTTTATCGTGTATATAAATATTC
3752564 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTAATATTA
1 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTAATATTA
3752629 ATTTAATATTAAAATGA
66 ATTTAATATTAAAATGA
3752646 TTAAGTTTAA
Statistics
Matches: 315, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
118 12 0.04
119 2 0.01
120 30 0.10
121 7 0.02
122 264 0.84
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (122 bp):
TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTAATATTA
ATTTAATATTAAAATGACTATCTTAACATTTATCGTTTATCGTGTATATAAATATTC
Found at i:3758899 original size:17 final size:17
Alignment explanation
Indices: 3758877--3758911 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3758867 TCGCGACTTG
3758877 GTGGCGATCAAGTTTGA
1 GTGGCGATCAAGTTTGA
3758894 GTGGCGATCAAGTTTGA
1 GTGGCGATCAAGTTTGA
3758911 G
1 G
3758912 CGTTGCTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.37, T:0.29
Consensus pattern (17 bp):
GTGGCGATCAAGTTTGA
Found at i:3765261 original size:35 final size:35
Alignment explanation
Indices: 3765207--3765275 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
3765197 TGTCCCATGA
*
3765207 AAATGTATCCATTGAATGATAAATTATCACTTTCT
1 AAATGTAACCATTGAATGATAAATTATCACTTTCT
* *
3765242 AAATGTAACTATTGCATGATAAATTATCACTTTC
1 AAATGTAACCATTGAATGATAAATTATCACTTTC
3765276 CAAAATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (35 bp):
AAATGTAACCATTGAATGATAAATTATCACTTTCT
Found at i:3766016 original size:22 final size:22
Alignment explanation
Indices: 3765988--3766032 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3765978 TAAATACAAA
3765988 TATTATTAATAAATTTATTATT
1 TATTATTAATAAATTTATTATT
3766010 TATTATTAATAAATTTATTATT
1 TATTATTAATAAATTTATTATT
3766032 T
1 T
3766033 TAACATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTATTAATAAATTTATTATT
Found at i:3772766 original size:182 final size:182
Alignment explanation
Indices: 3772443--3772819 Score: 551
Period size: 182 Copynumber: 2.1 Consensus size: 182
3772433 GTTTTTTTGG
* *
3772443 ATTGGGTCTTTAA-TGGTTCGAATCAGTTCAAGTTTTAATCACTTCACCTTCAAGTTAATTCAAA
1 ATTGGGTCATTAAGAGGTTCGAATCAGTTCAAGTTTTAATCACTTCACCTTCAAGTTAATTCAAA
* *
3772507 TTCAATTCAATTTGGGTTTAGAGTCAGGTGGTTTGAGATTTTTAATGATCAAATAGGATGGGGTT
66 TTCAATTCAATTTGGGTTTAGAGTCAGGTGGTTTGAGATTTTTAATGATCAAATAGGATGAGATT
* * *
3772572 GAATTAGAGTTTGAATTGATTGATTCGAATATTCAAATTCGGATATTTTCAA
131 GAATTAGAGTTTGAATCGATTGATTCAAATATTCAAATTCGAATATTTTCAA
* **
3772624 ATTGGGTCATTAAGAGGTTCGAATCAGTTCAAGTTTTAATCACTTTATGTTCAAGTTAATTCAAA
1 ATTGGGTCATTAAGAGGTTCGAATCAGTTCAAGTTTTAATCACTTCACCTTCAAGTTAATTCAAA
** * * *
3772689 TTTGATTCAATTTGGGTTTA-AGGTTAGGTGGTTTGAGTTTTTTAATGATCAAATTGGATGAGAT
66 TTCAATTCAATTTGGGTTTAGA-GTCAGGTGGTTTGAGATTTTTAATGATCAAATAGGATGAGAT
* * *
3772753 TGAATTTGAGTTTGAATCGATTGATTCAAATATTCAAATTTGAATTTTTTCAA
130 TGAATTAGAGTTTGAATCGATTGATTCAAATATTCAAATTCGAATATTTTCAA
* *
3772806 GTCGGGTCATTAAG
1 ATTGGGTCATTAAG
3772820 GATCCAGATC
Statistics
Matches: 174, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
181 13 0.07
182 161 0.93
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (182 bp):
ATTGGGTCATTAAGAGGTTCGAATCAGTTCAAGTTTTAATCACTTCACCTTCAAGTTAATTCAAA
TTCAATTCAATTTGGGTTTAGAGTCAGGTGGTTTGAGATTTTTAATGATCAAATAGGATGAGATT
GAATTAGAGTTTGAATCGATTGATTCAAATATTCAAATTCGAATATTTTCAA
Found at i:3777454 original size:16 final size:17
Alignment explanation
Indices: 3777430--3777462 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3777420 CTGGTGAGAG
*
3777430 TTCATTTCAT-TGGCCC
1 TTCACTTCATATGGCCC
3777446 TTCACTTCATATGGCCC
1 TTCACTTCATATGGCCC
3777463 ATTGCAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.15, C:0.33, G:0.12, T:0.39
Consensus pattern (17 bp):
TTCACTTCATATGGCCC
Found at i:3777569 original size:14 final size:14
Alignment explanation
Indices: 3777550--3777576 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3777540 ACAAAAGAAT
3777550 TATTTAATAAAAGA
1 TATTTAATAAAAGA
3777564 TATTTAATAAAAG
1 TATTTAATAAAAG
3777577 TCATCTGGCA
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:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
TATTTAATAAAAGA
Found at i:3777693 original size:2 final size:2
Alignment explanation
Indices: 3777688--3777715 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3777678 CCCACCCCCC
3777688 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3777716 ATTAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3778810 original size:23 final size:22
Alignment explanation
Indices: 3778774--3778818 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3778764 TACATAACTG
3778774 TTTAAAATATATATAATAATAAA
1 TTTAAAATATATATAA-AATAAA
*
3778797 TTTAAAAT-TAATATTAAATAAA
1 TTTAAAATAT-ATATAAAATAAA
3778819 ATAAAAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATATATATAAAATAAA
Found at i:3779104 original size:22 final size:22
Alignment explanation
Indices: 3779076--3779118 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3779066 AATTTATTCA
3779076 TATTTTTTTGAAAG-TATTTATG
1 TATTTTTTT-AAAGTTATTTATG
3779098 TATTTTTTTAAAGTTATTTAT
1 TATTTTTTTAAAGTTATTTAT
3779119 AAATTTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (22 bp):
TATTTTTTTAAAGTTATTTATG
Found at i:3779124 original size:22 final size:22
Alignment explanation
Indices: 3779077--3779125 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3779067 ATTTATTCAT
**
3779077 ATTTTTTTGAAAGTATTTATGT
1 ATTTTTTTGAAAGTATTTATAA
3779099 ATTTTTTT-AAAGTTATTTATAA
1 ATTTTTTTGAAAG-TATTTATAA
3779121 ATTTT
1 ATTTT
3779126 GAGGGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (22 bp):
ATTTTTTTGAAAGTATTTATAA
Found at i:3779125 original size:21 final size:20
Alignment explanation
Indices: 3779062--3779119 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
3779052 TAATACAAAA
* *
3779062 TTTAAATTTATTCATATTTT
1 TTTAAAGTTATTTATATTTT
3779082 TTTGAAAG-TATTTATGTATTTT
1 TTT-AAAGTTATTTA--TATTTT
3779104 TTTAAAGTTATTTATA
1 TTTAAAGTTATTTATA
3779120 AATTTTGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 10 0.31
21 7 0.22
22 15 0.47
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTAAAGTTATTTATATTTT
Found at i:3782075 original size:16 final size:16
Alignment explanation
Indices: 3782051--3782092 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3782041 AAAATTTATA
*
3782051 TATTCTTTAGAATTTT
1 TATTTTTTAGAATTTT
*
3782067 TATTTTTTATAATTTT
1 TATTTTTTAGAATTTT
3782083 TAATTTTTTA
1 T-ATTTTTTA
3782093 AAATATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
TATTTTTTAGAATTTT
Found at i:3782103 original size:23 final size:24
Alignment explanation
Indices: 3782077--3782122 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
3782067 TATTTTTTAT
*
3782077 AATTTTTAATTTTTTA-AAATATA
1 AATTTTGAATTTTTTATAAATATA
3782100 AATTTTGAATTTTTTATAAATAT
1 AATTTTGAATTTTTTATAAATAT
3782123 TTTGAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
AATTTTGAATTTTTTATAAATATA
Found at i:3782119 original size:18 final size:18
Alignment explanation
Indices: 3782096--3782161 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 18
3782086 TTTTTTAAAA
3782096 TATAAATTTTGAATTTTT
1 TATAAATTTTGAATTTTT
3782114 TATAAATATTTTGAATTTTT
1 TAT-AA-ATTTTGAATTTTT
* *
3782134 AAATTAATTTT-AATTCTTT
1 -TATAAATTTTGAATT-TTT
3782153 T-TAAATTTT
1 TATAAATTTT
3782162 TTTATTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 7 0.17
18 7 0.17
19 10 0.25
20 14 0.35
21 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (18 bp):
TATAAATTTTGAATTTTT
Found at i:3782126 original size:20 final size:20
Alignment explanation
Indices: 3782068--3782133 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
3782058 TAGAATTTTT
3782068 ATTTTTTAT-AAT-TTTT-A
1 ATTTTTTATAAATATTTTGA
*
3782085 ATTTTTTAAAATATAAATTTTGA
1 ATTTTTTATAA-AT--ATTTTGA
3782108 ATTTTTTATAAATATTTTGA
1 ATTTTTTATAAATATTTTGA
3782128 ATTTTT
1 ATTTTT
3782134 AAATTAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 8 0.20
18 1 0.02
19 2 0.05
20 13 0.32
22 6 0.15
23 11 0.27
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTTTTATAAATATTTTGA
Found at i:3782877 original size:29 final size:31
Alignment explanation
Indices: 3782844--3782901 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3782834 TTCAGGTATT
*
3782844 ACATTGGACA-TTT-TCAAAGTACAAATATC
1 ACATTAGACATTTTATCAAAGTACAAATATC
*
3782873 ACATTAGACATTTTATGAAAGTACAAATA
1 ACATTAGACATTTTATCAAAGTACAAATA
3782902 AAACACCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
30 3 0.12
31 13 0.52
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (31 bp):
ACATTAGACATTTTATCAAAGTACAAATATC
Found at i:3783395 original size:29 final size:29
Alignment explanation
Indices: 3783307--3783396 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 29
3783297 CCTAGTTTTC
* * * **
3783307 TTTGAAAATTCATATTAATCCTCTCAAAAT
1 TTTGAAAATTCTTATTAAACCT-TTAATTT
* *
3783337 TTTAAAAAAT-TTATCTAAACC-TT-ATGTT
1 TTTGAAAATTCTTAT-TAAACCTTTAAT-TT
3783365 TTTGAAAATTCTTATTAAACCTTTAATTT
1 TTTGAAAATTCTTATTAAACCTTTAATTT
3783394 TTT
1 TTT
3783397 TTAAGAAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
27 1 0.02
28 16 0.35
29 14 0.30
30 15 0.33
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTGAAAATTCTTATTAAACCTTTAATTT
Found at i:3783711 original size:9 final size:9
Alignment explanation
Indices: 3783697--3783748 Score: 77
Period size: 9 Copynumber: 5.8 Consensus size: 9
3783687 TTTGGTTAAA
3783697 AATTACCCG
1 AATTACCCG
*
3783706 AATTACTCG
1 AATTACCCG
3783715 AATTACCCG
1 AATTACCCG
*
3783724 AATTAACCG
1 AATTACCCG
*
3783733 AATTAACCG
1 AATTACCCG
3783742 AATTACC
1 AATTACC
3783749 GAAAAATACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:3786350 original size:200 final size:200
Alignment explanation
Indices: 3785989--3786374 Score: 549
Period size: 200 Copynumber: 1.9 Consensus size: 200
3785979 AAATACCCTC
*
3785989 ATTTTTCCTAACTAGTTGGACTAGGAAACCAAACACACATTCAGCCAAACCCCCTACTTAAATTC
1 ATTTTTCCTAACTAGTTGGACTAGAAAACCAAACACACATTCAGCCAAACCCCCTACTTAAATTC
* *
3786054 TGCTATAAGTACCTATATTTTATAAAAATTATGGATATAGTTTCTATATTTTTTTAGGTTTTGAA
66 TGCTATAAGTACCTATACTTTATAAAAATTATAGATATAGTTTCTATATTTTTTTAGGTTTTGAA
* * * *
3786119 ATTTTAATCTTGATTTAAACTGTAACAATTAAATCTGTTTGGTAAAATTCAGTTACCAGTAGATA
131 ATTTTAATCTTGACTCAAACTGTAACAATTAAATCTATTTGGTAAAATTCAATTACCAGTAGATA
3786184 TGCCT
196 TGCCT
* * ** *
3786189 ATTTTTCTTAACTAGTTGGACTAGAAAACCAAACACACATTCTGCCAAACCCTTGTACTTATATT
1 ATTTTTCCTAACTAGTTGGACTAGAAAACCAAACACACATTCAGCCAAACCC-CCTACTTAAATT
* * * * * *
3786254 TTGCTATAAGTCCCTATACTTTATGAAAATTGTAGATTTAGTTTCTATATTTTTTT-GGTTTTTA
65 CTGCTATAAGTACCTATACTTTATAAAAATTATAGATATAGTTTCTATATTTTTTTAGGTTTTGA
* * * * *
3786318 AATTTTAGTTTTGACTCAAATTGTAGCAATTAAATCTATTTGGTTAAATTCAATTAC
130 AATTTTAATCTTGACTCAAACTGTAACAATTAAATCTATTTGGTAAAATTCAATTAC
3786375 TAGTCTTGTA
Statistics
Matches: 162, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
200 104 0.64
201 58 0.36
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (200 bp):
ATTTTTCCTAACTAGTTGGACTAGAAAACCAAACACACATTCAGCCAAACCCCCTACTTAAATTC
TGCTATAAGTACCTATACTTTATAAAAATTATAGATATAGTTTCTATATTTTTTTAGGTTTTGAA
ATTTTAATCTTGACTCAAACTGTAACAATTAAATCTATTTGGTAAAATTCAATTACCAGTAGATA
TGCCT
Found at i:3793634 original size:34 final size:34
Alignment explanation
Indices: 3793595--3793660 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
3793585 CGATAATATA
3793595 TACTATTAGTATTATATAATTAAGGTATGTTAGT
1 TACTATTAGTATTATATAATTAAGGTATGTTAGT
3793629 TACTATTAGTATTATATAATTAAGGTATGTTA
1 TACTATTAGTATTATATAATTAAGGTATGTTA
3793661 ATTATGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (34 bp):
TACTATTAGTATTATATAATTAAGGTATGTTAGT
Found at i:3794369 original size:13 final size:12
Alignment explanation
Indices: 3794353--3794399 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
3794343 AAACTTATTA
3794353 TTAATTATTATAT
1 TTAATT-TTATAT
*
3794366 TTAAATTTAT-T
1 TTAATTTTATAT
3794377 ATTAATTGTTATAT
1 -TTAATT-TTATAT
3794391 TTAATTTTA
1 TTAATTTTA
3794400 GAAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 1 0.03
12 12 0.41
13 15 0.52
14 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (12 bp):
TTAATTTTATAT
Found at i:3794399 original size:25 final size:25
Alignment explanation
Indices: 3794341--3794399 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
3794331 ATAAAAAAAG
*
3794341 TTAAACTTATTATTAATTATTATAT
1 TTAAATTTATTATTAATTATTATAT
*
3794366 TTAAATTTATTATTAATTGTTATAT
1 TTAAATTTATTATTAATTATTATAT
*
3794391 TTAATTTTA
1 TTAAATTTA
3794400 GAAATTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TTAAATTTATTATTAATTATTATAT
Found at i:3795707 original size:40 final size:40
Alignment explanation
Indices: 3795640--3795873 Score: 274
Period size: 40 Copynumber: 5.9 Consensus size: 40
3795630 TTATTGTATG
*
3795640 ATTGCACATACATGCCCCTGTTTGTAC-TCTGGTACCCCTA
1 ATTGCACATACGTGCCCCTGTTTGTACTTC-GGTACCCCTA
* **
3795680 ATTACATGTACGTGCCCCTGTTTGTACTTCGGTACCCCTA
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTA
* * * *
3795720 ATGGCACATACGTGCCCCTGTTTGTACTTCGATACCCTTG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTA
* * * *
3795760 ATTGCACATACATG-CCCTGTTTGTACTTCAGTGCCCCTT
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTA
* * * *
3795799 ATTGTACATACGTGCCCCTATTTGTACTTTGGTACCCCTG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTA
* * *
3795839 GTTGCACATATGTGCCCCTGTTTGTAATTCGGTAC
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
3795874 TCTGAATGCA
Statistics
Matches: 161, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
39 32 0.20
40 127 0.79
41 2 0.01
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (40 bp):
ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTA
Found at i:3795717 original size:20 final size:20
Alignment explanation
Indices: 3795694--3795873 Score: 55
Period size: 20 Copynumber: 9.1 Consensus size: 20
3795684 CATGTACGTG
3795694 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
** * * * *
3795714 CCCCTAATGGCACATAC-GTG
1 CCCCTGTTTGTAC-TTCGGTA
*
3795734 CCCCTGTTTGTACTTCGATA
1 CCCCTGTTTGTACTTCGGTA
* * * * *
3795754 CCCTTGATTGCACATAC-AT-
1 CCCCTGTTTGTAC-TTCGGTA
* * *
3795773 GCCCTGTTTGTACTTCAGTG
1 CCCCTGTTTGTACTTCGGTA
* *
3795793 CCCCT-TATTGTACATAC-GTG
1 CCCCTGT-TTGTAC-TTCGGTA
* *
3795813 CCCCTATTTGTACTTTGGTA
1 CCCCTGTTTGTACTTCGGTA
* * * ** *
3795833 CCCCTGGTTGCACATATGTG
1 CCCCTGTTTGTACTTCGGTA
*
3795853 CCCCTGTTTGTAATTCGGTA
1 CCCCTGTTTGTACTTCGGTA
3795873 C
1 C
3795874 TCTGAATGCA
Statistics
Matches: 109, Mismatches: 42, Indels: 18
0.64 0.25 0.11
Matches are distributed among these distances:
18 2 0.02
19 14 0.13
20 86 0.79
21 7 0.06
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.36
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:3795854 original size:119 final size:119
Alignment explanation
Indices: 3795638--3795906 Score: 330
Period size: 119 Copynumber: 2.3 Consensus size: 119
3795628 AATTATTGTA
* *
3795638 TGATTGCACATACATGCCCCTGTTTGTAC-TCTGGTACCCCTAATTACATGTACGTGCCCCTGTT
1 TGATTGCACATACATGCCCCTGTTTGTACTTCTAGTACCCCTAATTACA-GTACGTGCCCCTATT
*
3795702 TGTACTTCGGTACCCCTAATGGCACATACGTGCCCCTGTTTGTACTTCGATACCC
65 TGTACTTCGGTACCCCTAATGGCACATACGTGCCCCTGTTTGTAATTCGATACCC
* *
3795757 TTGATTGCACATACATG-CCCTGTTTGTACTTC-AGTGCCCCTTATTGTACA-TACGTGCCCCTA
1 -TGATTGCACATACATGCCCCTGTTTGTACTTCTAGTACCCC-TAAT-TACAGTACGTGCCCCTA
* ** * * * *
3795819 TTTGTACTTTGGTACCCCTGGTTGCACATATGTGCCCCTGTTTGTAATTCGGTACTC
63 TTTGTACTTCGGTACCCCTAATGGCACATACGTGCCCCTGTTTGTAATTCGATACCC
* * * *
3795876 TGAATGCACTTCCATGCCCCTGTTTATACTT
1 TGATTGCACATACATGCCCCTGTTTGTACTT
3795907 GATAACTCTG
Statistics
Matches: 129, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
118 13 0.10
119 91 0.71
120 21 0.16
121 4 0.03
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (119 bp):
TGATTGCACATACATGCCCCTGTTTGTACTTCTAGTACCCCTAATTACAGTACGTGCCCCTATTT
GTACTTCGGTACCCCTAATGGCACATACGTGCCCCTGTTTGTAATTCGATACCC
Found at i:3795894 original size:79 final size:78
Alignment explanation
Indices: 3795642--3795906 Score: 271
Period size: 79 Copynumber: 3.3 Consensus size: 78
3795632 ATTGTATGAT
* * * **
3795642 TGCACATACATGCCCCTGTTTGTACTCTGGTACCCCTAATTACATGTACGTGCCCCTGTTTGTAC
1 TGCACATACATGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTAC
3795707 TTCGGTACCCCTAA
66 TTCGGTA-CCCTAA
* * * * *
3795721 TGGCACATACGTGCCCCTGTTTGTACTTCGATACCCTTGATTGCACATACATG-CCCTGTTTGTA
1 T-GCACATACATGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTA
* * *
3795785 CTTCAGTGCCCCTTAT
65 CTTCGGT-ACCC-TAA
* * * * * *
3795801 TGTACATACGTGCCCCTATTTGTACTTTGGTACCCCTGGTTGCACATATGTGCCCCTGTTTGTAA
1 TGCACATACATGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTAC
*
3795866 TTCGGTACTCTGAA
66 TTCGGTACCCT-AA
* * *
3795880 TGCACTTCCATGCCCCTGTTTATACTT
1 TGCACATACATGCCCCTGTTTGTACTT
3795907 GATAACTCTG
Statistics
Matches: 149, Mismatches: 32, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
78 1 0.01
79 88 0.59
80 60 0.40
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.35
Consensus pattern (78 bp):
TGCACATACATGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTAC
TTCGGTACCCTAA
Found at i:3803782 original size:40 final size:40
Alignment explanation
Indices: 3803699--3803961 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
3803689 TTGAATGCTG
* * * * * *
3803699 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
3803739 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
3803779 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
3803819 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
3803859 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
3803899 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
3803938 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
3803962 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:3803981 original size:79 final size:80
Alignment explanation
Indices: 3803738--3803996 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
3803728 AAGTGAATAT
* * * * * *
3803738 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
3803802 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
3803818 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
3803883 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
3803898 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
3803962 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
3803977 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
3803997 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:3811734 original size:40 final size:40
Alignment explanation
Indices: 3811651--3811913 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
3811641 TTGAATGCTG
* * * * * *
3811651 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
3811691 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
3811731 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
3811771 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
3811811 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
3811851 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
3811890 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
3811914 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:3811933 original size:79 final size:80
Alignment explanation
Indices: 3811690--3811948 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
3811680 AAGTGAATAT
* * * * * *
3811690 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
3811754 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
3811770 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
3811835 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
3811850 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
3811914 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
3811929 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
3811949 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:3819550 original size:38 final size:37
Alignment explanation
Indices: 3819485--3819598 Score: 99
Period size: 37 Copynumber: 3.0 Consensus size: 37
3819475 ATATACATAC
*
3819485 AATAATAAAAATCAATG--TAAACAATATATAATGAAG
1 AATAATAAAAAT-AAAGAATAAACAATATATAATGAAG
*
3819521 ATATAATAAAAATAAAGAATAAACAATATA-CATGACAG
1 A-ATAATAAAAATAAAGAATAAACAATATATAATGA-AG
* * *
3819559 AATAACAAACCAATATATAATAAAACAATATATACATGAA
1 AATAATAAA--AATAAAGAAT-AAACAATATATA-ATGAA
3819599 AGCATCTTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
36 4 0.06
37 22 0.35
38 14 0.22
39 8 0.13
40 10 0.16
41 1 0.02
42 4 0.06
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.23
Consensus pattern (37 bp):
AATAATAAAAATAAAGAATAAACAATATATAATGAAG
Found at i:3821138 original size:14 final size:14
Alignment explanation
Indices: 3821119--3821160 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
3821109 GGACCTTTAA
3821119 ATTATTTTGGTTTT
1 ATTATTTTGGTTTT
*
3821133 ATTATTTTTGTTTT
1 ATTATTTTGGTTTT
*
3821147 ATTTTTTTGGTTTT
1 ATTATTTTGGTTTT
3821161 TGTTTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (14 bp):
ATTATTTTGGTTTT
Found at i:3821166 original size:14 final size:14
Alignment explanation
Indices: 3821123--3821169 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
3821113 CTTTAAATTA
3821123 TTTTGGTTTTATTAT
1 TTTTGGTTTTATT-T
3821138 TTTT-GTTTTATTT
1 TTTTGGTTTTATTT
3821151 TTTTGGTTTT-TGTT
1 TTTTGGTTTTAT-TT
3821165 TTTTG
1 TTTTG
3821170 TGTGAGCCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.20
14 20 0.67
15 4 0.13
ACGTcount: A:0.06, C:0.00, G:0.15, T:0.79
Consensus pattern (14 bp):
TTTTGGTTTTATTT
Found at i:3825721 original size:39 final size:39
Alignment explanation
Indices: 3825687--3825855 Score: 234
Period size: 39 Copynumber: 4.3 Consensus size: 39
3825677 TTTAAGCTCA
* * *
3825687 GATATATTTCCAGCATGTAACCTGCGAACCTTAAGTCCG
1 GATATAATTCCAGCATATAGCCTGCGAACCTTAAGTCCG
3825726 GATTATAATTCCAGCATATAGCCTGC-AGACCTTAAGTCCG
1 GA-TATAATTCCAGCATATAGCCTGCGA-ACCTTAAGTCCG
* * *
3825766 GATATATTTCTAGCATATAGCCTGC-AGACCTTAAGTTCG
1 GATATAATTCCAGCATATAGCCTGCGA-ACCTTAAGTCCG
*
3825805 GATATAATTCCAGCATATAGCCTGCGGACCTTAAGTCCG
1 GATATAATTCCAGCATATAGCCTGCGAACCTTAAGTCCG
3825844 GATATAATTCCA
1 GATATAATTCCA
3825856 AATATCATGC
Statistics
Matches: 117, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
39 83 0.71
40 34 0.29
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (39 bp):
GATATAATTCCAGCATATAGCCTGCGAACCTTAAGTCCG
Found at i:3825841 original size:78 final size:79
Alignment explanation
Indices: 3825687--3825855 Score: 261
Period size: 78 Copynumber: 2.2 Consensus size: 79
3825677 TTTAAGCTCA
*
3825687 GATATATTTCCAGCATGTAACCTGCGAACCTTAAGTCCGGATTATAATTCCAGCATATAGCCTGC
1 GATATATTTCCAGCATATAACCTGCGAACCTTAAGTCCGGATTATAATTCCAGCATATAGCCTGC
3825752 AGACCTTAAGTCCG
66 AGACCTTAAGTCCG
* * *
3825766 GATATATTTCTAGCATATAGCCTGC-AGACCTTAAGTTCGGA-TATAATTCCAGCATATAGCCTG
1 GATATATTTCCAGCATATAACCTGCGA-ACCTTAAGTCCGGATTATAATTCCAGCATATAGCCTG
*
3825829 CGGACCTTAAGTCCG
65 CAGACCTTAAGTCCG
*
3825844 GATATAATTCCA
1 GATATATTTCCA
3825856 AATATCATGC
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
78 47 0.57
79 35 0.43
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (79 bp):
GATATATTTCCAGCATATAACCTGCGAACCTTAAGTCCGGATTATAATTCCAGCATATAGCCTGC
AGACCTTAAGTCCG
Found at i:3832287 original size:16 final size:17
Alignment explanation
Indices: 3832263--3832297 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3832253 TTTGTAGCCA
*
3832263 AAAGCAAAAA-AAAAAT
1 AAAGAAAAAAGAAAAAT
3832279 AAAGAAAAAAGAAAAAT
1 AAAGAAAAAAGAAAAAT
3832296 AA
1 AA
3832298 TACAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.83, C:0.03, G:0.09, T:0.06
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAAT
Found at i:3832579 original size:19 final size:19
Alignment explanation
Indices: 3832557--3832596 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
3832547 TTAATTCGGT
*
3832557 TTTGGGTTTTAAATTTGGG
1 TTTGGGTTTGAAATTTGGG
3832576 TTTGGGTTTGAAATTTGGG
1 TTTGGGTTTGAAATTTGGG
3832595 TT
1 TT
3832597 ATGTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.53
Consensus pattern (19 bp):
TTTGGGTTTGAAATTTGGG
Found at i:3834715 original size:49 final size:49
Alignment explanation
Indices: 3834656--3834830 Score: 242
Period size: 49 Copynumber: 3.5 Consensus size: 49
3834646 TGAGGTCACG
** *
3834656 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTGGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * * *
3834705 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCGCA
*
3834756 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
3834805 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
3834831 TGCGTACAAG
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 65 0.60
50 4 0.04
51 40 0.37
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:3834779 original size:51 final size:49
Alignment explanation
Indices: 3834649--3834843 Score: 237
Period size: 49 Copynumber: 3.9 Consensus size: 49
3834639 GCTATTGTGA
* * **
3834649 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
** * *
3834698 GGTCGTATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA-TT
* * * *
3834748 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * *
3834798 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACAAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
3834844 GATTCAGCTA
Statistics
Matches: 122, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 78 0.64
50 4 0.03
51 40 0.33
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
Found at i:3834824 original size:100 final size:100
Alignment explanation
Indices: 3834651--3834837 Score: 338
Period size: 100 Copynumber: 1.9 Consensus size: 100
3834641 TATTGTGAGG
** *
3834651 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTGGTCGTATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
3834716 AAGTGCAGGCTACTATGCGTACCTGATAACTTCGA
66 AAGTGCAGGCTACTATGCGTACCTGATAACTTCGA
*
3834751 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
3834816 AAGTGCAGGCTACTATGCGTAC
66 AAGTGCAGGCTACTATGCGTAC
3834838 AAGATAGATT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCTGATAACTTCGA
Found at i:3836474 original size:64 final size:64
Alignment explanation
Indices: 3836371--3836494 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 64
3836361 AGGCCTATGC
* * * * *
3836371 TTATGCCAAATAATTAGGATGTTATGATCGACATGAATCAATTGTTCCTAACTAGATGTGATGT
1 TTATGCCAAATAATTAGGATGCTATGATCGAAATAAATCAAATGCTCCTAACTAGATGTGATGT
* *
3836435 TTATGTCAAATAATTAGTATGCTATGATCGAAATAAATCAAATGCTCCTAACTAGATGTG
1 TTATGCCAAATAATTAGGATGCTATGATCGAAATAAATCAAATGCTCCTAACTAGATGTG
3836495 TTATAAATGA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (64 bp):
TTATGCCAAATAATTAGGATGCTATGATCGAAATAAATCAAATGCTCCTAACTAGATGTGATGT
Found at i:3837700 original size:14 final size:13
Alignment explanation
Indices: 3837673--3837727 Score: 76
Period size: 14 Copynumber: 4.2 Consensus size: 13
3837663 TGGCCTCTCC
3837673 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
*
3837686 TCTTCTTTCTCTTT
1 TTTTCTTT-TCTTT
3837700 TTTTCTTTTTCTTT
1 TTTTC-TTTTCTTT
3837714 TTTTCTTTT-TTT
1 TTTTCTTTTCTTT
3837726 TT
1 TT
3837728 GTGAAGGTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
12 5 0.13
13 11 0.29
14 19 0.50
15 3 0.08
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Found at i:3837706 original size:22 final size:22
Alignment explanation
Indices: 3837678--3837725 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3837668 TCTCCTTTTC
3837678 TTTTC-TTTTCTTCTTTCTCTTT
1 TTTTCTTTTTCTT-TTTCTCTTT
*
3837700 TTTTCTTTTTCTTTTTTTCTTT
1 TTTTCTTTTTCTTTTTCTCTTT
3837722 TTTT
1 TTTT
3837726 TTGTGAAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTCTTTTTCTTTTTCTCTTT
Found at i:3837725 original size:8 final size:8
Alignment explanation
Indices: 3837673--3837725 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
3837663 TGGCCTCTCC
3837673 TTTTCTTTT
1 TTTTC-TTT
3837682 CTTTTCTTCT
1 -TTTTCTT-T
*
3837692 TTCTCTTT
1 TTTTCTTT
3837700 TTTTC--T
1 TTTTCTTT
3837706 TTTTCTTT
1 TTTTCTTT
3837714 TTTTCTTT
1 TTTTCTTT
3837722 TTTT
1 TTTT
3837726 TTGTGAAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 6 0.16
8 18 0.47
9 8 0.21
10 6 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTCTTT
Found at i:3840191 original size:19 final size:19
Alignment explanation
Indices: 3840167--3840214 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
3840157 GGGAAAATTT
*
3840167 AATGCAAATGATGCAATGC
1 AATGCAAATGATGCAACGC
3840186 AATGCAAATGATGCAACGC
1 AATGCAAATGATGCAACGC
*
3840205 AATGAAAATG
1 AATGCAAATG
3840215 CATGGGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.19
Consensus pattern (19 bp):
AATGCAAATGATGCAACGC
Found at i:3844466 original size:19 final size:18
Alignment explanation
Indices: 3844442--3844480 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
3844432 TTATTTCAGT
3844442 TTTGGGTTTAAAATTTGGG
1 TTTGGGTTTAAAA-TTGGG
*
3844461 TTTGGGTTTGAAATTGGG
1 TTTGGGTTTAAAATTGGG
3844479 TT
1 TT
3844481 CTGTAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (18 bp):
TTTGGGTTTAAAATTGGG
Found at i:3845463 original size:46 final size:48
Alignment explanation
Indices: 3845391--3845493 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 48
3845381 GACAAGACAG
* * * *
3845391 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
*
3845437 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
3845485 GACAGGAAT
1 GACAGGAAT
3845494 AATTCATGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 27 0.54
47 1 0.02
48 22 0.44
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
Done.