Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_pilon, whole genome shotgun sequence
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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 18
Found at i:3492086 original size:19 final size:19
Alignment explanation
Indices: 3492038--3492088 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3492028 CAGTGCTTGA
3492038 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
3492057 AACCGAG-TTGACTGGTCTG
1 AACCG-GTTTGACCGGTCTG
3492076 -ACTCGGTTTGACC
1 AAC-CGGTTTGACC
3492089 CGACGCGACC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.11
19 23 0.85
20 1 0.04
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:3493964 original size:40 final size:39
Alignment explanation
Indices: 3493920--3494008 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 39
3493910 GCAAAGTTGA
* * *
3493920 CATCTTTGGTTGGTGGCTAACTTGTACACATTGATAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTACACA-TGAGAAATT
* * * *
3493960 CATCTTTAGTAGGTGGCCAACTTGTGCACATGGGAATTT
1 CATCTTTGGTAGGTGGCCAACTTGTACACATGAGAAATT
3493999 CATCTTTGGT
1 CATCTTTGGT
3494009 CCCTAAAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 15 0.37
40 26 0.63
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (39 bp):
CATCTTTGGTAGGTGGCCAACTTGTACACATGAGAAATT
Found at i:3495582 original size:13 final size:13
Alignment explanation
Indices: 3495564--3495595 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3495554 CCAGTATAAA
3495564 CATTGCCTCTTAT
1 CATTGCCTCTTAT
3495577 CATTGCCTCTTAT
1 CATTGCCTCTTAT
3495590 CATTGC
1 CATTGC
3495596 AGCCTAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.31, G:0.09, T:0.44
Consensus pattern (13 bp):
CATTGCCTCTTAT
Found at i:3497153 original size:18 final size:18
Alignment explanation
Indices: 3497130--3497179 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3497120 TATTTTATAT
3497130 ATATTAACTTAAATTCAC
1 ATATTAACTTAAATTCAC
* * *
3497148 ATATTAAATTAATTTTAC
1 ATATTAACTTAAATTCAC
*
3497166 ATCTTAACATTAAA
1 ATATTAAC-TTAAA
3497180 AAATATATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTAACTTAAATTCAC
Found at i:3497253 original size:30 final size:29
Alignment explanation
Indices: 3497204--3497308 Score: 95
Period size: 30 Copynumber: 3.5 Consensus size: 29
3497194 TTAATTTATT
* *
3497204 TATTTTATTTTATTTTTTTAAACCTAAAAATA
1 TATTTTA--TTATTATTTTAAA-TTAAAAATA
3497236 TATTTTATTATTATTTT-AATTAAAATAATA
1 TATTTTATTATTATTTTAAATT-AAA-AATA
* * *
3497266 TATTTTAATCTTATCTTAAATTAAAAATA
1 TATTTTATTATTATTTTAAATTAAAAATA
* *
3497295 TAATTTATTCTTAT
1 TATTTTATTATTAT
3497309 CCTAACTCAA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.02
29 21 0.33
30 30 0.48
31 4 0.06
32 7 0.11
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (29 bp):
TATTTTATTATTATTTTAAATTAAAAATA
Found at i:3497425 original size:24 final size:24
Alignment explanation
Indices: 3497393--3497451 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
3497383 AGTTAAGATA
*
3497393 AAAAT-AAAATATATTTTTTAGTT
1 AAAATAAAAATATATTTTTAAGTT
3497416 AAAATAAAAATATATTTTTAAGTT
1 AAAATAAAAATATATTTTTAAGTT
* *
3497440 AAGATAAGAATA
1 AAAATAAAAATA
3497452 AAAGATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 5 0.16
24 27 0.84
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (24 bp):
AAAATAAAAATATATTTTTAAGTT
Found at i:3497454 original size:30 final size:29
Alignment explanation
Indices: 3497383--3497522 Score: 119
Period size: 30 Copynumber: 4.9 Consensus size: 29
3497373 TTTTTTTTGT
* *
3497383 AGTTAAGATAAAAATAAAATATATTTTTT
1 AGTTAAGATAAGAATAAAATATATTTTTA
*
3497412 AGTT-A-A-AA-TA-AAAATATATTTTTA
1 AGTTAAGATAAGAATAAAATATATTTTTA
*
3497436 AGTTAAGATAAGAATAAAAGATATGTTTTA
1 AGTTAAGATAAGAATAAAATATAT-TTTTA
* ** *
3497466 AGTTAAAATAAGAATTAATTTATATTTAATA
1 AGTTAAGATAAGAA-TAAAATATATTT-TTA
* * *
3497497 ATTTAAGGTAAGAATAGAATATATTT
1 AGTTAAGATAAGAATAAAATATATTT
3497523 AATAATTTAA
Statistics
Matches: 88, Mismatches: 15, Indels: 15
0.75 0.13 0.13
Matches are distributed among these distances:
24 17 0.19
25 2 0.02
26 3 0.03
27 3 0.03
28 2 0.02
29 12 0.14
30 29 0.33
31 20 0.23
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (29 bp):
AGTTAAGATAAGAATAAAATATATTTTTA
Found at i:3497523 original size:36 final size:38
Alignment explanation
Indices: 3497462--3497532 Score: 87
Period size: 36 Copynumber: 1.9 Consensus size: 38
3497452 AAAGATATGT
*
3497462 TTTAAGTTAAAATAAGAATTAATTT-AT-ATTTAATAA
1 TTTAAGGTAAAATAAGAATTAATTTAATAATTTAATAA
3497498 TTTAAGGTAAGAAT-AGAA-TATATTTAATAATTTAA
1 TTTAAGGTAA-AATAAGAATTA-ATTTAATAATTTAA
3497533 GTCCGAGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
35 2 0.07
36 17 0.57
37 5 0.17
38 6 0.20
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.42
Consensus pattern (38 bp):
TTTAAGGTAAAATAAGAATTAATTTAATAATTTAATAA
Found at i:3499707 original size:9 final size:9
Alignment explanation
Indices: 3499679--3499712 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3499669 ATATTATTCT
3499679 TTAATTAAA
1 TTAATTAAA
*
3499688 TT-ATAAAA
1 TTAATTAAA
3499696 TTAATTAAA
1 TTAATTAAA
3499705 TTAATTAA
1 TTAATTAA
3499713 CATAAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:3500210 original size:23 final size:23
Alignment explanation
Indices: 3500164--3500210 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3500154 AGTAAATTCG
*
3500164 AAATAAAAATAAAATATATGATT
1 AAATAAAAATAAAATAAATGATT
* *
3500187 AAATAAAAATAATATAAATTATT
1 AAATAAAAATAAAATAAATGATT
3500210 A
1 A
3500211 GTCAATATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
AAATAAAAATAAAATAAATGATT
Found at i:3500627 original size:23 final size:24
Alignment explanation
Indices: 3500601--3500652 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
3500591 TCACCGGCCA
*
3500601 ACCACCTG-CCGGTCACTATT-AC
1 ACCACCTGCCCGATCACTATTCAC
3500623 GACCA-CTGCCCGATCACTATTCAC
1 -ACCACCTGCCCGATCACTATTCAC
3500647 ACCACC
1 ACCACC
3500653 GGTCACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 3 0.12
23 19 0.76
24 3 0.12
ACGTcount: A:0.25, C:0.44, G:0.12, T:0.19
Consensus pattern (24 bp):
ACCACCTGCCCGATCACTATTCAC
Found at i:3501391 original size:3 final size:3
Alignment explanation
Indices: 3501383--3501441 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
3501373 ATATTTGTTA
* **
3501383 AAT AAT AAT AAT AAT AAT -AT ATAT AAT ATT AAT AAT AAT AAT TTT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
3501428 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
3501442 AATGAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:3501654 original size:45 final size:45
Alignment explanation
Indices: 3501600--3501693 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
3501590 AGTCTTATAA
3501600 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAG
1 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAG
3501645 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAG
1 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAG
3501690 ATGA
1 ATGA
3501694 ACATCATGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.22
Consensus pattern (45 bp):
ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAG
Found at i:3501706 original size:29 final size:29
Alignment explanation
Indices: 3501664--3501722 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3501654 AGGTTTTGAA
3501664 AACATCATGCACTGAAGGGCTTACAGATG
1 AACATCATGCACTGAAGGGCTTACAGATG
3501693 AACATCATGCACTGAAGGGCTTACAGATG
1 AACATCATGCACTGAAGGGCTTACAGATG
3501722 A
1 A
3501723 CCCGAAGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (29 bp):
AACATCATGCACTGAAGGGCTTACAGATG
Found at i:3501740 original size:74 final size:74
Alignment explanation
Indices: 3501619--3501767 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
3501609 AGGTTTTGAA
3501619 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
3501684 TTACAGATG
66 TTACAGATG
3501693 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
3501758 TTACAGATG
66 TTACAGATG
3501767 A
1 A
3501768 CCCGAAGGTT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (74 bp):
AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
TTACAGATG
Found at i:3501745 original size:45 final size:45
Alignment explanation
Indices: 3501693--3502014 Score: 590
Period size: 45 Copynumber: 7.2 Consensus size: 45
3501683 CTTACAGATG
3501693 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
3501738 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
*
3501783 AACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
*
3501828 AACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
* *
3501873 AACATCATGCACTGAAGGGTTTACAGATGACCCGAATGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
3501918 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
*
3501963 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
*
3502008 AATATCA
1 AACATCA
3502015 AAAAGCTCCC
Statistics
Matches: 269, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 269 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (45 bp):
AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAA
Found at i:3501819 original size:20 final size:20
Alignment explanation
Indices: 3501794--3501865 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
3501784 ACATCATGCA
3501794 CTGAAGGGCTTACAGATGAC
1 CTGAAGGGCTTACAGATGAC
** *
3501814 CTGAAGGTTTTGAAAACATCATG-C
1 CTGAAGGGCTT----ACA-GATGAC
3501838 ACTGAAGGGCTTACAGATGAC
1 -CTGAAGGGCTTACAGATGAC
3501859 CTGAAGG
1 CTGAAGG
3501866 TTTTGAAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 19 0.49
21 4 0.10
24 4 0.10
25 12 0.31
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (20 bp):
CTGAAGGGCTTACAGATGAC
Found at i:3502774 original size:22 final size:22
Alignment explanation
Indices: 3502713--3502776 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
3502703 AAATTCAATA
* * *
3502713 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
3502735 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
3502757 AATCTATCATCTTTGAAGAG
1 AATCTATCATCTTTGAAGAG
3502777 TGTAGATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:3510859 original size:9 final size:9
Alignment explanation
Indices: 3510831--3510864 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3510821 ATATTATTCT
3510831 TTAATTAAA
1 TTAATTAAA
*
3510840 TT-ATAAAA
1 TTAATTAAA
3510848 TTAATTAAA
1 TTAATTAAA
3510857 TTAATTAA
1 TTAATTAA
3510865 CATAAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:3511365 original size:23 final size:23
Alignment explanation
Indices: 3511294--3511365 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
3511284 TATGTGATAA
*
3511294 AAATAATAAATAAGTATTAAATT-TG
1 AAATAA-AAATAA-TA-TAAATTATT
* * *
3511319 AAATAAAAATAAAATATATGATT
1 AAATAAAAATAATATAAATTATT
3511342 AAATAAAAATAATATAAATTATT
1 AAATAAAAATAATATAAATTATT
3511365 A
1 A
3511366 GTCAATATTC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 4 0.10
23 23 0.59
24 6 0.15
25 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATAAAAATAATATAAATTATT
Found at i:3511774 original size:23 final size:22
Alignment explanation
Indices: 3511748--3511831 Score: 93
Period size: 23 Copynumber: 3.9 Consensus size: 22
3511738 AAACTCTGTT
3511748 CACCGGCCGGTCACTATTACGAC
1 CACCGGCCGGTCACTATT-CGAC
* *
3511771 CACCGGTCGGTTACTATTCCGAC
1 CACCGGCCGGTCACTATT-CGAC
*
3511794 CACTGGCCGGTCACTATTC-A-
1 CACCGGCCGGTCACTATTCGAC
*
3511814 CGCC-GCCGGTCACTATTC
1 CACCGGCCGGTCACTATTC
3511832 TGGGTACTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.26
20 2 0.04
21 1 0.02
22 1 0.02
23 35 0.66
ACGTcount: A:0.18, C:0.38, G:0.21, T:0.23
Consensus pattern (22 bp):
CACCGGCCGGTCACTATTCGAC
Found at i:3512301 original size:29 final size:29
Alignment explanation
Indices: 3512262--3512318 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
3512252 GTGACGTCAT
* *
3512262 GGCGGCGTCGGAGTAGACCACTTGGAGGC
1 GGCGACGTCGGAATAGACCACTTGGAGGC
*
3512291 GGCGACGTCGGAATGGACCACTTGGAGG
1 GGCGACGTCGGAATAGACCACTTGGAGG
3512319 TAGTGGCCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.19, C:0.23, G:0.44, T:0.14
Consensus pattern (29 bp):
GGCGACGTCGGAATAGACCACTTGGAGGC
Found at i:3512548 original size:3 final size:3
Alignment explanation
Indices: 3512540--3512597 Score: 64
Period size: 3 Copynumber: 18.7 Consensus size: 3
3512530 ATATTTGTTA
* *
3512540 AAT AAT AAT AAT AAT ATAT ATAT AAT ATT AAT AAT AAT AAT -TT CAAT
1 AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT -AAT
3512587 AAT AAT AAT AA
1 AAT AAT AAT AA
3512598 AATGAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 1 0.02
3 39 0.81
4 8 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:3512918 original size:31 final size:31
Alignment explanation
Indices: 3512845--3512907 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
3512835 TACATCGGGT
* *
3512845 ACCATATTGCAAATGGACTAAATGTTGAGGG
1 ACCATATTACAAACGGACTAAATGTTGAGGG
*
3512876 ACCATATTACAAACGGACTAAATGTTGGGGG
1 ACCATATTACAAACGGACTAAATGTTGAGGG
3512907 A
1 A
3512908 TTGTATTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (31 bp):
ACCATATTACAAACGGACTAAATGTTGAGGG
Found at i:3513382 original size:21 final size:21
Alignment explanation
Indices: 3513345--3513384 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3513335 TGGGATTAGC
*
3513345 GTAATTACATGAGTTACAAAA
1 GTAATTACACGAGTTACAAAA
3513366 GTAATTACAACGA-TTACAA
1 GTAATTAC-ACGAGTTACAA
3513385 TCTACTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (21 bp):
GTAATTACACGAGTTACAAAA
Found at i:3515059 original size:16 final size:16
Alignment explanation
Indices: 3515038--3515080 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
3515028 AGTCTGACTC
3515038 GTTGACTTTGAATAGT
1 GTTGACTTTGAATAGT
*
3515054 GTTGACTTTGACTAGT
1 GTTGACTTTGAATAGT
*
3515070 TTTGACTTTGA
1 GTTGACTTTGA
3515081 TCGAAAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.47
Consensus pattern (16 bp):
GTTGACTTTGAATAGT
Found at i:3521912 original size:23 final size:21
Alignment explanation
Indices: 3521860--3521921 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
3521850 TTTTGGTGCA
*
3521860 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
3521880 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
3521901 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
3521922 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:3528942 original size:15 final size:15
Alignment explanation
Indices: 3528909--3528939 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3528899 CATAAATACT
3528909 AATAAAACTAAACTA
1 AATAAAACTAAACTA
3528924 AATAAAA-TAAACTA
1 AATAAAACTAAACTA
3528938 AA
1 AA
3528940 ATAGTTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAAACTAAACTA
Found at i:3538804 original size:14 final size:14
Alignment explanation
Indices: 3538771--3538798 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3538761 TTCCTTACTG
3538771 TGTGATTCACAAGA
1 TGTGATTCACAAGA
3538785 TGTGATTCACAAGA
1 TGTGATTCACAAGA
3538799 CTTGATAAAT
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:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
TGTGATTCACAAGA
Found at i:3539255 original size:33 final size:34
Alignment explanation
Indices: 3539218--3539287 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 34
3539208 ACGAAATTAG
3539218 TTTATAACAGAAGGTTATAAATATAAAA-GGAAT
1 TTTATAACAGAAGGTTATAAATATAAAAGGGAAT
* *
3539251 TTTATAACATAAGGTTATAAGTATAAAAGGGAAT
1 TTTATAACAGAAGGTTATAAATATAAAAGGGAAT
3539285 TTT
1 TTT
3539288 GTACAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 26 0.76
34 8 0.24
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (34 bp):
TTTATAACAGAAGGTTATAAATATAAAAGGGAAT
Found at i:3544900 original size:30 final size:30
Alignment explanation
Indices: 3544866--3545004 Score: 78
Period size: 31 Copynumber: 4.7 Consensus size: 30
3544856 TATTTTAAAG
3544866 TTAAAATAAGAATAAAATATATTTAATAAT
1 TTAAAATAAGAATAAAATATATTTAATAAT
* * * *
3544896 TTAAAGTAATAATATAATATA-AT-AT-AT
1 TTAAAATAAGAATAAAATATATTTAATAAT
* * * * *
3544923 TT--AGTAA-ATTAAGTATATACTTTAAAAAA
1 TTAAAATAAGAATAA-AATATA-TTTAATAAT
*
3544952 TTAAAATAATAATAAAATATATTTTTTAA-AAT
1 TTAAAATAAGAATAAAATATA---TTTAATAAT
*
3544984 TTAGAA-AAGAATAAAATATAT
1 TTAAAATAAGAATAAAATATAT
3545005 ATATTTTTAA
Statistics
Matches: 82, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
24 3 0.04
25 10 0.12
27 5 0.06
28 4 0.05
29 4 0.05
30 18 0.22
31 22 0.27
32 11 0.13
33 5 0.06
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (30 bp):
TTAAAATAAGAATAAAATATATTTAATAAT
Found at i:3544923 original size:35 final size:36
Alignment explanation
Indices: 3544859--3544934 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
3544849 GTTAAAGTAT
3544859 TTTAAAGTTAAAATAAGAATAAAATATATTTAATAA
1 TTTAAAGTTAAAATAAGAATAAAATATATTTAATAA
* * *
3544895 TTTAAAG-TAATAAT-ATAATATAATATATTTAGTAA
1 TTTAAAGTTAA-AATAAGAATAAAATATATTTAATAA
*
3544930 ATTAA
1 TTTAA
3544935 GTATATACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 25 0.71
36 10 0.29
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (36 bp):
TTTAAAGTTAAAATAAGAATAAAATATATTTAATAA
Found at i:3544980 original size:33 final size:31
Alignment explanation
Indices: 3544947--3545039 Score: 82
Period size: 32 Copynumber: 2.9 Consensus size: 31
3544937 ATATACTTTA
*
3544947 AAAAATTAAAATAATAATAAAATATATTTTTT
1 AAAAATTAAAA-AAGAATAAAATATATTTTTT
* *
3544979 AAAATTTAGAAAAGAATAAAATATATATATTTT
1 AAAAATTAAAAAAGAATAAAATATAT-T-TTTT
* * *
3545012 -TAAATCAAAAGAAAAATAAAATAT-TTTT
1 AAAAATTAAAA-AAGAATAAAATATATTTT
3545040 AAATTCAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
30 2 0.04
31 15 0.30
32 17 0.34
33 16 0.32
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (31 bp):
AAAAATTAAAAAAGAATAAAATATATTTTTT
Found at i:3546408 original size:15 final size:15
Alignment explanation
Indices: 3546356--3546408 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
3546346 ATATTTAGTT
* *
3546356 GGGCGGGAGGATGTG
1 GGGCGGGTGGATGCG
*
3546371 GGGCGGGCGGATGCG
1 GGGCGGGTGGATGCG
*
3546386 GGGTGGGTGGATGCG
1 GGGCGGGTGGATGCG
3546401 GGGCGGGT
1 GGGCGGGT
3546409 AAGGTCTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.11, G:0.68, T:0.13
Consensus pattern (15 bp):
GGGCGGGTGGATGCG
Found at i:3546881 original size:25 final size:23
Alignment explanation
Indices: 3546853--3546903 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
3546843 TACCAAAAAG
*
3546853 TAAAGAAAAATGTGCTACAAAGGCA
1 TAAAGAAAAATGT-C-ACAAAGACA
* *
3546878 TAAATAAACATGTCACAAAGACA
1 TAAAGAAAAATGTCACAAAGACA
3546901 TAA
1 TAA
3546904 TTATTATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 11 0.48
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.18
Consensus pattern (23 bp):
TAAAGAAAAATGTCACAAAGACA
Found at i:3549854 original size:21 final size:21
Alignment explanation
Indices: 3549830--3549877 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
3549820 AACATGACAT
3549830 CCATAACAACAAACTTGAAAC
1 CCATAACAACAAACTTGAAAC
* *
3549851 CCATAACAACCAACTTGAAAT
1 CCATAACAACAAACTTGAAAC
3549872 CCATAA
1 CCATAA
3549878 TAATAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.29, G:0.04, T:0.17
Consensus pattern (21 bp):
CCATAACAACAAACTTGAAAC
Found at i:3549938 original size:3 final size:3
Alignment explanation
Indices: 3549928--3549973 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
3549918 CCAAAAAAAA
*
3549928 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAC TAT TACT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
3549972 TA
1 TA
3549974 ATTACATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.11
3 32 0.84
4 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3550157 original size:28 final size:28
Alignment explanation
Indices: 3550115--3550181 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
3550105 CCCAGCATTT
*
3550115 GACCCGGATCAAGACTCGAATCTGGATCC
1 GACCC-GATCCAGACTCGAATCTGGATCC
*
3550144 GACCCGATCCAGACTTGAATCTGGATCC
1 GACCCGATCCAGACTCGAATCTGGATCC
3550172 GACCCGATCC
1 GACCCGATCC
3550182 TTTAGGGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 31 0.86
29 5 0.14
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.18
Consensus pattern (28 bp):
GACCCGATCCAGACTCGAATCTGGATCC
Found at i:3551065 original size:11 final size:11
Alignment explanation
Indices: 3551049--3551073 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3551039 TTTTCCTAAT
3551049 TTTGTCTTATA
1 TTTGTCTTATA
3551060 TTTGTCTTATA
1 TTTGTCTTATA
3551071 TTT
1 TTT
3551074 TATTTTAGTC
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTGTCTTATA
Found at i:3551410 original size:30 final size:30
Alignment explanation
Indices: 3551265--3551670 Score: 239
Period size: 30 Copynumber: 13.6 Consensus size: 30
3551255 TGTTAATACC
* * * *
3551265 ATTTTAGTCCCTTAAGTTTCTA-TTTTACC
1 ATTTTAGTCCTTTAATTTTCTATTTTTGCT
* * *
3551294 ATTTTAGTCAC-TTAACTATT-TGTTTTTACT
1 ATTTTAGTC-CTTTAA-TTTTCTATTTTTGCT
* *
3551324 ATTTTAGTCCTTTAAATATT-TATTTATGCT
1 ATTTTAGTCCTTT-AATTTTCTATTTTTGCT
* * *
3551354 ATTTTAATCCCTTAAGTTT-TAGTTTTTGCT
1 ATTTTAGTCCTTTAATTTTCTA-TTTTTGCT
*
3551384 ATTTTAGTCCTTTTATTTTCTATTTTTGCT
1 ATTTTAGTCCTTTAATTTTCTATTTTTGCT
* * * * **
3551414 A-TTTAGACCCTTAAGTTTCTACTTTTATT
1 ATTTTAGTCCTTTAATTTTCTATTTTTGCT
* *
3551443 ATTTTAG-CCATTTAAGTTTT-TATTTTTTCC
1 ATTTTAGTCC-TTTAA-TTTTCTATTTTTGCT
* * *
3551473 ATTTTAGTCCTTTAAATTTCTATTTGTGTT
1 ATTTTAGTCCTTTAATTTTCTATTTTTGCT
* * * * * *
3551503 ATTTTTGTCATTTGAGTTTATGTTTTTG-T
1 ATTTTAGTCCTTTAATTTTCTATTTTTGCT
* *
3551532 -TGTTTAGTCCTTTAAGTTTCTATTTTTCCT
1 AT-TTTAGTCCTTTAATTTTCTATTTTTGCT
* * *
3551562 ATTTTAATCCTTTAATTTTTTATTTGTGCT
1 ATTTTAGTCCTTTAATTTTCTATTTTTGCT
* * *
3551592 A-TTTACGTCCCTAAAGTTTT-TGTTTTTGCT
1 ATTTTA-GTCCTTTAA-TTTTCTATTTTTGCT
* *
3551622 ATTTTAGT-CTTGTAAATTTCTATTTTTTTTCT
1 ATTTTAGTCCTT-TAATTTTCTA--TTTTTGCT
3551654 A-TTTAGTCCTTT-ATTTT
1 ATTTTAGTCCTTTAATTTT
3551671 ACTAAGCATG
Statistics
Matches: 291, Mismatches: 63, Indels: 45
0.73 0.16 0.11
Matches are distributed among these distances:
28 1 0.00
29 78 0.27
30 176 0.60
31 25 0.09
32 11 0.04
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.59
Consensus pattern (30 bp):
ATTTTAGTCCTTTAATTTTCTATTTTTGCT
Found at i:3551419 original size:119 final size:118
Alignment explanation
Indices: 3551265--3551664 Score: 344
Period size: 119 Copynumber: 3.3 Consensus size: 118
3551255 TGTTAATACC
* * * * *
3551265 ATTTTAGTCCCTTAAGTTTCTA-TTTTACCATTTTAGTCACTTAACTATT-TGTTTTTACTATTT
1 ATTTTAGTCCTTTAAGTTTCTATTTTTGCTA-TTTAGTC-CTTAAGT-TTCTATTTTTACTATTT
* *
3551328 TAGTCCTTTAAATATTTATTTATGCTATTTTAATCCCTTAAGTTTTAGTTTTTGCT
63 TAGTCCTTTAAATTTTTATTTATGCTATTTTAGTCCCTTAAGTTTTAGTTTTTGCT
* * * * *
3551384 ATTTTAGTCCTTTTATTTTCTATTTTTGCTATTTAGACCCTTAAGTTTCTACTTTTATTATTTTA
1 ATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTAG-TCCTTAAGTTTCTATTTTTACTATTTTA
* * * * * * * *
3551449 G-CCATTTAAGTTTTTATTTTTTCCATTTTAGTCCTTTAAATTTCTA-TTTGTGTT
65 GTCC-TTTAAATTTTTATTTATGCTATTTTAGTCCCTTAAGTTT-TAGTTTTTGCT
* * * * * * * *
3551503 ATTTTTGTCATTTGAGTTTATGTTTTTGTTGTTTAGTCCTTTAAGTTTCTATTTTTCCTATTTTA
1 ATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTAGTCC-TTAAGTTTCTATTTTTACTATTTTA
* * * * *
3551568 ATCCTTTAATTTTTTATTTGTGCTA-TTTACGTCCCTAAAGTTTTTGTTTTTGCT
65 GTCCTTTAAATTTTTATTTATGCTATTTTA-GTCCCTTAAGTTTTAGTTTTTGCT
* *
3551622 ATTTTAGT-CTTGTAAATTTCTATTTTTTTTCTATTTAGTCCTT
1 ATTTTAGTCCTT-TAAGTTTCTA--TTTTTGCTATTTAGTCCTT
3551665 TATTTTACTA
Statistics
Matches: 217, Mismatches: 52, Indels: 23
0.74 0.18 0.08
Matches are distributed among these distances:
118 13 0.06
119 177 0.82
120 13 0.06
121 14 0.06
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.59
Consensus pattern (118 bp):
ATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTAGTCCTTAAGTTTCTATTTTTACTATTTTAG
TCCTTTAAATTTTTATTTATGCTATTTTAGTCCCTTAAGTTTTAGTTTTTGCT
Found at i:3551610 original size:89 final size:88
Alignment explanation
Indices: 3551266--3551670 Score: 271
Period size: 89 Copynumber: 4.6 Consensus size: 88
3551256 GTTAATACCA
* * * *
3551266 TTTTAGTCCCTTAAGTTTCTA-TTTTACC-ATTTTAGTCAC-TTAACTATTTGT-TTT-TACTAT
1 TTTTAGTCCTTTAAGTTTCTAGTTTTTCCTATTTTAGTC-CTTTAA-T-TTTCTATTTGTGCTA-
* * * *
3551326 TTTAGTCCTTTAAATATT-TATTTATGCT
62 TTTAGTCCCTTAAGT-TTATGTTTTTG-T
* * * * *
3551354 ATTTTAATCCCTTAAGTTT-TAGTTTTTGCTATTTTAGTCCTTTTATTTTCTATTTTTGCTATTT
1 -TTTTAGTCCTTTAAGTTTCTAGTTTTTCCTATTTTAGTCCTTTAATTTTCTATTTGTGCTATTT
* * *
3551418 AGACCCTTAAGTTTCTACTTTTAT-T
65 AGTCCCTTAAGTTTAT-GTTTT-TGT
* * * *
3551443 ATTTTAG-CCATTTAAGTTTTTATTTTTTCC-ATTTTAGTCCTTTAAATTTCTATTTGTGTTATT
1 -TTTTAGTCC-TTTAAGTTTCTAGTTTTTCCTATTTTAGTCCTTTAATTTTCTATTTGTGCTA-T
* ** *
3551506 TTTGTCATTTGAGTTTATGTTTTTGT
63 TTAGTCCCTTAAGTTTATGTTTTTGT
* *
3551532 TGTTTAGTCCTTTAAGTTTCTA-TTTTTCCTATTTTAATCCTTTAATTTTTTATTTGTGCTATTT
1 T-TTTAGTCCTTTAAGTTTCTAGTTTTTCCTATTTTAGTCCTTTAATTTTCTATTTGTGCTATTT
* *
3551596 ACGTCCCTAAAGTTTTTGTTTTTGCT
65 A-GTCCCTTAAGTTTATGTTTTTG-T
* * *
3551622 ATTTTAGT-CTTGTAAATTTCTATTTTTTTTCTA-TTTAGTCCTTT-ATTTT
1 -TTTTAGTCCTT-TAAGTTTCTA-GTTTTTCCTATTTTAGTCCTTTAATTTT
3551671 ACTAAGCATG
Statistics
Matches: 255, Mismatches: 40, Indels: 41
0.76 0.12 0.12
Matches are distributed among these distances:
88 22 0.09
89 150 0.59
90 63 0.25
91 12 0.05
92 8 0.03
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.60
Consensus pattern (88 bp):
TTTTAGTCCTTTAAGTTTCTAGTTTTTCCTATTTTAGTCCTTTAATTTTCTATTTGTGCTATTTA
GTCCCTTAAGTTTATGTTTTTGT
Found at i:3557100 original size:36 final size:38
Alignment explanation
Indices: 3557037--3557138 Score: 109
Period size: 38 Copynumber: 2.7 Consensus size: 38
3557027 ATCTTCTTAA
* * * *
3557037 AAAAATAAAGTGTCGTCTCGCTAGAGAC-AGTTT-TCTT
1 AAAAATAAA-TTTTGTCTCGCTTGAGACAACTTTCTCTT
3557074 AAAAATAAATTTTGTCTCGCTTGAGACAACTTTCTCTT
1 AAAAATAAATTTTGTCTCGCTTGAGACAACTTTCTCTT
* * * *
3557112 TAAAACAAATTCTGTCTTGCTTGAGAC
1 AAAAATAAATTTTGTCTCGCTTGAGAC
3557139 TTTTTCCACA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 15 0.27
37 13 0.24
38 27 0.49
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (38 bp):
AAAAATAAATTTTGTCTCGCTTGAGACAACTTTCTCTT
Found at i:3557489 original size:28 final size:30
Alignment explanation
Indices: 3557457--3557518 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
3557447 CTTGAGACAA
*
3557457 TTTCTCTT-G-AAACAAATCTTTGAATCTG
1 TTTCTCTTGGAAAAAAAATCTTTGAATCTG
* *
3557485 TTTCTTTTGGAAAAAAAATCTTTGAGTCTG
1 TTTCTCTTGGAAAAAAAATCTTTGAATCTG
3557515 TTTC
1 TTTC
3557519 ACTTAACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 7 0.24
29 1 0.03
30 21 0.72
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (30 bp):
TTTCTCTTGGAAAAAAAATCTTTGAATCTG
Found at i:3557860 original size:64 final size:66
Alignment explanation
Indices: 3557699--3557868 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 66
3557689 TTTGAGATTG
* *
3557699 TTTCCCTTAAAACGAATTTTGTCTCATTTGAGATAGTTTTCCATGAAACATCGATCTTTAAGAAC
1 TTTCCCTTAAAACGAATTTTGTCTCATTTGAGACAGTTTCCCATGAAACATCGATCTTTAAGAAC
*
3557764 G
66 A
* ** * * * * *
3557765 TTTCCCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTTAAACGTC-ATCTTTGAG-TC
1 TTTCCCTTAAAACGAATTTTGTCTCATTTGAGACAGTTTCCCATGAAACATCGATCTTTAAGAAC
3557828 A
66 A
* *
3557829 TTTCCCTTGAAACGAATTTTGTCTCTTTTGAGACAGTTTC
1 TTTCCCTTAAAACGAATTTTGTCTCATTTGAGACAGTTTC
3557869 TTTTGAAACA
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 37 0.42
65 8 0.09
66 44 0.49
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (66 bp):
TTTCCCTTAAAACGAATTTTGTCTCATTTGAGACAGTTTCCCATGAAACATCGATCTTTAAGAAC
A
Found at i:3558186 original size:133 final size:133
Alignment explanation
Indices: 3557964--3558300 Score: 462
Period size: 133 Copynumber: 2.5 Consensus size: 133
3557954 CCAGCCATCC
* * * *
3557964 TCATCACGTAGGAATCGTATCATCCCCTAACCAGACCTCCTCATCATGTAGGA-TCCGTGTCACC
1 TCATCACGTATGAGTCGTGTCATCCCC-GACCAGACCTCCTCATCATGTAGGAGT-CGTGTCACC
* *
3558028 CCTAGATAATTAGCCGTCTGAATCGCATAGGAACCAAGTTATCACCCTTTCTAAAGATGGCAAGA
64 CCTAGATAACTAGCCGTCTGAATCGCATAGGAACCAAGTTATCACCCTTCCTAAAGATGGCAAGA
3558093 ACTCT
129 ACTCT
* * * * *
3558098 TCATCACGTATGAGTCATGTCATCCCCGACCAGACCTCATCATCACGTATGAGTTGTGTCACCCC
1 TCATCACGTATGAGTCGTGTCATCCCCGACCAGACCTCCTCATCATGTAGGAGTCGTGTCACCCC
* * * *
3558163 TAGATAACTAGCCGTTCT-CATCGCGTAGGAACCTAGTTATCACCCTTCCTAAAGATGGCTAGAA
66 TAGATAACTAGCCG-TCTGAATCGCATAGGAACCAAGTTATCACCCTTCCTAAAGATGGCAAGAA
3558227 CTCT
130 CTCT
* *
3558231 TCATCACGTATGAGTCGTGTCATCCACCGACCAGATCTCCTCATCATGTAGGAGACGTGTCACCC
1 TCATCACGTATGAGTCGTGTCATCC-CCGACCAGACCTCCTCATCATGTAGGAGTCGTGTCACCC
*
3558296 TTAGA
65 CTAGA
3558301 CGACCAAAAC
Statistics
Matches: 177, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
133 113 0.64
134 64 0.36
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.26
Consensus pattern (133 bp):
TCATCACGTATGAGTCGTGTCATCCCCGACCAGACCTCCTCATCATGTAGGAGTCGTGTCACCCC
TAGATAACTAGCCGTCTGAATCGCATAGGAACCAAGTTATCACCCTTCCTAAAGATGGCAAGAAC
TCT
Found at i:3558333 original size:43 final size:40
Alignment explanation
Indices: 3558225--3558334 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 40
3558215 AGATGGCTAG
* * *
3558225 AACTCTTCATCACGTATGAGTCGTGTCATCCACCGACCAG
1 AACTCTTCATCACGTATGAGTCGTGTCACCCAACGACCAA
* * * * *
3558265 ATCTCCTCATCATGTAGGAGACGTGTCACCCTTAGACGACCAA
1 AACTCTTCATCACGTATGAGTCGTGTCACCC--A-ACGACCAA
*
3558308 AACTCTTCATCGCGTATGAGTCGTGTC
1 AACTCTTCATCACGTATGAGTCGTGTC
3558335 GTCCCCAAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
40 25 0.47
42 1 0.02
43 27 0.51
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (40 bp):
AACTCTTCATCACGTATGAGTCGTGTCACCCAACGACCAA
Found at i:3558522 original size:3 final size:3
Alignment explanation
Indices: 3558502--3558548 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
3558492 CTACCAAAAA
3558502 ATT ATT -TT ATT ATT -TT ATT ATT ATT ATT ATT ATT ACTT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
3558545 ATT A
1 ATT A
3558549 ATTACATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.15
3 32 0.80
4 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:3559142 original size:6 final size:6
Alignment explanation
Indices: 3559131--3559164 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
3559121 AAAAAATATC
3559131 AAAAGA AAAAGA AAAAG- AAAAGA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAG
3559165 TTTACTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:3559145 original size:11 final size:11
Alignment explanation
Indices: 3559131--3559162 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
3559121 AAAAAATATC
3559131 AAAAGAAAAAGA
1 AAAAG-AAAAGA
3559143 AAAAGAAAAGA
1 AAAAGAAAAGA
3559154 AAAAGAAAA
1 AAAAGAAAA
3559163 AGTTTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:3559151 original size:17 final size:17
Alignment explanation
Indices: 3559131--3559164 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3559121 AAAAAATATC
3559131 AAAAGAAAAAGAAAAAG
1 AAAAGAAAAAGAAAAAG
3559148 AAAAGAAAAAGAAAAAG
1 AAAAGAAAAAGAAAAAG
3559165 TTTACTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAAG
Found at i:3560046 original size:30 final size:30
Alignment explanation
Indices: 3559964--3560361 Score: 293
Period size: 30 Copynumber: 13.4 Consensus size: 30
3559954 TGATAATACC
*
3559964 ATTTTAGTCCCTTAAGTTTCTG-TTTTGCT
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTGCT
* *
3559993 GTTTTA-TCAC-TTAA-TTGTCTGTTTTTACT
1 ATTTTAGTC-CTTTAAGTT-TCTGTTTTTGCT
* * *
3560022 ATTTTAGTCCTTTAAATCTCTGTTTATGCT
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTGCT
* *
3560052 ATTTTAATCAC-TTAAGTTTCAGTTTTTGCT
1 ATTTTAGTC-CTTTAAGTTTCTGTTTTTGCT
* *
3560082 ATTTTAGTACTTTTAA-TTTCTATTTTTGCT
1 ATTTTAGT-CCTTTAAGTTTCTGTTTTTGCT
* * ** *
3560112 A-TTTAGACCCTTAAGTTTCTAATTTTACT
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTGCT
* * *
3560141 ATTTTAG-CCTTTTAAGTTTTTATTTTTTCT
1 ATTTTAGTCC-TTTAAGTTTCTGTTTTTGCT
* * *
3560171 ATTTTAGTCCTTTAAATTTCTATTTGTGCT
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTGCT
* * *
3560201 ATTTTGGTCCTTTGAGTTTATGTTTTTGCT
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTGCT
* * *
3560231 -GTTTAGTCCTTTAAGTTTAT-TTTTTCCT
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTGCT
* * *
3560259 ATTTTATTCCTTTACA-TTTTTGTTTGTGCT
1 ATTTTAGTCCTTTA-AGTTTCTGTTTTTGCT
* *
3560289 A-TTTATGTCCCTTAAGTTTTTGTTTTTGCT
1 ATTTTA-GTCCTTTAAGTTTCTGTTTTTGCT
* * * *
3560319 ATTTCAGT-CTTGTAAATTTTTGTTTTTTTCT
1 ATTTTAGTCCTT-TAAGTTTCTG-TTTTTGCT
3560350 A-TTTAGTCCTTT
1 ATTTTAGTCCTTT
3560362 TTTTACTAAG
Statistics
Matches: 296, Mismatches: 51, Indels: 43
0.76 0.13 0.11
Matches are distributed among these distances:
27 2 0.01
28 22 0.07
29 77 0.26
30 172 0.58
31 23 0.08
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (30 bp):
ATTTTAGTCCTTTAAGTTTCTGTTTTTGCT
Found at i:3560140 original size:119 final size:117
Alignment explanation
Indices: 3560015--3560322 Score: 298
Period size: 119 Copynumber: 2.6 Consensus size: 117
3560005 AATTGTCTGT
* * *
3560015 TTTTACTATTTTAGTCCTTTAAATCTCTGTTTATGCTATTTTAATCACTTAAGTTTCAGTTTTTG
1 TTTTACTATTTTAGTCCTTTAAATTTTTGTTTATGCTATTTTAGTC-CTTAAGTTTCAGTTTTTG
* * *
3560080 CTATTTTAGTACTTTTAATTTCTATTTTTGCTATTTAGACCCTTAAGTTTCTAA
65 CTATTTTAGTACTTTGAATTTATATTTTTGCTATTTAGACCCTTAAGTTTAT-A
* * * * * *
3560134 TTTTACTATTTTAG-CCTTTTAAGTTTTTATTTTTTCTATTTTAGTCCTTTAAATTTCTA-TTTG
1 TTTTACTATTTTAGTCC-TTTAAATTTTTGTTTATGCTATTTTAGTCC-TTAAGTTTC-AGTTTT
* * * * * * * *
3560197 TGCTATTTTGGTCCTTTGAGTTTATGTTTTTGCTGTTTAGTCCTTTAAGTTTATT
63 TGCTATTTTAGTACTTTGAATTTATATTTTTGCTATTTAGACCCTTAAGTTTATA
* * * * **
3560252 TTTTCCTATTTTATTCCTTTACATTTTTGTTTGTGCTA-TTTATGTCCCTTAAGTTTTTGTTTTT
1 TTTTACTATTTTAGTCCTTTAAATTTTTGTTTATGCTATTTTA-GT-CCTTAAGTTTCAGTTTTT
3560316 GCTATTT
64 GCTATTT
3560323 CAGTCTTGTA
Statistics
Matches: 151, Mismatches: 31, Indels: 15
0.77 0.16 0.08
Matches are distributed among these distances:
117 4 0.03
118 51 0.34
119 95 0.63
120 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (117 bp):
TTTTACTATTTTAGTCCTTTAAATTTTTGTTTATGCTATTTTAGTCCTTAAGTTTCAGTTTTTGC
TATTTTAGTACTTTGAATTTATATTTTTGCTATTTAGACCCTTAAGTTTATA
Found at i:3560236 original size:89 final size:88
Alignment explanation
Indices: 3560074--3560361 Score: 287
Period size: 88 Copynumber: 3.2 Consensus size: 88
3560064 TAAGTTTCAG
* * * * * * * ** *
3560074 TTTTTGCTATTTTAGTACTTTTAATTTCTATTTTTGCTATTTAGACCCTTAAGTTTCTAATTTTA
1 TTTTTTCTATTTTAGTCCTTTAAATTTCTATTTGTGCTATTTTGTCCCTTAAGTTTATGTTTTTG
3560139 CTATTTTAGCCTTTTAAGTTTTTA
66 CTA-TTTAGCCTTTTAAGTTTTTA
* *
3560163 TTTTTTCTATTTTAGTCCTTTAAATTTCTATTTGTGCTATTTTGGTCCTTTGAGTTTATGTTTTT
1 TTTTTTCTATTTTAGTCCTTTAAATTTCTATTTGTGCTATTTT-GTCCCTTAAGTTTATGTTTTT
*
3560228 GCTGTTTAGTCC-TTTAAG--TTTA
65 GCTATTTAG-CCTTTTAAGTTTTTA
* * * * *
3560250 TTTTTTCCTATTTTATTCCTTTACATTTTTGTTTGTGCTATTTATGTCCCTTAAGTTTTTGTTTT
1 TTTTTT-CTATTTTAGTCCTTTAAATTTCTATTTGTGCTATTT-TGTCCCTTAAGTTTATGTTTT
* * * *
3560315 TGCTATTTCAGTCTTGTAAATTTTTGT
64 TGCTATTT-AGCCTTTTAAGTTTTT-A
3560342 TTTTTTCTA-TTTAGTCCTTT
1 TTTTTTCTATTTTAGTCCTTT
3560362 TTTTACTAAG
Statistics
Matches: 164, Mismatches: 26, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
87 10 0.06
88 57 0.35
89 56 0.34
90 29 0.18
91 6 0.04
92 6 0.04
ACGTcount: A:0.16, C:0.12, G:0.10, T:0.61
Consensus pattern (88 bp):
TTTTTTCTATTTTAGTCCTTTAAATTTCTATTTGTGCTATTTTGTCCCTTAAGTTTATGTTTTTG
CTATTTAGCCTTTTAAGTTTTTA
Found at i:3564812 original size:41 final size:41
Alignment explanation
Indices: 3564763--3564913 Score: 153
Period size: 41 Copynumber: 3.7 Consensus size: 41
3564753 AGAACGATTC
* * *
3564763 TTTT-GCGGCATTTGTTTAGAAACGCCACTAATGTACTAGG
1 TTTTAGCGGCGTTTGTTTAGAAATGCCACTAAAGTACTAGG
* * * * *
3564803 TTTTAGCGGCGTTAGTTTAAAAATGCCACTAAAGAACGA-C
1 TTTTAGCGGCGTTTGTTTAGAAATGCCACTAAAGTACTAGG
* **
3564843 TCTTTTGCAACGTTTGTTTAGAAATGCCACTAAAGTACTAGG
1 T-TTTAGCGGCGTTTGTTTAGAAATGCCACTAAAGTACTAGG
* * *
3564885 TTTTAGTGGCGTTTGTCTAAAAATGCCAC
1 TTTTAGCGGCGTTTGTTTAGAAATGCCAC
3564914 AATATATGTA
Statistics
Matches: 86, Mismatches: 22, Indels: 5
0.76 0.19 0.04
Matches are distributed among these distances:
40 5 0.06
41 80 0.93
42 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTGTTTAGAAATGCCACTAAAGTACTAGG
Found at i:3564835 original size:82 final size:82
Alignment explanation
Indices: 3564739--3564913 Score: 269
Period size: 82 Copynumber: 2.1 Consensus size: 82
3564729 ATTTGTTTCA
* ** *
3564739 AAAAATGCCACTAAAGAACGATTCTTTTGCGGCATTTGTTTAGAAACGCCACTAATGTACTAGGT
1 AAAAATGCCACTAAAGAACGACTCTTTTGCAACATTTGTTTAGAAACGCCACTAAAGTACTAGGT
*
3564804 TTTAGCGGCGTTAGTTT
66 TTTAGCGGCGTTAGTCT
* *
3564821 AAAAATGCCACTAAAGAACGACTCTTTTGCAACGTTTGTTTAGAAATGCCACTAAAGTACTAGGT
1 AAAAATGCCACTAAAGAACGACTCTTTTGCAACATTTGTTTAGAAACGCCACTAAAGTACTAGGT
* *
3564886 TTTAGTGGCGTTTGTCT
66 TTTAGCGGCGTTAGTCT
3564903 AAAAATGCCAC
1 AAAAATGCCAC
3564914 AATATATGTA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (82 bp):
AAAAATGCCACTAAAGAACGACTCTTTTGCAACATTTGTTTAGAAACGCCACTAAAGTACTAGGT
TTTAGCGGCGTTAGTCT
Found at i:3564954 original size:82 final size:82
Alignment explanation
Indices: 3564739--3564963 Score: 238
Period size: 82 Copynumber: 2.7 Consensus size: 82
3564729 ATTTGTTTCA
** * * ** *
3564739 AAAAATGCCACTAAAGAACGATTCTTTTGCGGCATTTGTTTAGAAACGCCACTAATGTACTAGGT
1 AAAAATGCCACTAAAGAACGACCCTATTACAACATTTGTTTAGAAACGCCACTAAAGTACTAGGT
*
3564804 TTTAGCGGCGTTAGTTT
66 TTTAGCGGCGTTAGTCT
* * * * *
3564821 AAAAATGCCACTAAAGAACGACTCTTTTGCAACGTTTGTTTAGAAATGCCACTAAAGTACTAGGT
1 AAAAATGCCACTAAAGAACGACCCTATTACAACATTTGTTTAGAAACGCCACTAAAGTACTAGGT
* *
3564886 TTTAGTGGCGTTTGTCT
66 TTTAGCGGCGTTAGTCT
* * * * *
3564903 AAAAATGCCAC-AATA-TATGTACCCTATTACGACATTTATTTAAAAACGCCACTAAAGTACT
1 AAAAATGCCACTAA-AGAACG-ACCCTATTACAACATTTGTTTAGAAACGCCACTAAAGTACT
3564964 TATATGTTGC
Statistics
Matches: 122, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
81 4 0.03
82 118 0.97
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (82 bp):
AAAAATGCCACTAAAGAACGACCCTATTACAACATTTGTTTAGAAACGCCACTAAAGTACTAGGT
TTTAGCGGCGTTAGTCT
Found at i:3568304 original size:21 final size:21
Alignment explanation
Indices: 3568280--3568339 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
3568270 CCTCTTCACC
*
3568280 AAACCCCAAACCCTAAATAAT
1 AAACCCAAAACCCTAAATAAT
*** * *
3568301 AAACATTAAACTCTAAATCAT
1 AAACCCAAAACCCTAAATAAT
*
3568322 AAACCCAAAACCTTAAAT
1 AAACCCAAAACCCTAAAT
3568340 CGCAAATCTT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACCCAAAACCCTAAATAAT
Found at i:3568380 original size:21 final size:20
Alignment explanation
Indices: 3568307--3568381 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 20
3568297 TAATAAACAT
**
3568307 TAAACTCTAAATCATAAACCC
1 TAAACT-TAAATCGCAAACCC
* * *
3568328 AAAACCTTAAATCGCAAATCT
1 TAAA-CTTAAATCGCAAACCC
3568349 TAAACTATAAACTC-CAAACCC
1 TAAACT-TAAA-TCGCAAACCC
3568370 TAAAGCTTAAAT
1 TAAA-CTTAAAT
3568382 TTTGAACCCT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
20 3 0.07
21 33 0.79
22 6 0.14
ACGTcount: A:0.48, C:0.25, G:0.03, T:0.24
Consensus pattern (20 bp):
TAAACTTAAATCGCAAACCC
Found at i:3568446 original size:21 final size:21
Alignment explanation
Indices: 3568420--3568462 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3568410 AAAAAAAGAA
*
3568420 AAAAATA-TTATTTTTTGAGTT
1 AAAAATATTTATTTATTG-GTT
3568441 AAAAATATTTATTTATTGGTT
1 AAAAATATTTATTTATTGGTT
3568462 A
1 A
3568463 TAAACTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (21 bp):
AAAAATATTTATTTATTGGTT
Found at i:3568585 original size:21 final size:21
Alignment explanation
Indices: 3568548--3568598 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
3568538 ATATAACCCC
* * *
3568548 AAACCCTAAAGCTTAAATTTT
1 AAACCCTAAAGCATAAACTCT
*
3568569 AAACCCTAAATCATAAACTCT
1 AAACCCTAAAGCATAAACTCT
3568590 -AACCCTAAA
1 AAACCCTAAA
3568599 AATAATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.47, C:0.25, G:0.02, T:0.25
Consensus pattern (21 bp):
AAACCCTAAAGCATAAACTCT
Found at i:3571209 original size:3 final size:3
Alignment explanation
Indices: 3571201--3571241 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
3571191 TTTTGTTTTA
* *
3571201 TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3571242 AATAAATACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3583646 original size:45 final size:45
Alignment explanation
Indices: 3583582--3584107 Score: 849
Period size: 45 Copynumber: 11.7 Consensus size: 45
3583572 AAAATATTTT
3583582 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* *
3583627 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAACATTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* *
3583672 GGGTCATCTATAAACCCTTCAGTGCATGATGTTTTTCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAACCTTC
* * *
3583718 GGGTCATCTGTATGCCCTTCAGTGCAAGATGTTTTCAAAACCTCC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
3583763 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* * *
3583808 AGGTCATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAACCTTT
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
3583853 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
3583898 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
*
3583943 GGGTCATCTTTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
*
3583988 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCGAAACCTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* **
3584033 GGGTCATCTGTAAGCCCTTCAGGGCATGATG-TTT-AAAATATTTC
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA-CCTTC
* * * *
3584077 AGGTCATCTGTAAGACCTACAGTGCAAGATG
1 GGGTCATCTGTAAGCCCTTCAGTGCATGATG
3584108 ATATGACCTT
Statistics
Matches: 447, Mismatches: 32, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
43 3 0.01
44 32 0.07
45 373 0.83
46 39 0.09
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (45 bp):
GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
Found at i:3584271 original size:3 final size:3
Alignment explanation
Indices: 3584263--3584319 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
3584253 TCATTTCATT
** **
3584263 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA AAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3584311 TTA TTA TTA
1 TTA TTA TTA
3584320 AATAAATACA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3584288 original size:18 final size:18
Alignment explanation
Indices: 3584265--3584316 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
3584255 ATTTCATTTT
3584265 ATTATTATTATTATTAAA
1 ATTATTATTATTATTAAA
3584283 ATTATTATTATTATTAAA
1 ATTATTATTATTATTAAA
3584301 ATTATTATTATTATTA
1 ATTATTATTATTATTA
3584317 TTAAATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATTATTATTATTAAA
Found at i:3584757 original size:13 final size:13
Alignment explanation
Indices: 3584741--3584767 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3584731 AAAAAGAAAA
3584741 GAGAACAAGAACG
1 GAGAACAAGAACG
3584754 GAGAACAAGAACG
1 GAGAACAAGAACG
3584767 G
1 G
3584768 TGATATTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (13 bp):
GAGAACAAGAACG
Found at i:3585470 original size:24 final size:23
Alignment explanation
Indices: 3585386--3585470 Score: 62
Period size: 24 Copynumber: 3.4 Consensus size: 23
3585376 TTTCGATATG
* *
3585386 TTTAAATTATTACTTTAATTATTAT
1 TTTAAATTAATA-TTTATTTATT-T
* * * *
3585411 TTTATATAAATATATATATATTT
1 TTTAAATTAATATTTATTTATTT
3585434 GTTTAAAGTTTAATATTTATTTATTT
1 -TTTAAA--TTAATATTTATTTATTT
3585460 TTTAATATTAA
1 TTTAA-ATTAA
3585471 GAAATTGGTT
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
23 1 0.02
24 16 0.35
25 14 0.30
26 15 0.33
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTAAATTAATATTTATTTATTT
Found at i:3585555 original size:2 final size:2
Alignment explanation
Indices: 3585548--3585599 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3585538 ATAAAAATGA
3585548 AT AT AT AT 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 AT AT AT AT
3585590 AT AT AT AT AT
1 AT AT AT AT AT
3585600 TCTTAAAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3588294 original size:20 final size:20
Alignment explanation
Indices: 3588271--3588326 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3588261 ATTGGGGTCT
**
3588271 GATGGTATCGATACTATGGC
1 GATGGTATCGATACTATAAC
*
3588291 GATGGTATCAATACTATAAC
1 GATGGTATCGATACTATAAC
*
3588311 AATGGTATCGATACTA
1 GATGGTATCGATACTA
3588327 CTATACATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (20 bp):
GATGGTATCGATACTATAAC
Found at i:3598493 original size:41 final size:40
Alignment explanation
Indices: 3598436--3598575 Score: 190
Period size: 41 Copynumber: 3.4 Consensus size: 40
3598426 CATGATAAAC
3598436 TTCACTTCGGATTATTAGTGGATTCACATTTTGGGATGAAT
1 TTCACTTCGGATTATTAGTGGATTCAC-TTTTGGGATGAAT
*
3598477 TTCACTTTGGATTATTAGTGGATTCACTTTTCGGGATGAAT
1 TTCACTTCGGATTATTAGTGGATTCACTTTT-GGGATGAAT
* * *
3598518 TTCACTTCAGATTATTAGTGGATTCACCCTTTGGAATGAAT
1 TTCACTTCGGATTATTAGTGGATTCA-CTTTTGGGATGAAT
* * *
3598559 CTCAGTTTGGATTATTA
1 TTCACTTCGGATTATTA
3598576 ACGGCTCCTC
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
40 4 0.05
41 80 0.91
42 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (40 bp):
TTCACTTCGGATTATTAGTGGATTCACTTTTGGGATGAAT
Found at i:3608134 original size:3 final size:3
Alignment explanation
Indices: 3608126--3608213 Score: 149
Period size: 3 Copynumber: 29.3 Consensus size: 3
3608116 TATTTCTATG
* * *
3608126 ATA ATA ATA ATA ATA ATA AGA ATA ATA ATA AGA AGA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3608174 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3608214 CAACAACAAC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3609798 original size:31 final size:31
Alignment explanation
Indices: 3609720--3609798 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
3609710 TCAAGTTTGT
* *
3609720 ATTCAAATAATGCACAATATGTCAGGTTTAC
1 ATTCAGATAATGCACAGTATGTCAGGTTTAC
*
3609751 ATTCAGATAATGCACAGTATGTCATG-TTAGC
1 ATTCAGATAATGCACAGTATGTCAGGTTTA-C
*
3609782 TTTCAGATAATGCACAG
1 ATTCAGATAATGCACAG
3609799 GAGTATCAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 3 0.07
31 40 0.93
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (31 bp):
ATTCAGATAATGCACAGTATGTCAGGTTTAC
Found at i:3614981 original size:12 final size:12
Alignment explanation
Indices: 3614960--3615024 Score: 64
Period size: 12 Copynumber: 5.4 Consensus size: 12
3614950 ATGACTTGAA
3614960 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
3614972 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
3614984 TTCTGTTCTG-T
1 TTCTGTTCTGAT
*
3614995 TATGTGTTCTGAAT
1 T-TCTGTTCTG-AT
3615009 TT-TGTTCTGAT
1 TTCTGTTCTGAT
3615020 TTCTG
1 TTCTG
3615025 ATATCTCTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 6 0.14
12 33 0.75
13 3 0.07
14 2 0.05
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:3614986 original size:24 final size:24
Alignment explanation
Indices: 3614932--3615026 Score: 97
Period size: 24 Copynumber: 4.0 Consensus size: 24
3614922 ATTTCCAACT
*
3614932 TGAATTCTGTTCTGA-TACATGA-C
1 TGAATTCTGTTCTGATTTC-TGATC
3614955 TTGAATTCTGTTCTGATTTCTGATC
1 -TGAATTCTGTTCTGATTTCTGATC
* * *
3614980 TGGATTCTGTTCTG-TTATGTGTTC
1 TGAATTCTGTTCTGATT-TCTGATC
*
3615004 TGAATTTTGTTCTGATTTCTGAT
1 TGAATTCTGTTCTGATTTCTGAT
3615027 ATCTCTGTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.03
24 52 0.88
25 5 0.08
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:3614987 original size:48 final size:48
Alignment explanation
Indices: 3614935--3615026 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
3614925 TCCAACTTGA
3614935 ATTCTGTTCTGATACATGACT-TGAATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATACATG-CTCTGAATTCTGTTCTGATTTCTGATCTGG
* ** * *
3614983 ATTCTGTTCTGTTATGTGTTCTGAATTTTGTTCTGATTTCTGAT
1 ATTCTGTTCTGATACATGCTCTGAATTCTGTTCTGATTTCTGAT
3615027 ATCTCTGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
47 1 0.03
48 37 0.97
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.51
Consensus pattern (48 bp):
ATTCTGTTCTGATACATGCTCTGAATTCTGTTCTGATTTCTGATCTGG
Found at i:3619680 original size:24 final size:25
Alignment explanation
Indices: 3619650--3619720 Score: 92
Period size: 24 Copynumber: 2.9 Consensus size: 25
3619640 ATACATGACT
3619650 TGAATTCTGTTCTGATTTTTGATT-
1 TGAATTCTGTTCTGATTTTTGATTC
* *
3619674 TGGATTCTGTTCTGATATTTG-TTC
1 TGAATTCTGTTCTGATTTTTGATTC
* *
3619698 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATTTTTGAT
3619721 ATCTTCGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 2 0.05
24 36 0.92
25 1 0.03
ACGTcount: A:0.15, C:0.10, G:0.18, T:0.56
Consensus pattern (25 bp):
TGAATTCTGTTCTGATTTTTGATTC
Found at i:3619698 original size:12 final size:13
Alignment explanation
Indices: 3619677--3619718 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
3619667 TTTGATTTGG
3619677 ATTCTGTTCTGAT
1 ATTCTGTTCTGAT
3619690 ATT-TGTTCTGA-
1 ATTCTGTTCTGAT
*
3619701 ATTCTGTTTTGAT
1 ATTCTGTTCTGAT
3619714 -TTCTG
1 ATTCTG
3619719 ATATCTTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.14, C:0.12, G:0.17, T:0.57
Consensus pattern (13 bp):
ATTCTGTTCTGAT
Found at i:3623898 original size:2 final size:2
Alignment explanation
Indices: 3623886--3623928 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
3623876 ATGAAACAAC
*
3623886 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3623929 CTCATATGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3625098 original size:47 final size:47
Alignment explanation
Indices: 3625029--3625122 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
3625019 TTATTCAAGC
3625029 ATAGTACATCAATTTTTAAACAATTGTTT-CTTCAATCCCATAATTTT
1 ATAGTACATCAATTTTTAAACAATT-TTTGCTTCAATCCCATAATTTT
*
3625076 ATAGTACATCAATTTTTAAACAATTTTTGCTTCATTCCCATAATTTT
1 ATAGTACATCAATTTTTAAACAATTTTTGCTTCAATCCCATAATTTT
3625123 CATAATATAC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 3 0.07
47 42 0.93
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (47 bp):
ATAGTACATCAATTTTTAAACAATTTTTGCTTCAATCCCATAATTTT
Found at i:3625136 original size:47 final size:47
Alignment explanation
Indices: 3625033--3625137 Score: 151
Period size: 47 Copynumber: 2.2 Consensus size: 47
3625023 TCAAGCATAG
*
3625033 TACATCAATTTTTAAACAATTGTTTCTTCAATCCCATAATTTTATAG
1 TACATCAATTTTTAAACAATTGTTTCTTCAATCCCATAATTTTATAA
*
3625080 TACATCAATTTTTAAACAATT-TTTGCTTCATTCCCATAATTTTCATAA
1 TACATCAATTTTTAAACAATTGTTT-CTTCAATCCCATAATTTT-ATAA
*
3625128 TATA-CAATTT
1 TACATCAATTT
3625138 GGTCCTTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
46 3 0.06
47 44 0.83
48 6 0.11
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (47 bp):
TACATCAATTTTTAAACAATTGTTTCTTCAATCCCATAATTTTATAA
Found at i:3626269 original size:29 final size:31
Alignment explanation
Indices: 3626202--3626271 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 31
3626192 AAATTAGAAC
*
3626202 TTGGTCCCTAAACGTTTCCAAACTTTACACT
1 TTGGTCACTAAACGTTTCCAAACTTTACACT
* * * *
3626233 TTAG-CACTAAAC-TTT-CAAATTTTATATT
1 TTGGTCACTAAACGTTTCCAAACTTTACACT
3626261 TTGGTCACTAA
1 TTGGTCACTAA
3626272 TAAAAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 13 0.41
29 9 0.28
30 7 0.22
31 3 0.09
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (31 bp):
TTGGTCACTAAACGTTTCCAAACTTTACACT
Found at i:3629960 original size:2 final size:2
Alignment explanation
Indices: 3629953--3629988 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3629943 TAAAACCAAA
3629953 AT 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 AT
3629989 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3629993 original size:2 final size:2
Alignment explanation
Indices: 3629988--3630049 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
3629978 TATATATATA
3629988 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
3630030 TA TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG
3630050 AAACTGCGTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3631475 original size:57 final size:57
Alignment explanation
Indices: 3631412--3631539 Score: 179
Period size: 57 Copynumber: 2.2 Consensus size: 57
3631402 TTGATTCCTT
* * * *
3631412 TGCTATGTTAAATGCTATGAGTA-AT-TATTCTATGTGAATAAATGATAATTTGAGTAA
1 TGCTATGTGAAATACTATGAGTATATGT-TT-TATGTGAACAAATGATAATTTGAATAA
3631469 TGCTATGTGAAATACTATGAGTATATGTTTTATGTGAACAAATGATAATTTGAATAA
1 TGCTATGTGAAATACTATGAGTATATGTTTTATGTGAACAAATGATAATTTGAATAA
*
3631526 TACTATGTGAAATA
1 TGCTATGTGAAATA
3631540 ATTATATGGT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
57 59 0.92
58 4 0.06
59 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.39
Consensus pattern (57 bp):
TGCTATGTGAAATACTATGAGTATATGTTTTATGTGAACAAATGATAATTTGAATAA
Found at i:3631643 original size:23 final size:23
Alignment explanation
Indices: 3631610--3631660 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3631600 GAGGTGAAGG
*
3631610 TTCTACACGGTCCTTCGGGTCAA
1 TTCTACACGGTCCTTCGGGACAA
*
3631633 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACACGGTCCTTCGGGACAA
*
3631656 GTCTA
1 TTCTA
3631661 TGTGGCACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (23 bp):
TTCTACACGGTCCTTCGGGACAA
Found at i:3631701 original size:24 final size:24
Alignment explanation
Indices: 3631657--3631710 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3631647 TCGGGACAAG
* *
3631657 TCTATGTGGCACTTCAATGCATAT
1 TCTACGTGGCACTTCAATGCAAAT
**
3631681 TCTACGTGGCACTTCGGTGCAAAT
1 TCTACGTGGCACTTCAATGCAAAT
*
3631705 TATACG
1 TCTACG
3631711 CGGTAGTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (24 bp):
TCTACGTGGCACTTCAATGCAAAT
Found at i:3634118 original size:21 final size:20
Alignment explanation
Indices: 3634075--3634119 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
3634065 ATCATAAGTA
* *
3634075 TTAACCCTAAATCTTAAATC
1 TTAACCCTAAATCTGAAACC
*
3634095 TTAACCACTTAATCTGAAACC
1 TTAACC-CTAAATCTGAAACC
3634116 TTAA
1 TTAA
3634120 AACCTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.33
Consensus pattern (20 bp):
TTAACCCTAAATCTGAAACC
Found at i:3634199 original size:20 final size:20
Alignment explanation
Indices: 3634176--3634213 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3634166 TTAGTTATAA
3634176 ATTT-TTATTATATCTAATTT
1 ATTTATTATTA-ATCTAATTT
*
3634196 ATTTATTTTTAATCTAAT
1 ATTTATTATTAATCTAAT
3634214 GGCTATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTATTATTAATCTAATTT
Found at i:3635704 original size:19 final size:19
Alignment explanation
Indices: 3635680--3635716 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3635670 TAACGCGAGA
3635680 TCTCCAAGAATTTAAAGCG
1 TCTCCAAGAATTTAAAGCG
*
3635699 TCTCCAAGAATTTGAAGC
1 TCTCCAAGAATTTAAAGC
3635717 ATCAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (19 bp):
TCTCCAAGAATTTAAAGCG
Found at i:3637128 original size:219 final size:219
Alignment explanation
Indices: 3636742--3637178 Score: 777
Period size: 219 Copynumber: 2.0 Consensus size: 219
3636732 TCGAATAAAA
*
3636742 TCTAGCGTGTCAGAATGAACTCACGATCTGTAAAATGTGAGGTTGTTTTTTGTAGGATCTCGCGC
1 TCTAGCGTGTCAGAATGAACTCACGATCTGTAAAACGTGAGGTTGTTTTTTGTAGGATCTCGCGC
* * *
3636807 CCTACAGCACACGAGGTCCATTCATTTTCATGCCATAATTCATTTGTTTATATTCATGCTCGAGG
66 CCTACAGCACACGAGGTCCATTCATTTTCAGGCCACAATTCATTTGTTTATATGCATGCTCGAGG
3636872 CATTTTCCCGGGTTGTAAATTGGAAATTTTGTGTAATTTATAAGATTAGCAGCATAGTATTTAAA
131 CATTTTCCCGGGTTGTAAATTGGAAATTTTGTGTAATTTATAAGATTAGCAGCATAGTATTTAAA
3636937 CTTATTTTTCCGTTGAGTCTAATT
196 CTTATTTTTCCGTTGAGTCTAATT
3636961 TCTAGCGTGTCAGAATGAACTCACGATCTGTAAAACGTGAGGTTGTTTTTTCGTAGGATCTCGCG
1 TCTAGCGTGTCAGAATGAACTCACGATCTGTAAAACGTGAGGTTGTTTTTT-GTAGGATCTCGCG
* *
3637026 CCTTACAGCACACGAGGTCCATTCATTTTCAGGCCACAATTCATTTGTTTATATGCATGTTCGAG
65 CCCTACAGCACACGAGGTCCATTCATTTTCAGGCCACAATTCATTTGTTTATATGCATGCTCGAG
* * *
3637091 GCATTTTCCCGGGTT-TATATTGGAAATTTTTTGTAATTTATAAGATTAGCAGCGTAGTATTTAA
130 GCATTTTCCCGGGTTGTAAATTGGAAATTTTGTGTAATTTATAAGATTAGCAGCATAGTATTTAA
3637155 ACTTATTTTTCCGTTGAGTCTAAT
195 ACTTATTTTTCCGTTGAGTCTAAT
3637179 AACCGCACAT
Statistics
Matches: 208, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
219 120 0.58
220 88 0.42
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (219 bp):
TCTAGCGTGTCAGAATGAACTCACGATCTGTAAAACGTGAGGTTGTTTTTTGTAGGATCTCGCGC
CCTACAGCACACGAGGTCCATTCATTTTCAGGCCACAATTCATTTGTTTATATGCATGCTCGAGG
CATTTTCCCGGGTTGTAAATTGGAAATTTTGTGTAATTTATAAGATTAGCAGCATAGTATTTAAA
CTTATTTTTCCGTTGAGTCTAATT
Found at i:3640318 original size:21 final size:21
Alignment explanation
Indices: 3640294--3640333 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3640284 GTTGACCGGC
3640294 CGTTGACC-GACCGTTGACTGT
1 CGTTGACCAG-CCGTTGACTGT
*
3640315 CGTTGATCAGCCGTTGACT
1 CGTTGACCAGCCGTTGACT
3640334 TTTCTGGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (21 bp):
CGTTGACCAGCCGTTGACTGT
Found at i:3644366 original size:6 final size:6
Alignment explanation
Indices: 3644348--3644389 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
3644338 TATTATAAAA
* *
3644348 TATATT TTTA-T TATAAT TATATT TATATT TATATT TATATT T
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT T
3644390 TTATATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:3645233 original size:46 final size:46
Alignment explanation
Indices: 3645126--3645268 Score: 205
Period size: 46 Copynumber: 3.0 Consensus size: 46
3645116 TTAAAACCTT
* * *
3645126 GATTCATCTTCACTACTGCAATTTACACAACCCTCCTAAACTTTCTCTCATA
1 GATTCATCTT--C-ACTGCTATTTACACCACCCT-C--AACTCTCTCTCATA
3645178 GATTCATCTTCACTGCTATTTACACCACCCTCAACTCTCTCTCATA
1 GATTCATCTTCACTGCTATTTACACCACCCTCAACTCTCTCTCATA
3645224 GATTCATCTTCACTGCTATTTACACCACCCTCAACTCTCTCTCAT
1 GATTCATCTTCACTGCTATTTACACCACCCTCAACTCTCTCTCAT
3645269 CCTCAACAAT
Statistics
Matches: 88, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
46 58 0.66
48 1 0.01
49 18 0.20
50 1 0.01
52 10 0.11
ACGTcount: A:0.25, C:0.36, G:0.04, T:0.35
Consensus pattern (46 bp):
GATTCATCTTCACTGCTATTTACACCACCCTCAACTCTCTCTCATA
Found at i:3658670 original size:19 final size:18
Alignment explanation
Indices: 3658621--3658680 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
3658611 AAATAGAAGG
3658621 TAACATTATAGGTTG-AA
1 TAACATTATAGGTTGTAA
* *
3658638 TGAAAAATATTAGGTTGTAGA
1 T-AACATTA-TAGGTTGTA-A
3658659 TAACATTATAGGTTGTACA
1 TAACATTATAGGTTGTA-A
3658678 TAA
1 TAA
3658681 TCAGTGACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.03
18 5 0.15
19 20 0.59
20 6 0.18
21 2 0.06
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (18 bp):
TAACATTATAGGTTGTAA
Found at i:3658733 original size:6 final size:6
Alignment explanation
Indices: 3658722--3658751 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3658712 ATCGAAGCAA
3658722 TTACAT TTACAT TTACAT TTACAT TTACAT
1 TTACAT TTACAT TTACAT TTACAT TTACAT
3658752 AACTATTTAT
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:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TTACAT
Found at i:3658759 original size:18 final size:18
Alignment explanation
Indices: 3658722--3658760 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3658712 ATCGAAGCAA
*
3658722 TTACATTTACATTTACAT
1 TTACATTTACATTAACAT
3658740 TTACATTTACA-TAACTAT
1 TTACATTTACATTAAC-AT
3658758 TTA
1 TTA
3658761 TTACTACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (18 bp):
TTACATTTACATTAACAT
Found at i:3661296 original size:117 final size:116
Alignment explanation
Indices: 3661078--3661303 Score: 267
Period size: 117 Copynumber: 1.9 Consensus size: 116
3661068 CATCATTGTT
* * * *
3661078 AGGCATAAGTTGGAAGATTGGATATGTGAAGAATGTTTGTCTTCCAACGCATGAATCCAACCCGT
1 AGGCATAAGGTAGAAGATTGGATATGTGAAGAATGCTTGTCTTCCAACGCATGAATCCAACCCAT
* *
3661143 TCAACTCGTTTGGATAGAAATGAGAAGAAACAAACAATAAATGTGTTTTTTG
66 TCAACTCGTTCGGATAGAAATGAGAAG-AACAAACAAAAAATGTGTTTTTTG
** * *
3661195 AGGCATAAGGTAGAAGATTGGATATGTGAAGAATGCCTT-TCTTTTAATGCATGACTCCAACCCA
1 AGGCATAAGGTAGAAGATTGGATATGTGAAGAATG-CTTGTCTTCCAACGCATGAATCCAACCCA
* * * * *
3661259 TTCAGCTTGTTCGGTTAGAATTGATAAG-ACGAGAACAAAAAATGT
65 TTCAACTCGTTCGGATAGAAATGAGAAGAAC-A-AACAAAAAATGT
3661304 AAACAAAACA
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
115 2 0.02
116 1 0.01
117 86 0.95
118 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (116 bp):
AGGCATAAGGTAGAAGATTGGATATGTGAAGAATGCTTGTCTTCCAACGCATGAATCCAACCCAT
TCAACTCGTTCGGATAGAAATGAGAAGAACAAACAAAAAATGTGTTTTTTG
Found at i:3666554 original size:27 final size:27
Alignment explanation
Indices: 3666524--3666580 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
3666514 CTCTCAAATT
* *
3666524 TTTTTAAACTTTTTC-TTCTCTCTTTTA
1 TTTTT-AACTTTTACTTTCTCTCTTTCA
*
3666551 TTTTTAACTTTTACTTTTTCTCTTTCA
1 TTTTTAACTTTTACTTTCTCTCTTTCA
3666578 TTT
1 TTT
3666581 CTTCATCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTTAACTTTTACTTTCTCTCTTTCA
Found at i:3669363 original size:20 final size:20
Alignment explanation
Indices: 3669338--3669383 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
3669328 AAGATACAGC
3669338 TGTACGAGGACATCTGGCTT
1 TGTACGAGGACATCTGGCTT
3669358 TGTACGAGGACATCTGGCTT
1 TGTACGAGGACATCTGGCTT
3669378 TGTACG
1 TGTACG
3669384 TGAAATGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (20 bp):
TGTACGAGGACATCTGGCTT
Found at i:3670964 original size:31 final size:31
Alignment explanation
Indices: 3670920--3670997 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
3670910 TTCTTTTTCA
3670920 TATCTATTTTTTCTTTCTTTCCTTTATTCTTC
1 TATCT-TTTTTTCTTTCTTTCCTTTATTCTTC
*
3670952 TATCTTTTTTTCTTTCTTTCTTTTATTCTTC
1 TATCTTTTTTTCTTTCTTTCCTTTATTCTTC
3670983 TATCTTTTTTTCTTT
1 TATCTTTTTTTCTTT
3670998 TTTTGTGGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 40 0.89
32 5 0.11
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (31 bp):
TATCTTTTTTTCTTTCTTTCCTTTATTCTTC
Found at i:3670998 original size:8 final size:8
Alignment explanation
Indices: 3670926--3671001 Score: 57
Period size: 8 Copynumber: 9.8 Consensus size: 8
3670916 TTCATATCTA
3670926 TTTTTTCT
1 TTTTTTCT
* *
3670934 TTCTTTCC
1 TTTTTTCT
*
3670942 TTTATTC-
1 TTTTTTCT
* *
3670949 TTCTATCT
1 TTTTTTCT
3670957 TTTTTTCT
1 TTTTTTCT
*
3670965 TTCTTTCT
1 TTTTTTCT
*
3670973 TTTATTC-
1 TTTTTTCT
* *
3670980 TTCTATCT
1 TTTTTTCT
3670988 TTTTTTCT
1 TTTTTTCT
3670996 TTTTTT
1 TTTTTT
3671002 GTGGTAGATG
Statistics
Matches: 49, Mismatches: 17, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
7 8 0.16
8 41 0.84
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCT
Found at i:3675641 original size:13 final size:13
Alignment explanation
Indices: 3675612--3675658 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
3675602 TCGAATACCT
3675612 AAAAATATATTTT-
1 AAAAATA-ATTTTA
3675625 -AAAATAATTTTAA
1 AAAAATAATTTT-A
3675638 AAAAATAATTTTA
1 AAAAATAATTTTA
*
3675651 AAAGATAA
1 AAAAATAA
3675659 AAAAATTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 5 0.17
12 6 0.20
13 8 0.27
14 11 0.37
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:3675644 original size:14 final size:14
Alignment explanation
Indices: 3675625--3675653 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3675615 AATATATTTT
3675625 AAAATAATTTTAAA
1 AAAATAATTTTAAA
3675639 AAAATAATTTTAAA
1 AAAATAATTTTAAA
3675653 A
1 A
3675654 GATAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATAATTTTAAA
Found at i:3677811 original size:139 final size:139
Alignment explanation
Indices: 3677543--3677895 Score: 528
Period size: 139 Copynumber: 2.5 Consensus size: 139
3677533 AAGCTAAAGT
* * * *
3677543 TCTTCTCATTATGAACTTTTTTTCCATT-ATCGGATGAGTTATTCTCATTATGAACTCTCCACTG
1 TCTTCTCATTATGAACTTATTCTCC-TTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * * *
3677607 GAAAGGTTGATCCCTTGAGTGAGGTGTTACTGATTCAACTCCATATATGACGAATCGAGCCAAGG
65 GAAATGTTGATCCCTCGAGTGAGGTATTACTGATTCAACTCCATATACGACGAATCGAGCCAAGG
3677672 TCGAACAAGC
130 TCGAACAAGC
3677682 TCTTCTCATTATGAACTTATTCTCCTTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGG
1 TCTTCTCATTATGAACTTATTCTCCTTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * * * * *
3677747 AAATGTTGATCCCTCGAGTGAGGTATTGCTGATTCAATTCCATATGCGATGAATTGAGCTAAGGT
66 AAATGTTGATCCCTCGAGTGAGGTATTACTGATTCAACTCCATATACGACGAATCGAGCCAAGGT
3677812 CGAACAAGC
131 CGAACAAGC
* * * *
3677821 TCTTCTTATTATGAACTTCTTCTCCTTCATCGGATGATTTCTTCTCATTATGAACTCTCCATTTG
1 TCTTCTCATTATGAACTTATTCTCCTTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGG
3677886 AAATGTTGAT
66 AAATGTTGAT
3677896 TGGTTCATCT
Statistics
Matches: 195, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
138 2 0.01
139 193 0.99
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (139 bp):
TCTTCTCATTATGAACTTATTCTCCTTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGG
AAATGTTGATCCCTCGAGTGAGGTATTACTGATTCAACTCCATATACGACGAATCGAGCCAAGGT
CGAACAAGC
Found at i:3678940 original size:42 final size:41
Alignment explanation
Indices: 3678840--3678940 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 41
3678830 ATGGATGTCT
* * *
3678840 CGAATGACTTATCATCTTGCTCGAAAGACTTATAGATGACC
1 CGAAGGACTTATCATCATGCTCAAAAGACTTATAGATGACC
* * *
3678881 CGAAGGATTTAAGCATCATGCTCAAAAGACTTACT-GATGGCC
1 CGAAGGACTT-ATCATCATGCTCAAAAGACTTA-TAGATGACC
3678923 CGGAA-GACTTATTCATCA
1 C-GAAGGACTTA-TCATCA
3678941 AGAAACCCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
41 9 0.19
42 35 0.73
43 4 0.08
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (41 bp):
CGAAGGACTTATCATCATGCTCAAAAGACTTATAGATGACC
Found at i:3678941 original size:275 final size:274
Alignment explanation
Indices: 3678430--3678972 Score: 849
Period size: 275 Copynumber: 2.0 Consensus size: 274
3678420 AGTTTTCATC
*
3678430 AAGGAACCTCTAAAAATTAGGCTTAGCTTCCTTTAAAAATTCTTTGGAGATAATCATCAAGAAAC
1 AAGGAACCTCTAAAAATTAGGCTTAGCTTCCTTTAAAAACTCTTTGGAGATAATCATCAAGAAAC
* * * * *
3678495 CCATGAAAATCAGTCTTAGTTTCTAAAAACTCATTTAAAAACAACCTTCCCGAAGGACTTATGGA
66 CCATAAAAATCAGGCTTAATTTCTAAAAACTCATTTAAAAACAACCTGCCCGAAGGACATATGGA
* *
3678560 TTGTCTGAAGGACTTGTCATCTTGCTCGAAAGACTTATAGCTGACCCAAAAGATTTAAGCATCAT
131 TTGTCTGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCAAAAGATTTAAGCATCAT
* *
3678625 GCTCGAAAGACTTACTGATGTCCCGAAGGAATTACTCATCAAGAAACCCTTGAAAATCAAGCTTA
196 GCTCAAAAGACTTACTGATGGCCCGAAGGAATTACTCATCAAGAAACCCTTGAAAATCAAGCTTA
3678690 GTTTCTTAGCTGTT
261 GTTTCTTAGCTGTT
3678704 AAGGAACC-CTTAAAAATTAGGCTTAGCTTCCTTTTAAAAACTCTTTGGAGATAATCATCAAGAA
1 AAGGAACCTC-TAAAAATTAGGCTTAGCTTCC-TTTAAAAACTCTTTGGAGATAATCATCAAGAA
* * * *
3678768 ACCCCTAAAAATCAGGCTTAATTTCTAAAAACTCATTTGAAAACATCCTGCCCGAAGGTCATATG
64 ACCCATAAAAATCAGGCTTAATTTCTAAAAACTCATTTAAAAACAACCTGCCCGAAGGACATATG
* * *
3678833 GA-TGTCTCGAATGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGCAT
129 GATTGTCT-GAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCAAAAGATTTAAGCAT
* * *
3678897 CATGCTCAAAAGACTTACTGATGGCCCGGAA-GACTTATTCATCAAGAAACCCTTTAAAATCAAG
193 CATGCTCAAAAGACTTACTGATGGCCC-GAAGGAATTACTCATCAAGAAACCCTTGAAAATCAAG
3678961 CTTAGTTTCTTA
257 CTTAGTTTCTTA
3678973 AAATCTTTCA
Statistics
Matches: 245, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
273 1 0.00
274 34 0.14
275 207 0.84
276 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (274 bp):
AAGGAACCTCTAAAAATTAGGCTTAGCTTCCTTTAAAAACTCTTTGGAGATAATCATCAAGAAAC
CCATAAAAATCAGGCTTAATTTCTAAAAACTCATTTAAAAACAACCTGCCCGAAGGACATATGGA
TTGTCTGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCAAAAGATTTAAGCATCAT
GCTCAAAAGACTTACTGATGGCCCGAAGGAATTACTCATCAAGAAACCCTTGAAAATCAAGCTTA
GTTTCTTAGCTGTT
Found at i:3679077 original size:54 final size:53
Alignment explanation
Indices: 3678995--3679351 Score: 344
Period size: 54 Copynumber: 6.6 Consensus size: 53
3678985 TTTCAGTTAT
* * *
3678995 CATCAAAAAACTCCTAAAAATCAGGCTTAGTTTCTTTGAAAATCCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTT-AAAATTCATTTGAAAA
* * *
3679049 CATCAAGAAACCCCT-AAAATCTATGCTTAATTTATTTGAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATC-AGGCTTAGTTTCTTT-AAAATTCATTTGAAAA
* * * * * *
3679103 CATTAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCATATTCATCTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTAAAATTCATTTGAAAA
* * * *
3679156 TATCAAGAAACCCAT-AAAATTAGGATTA-TGTTCTTTAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGT-TTCTTTAAAATTCATTTGAAAA
* ** *
3679208 CATCAAGAAACCCCTAAAAATCAGACTTAGTTTCTTTGAAAGGTCATTTAAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTT-AAAATTCATTTGAAAA
** *
3679262 TCATCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAGCTT-ATTTGAAAA
1 -CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTAAAA--TTCATTTGAAAA
** ** * *
3679317 TTGTCAAGAAACTTCTGAAAATCAGACTTAGTTTC
1 -CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTC
3679352 CAAAAAAACA
Statistics
Matches: 255, Mismatches: 39, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
52 44 0.17
53 47 0.18
54 83 0.33
55 80 0.31
56 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (53 bp):
CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTAAAATTCATTTGAAAA
Found at i:3679216 original size:105 final size:108
Alignment explanation
Indices: 3678995--3679248 Score: 336
Period size: 105 Copynumber: 2.4 Consensus size: 108
3678985 TTTCAGTTAT
* * *
3678995 CATCAAAAAACTCCTAAAAATCAGGCTTAGTTTCTTTGAAAATCCATTTGAAAACATCAAGAAAC
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTGAAAATCCATCTGAAAACATCAAGAAAC
* * *
3679060 CCCTAAAATCTATGCTTAATTTATTTGAAAATTCATTTGAAAA
66 CCATAAAATCTAGGATTAATTTATTTGAAAATTCATTTGAAAA
* * * * * * *
3679103 CATTAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTT-CATATTCATCTGAAAATATCAAGAAAC
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTGAAAATCCATCTGAAAACATCAAGAAAC
*
3679167 CCATAAAAT-TAGGATT-ATGTTCTTT-AAAATTCATTTGAAAA
66 CCATAAAATCTAGGATTAAT-TTATTTGAAAATTCATTTGAAAA
*
3679208 CATCAAGAAACCCCTAAAAATCAGACTTAGTTTCTTTGAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTGAAA
3679249 GGTCATTTAA
Statistics
Matches: 124, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
105 51 0.41
106 11 0.09
107 30 0.24
108 32 0.26
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (108 bp):
CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTGAAAATCCATCTGAAAACATCAAGAAAC
CCATAAAATCTAGGATTAATTTATTTGAAAATTCATTTGAAAA
Found at i:3679273 original size:55 final size:54
Alignment explanation
Indices: 3678993--3679351 Score: 333
Period size: 55 Copynumber: 6.7 Consensus size: 54
3678983 TTTTTCAGTT
* * * *
3678993 ATCATCAAAAAACTCCTAAAAATCAGGCTTAGTTTCTTTGAAAATCCATTTGAAA
1 ATCATCAAGAAACCCCTAAAAATCAGACTTAGTTTCTTTG-AAATTCATTTGAAA
* *
3679048 A-CATCAAGAAACCCCT-AAAATCTATG-CTTAATTTATTTGAAAATTCATTTGAAA
1 ATCATCAAGAAACCCCTAAAAATC-A-GACTTAGTTTCTTTG-AAATTCATTTGAAA
* * * * * * *
3679102 A-CATTAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCATATTCATCTGAAA
1 ATCATCAAGAAACCCCTAAAAATCAGACTTAGTTTCTTTGAAATTCATTTGAAA
* * *
3679155 AT-ATCAAGAAACCCAT-AAAATTAGGA-TTA-TGTTCTTTAAAATTCATTTGAAA
1 ATCATCAAGAAACCCCTAAAAATCA-GACTTAGT-TTCTTTGAAATTCATTTGAAA
* *
3679207 A-CATCAAGAAACCCCTAAAAATCAGACTTAGTTTCTTTGAAAGGTCATTTAAAA
1 ATCATCAAGAAACCCCTAAAAATCAGACTTAGTTTCTTTGAAA-TTCATTTGAAA
** *
3679261 ATCATCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAGCTT-ATTTGAAA
1 ATCATCAAGAAACCCCTAAAAATCAGACTTAGTTTCTTTGAAA--TTCATTTGAAA
** ** *
3679316 ATTGTCAAGAAACTTCTGAAAATCAGACTTAGTTTC
1 ATCATCAAGAAACCCCTAAAAATCAGACTTAGTTTC
3679352 CAAAAAAACA
Statistics
Matches: 256, Mismatches: 34, Indels: 28
0.81 0.11 0.09
Matches are distributed among these distances:
52 44 0.17
53 51 0.20
54 75 0.29
55 85 0.33
56 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (54 bp):
ATCATCAAGAAACCCCTAAAAATCAGACTTAGTTTCTTTGAAATTCATTTGAAA
Found at i:3681369 original size:11 final size:11
Alignment explanation
Indices: 3681353--3681382 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3681343 CTTCTTTCTT
3681353 CTTTTTCTCTC
1 CTTTTTCTCTC
3681364 CTTTTTCTCTC
1 CTTTTTCTCTC
*
3681375 TTTTTTCT
1 CTTTTTCT
3681383 TTTTCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTTTTCTCTC
Found at i:3681384 original size:17 final size:17
Alignment explanation
Indices: 3681364--3681444 Score: 75
Period size: 17 Copynumber: 5.0 Consensus size: 17
3681354 TTTTTCTCTC
3681364 CTTTTTCTCTCTTTTTT
1 CTTTTTCTCTCTTTTTT
3681381 CTTTTTCTCT-TTTTCTT
1 CTTTTTCTCTCTTTT-TT
*
3681398 CTGTTT-TCTC---TTT
1 CTTTTTCTCTCTTTTTT
*
3681411 CTTTTTATCT-TTTTTCT
1 CTTTTTCTCTCTTTTT-T
*
3681428 GTTTTTCTCTCTTTTTT
1 CTTTTTCTCTCTTTTTT
3681445 TCTTCTTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
13 7 0.13
14 4 0.08
16 9 0.17
17 27 0.52
18 5 0.10
ACGTcount: A:0.01, C:0.21, G:0.02, T:0.75
Consensus pattern (17 bp):
CTTTTTCTCTCTTTTTT
Found at i:3681414 original size:30 final size:29
Alignment explanation
Indices: 3681378--3681474 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 29
3681368 TTCTCTCTTT
*
3681378 TTTCTTTTTCTCTTTTTCTTCTGTTTTCTC
1 TTTCTTTTTATCTTTTTCTTCTGTTTT-TC
3681408 TTTCTTTTTATC-TTTT-TTCTGTTTTTC
1 TTTCTTTTTATCTTTTTCTTCTGTTTTTC
* * ** *
3681435 TCTCTTTTTTTCTTCTTTCCCCTATTTTTAC
1 TTTCTTTTTATCTT-TTTCTTCTGTTTTT-C
3681466 TTTCTTTTT
1 TTTCTTTTT
3681475 GTGTGTGTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
27 12 0.21
28 10 0.18
29 7 0.12
30 18 0.32
31 9 0.16
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTCTTTTTATCTTTTTCTTCTGTTTTTC
Found at i:3681451 original size:11 final size:11
Alignment explanation
Indices: 3681347--3681452 Score: 57
Period size: 10 Copynumber: 9.9 Consensus size: 11
3681337 TATTTTCTTC
3681347 TTTCTTCTTTT
1 TTTCTTCTTTT
* *
3681358 TCTCTCCTTTT
1 TTTCTTCTTTT
3681369 TCTCTCTT-TTTT
1 T-T-TCTTCTTTT
*
3681381 CTTT-TTCTCTT
1 -TTTCTTCTTTT
*
3681392 TTTCTTC-TGT
1 TTTCTTCTTTT
3681402 TTTC-TCTTTCT
1 TTTCTTCTTT-T
3681413 TTT-TATC-TTT
1 TTTCT-TCTTTT
*
3681423 TTTC-TGTTTT
1 TTTCTTCTTTT
*
3681433 TCTC-TCTTTT
1 TTTCTTCTTTT
3681443 TTTCTTCTTT
1 TTTCTTCTTT
3681453 CCCCTATTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 24
0.66 0.11 0.22
Matches are distributed among these distances:
9 3 0.04
10 29 0.41
11 28 0.39
12 7 0.10
13 4 0.06
ACGTcount: A:0.01, C:0.23, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTCTTCTTTT
Found at i:3688000 original size:23 final size:21
Alignment explanation
Indices: 3687948--3688009 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
3687938 TTTTGGTGCA
*
3687948 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
3687968 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
3687989 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
3688010 ACAAGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:3688023 original size:21 final size:21
Alignment explanation
Indices: 3687949--3688029 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
3687939 TTTGGTGCAG
* **
3687949 AGGGAATCGA-TCCCCCCTTG
1 AGGGAACCGATTCCCCCCTCA
* *
3687969 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCC-CTCA
*
3687991 AGGGGAACCGATTCCCCCCACA
1 A-GGGAACCGATTCCCCCCTCA
* *
3688013 AGGGAATCGATACCCCC
1 AGGGAACCGATTCCCCC
3688030 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.18
21 20 0.41
22 4 0.08
23 16 0.33
ACGTcount: A:0.25, C:0.36, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCCTCA
Found at i:3696333 original size:20 final size:20
Alignment explanation
Indices: 3696310--3696352 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3696300 AATCCACCAC
*
3696310 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
3696330 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
3696350 ATG
1 ATG
3696353 GTCCAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:3703871 original size:3 final size:3
Alignment explanation
Indices: 3703854--3703899 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
3703844 TTTGGACTTG
* *
3703854 TAA TAA TAT TAAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3703900 CGGGACGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3713919 original size:73 final size:73
Alignment explanation
Indices: 3713831--3713982 Score: 270
Period size: 73 Copynumber: 2.1 Consensus size: 73
3713821 GATAACAATT
* *
3713831 CTATCAACTGCATTAAGAATTTACAAGAAGGCTGTCAACTAAAAGATTATAAAAATGACAATACA
1 CTATCAACAGCATTAAGAATTTACAAGAAGGCTGTCAACTAAAAGATTATAAAAATGAAAATACA
3713896 CACTCTAC
66 CACTCTAC
*
3713904 CTATCAACAGCATTAAGAATTTACTAGAAGGCTGTCAACTAAAAGATTATAAAAATGAAAATACA
1 CTATCAACAGCATTAAGAATTTACAAGAAGGCTGTCAACTAAAAGATTATAAAAATGAAAATACA
3713969 CACTCTAC
66 CACTCTAC
3713977 CT-TCAA
1 CTATCAA
3713983 ATTTATACTA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 4 0.05
73 72 0.95
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (73 bp):
CTATCAACAGCATTAAGAATTTACAAGAAGGCTGTCAACTAAAAGATTATAAAAATGAAAATACA
CACTCTAC
Found at i:3719450 original size:18 final size:18
Alignment explanation
Indices: 3719427--3719461 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3719417 TTCCATCCGG
*
3719427 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
3719445 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
3719462 GTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:3720623 original size:5 final size:5
Alignment explanation
Indices: 3720613--3720686 Score: 58
Period size: 5 Copynumber: 13.0 Consensus size: 5
3720603 GTCGAGTCAA
*
3720613 CGGGT CGGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT AAATGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT ---CGGGT CGGGT
3720664 CGGGT AAACGGGT CGGGT CGGGT
1 CGGGT ---CGGGT CGGGT CGGGT
3720687 TGTGACCGGT
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
5 44 0.76
8 14 0.24
ACGTcount: A:0.11, C:0.18, G:0.53, T:0.19
Consensus pattern (5 bp):
CGGGT
Done.