Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 8 of 295
Found at i:2486141 original size:26 final size:26
Alignment explanation
Indices: 2486112--2486164 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2486102 TTTACAGTTT
2486112 TACCCTTAGGAGATAAATT-ACCAAAA
1 TACCCTTAGG-GATAAATTGACCAAAA
* *
2486138 TACCCTTAGGGTTAAATTGACCTAAA
1 TACCCTTAGGGATAAATTGACCAAAA
2486164 T
1 T
2486165 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (26 bp):
TACCCTTAGGGATAAATTGACCAAAA
Found at i:2487680 original size:35 final size:34
Alignment explanation
Indices: 2487634--2487743 Score: 96
Period size: 35 Copynumber: 3.2 Consensus size: 34
2487624 TTGACTTGGC
*
2487634 TTTATTAATGGAAAATTTAGGTCTTCATTTTTCGT
1 TTTATTAATGGAAAATTTAAGTCTTCA-TTTTCGT
* * ** * * *
2487669 TTTATTCATGGAAATTTTACTTCTTTGATTTTGGA
1 TTTATTAATGGAAAATTTAAGTC-TTCATTTTCGT
* *
2487704 TTTATTAATGGAAACTTTAAGTCTTCAGTTT-GCT
1 TTTATTAATGGAAAATTTAAGTCTTCATTTTCG-T
2487738 TTTATT
1 TTTATT
2487744 CTTGTAAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
33 1 0.02
34 12 0.20
35 43 0.73
36 3 0.05
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.53
Consensus pattern (34 bp):
TTTATTAATGGAAAATTTAAGTCTTCATTTTCGT
Found at i:2487710 original size:70 final size:68
Alignment explanation
Indices: 2487620--2487771 Score: 189
Period size: 70 Copynumber: 2.2 Consensus size: 68
2487610 ATTCCAACTT
* * * * *
2487620 AGTTTTGA-CTTGGCTTTATTAATGGAAAATTTAGGTCTTCATTTTTCGTTTTATTCATGGAAAT
1 AGTTTTGATTTTGGATTTATTAATGGAAAATTTAAGTCTTCAGTTTGC-TTTTATTCATGGAAAT
2487684 TTTA
65 TTTA
** * * *
2487688 CTTCTTTGATTTTGGATTTATTAATGGAAACTTTAAGTCTTCAGTTTGCTTTTATTCTTGTAAAT
1 AGT-TTTGATTTTGGATTTATTAATGGAAAATTTAAGTCTTCAGTTTGCTTTTATTCATGGAAAT
2487753 TTTA
65 TTTA
2487757 AGTTTTGATTTTGGA
1 AGTTTTGATTTTGGA
2487772 AATTTTAGAT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
68 13 0.19
69 24 0.34
70 33 0.47
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.52
Consensus pattern (68 bp):
AGTTTTGATTTTGGATTTATTAATGGAAAATTTAAGTCTTCAGTTTGCTTTTATTCATGGAAATT
TTA
Found at i:2487784 original size:16 final size:15
Alignment explanation
Indices: 2487759--2487789 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2487749 AAATTTTAAG
2487759 TTTTGATTTTGGAAA
1 TTTTGATTTTGGAAA
2487774 TTTTAGATTTTGGAAA
1 TTTT-GATTTTGGAAA
2487790 AAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (15 bp):
TTTTGATTTTGGAAA
Found at i:2487885 original size:25 final size:26
Alignment explanation
Indices: 2487857--2487910 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2487847 TACTACTTTT
2487857 TAATTACCTAG-AAAATATTTAAACA
1 TAATTACCTAGAAAAATATTTAAACA
*** *
2487882 TAATTTTTTAGAAAAATATTTAAATA
1 TAATTACCTAGAAAAATATTTAAACA
2487908 TAA
1 TAA
2487911 ACATATAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (26 bp):
TAATTACCTAGAAAAATATTTAAACA
Found at i:2489812 original size:22 final size:23
Alignment explanation
Indices: 2489762--2489812 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
2489752 TCAAACATAA
2489762 ATAATA-AATTTTATAAACTTAT
1 ATAATATAATTTTATAAACTTAT
*
2489784 A-ACTATAATTTTAT-AA-TTAT
1 ATAATATAATTTTATAAACTTAT
2489804 ATTAATATA
1 A-TAATATA
2489813 TAATTTCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 5 0.21
21 5 0.21
22 14 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATATAATTTTATAAACTTAT
Found at i:2493394 original size:30 final size:31
Alignment explanation
Indices: 2493336--2493398 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
2493326 ATTAACAAGT
2493336 AAATGCCTCTAAAATAATAAAAAAAATTAAC
1 AAATGCCTCTAAAATAATAAAAAAAATTAAC
* *
2493367 AAATGCCTTTAAAATAAT-AACAAAATTAAC
1 AAATGCCTCTAAAATAATAAAAAAAATTAAC
2493397 AA
1 AA
2493399 GAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.24
Consensus pattern (31 bp):
AAATGCCTCTAAAATAATAAAAAAAATTAAC
Found at i:2498659 original size:21 final size:21
Alignment explanation
Indices: 2498633--2498673 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2498623 CAGAGAACGA
* *
2498633 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2498654 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2498674 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2500598 original size:16 final size:16
Alignment explanation
Indices: 2500565--2500598 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2500555 GGAGATTGTT
* *
2500565 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
2500581 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
2500597 AA
1 AA
2500599 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:2503910 original size:35 final size:35
Alignment explanation
Indices: 2503871--2503943 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
2503861 AAATTGAAAT
*
2503871 TAAATTAAAAATATATATTTATACTTAAATAACTC
1 TAAATTAAAAAAATATATTTATACTTAAATAACTC
2503906 TAAATTAAAAAAATATATTTATACTTAAATAACTC
1 TAAATTAAAAAAATATATTTATACTTAAATAACTC
2503941 TAA
1 TAA
2503944 CATATGCAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.38
Consensus pattern (35 bp):
TAAATTAAAAAAATATATTTATACTTAAATAACTC
Found at i:2504037 original size:11 final size:11
Alignment explanation
Indices: 2504023--2504047 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2504013 ATATCCAAAT
2504023 AATAATAGTAA
1 AATAATAGTAA
2504034 AATAATAGTAA
1 AATAATAGTAA
2504045 AAT
1 AAT
2504048 GGTAGCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (11 bp):
AATAATAGTAA
Found at i:2506282 original size:11 final size:11
Alignment explanation
Indices: 2506266--2506299 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2506256 TTTATTTGTG
2506266 AAAAATAAAAT
1 AAAAATAAAAT
2506277 AAAAATAAAAT
1 AAAAATAAAAT
2506288 --AAATAAAAT
1 AAAAATAAAAT
2506297 AAA
1 AAA
2506300 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:2506293 original size:4 final size:5
Alignment explanation
Indices: 2506267--2506299 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
2506257 TTATTTGTGA
2506267 AAAAT AAAAT AAAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAA
2506300 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:2520916 original size:46 final size:46
Alignment explanation
Indices: 2520856--2521074 Score: 305
Period size: 46 Copynumber: 4.8 Consensus size: 46
2520846 TTTGACATGA
* * * * * *
2520856 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATGTCAGGT
** *
2520902 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTT-ATGTCAGGT
* *
2520948 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATGTCAGGT
* *
2520994 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATGTCAGGT
2521040 TGCCATGGTATCTTTCAACCATGGTCTTACACATT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATT
2521075 CCCGCGAACC
Statistics
Matches: 160, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
45 4 0.03
46 153 0.96
47 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATGTCAGGT
Found at i:2524437 original size:28 final size:28
Alignment explanation
Indices: 2524405--2524462 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
2524395 GGAGGCTTGT
2524405 GAAGTATGTCAGCTAGGAAACCAAATCA
1 GAAGTATGTCAGCTAGGAAACCAAATCA
* *
2524433 GAAGTATGTCAGCTAGGAAAGCAAGTCA
1 GAAGTATGTCAGCTAGGAAACCAAATCA
2524461 GA
1 GA
2524463 CTTCCATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.17
Consensus pattern (28 bp):
GAAGTATGTCAGCTAGGAAACCAAATCA
Found at i:2528355 original size:23 final size:22
Alignment explanation
Indices: 2528312--2528369 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
2528302 AAAAGGTATC
* *
2528312 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
2528333 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
2528356 TGCATATCATATCT
1 TACAAATCATATCT
2528370 AAGATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:2528383 original size:22 final size:19
Alignment explanation
Indices: 2528339--2528386 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2528329 AGATTACAAA
2528339 ATCATATCTTCTAAGATTG
1 ATCATATCTTCTAAGATTG
2528358 --CATATCATATCTAAGATTG
1 ATCATATC-T-TCTAAGATTG
2528377 TATCATATCT
1 -ATCATATCT
2528387 AAGATTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
17 6 0.25
18 1 0.04
19 10 0.42
21 1 0.04
22 6 0.25
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (19 bp):
ATCATATCTTCTAAGATTG
Found at i:2528427 original size:36 final size:36
Alignment explanation
Indices: 2528351--2528428 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
2528341 CATATCTTCT
*
2528351 AAGATTGCATATCATATCTAAGATTGTATCATATCT
1 AAGATTGCATATCATATCTAAGATTGTATCATATCG
2528387 AAGATTGCATATCATATCTAAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCTAAGATTG--TATCATATCG
2528423 AAGATT
1 AAGATT
2528429 AGATTTCCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 32 0.82
37 1 0.03
38 6 0.15
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (36 bp):
AAGATTGCATATCATATCTAAGATTGTATCATATCG
Found at i:2528428 original size:17 final size:19
Alignment explanation
Indices: 2528348--2528420 Score: 132
Period size: 19 Copynumber: 3.9 Consensus size: 19
2528338 AATCATATCT
2528348 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2528367 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
2528384 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2528403 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
2528421 TGAAGATTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.33
19 35 0.67
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2531832 original size:9 final size:9
Alignment explanation
Indices: 2531814--2531850 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2531804 AAGTTGGCCT
*
2531814 ACATGCAGC
1 ACATGAAGC
*
2531823 ACATGTAGC
1 ACATGAAGC
2531832 ACATGAAGC
1 ACATGAAGC
2531841 ACATGAAGC
1 ACATGAAGC
2531850 A
1 A
2531851 GCCAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (9 bp):
ACATGAAGC
Found at i:2540063 original size:21 final size:21
Alignment explanation
Indices: 2540037--2540077 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2540027 ATCTGCTCAA
* *
2540037 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2540058 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2540078 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2545959 original size:15 final size:15
Alignment explanation
Indices: 2545939--2545970 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2545929 AAGTTTGTCA
2545939 AATTATTCAATTCTG
1 AATTATTCAATTCTG
2545954 AATTATTCAATTCTG
1 AATTATTCAATTCTG
2545969 AA
1 AA
2545971 ATTCAATCCC
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:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (15 bp):
AATTATTCAATTCTG
Found at i:2546929 original size:20 final size:20
Alignment explanation
Indices: 2546904--2546953 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2546894 TGGCTTAAAA
2546904 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2546924 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2546941 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2546954 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2551568 original size:20 final size:20
Alignment explanation
Indices: 2551543--2551592 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2551533 TGGCTTAAAA
2551543 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2551563 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2551580 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2551593 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2553154 original size:13 final size:13
Alignment explanation
Indices: 2553136--2553164 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2553126 ATGATCGAAT
2553136 ACAAAAAAAAATG
1 ACAAAAAAAAATG
2553149 AC-AAAAAAAATG
1 ACAAAAAAAAATG
2553161 ACAA
1 ACAA
2553165 TGATAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.76, C:0.10, G:0.07, T:0.07
Consensus pattern (13 bp):
ACAAAAAAAAATG
Found at i:2553156 original size:12 final size:12
Alignment explanation
Indices: 2553139--2553164 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2553129 ATCGAATACA
2553139 AAAAAAAATGAC
1 AAAAAAAATGAC
2553151 AAAAAAAATGAC
1 AAAAAAAATGAC
2553163 AA
1 AA
2553165 TGATAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAAATGAC
Found at i:2553873 original size:3 final size:3
Alignment explanation
Indices: 2553867--2553897 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
2553857 TATCAAAAAC
2553867 TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
2553898 ATGTATACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2565436 original size:21 final size:21
Alignment explanation
Indices: 2565410--2565450 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2565400 ATCTGCTCAA
* *
2565410 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2565431 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2565451 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2576591 original size:31 final size:31
Alignment explanation
Indices: 2576556--2576628 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
2576546 ACCCAGCTTC
*
2576556 AAAAAGTTATTAAATG-AGCAA-TAAATTATTT
1 AAAAA-TT-TTAAATGAAGCAACTAAACTATTT
* *
2576587 AAAAATTTTCATTGAAGCAACTAAACTATTT
1 AAAAATTTTAAATGAAGCAACTAAACTATTT
2576618 AAAAGATTTTA
1 AAAA-ATTTTA
2576629 TTTAATTTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 5 0.14
30 7 0.20
31 18 0.51
32 5 0.14
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (31 bp):
AAAAATTTTAAATGAAGCAACTAAACTATTT
Found at i:2586761 original size:24 final size:24
Alignment explanation
Indices: 2586698--2586749 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2586688 TTTCTAGAAG
* * *
2586698 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
2586722 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
2586746 ATTT
1 ATTT
2586750 TGCTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:2598574 original size:78 final size:78
Alignment explanation
Indices: 2598445--2598606 Score: 315
Period size: 78 Copynumber: 2.1 Consensus size: 78
2598435 TGTGTATTCA
2598445 CCTTTAAGAGATCATGAGGTATAATATGTCTAAGGTTCTAGCATTTGCAACCCATTAATTATTCC
1 CCTTTAAGAGATCATGAGGTATAATATGTCTAAGGTTCTAGCATTTGCAACCCATTAATTATTCC
*
2598510 TAAGCTCTTCCCT
66 CAAGCTCTTCCCT
2598523 CCTTTAAGAGATCATGAGGTATAATATGTCTAAGGTTCTAGCATTTGCAACCCATTAATTATTCC
1 CCTTTAAGAGATCATGAGGTATAATATGTCTAAGGTTCTAGCATTTGCAACCCATTAATTATTCC
2598588 CAAGCTCTTCCCT
66 CAAGCTCTTCCCT
2598601 CCTTTA
1 CCTTTA
2598607 TGCAAAAGGA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 83 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (78 bp):
CCTTTAAGAGATCATGAGGTATAATATGTCTAAGGTTCTAGCATTTGCAACCCATTAATTATTCC
CAAGCTCTTCCCT
Found at i:2607270 original size:21 final size:21
Alignment explanation
Indices: 2607246--2607315 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
2607236 GTTAAGAAAC
2607246 GAGAAGACAAAGTTGTGAATG
1 GAGAAGACAAAGTTGTGAATG
* **
2607267 GAGAAG-CTGATAGCTT-TGAAAC
1 GAGAAGAC--AAAG-TTGTGAATG
2607289 GAGAAGACAAAGTTGTGAATG
1 GAGAAGACAAAGTTGTGAATG
2607310 GAGAAG
1 GAGAAG
2607316 CTGATAGCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
20 3 0.08
21 19 0.50
22 13 0.34
23 3 0.08
ACGTcount: A:0.41, C:0.07, G:0.33, T:0.19
Consensus pattern (21 bp):
GAGAAGACAAAGTTGTGAATG
Found at i:2607289 original size:43 final size:43
Alignment explanation
Indices: 2607241--2607327 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
2607231 AAATTGTTAA
2607241 GAAACGAGAAGACAAAGTTGTGAATGGAGAAGCTGATAGCTTT
1 GAAACGAGAAGACAAAGTTGTGAATGGAGAAGCTGATAGCTTT
2607284 GAAACGAGAAGACAAAGTTGTGAATGGAGAAGCTGATAGCTTT
1 GAAACGAGAAGACAAAGTTGTGAATGGAGAAGCTGATAGCTTT
2607327 G
1 G
2607328 GCAATGACTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.39, C:0.09, G:0.31, T:0.21
Consensus pattern (43 bp):
GAAACGAGAAGACAAAGTTGTGAATGGAGAAGCTGATAGCTTT
Found at i:2608585 original size:26 final size:26
Alignment explanation
Indices: 2608549--2608603 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
2608539 CAAACATATC
*
2608549 CCATAGATACCACTCGATATCAAGCA
1 CCATAGATACCACTCAATATCAAGCA
2608575 CCATAGATACCACTCAATATCAAGCA
1 CCATAGATACCACTCAATATCAAGCA
2608601 CCA
1 CCA
2608604 CCATGAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.40, C:0.33, G:0.09, T:0.18
Consensus pattern (26 bp):
CCATAGATACCACTCAATATCAAGCA
Found at i:2620485 original size:17 final size:17
Alignment explanation
Indices: 2620463--2620498 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2620453 TCATTTAATC
2620463 AATAATCAATAATCAAT
1 AATAATCAATAATCAAT
2620480 AATAATCAATAATCAAT
1 AATAATCAATAATCAAT
2620497 AA
1 AA
2620499 GATAAACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATCAATAATCAAT
Found at i:2620511 original size:20 final size:17
Alignment explanation
Indices: 2620463--2620516 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
2620453 TCATTTAATC
*
2620463 AATAATCAATAATCAAT
1 AATAACCAATAATCAAT
*
2620480 AATAATCAATAATCAAT
1 AATAACCAATAATCAAT
2620497 AAGATAAACCAATAATCAAT
1 -A-AT-AACCAATAATCAAT
2620517 TAATCTCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 17 0.52
18 1 0.03
19 2 0.06
20 13 0.39
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.26
Consensus pattern (17 bp):
AATAACCAATAATCAAT
Found at i:2620516 original size:7 final size:7
Alignment explanation
Indices: 2620458--2620498 Score: 55
Period size: 7 Copynumber: 5.4 Consensus size: 7
2620448 GTAAGTCATT
2620458 TAATCAA
1 TAATCAA
2620465 TAATCAA
1 TAATCAA
2620472 TAATCAATAA
1 TAATC---AA
2620482 TAATCAA
1 TAATCAA
2620489 TAATCAA
1 TAATCAA
2620496 TAA
1 TAA
2620499 GATAAACCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 24 0.77
10 7 0.23
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (7 bp):
TAATCAA
Found at i:2628498 original size:15 final size:15
Alignment explanation
Indices: 2628478--2628518 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
2628468 ATAGTTATAT
*
2628478 ATTATTTTATAAAGA
1 ATTATTTTATAAAAA
2628493 ATTA--TTATAAAAA
1 ATTATTTTATAAAAA
2628506 ATTATTTTA-AAAA
1 ATTATTTTATAAAA
2628519 TTGATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 12 0.52
14 4 0.17
15 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
ATTATTTTATAAAAA
Found at i:2628583 original size:19 final size:19
Alignment explanation
Indices: 2628559--2628598 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2628549 TAAATAATAA
2628559 TTAGCTTAATTATTAAGAG
1 TTAGCTTAATTATTAAGAG
2628578 TTAGCTTAATTATTAAGAG
1 TTAGCTTAATTATTAAGAG
2628597 TT
1 TT
2628599 GAATTAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (19 bp):
TTAGCTTAATTATTAAGAG
Found at i:2628843 original size:17 final size:17
Alignment explanation
Indices: 2628821--2628853 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2628811 ATAATGTACG
*
2628821 TTCAAATGTTGAAAATC
1 TTCAAATATTGAAAATC
2628838 TTCAAATATTGAAAAT
1 TTCAAATATTGAAAAT
2628854 GACATAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (17 bp):
TTCAAATATTGAAAATC
Found at i:2634853 original size:21 final size:21
Alignment explanation
Indices: 2634829--2634868 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2634819 TGAAAGAGGG
2634829 ACACGAC-AGTGTGATAGAGAC
1 ACACGACTA-TGTGATAGAGAC
*
2634850 ACACGCCTATGTGATAGAG
1 ACACGACTATGTGATAGAG
2634869 TTACATAGTC
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:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (21 bp):
ACACGACTATGTGATAGAGAC
Found at i:2636674 original size:18 final size:18
Alignment explanation
Indices: 2636651--2636694 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2636641 TCTACACTTC
*
2636651 TGAGCTCATCC-AAAGTTG
1 TGAGCTCA-CCTAAAGATG
2636669 TGAGCTCACCTAAAGATG
1 TGAGCTCACCTAAAGATG
*
2636687 CGAGCTCA
1 TGAGCTCA
2636695 ACTCAAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (18 bp):
TGAGCTCACCTAAAGATG
Found at i:2640526 original size:21 final size:21
Alignment explanation
Indices: 2640500--2640540 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2640490 ATCTGCTCAA
*
2640500 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
2640521 ACTCCACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
2640541 TCGCTTGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:2648577 original size:23 final size:22
Alignment explanation
Indices: 2648526--2648577 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
2648516 CCTCGTCTTT
*
2648526 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
2648548 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
2648571 TTCTTTT
1 TTCTTTT
2648578 TCAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:2652738 original size:15 final size:15
Alignment explanation
Indices: 2652701--2652750 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
2652691 ATTTACTATA
2652701 TTATTTAT-TTTA-G
1 TTATTTATATTTATG
2652714 -TATTTAATATTTATG
1 TTATTT-ATATTTATG
2652729 TTATTTATATTTCAT-
1 TTATTTATATTT-ATG
2652744 TTATTTA
1 TTATTTA
2652751 CACATTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.16
13 2 0.06
14 4 0.12
15 14 0.44
16 7 0.22
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (15 bp):
TTATTTATATTTATG
Found at i:2654939 original size:29 final size:30
Alignment explanation
Indices: 2654907--2654963 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2654897 ATAATGACAA
*
2654907 AATTTTATA-CTTAAAAAATATAAAAATTT
1 AATTTAATATCTTAAAAAATATAAAAATTT
* *
2654936 AATTTAATATTTTAAAAATTATAAAAAT
1 AATTTAATATCTTAAAAAATATAAAAAT
2654964 ATAAATCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
AATTTAATATCTTAAAAAATATAAAAATTT
Found at i:2659995 original size:26 final size:24
Alignment explanation
Indices: 2659965--2660014 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
2659955 TAAATAAAAA
*
2659965 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
2659991 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
2660015 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:2660034 original size:21 final size:21
Alignment explanation
Indices: 2659985--2660043 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2659975 ATAATAAATC
*
2659985 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
2660005 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
2660027 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
2660044 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:2662759 original size:28 final size:28
Alignment explanation
Indices: 2662704--2662806 Score: 122
Period size: 28 Copynumber: 3.8 Consensus size: 28
2662694 AGCATGGCTG
* * *
2662704 CCAGA-ACAGAT-ATTGTGACAGAGTCA
1 CCAGATACAGATAATTGTGGCAGGGCCA
2662730 CCAGATACAGATAATTGTGGCAGGGCCA
1 CCAGATACAGATAATTGTGGCAGGGCCA
* *
2662758 CCAGAAACAGATATTTGTGGCAGGGCCA
1 CCAGATACAGATAATTGTGGCAGGGCCA
* *
2662786 CCAAAT-CAGATATTTGTGGCA
1 CCAGATACAGATAATTGTGGCA
2662807 TAGCCATCAG
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
26 5 0.07
27 21 0.31
28 42 0.62
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.20
Consensus pattern (28 bp):
CCAGATACAGATAATTGTGGCAGGGCCA
Found at i:2662818 original size:55 final size:55
Alignment explanation
Indices: 2662704--2662818 Score: 135
Period size: 55 Copynumber: 2.1 Consensus size: 55
2662694 AGCATGGCTG
* * *
2662704 CCAG-AACAGATATTGTGACAGAGTCACCAGATACAGATAATTGTGGCAGGGCCA
1 CCAGAAACAGATATTGTGACAGAGCCACCAAATACAGATAATTGTGGCAGAGCCA
* * * *
2662758 CCAGAAACAGATATTTGTGGCAGGGCCACCAAAT-CAGATATTTGTGGCATAGCCA
1 CCAGAAACAGATA-TTGTGACAGAGCCACCAAATACAGATAATTGTGGCAGAGCCA
*
2662813 TCAGAA
1 CCAGAA
2662819 TGCTTCCTCC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
54 4 0.08
55 31 0.61
56 16 0.31
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (55 bp):
CCAGAAACAGATATTGTGACAGAGCCACCAAATACAGATAATTGTGGCAGAGCCA
Found at i:2664060 original size:18 final size:18
Alignment explanation
Indices: 2664013--2664063 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
2664003 AGCTATAGAG
2664013 GAAAAGAAGAAGAAGAGGA
1 GAAAAGAAGAAG-AGAGGA
* *
2664032 -AATAGATGAAGAGAGGA
1 GAAAAGAAGAAGAGAGGA
2664049 GAAAAGAAGAAGAGA
1 GAAAAGAAGAAGAGA
2664064 AAAGAATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.04
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAGGA
Found at i:2664069 original size:18 final size:18
Alignment explanation
Indices: 2664013--2664069 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
2664003 AGCTATAGAG
*
2664013 GAAAAGAAGAAGA-AGAG
1 GAAAAGAAGAAGAGAGAA
* *
2664030 GAAATAGATGAAGAGAGGA
1 GAAA-AGAAGAAGAGAGAA
*
2664049 GAAAAGAAGAAGAGAAAA
1 GAAAAGAAGAAGAGAGAA
2664067 GAA
1 GAA
2664070 TTGTCAGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 4 0.12
18 22 0.69
19 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAGAA
Found at i:2664705 original size:15 final size:15
Alignment explanation
Indices: 2664682--2664711 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2664672 TAAACTAACC
*
2664682 TAAACATAATAATAA
1 TAAAAATAATAATAA
2664697 TAAAAATAATAATAA
1 TAAAAATAATAATAA
2664712 CAATAACGCC
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:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAAATAATAATAA
Found at i:2668020 original size:39 final size:39
Alignment explanation
Indices: 2667900--2668020 Score: 215
Period size: 39 Copynumber: 3.1 Consensus size: 39
2667890 AATTATATTA
* *
2667900 CCAGCACAAAGCCTGCGGGACTTTAGCCCGAATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
2667939 CCAACACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
2667978 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
2668017 CCAG
1 CCAG
2668021 TGTCTTGAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Found at i:2673041 original size:37 final size:36
Alignment explanation
Indices: 2672983--2673054 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
2672973 TTATTTTTAT
* *
2672983 TTTTATTTTTTTTATTTATTATTTTCCTTTATTTTC
1 TTTTATTTTTATTATTTATTATTTTACTTTATTTTC
*
2673019 TTTTATTATTTATTATTTATTATTTTATTTTATTTT
1 TTTTATT-TTTATTATTTATTATTTTACTTTATTTT
2673055 AGTTAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (36 bp):
TTTTATTTTTATTATTTATTATTTTACTTTATTTTC
Found at i:2673051 original size:10 final size:10
Alignment explanation
Indices: 2672972--2673055 Score: 55
Period size: 10 Copynumber: 7.9 Consensus size: 10
2672962 CAACCCAATC
2672972 TTTATTTTTATT
1 TTTA-TTTTA-T
2672984 TTTATTTT-T
1 TTTATTTTAT
2672993 TTTATTTATTAT
1 TTTA-TT-TTAT
**
2673005 TTTCCTTTAT
1 TTTATTTTAT
*
2673015 TTTCTTTTATT
1 TTTATTTTA-T
2673026 ATTTATTATT-T
1 -TTTATT-TTAT
*
2673037 ATTATTTTAT
1 TTTATTTTAT
2673047 TTTATTTTA
1 TTTATTTTA
2673056 GTTAAATATT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
9 7 0.12
10 28 0.47
11 9 0.15
12 13 0.22
13 2 0.03
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:2673208 original size:42 final size:42
Alignment explanation
Indices: 2673162--2673266 Score: 149
Period size: 42 Copynumber: 2.5 Consensus size: 42
2673152 ATCCATGGTA
2673162 CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTGCT-G
1 CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTG-TAG
* * *
2673204 CCAAACAGTTCTATTCCAGCCCAGAATGTCATATCTCTGTAG
1 CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTGTAG
* *
2673246 CCAAACAGTCCTATTTCAGCC
1 CCAAACAGTTCTATTCCAGCC
2673267 TTAGAATCCC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.02
42 56 0.98
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.26
Consensus pattern (42 bp):
CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTGTAG
Found at i:2674256 original size:118 final size:118
Alignment explanation
Indices: 2674048--2674278 Score: 363
Period size: 118 Copynumber: 2.0 Consensus size: 118
2674038 TGTTTTCCAT
* * *
2674048 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTTTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
* *
2674113 CTACTTCGCGTTAAAAGGTTGTGTGATGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTAGCGTCAAAAGGTTGTGTGATGTGACAAGTAAAACTCCGCTAGCCGA
**
2674166 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
****
2674231 CTACTTAGCGTCAAAAGGTTGTGTGATGTGTTGGGTAAAACTCCGCTA
66 CTACTTAGCGTCAAAAGGTTGTGTGATGTGACAAGTAAAACTCCGCTA
2674279 ACCGGAAATA
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
118 102 1.00
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTAGCGTCAAAAGGTTGTGTGATGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:2678392 original size:28 final size:28
Alignment explanation
Indices: 2678337--2678450 Score: 117
Period size: 28 Copynumber: 4.2 Consensus size: 28
2678327 AGCATGGCTG
* *
2678337 CCAGA-ACAGAT-ATTGTGACAGAGTCA
1 CCAGATACAGATAATTGTGGCAGAGCCA
*
2678363 CCAGATACAGATAATTGTGGCAGGGCCA
1 CCAGATACAGATAATTGTGGCAGAGCCA
* * * * *
2678391 CCAGAAATAGATATTTGTCGCAGGGCCA
1 CCAGATACAGATAATTGTGGCAGAGCCA
* *
2678419 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATAATTGTGGCAGAGCCA
2678446 CCAGA
1 CCAGA
2678451 ATGCTTCCTC
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
26 5 0.07
27 28 0.38
28 41 0.55
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (28 bp):
CCAGATACAGATAATTGTGGCAGAGCCA
Found at i:2680362 original size:15 final size:15
Alignment explanation
Indices: 2680339--2680368 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2680329 TAAACTAACC
*
2680339 TAAACATAATAATAA
1 TAAAAATAATAATAA
2680354 TAAAAATAATAATAA
1 TAAAAATAATAATAA
2680369 CAATAAAGAA
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:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAAATAATAATAA
Found at i:2682902 original size:3 final size:3
Alignment explanation
Indices: 2682894--2682919 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2682884 ACTGTCTATG
2682894 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2682920 GACAAGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2686246 original size:22 final size:23
Alignment explanation
Indices: 2686211--2686259 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
2686201 AATATAACCT
*
2686211 ATTCTGAAATAAAATTTAAACAG
1 ATTCTGAAAAAAAATTTAAACAG
*
2686234 ATTCT-AAAAAAAATTTAAATAG
1 ATTCTGAAAAAAAATTTAAACAG
2686256 ATTC
1 ATTC
2686260 CCTAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (23 bp):
ATTCTGAAAAAAAATTTAAACAG
Found at i:2687282 original size:24 final size:25
Alignment explanation
Indices: 2687236--2687282 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2687226 CAAAAATACT
2687236 AAAAAAATAAAAATAAATATTTTCC
1 AAAAAAATAAAAATAAATATTTTCC
* *
2687261 AAAAAATTGAAAATAAAT-TTTT
1 AAAAAAATAAAAATAAATATTTT
2687283 AAAAATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAAAAATAAAAATAAATATTTTCC
Found at i:2687365 original size:30 final size:30
Alignment explanation
Indices: 2687331--2687390 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2687321 ACTTAACAAG
*
2687331 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
2687361 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
2687391 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:2700902 original size:30 final size:30
Alignment explanation
Indices: 2700842--2700903 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
2700832 ATTCTCTATA
** *
2700842 TTTATAATTTTTAAAGGATTAAATTAAATT
1 TTTATAATTTTTAAAGGACGAAAGTAAATT
*
2700872 TTTATAA-TTTTAGAGGACGAAAGTACAATT
1 TTTATAATTTTTAAAGGACGAAAGTA-AATT
2700902 TT
1 TT
2700904 ACCTTTACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.45
Consensus pattern (30 bp):
TTTATAATTTTTAAAGGACGAAAGTAAATT
Found at i:2707417 original size:11 final size:11
Alignment explanation
Indices: 2707402--2707441 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2707392 GTTTTCTCCA
2707402 TATTTTGCTAT
1 TATTTTGCTAT
* *
2707413 CATTTTACTAT
1 TATTTTGCTAT
*
2707424 TATGTTGCTAT
1 TATTTTGCTAT
2707435 TATTTTG
1 TATTTTG
2707442 TTGTTATTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:2707537 original size:29 final size:30
Alignment explanation
Indices: 2707478--2707539 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
2707468 ATTTATTTTA
*
2707478 TTGTTAATTTTCTTATTATTTTAAAGGTAT
1 TTGTTAATTTTCTTATTATTTTAAAGCTAT
2707508 TTGTTAATTTT-TTATTATTTTAGAA-CTAT
1 TTGTTAATTTTCTTATTATTTTA-AAGCTAT
2707537 TTG
1 TTG
2707540 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.61
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAAAGCTAT
Found at i:2708671 original size:8 final size:8
Alignment explanation
Indices: 2708638--2708672 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
2708628 TAATATAATC
2708638 ATTTTTA-
1 ATTTTTAT
2708645 ATTTTTAT
1 ATTTTTAT
2708653 AATTTTTAT
1 -ATTTTTAT
2708662 ATTTTTAT
1 ATTTTTAT
2708670 ATT
1 ATT
2708673 CTAAAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.27
8 11 0.42
9 8 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
ATTTTTAT
Found at i:2710042 original size:26 final size:24
Alignment explanation
Indices: 2710013--2710113 Score: 59
Period size: 23 Copynumber: 4.0 Consensus size: 24
2710003 TTAGTCATGC
2710013 TATTATATTTATTACTGTTATTATTA
1 TATTAT-TTTATTA-TGTTATTATTA
*
2710039 TATT-TTTT-TTAGTGTT-CTATTA
1 TATTATTTTATTA-TGTTATTATTA
2710061 TTATTATTTTATTTGATGCTTATATATATA
1 -TATTATTTTA-TT-ATG-TTAT-TAT-TA
*
2710091 TATTATATTA-TATAG-TATTATTA
1 TATTATTTTATTAT-GTTATTATTA
2710114 ATAGCTTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 23
0.69 0.05 0.26
Matches are distributed among these distances:
22 5 0.08
23 13 0.21
24 10 0.16
25 4 0.07
26 10 0.16
27 5 0.08
29 12 0.20
30 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (24 bp):
TATTATTTTATTATGTTATTATTA
Found at i:2710262 original size:3 final size:3
Alignment explanation
Indices: 2710254--2710292 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2710244 TGTATTTCTA
*
2710254 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2710293 ATAGTAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2714149 original size:16 final size:16
Alignment explanation
Indices: 2714128--2714167 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2714118 CGCAACTCAT
*
2714128 TTTTTTAATAATATAA
1 TTTTTTAAAAATATAA
*
2714144 TTTTTTAAAAATATTA
1 TTTTTTAAAAATATAA
2714160 TTATTTTA
1 TT-TTTTA
2714168 TTATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTTAAAAATATAA
Found at i:2717616 original size:11 final size:11
Alignment explanation
Indices: 2717581--2717608 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2717571 GAGAGTAAGA
2717581 AATTTTAATGT
1 AATTTTAATGT
2717592 AATTTTAATGT
1 AATTTTAATGT
2717603 AATTTT
1 AATTTT
2717609 GATATAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
AATTTTAATGT
Found at i:2718818 original size:7 final size:7
Alignment explanation
Indices: 2718800--2718845 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
2718790 TAAAATTATT
2718800 TAAAAT-
1 TAAAATA
2718806 TAAAATA
1 TAAAATA
2718813 TAAAATA
1 TAAAATA
2718820 TAAAATA
1 TAAAATA
*
2718827 TAAATGTA
1 TAAA-ATA
2718835 TAAAA-A
1 TAAAATA
2718841 TAAAA
1 TAAAA
2718846 ACATATAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 12 0.33
7 18 0.50
8 6 0.17
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (7 bp):
TAAAATA
Found at i:2722254 original size:20 final size:21
Alignment explanation
Indices: 2722231--2722280 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
2722221 ATATATATTT
2722231 TTAATTTTTAAAAAATT-AAA
1 TTAATTTTTAAAAAATTAAAA
*
2722251 TTAATTTTTAAAAATTTAAAA
1 TTAATTTTTAAAAAATTAAAA
2722272 TATAATTTT
1 T-TAATTTT
2722281 ATAATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 16 0.59
21 4 0.15
22 7 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATTTTTAAAAAATTAAAA
Found at i:2726900 original size:29 final size:29
Alignment explanation
Indices: 2726868--2726924 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2726858 TCCTTAACTC
2726868 AAACTTTTGAAAAATTACAATTTTGCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCT
* * * *
2726897 AAACTTTTGCATATTTACACTTTTGCCC
1 AAACTTTTGAAAAATTACAATTTTGCCC
2726925 CTAGGCTCGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (29 bp):
AAACTTTTGAAAAATTACAATTTTGCCCT
Found at i:2728946 original size:20 final size:20
Alignment explanation
Indices: 2728910--2728947 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2728900 TAATTGAAAA
*
2728910 TTAAAAAGATATTAAAATTT
1 TTAAAAAGATATGAAAATTT
2728930 TTAAAAA-ATTATGAAAAT
1 TTAAAAAGA-TATGAAAAT
2728948 AGTTTCCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
TTAAAAAGATATGAAAATTT
Found at i:2733836 original size:493 final size:492
Alignment explanation
Indices: 2732908--2733881 Score: 1545
Period size: 493 Copynumber: 2.0 Consensus size: 492
2732898 CCTTTACATC
* * * *
2732908 CTTCATTGATCCTTCGAGTTTACCCACACGTTCCTCTACTGCTAACAGCGTCTCCTTCAAAGACT
1 CTTCATTGATCCCTCGAGTTTACCCACACATTCCTCTACTGCTAACAGCATCTCCCTCAAAGACT
2732973 TTTTGACCCACCTTTGTTCAAAATCTTCTTTCGACATCCCAACGGTTCCTTCAAACCAACAGCTC
66 TTTTGACCCACCTTTGTTCAAAATCTTCTTTCGACATCCCAACGGTTCCTTCAAACCAACAGCTC
* * * *
2733038 GGATACCACTTGTCACGGGGCTAGATCTTTCGTCTTGCGATTCGTGAGGCCTTAGGCGATTCATT
131 GGATACCACTTGTCACGGGGCTAGATCTTTCGTCTCGCGATCCGTGAGGCCTTAAGCGATCCATT
* * * *
2733103 CGCCCAAATTCTCCTAAGTCAGCCTTTACCCAAGCGAGGATTTCTTTAAAACTCCTCCAAGGCAC
196 CGCCCAAACTCACCTAAGTCAACCTTTACCCAAGCGAGGATTCCTTTAAAACTCCTCCAAGGCAC
*
2733168 CAATTTGTATAGTAGAAGTGATTTATGCCAAAAGAAGCAACAAAAGAACAACAGAAAGAACGCAC
261 CAATTTGTATAGTAGAAGCGATTTATGCCAAAAGAAGCAACAAAAGAACAACAGAAAGAACGCAC
* * * * *
2733233 ATAAGGTGTTTGAGTAAATGCTCTTAATATCCTCTTATTGACAAAGATTAATGAAACAATGAATA
326 ACAAGGTGTTTGAGTAAATACTCTCAATATCCTCTTATTCACAAAGAATAATGAAACAATGAATA
*
2733298 GAGTGAGTATAAATGAGGGGGTGGCTCTCTATTTATAGCTGAGCTCCCCTAAAACCAACGGTCAA
391 GAGTGAGTACAAATGAGGGGGTGGCTCTCTATTTATAGCTGAGCTCCCC-AAAACCAACGGTCAA
* *
2733363 TATTACAATACATCAAAGGATGAGATTACCCACACGTT
455 GATTACAATACATCAAAGGACGAGATTACCCACACGTT
* *
2733401 CTTCATTGATCCCTCGAGTTTACCCACACATTCCTCTACTGTTGACAGCATCTCCCTCAAAGACT
1 CTTCATTGATCCCTCGAGTTTACCCACACATTCCTCTACTGCTAACAGCATCTCCCTCAAAGACT
* * * *
2733466 TTTTGGCCCACCTTTGTTCAAACTCTTCTTTCGACATCCCAACGGTTCCTTTC-AATCAATAGCT
66 TTTTGACCCACCTTTGTTCAAAATCTTCTTTCGACATCCCAACGGTTCC-TTCAAACCAACAGCT
* * *
2733530 CGGATACCACTTGTCACGGGGCTAGATCTTTCGTCTCGCGATCCGTGCGGTCTTAAGCGATCCGT
130 CGGATACCACTTGTCACGGGGCTAGATCTTTCGTCTCGCGATCCGTGAGGCCTTAAGCGATCCAT
* * * * * *
2733595 TCGTCCAAACTCACCTAAGTCAACCTTTACTCAAGTGATGATTCCTTTAGAACTCCTCCAATGCA
195 TCGCCCAAACTCACCTAAGTCAACCTTTACCCAAGCGAGGATTCCTTTAAAACTCCTCCAAGGCA
*
2733660 CCAATTTGTATAGTAGAAGCGATTTATGCCTAAAGAAGCAACAAAAGAACAACAGAAAGAACGCA
260 CCAATTTGTATAGTAGAAGCGATTTATGCCAAAAGAAGCAACAAAAGAACAACAGAAAGAACGCA
2733725 CACAAGGTGTTTGAGTAAATACTCTCAATATCCTCTTATTCACAAAGAATAATGAAACAATGAAT
325 CACAAGGTGTTTGAGTAAATACTCTCAATATCCTCTTATTCACAAAGAATAATGAAACAATGAAT
* * * *
2733790 GGAGTGAGTACAAATGAGGGGGTGGCTTTCTATTTATAGTTGAGCTCCCCAACACCAACGGTCAA
390 AGAGTGAGTACAAATGAGGGGGTGGCTCTCTATTTATAGCTGAGCTCCCCAAAACCAACGGTCAA
*
2733855 GATTACAATACATCAACGGACGAGATT
455 GATTACAATACATCAAAGGACGAGATT
2733882 TATCCTATCC
Statistics
Matches: 438, Mismatches: 42, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
492 38 0.09
493 397 0.91
494 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (492 bp):
CTTCATTGATCCCTCGAGTTTACCCACACATTCCTCTACTGCTAACAGCATCTCCCTCAAAGACT
TTTTGACCCACCTTTGTTCAAAATCTTCTTTCGACATCCCAACGGTTCCTTCAAACCAACAGCTC
GGATACCACTTGTCACGGGGCTAGATCTTTCGTCTCGCGATCCGTGAGGCCTTAAGCGATCCATT
CGCCCAAACTCACCTAAGTCAACCTTTACCCAAGCGAGGATTCCTTTAAAACTCCTCCAAGGCAC
CAATTTGTATAGTAGAAGCGATTTATGCCAAAAGAAGCAACAAAAGAACAACAGAAAGAACGCAC
ACAAGGTGTTTGAGTAAATACTCTCAATATCCTCTTATTCACAAAGAATAATGAAACAATGAATA
GAGTGAGTACAAATGAGGGGGTGGCTCTCTATTTATAGCTGAGCTCCCCAAAACCAACGGTCAAG
ATTACAATACATCAAAGGACGAGATTACCCACACGTT
Found at i:2736610 original size:54 final size:55
Alignment explanation
Indices: 2736552--2736680 Score: 149
Period size: 53 Copynumber: 2.4 Consensus size: 55
2736542 AATTCATTTT
* **
2736552 AAATATTAAAAT-T-AAAATATTTTAAGAAAAAATTTAAAGTTGAATTCAAAATAA
1 AAATATTAAAATATAAAAATAATTTAAG-AAAAATTTAAAGTCAAATTCAAAATAA
* *
2736606 AAATA--AAAATATAAAAATAATTTAAGAAAAATTTGAAGTCAAATTCAAAATAT
1 AAATATTAAAATATAAAAATAATTTAAGAAAAATTTAAAGTCAAATTCAAAATAA
* *
2736659 AAATATTAGAATAATAATAATA
1 AAATATTAAAAT-ATAAAAATA
2736681 GGATTCAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
52 5 0.08
53 29 0.46
54 17 0.27
55 4 0.06
56 8 0.13
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.31
Consensus pattern (55 bp):
AAATATTAAAATATAAAAATAATTTAAGAAAAATTTAAAGTCAAATTCAAAATAA
Found at i:2738116 original size:29 final size:31
Alignment explanation
Indices: 2738083--2738153 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 31
2738073 AATAGTTTAT
*
2738083 ATTTT-ATAATTTTT-GAAGGA-TTAAATTA-A
1 ATTTTAAT-ATTTTTAG-AGGAGTTAAAATACA
2738112 ATTTTAATATTTTTAGAGGAGTTAAAATACA
1 ATTTTAATATTTTTAGAGGAGTTAAAATACA
*
2738143 ATTTTACTATT
1 ATTTTAATATT
2738154 ATTAATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 15 0.42
30 10 0.28
31 11 0.31
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (31 bp):
ATTTTAATATTTTTAGAGGAGTTAAAATACA
Found at i:2744672 original size:14 final size:14
Alignment explanation
Indices: 2744653--2744679 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2744643 TACTTCTTGC
2744653 TTCAGTTTTGCAAA
1 TTCAGTTTTGCAAA
2744667 TTCAGTTTTGCAA
1 TTCAGTTTTGCAA
2744680 CTTTGTTTGA
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:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (14 bp):
TTCAGTTTTGCAAA
Found at i:2746161 original size:11 final size:11
Alignment explanation
Indices: 2746145--2746187 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
2746135 TAGAATATAC
2746145 CCCATACCTTG
1 CCCATACCTTG
*
2746156 CCCATACCTTT
1 CCCATACCTTG
*
2746167 CCCATACC-TA
1 CCCATACCTTG
2746177 CCCATACCTTG
1 CCCATACCTTG
2746188 GAAAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:2746182 original size:21 final size:22
Alignment explanation
Indices: 2746145--2746186 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2746135 TAGAATATAC
*
2746145 CCCATACCTTGCCCATACCTTT
1 CCCATACCTTACCCATACCTTT
2746167 CCCATACC-TACCCATACCTT
1 CCCATACCTTACCCATACCTT
2746187 GGAAAGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (22 bp):
CCCATACCTTACCCATACCTTT
Found at i:2746740 original size:22 final size:22
Alignment explanation
Indices: 2746709--2746751 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2746699 ATAATAATAA
2746709 AAAAAATTTATAACATATTTTG
1 AAAAAATTTATAACATATTTTG
*
2746731 AAAAACTTTATAACATATTTT
1 AAAAAATTTATAACATATTTT
2746752 AACTTAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAAAATTTATAACATATTTTG
Found at i:2757078 original size:21 final size:22
Alignment explanation
Indices: 2757016--2757078 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
2757006 ATAATACATT
*
2757016 TAAAATATTAAAAACATT-AAAA
1 TAAAATTTTAAAAA-ATTGAAAA
*
2757038 TAAATATTTTCAATAAATTGAAAA
1 TAAA-ATTTT-AAAAAATTGAAAA
2757062 T-AAATTTTAAAAAATTG
1 TAAAATTTTAAAAAATTG
2757079 TGTATACTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 8 0.23
22 9 0.26
23 9 0.26
24 9 0.26
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (22 bp):
TAAAATTTTAAAAAATTGAAAA
Found at i:2757715 original size:18 final size:18
Alignment explanation
Indices: 2757682--2757716 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2757672 ATACAGCTTG
*
2757682 TATGCATGCTGTAGCAAT
1 TATGCATGCTGCAGCAAT
*
2757700 TATGCATGTTGCAGCAA
1 TATGCATGCTGCAGCAA
2757717 CATATTTTCT
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:0.23, T:0.31
Consensus pattern (18 bp):
TATGCATGCTGCAGCAAT
Found at i:2759203 original size:16 final size:15
Alignment explanation
Indices: 2759184--2759218 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2759174 TAATTTAATC
*
2759184 ATTTTATTTTTTATAA
1 ATTTTATATTTTA-AA
2759200 ATTTTATATTTTAAA
1 ATTTTATATTTTAAA
2759215 ATTT
1 ATTT
2759219 CAATCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTATATTTTAAA
Found at i:2763659 original size:20 final size:18
Alignment explanation
Indices: 2763634--2763670 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
2763624 ATTGCTAAGT
2763634 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
2763654 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
2763671 TATGAGTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:2764281 original size:46 final size:46
Alignment explanation
Indices: 2764231--2764402 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
2764221 TGAGCATCCA
*
2764231 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * * *
2764277 AACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCG
* * *
2764324 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
*
2764370 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2764403 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.57
47 26 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:2764383 original size:93 final size:93
Alignment explanation
Indices: 2764224--2764394 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
2764214 GGATGGTTGA
* **
2764224 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
2764289 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
2764317 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2764382 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
2764395 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2767032 original size:46 final size:45
Alignment explanation
Indices: 2766978--2767142 Score: 165
Period size: 46 Copynumber: 3.6 Consensus size: 45
2766968 CGAGGGCTAG
2766978 TGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCCAGA
1 TGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGAGAGCCA-A
* ** **
2767025 -GTAAGACATGTCTGGGACATGCATCGGCCTTGAGATGTTAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCC-ACAGATGAGAGCCAA
* * * * * *
2767070 TGTCAGACATGTCTGGGACATGCGTCGGCTAC-GA-GATGTGCTAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCACAGATGA-GAGCCAA
*
2767114 TGTAAGACATGTCTGGGACATGCGTCAGC
1 TGTAAGACATGTCTGGGACATGCATCAGC
2767143 ACGGTTACAT
Statistics
Matches: 99, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
43 1 0.01
44 33 0.33
45 1 0.01
46 62 0.63
47 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (45 bp):
TGTAAGACATGTCTGGGACATGCATCAGCCACAGATGAGAGCCAA
Found at i:2769978 original size:20 final size:18
Alignment explanation
Indices: 2769953--2769989 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
2769943 ATTGCTAAGT
2769953 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
2769973 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
2769990 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:2770701 original size:93 final size:93
Alignment explanation
Indices: 2770542--2770712 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
2770532 GGATGGTTGA
* *
2770542 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCTCGAACTCGTTGAGT
*
2770607 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
2770635 GCATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCTCGAACTCGTTGAGT
2770700 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
2770713 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCTCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2770719 original size:46 final size:46
Alignment explanation
Indices: 2770551--2770720 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 46
2770541 AGCATCCGAA
* * * *
2770551 CTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATGTTCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAG
* * * *
2770597 CTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGGCATCTGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC-TC-GAG
2770644 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAG
2770690 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2770721 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 58 0.56
47 26 0.25
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAG
Found at i:2773318 original size:15 final size:16
Alignment explanation
Indices: 2773288--2773336 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2773278 GTATTTGGAA
2773288 TTTTATTTGTGTGTTT
1 TTTTATTTGTGTGTTT
*
2773304 TTTTATTTTTG-GTTT
1 TTTTATTTGTGTGTTT
* * *
2773319 TTTAATTTCTATGTTT
1 TTTTATTTGTGTGTTT
2773335 TT
1 TT
2773337 ATTCTAATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.10, C:0.02, G:0.12, T:0.76
Consensus pattern (16 bp):
TTTTATTTGTGTGTTT
Found at i:2774716 original size:33 final size:33
Alignment explanation
Indices: 2774679--2774745 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2774669 GCATTATTGT
2774679 TGTTGAATTTCATTCCTGATGAATATGATCATC
1 TGTTGAATTTCATTCCTGATGAATATGATCATC
2774712 TGTTGAATTTCATTCCTGATGAATATGATCATC
1 TGTTGAATTTCATTCCTGATGAATATGATCATC
2774745 T
1 T
2774746 TACCACCACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTTGAATTTCATTCCTGATGAATATGATCATC
Found at i:2779507 original size:37 final size:36
Alignment explanation
Indices: 2779466--2779535 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 36
2779456 TAGTGATAAA
* *
2779466 AATAAAAATAATGACAATGACAATAGAGAGTAATGGC
1 AATAAAAATAATAACAATGAAAATA-AGAGTAATGGC
* *
2779503 AATAATAATAATAATAATGAAAATAAGAGTAAT
1 AATAAAAATAATAACAATGAAAATAAGAGTAAT
2779536 ATTAGTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 8 0.28
37 21 0.72
ACGTcount: A:0.59, C:0.04, G:0.14, T:0.23
Consensus pattern (36 bp):
AATAAAAATAATAACAATGAAAATAAGAGTAATGGC
Found at i:2785396 original size:24 final size:24
Alignment explanation
Indices: 2785369--2785420 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2785359 TTAGTAAGTC
*
2785369 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2785393 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2785417 AAAT
1 AAAT
2785421 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2787350 original size:24 final size:24
Alignment explanation
Indices: 2787323--2787374 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2787313 TTAGTAAGTC
*
2787323 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2787347 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2787371 AAAT
1 AAAT
2787375 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2788495 original size:3 final size:3
Alignment explanation
Indices: 2788487--2788515 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2788477 AACACCATTG
2788487 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2788516 AGTGCACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2795245 original size:13 final size:13
Alignment explanation
Indices: 2795222--2795253 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
2795212 CTAATAACAA
2795222 CACCAACTTATAAC
1 CACC-ACTTATAAC
2795236 CACCACTTATAAC
1 CACCACTTATAAC
2795249 CACCA
1 CACCA
2795254 TTAAAGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.19
Consensus pattern (13 bp):
CACCACTTATAAC
Found at i:2795896 original size:25 final size:26
Alignment explanation
Indices: 2795852--2795903 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
2795842 AACACTTAAA
*
2795852 AATAATATATATCAATAT-AACTAAC
1 AATAATATAAATCAATATAAACTAAC
2795877 AATAATATAAAT-AATAATAAACTAAC
1 AATAATATAAATCAAT-ATAAACTAAC
2795903 A
1 A
2795904 CTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 3 0.12
25 13 0.54
26 8 0.33
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (26 bp):
AATAATATAAATCAATATAAACTAAC
Found at i:2796779 original size:25 final size:25
Alignment explanation
Indices: 2796745--2796798 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
2796735 TTAATTTAAC
*
2796745 TTTTTTATTTGT-AAATTTTAATAT
1 TTTTTTATTTATAAAATTTTAATAT
2796769 ATTTTTTATTTATAAAATTTTAATAT
1 -TTTTTTATTTATAAAATTTTAATAT
2796795 TTTT
1 TTTT
2796799 AAAATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTTTATTTATAAAATTTTAATAT
Found at i:2796814 original size:17 final size:17
Alignment explanation
Indices: 2796760--2796815 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
2796750 TATTTGTAAA
* *
2796760 TTTTAATATATTTTTTAT
1 TTTTAAAATA-TTTATAT
*
2796778 TTATAAAAT-TTTAATAT
1 TTTTAAAATATTT-ATAT
2796795 TTTTAAAATATTTATAT
1 TTTTAAAATATTTATAT
2796812 TTTT
1 TTTT
2796816 TTTATACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 3 0.09
17 19 0.59
18 10 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTAAAATATTTATAT
Found at i:2797541 original size:122 final size:122
Alignment explanation
Indices: 2797393--2797614 Score: 372
Period size: 122 Copynumber: 1.8 Consensus size: 122
2797383 ATACTCTTAA
* * **
2797393 TTTTAATAATTTAATCATCTACTTTTCGGATTTAAAAATTTAGGATCCATTATTACCATTGTTAA
1 TTTTAATAATTTAATCATCTACTTTTCGGATTTAAAAATTCAGGACCCATTATTACCACCGTTAA
*
2797458 CATTCTTCTATTAAATTCATTGGTGTGACGTTTTGAAACTTAGTCTCCAAACTTTTT
66 AATTCTTCTATTAAATTCATTGGTGTGACGTTTTGAAACTTAGTCTCCAAACTTTTT
* *
2797515 TTTTAATAATTTATTTATCTACTTTTCGGATTTAAAAATTCAGGACCCATTATTACCACCGTTAA
1 TTTTAATAATTTAATCATCTACTTTTCGGATTTAAAAATTCAGGACCCATTATTACCACCGTTAA
*
2797580 AATTCTTCTATTAAATTTATTGGTGTGACGTTTTG
66 AATTCTTCTATTAAATTCATTGGTGTGACGTTTTG
2797615 GAATTTAATA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
122 92 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.46
Consensus pattern (122 bp):
TTTTAATAATTTAATCATCTACTTTTCGGATTTAAAAATTCAGGACCCATTATTACCACCGTTAA
AATTCTTCTATTAAATTCATTGGTGTGACGTTTTGAAACTTAGTCTCCAAACTTTTT
Found at i:2798458 original size:17 final size:16
Alignment explanation
Indices: 2798425--2798467 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
2798415 TAATTTATTA
2798425 AATAAAA-ATTATCTT
1 AATAAAATATTATCTT
*
2798440 AACTAAAATATTATTTT
1 AA-TAAAATATTATCTT
2798457 AATAAAATATT
1 AATAAAATATT
2798468 TAAATTTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 2 0.08
16 14 0.56
17 9 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAAAATATTATCTT
Found at i:2803078 original size:12 final size:12
Alignment explanation
Indices: 2803063--2803112 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2803053 ATTTAATTTA
2803063 ATATTTATCTAG
1 ATATTTATCTAG
* *
2803075 ATATTAATAT-G
1 ATATTTATCTAG
*
2803086 ATATTTAATTTAG
1 ATATTT-ATCTAG
2803099 -TATTTATCTAG
1 ATATTTATCTAG
2803110 ATA
1 ATA
2803113 ATATTTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
11 11 0.37
12 18 0.60
13 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATTTATCTAG
Found at i:2803084 original size:35 final size:35
Alignment explanation
Indices: 2803043--2803112 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
2803033 TTTAATGAAT
*
2803043 TTAATATTAAATTTAATTTAATATTTATCTAGATA
1 TTAATATGAAATTTAATTTAATATTTATCTAGATA
* *
2803078 TTAATATGATATTTAATTTAGTATTTATCTAGATA
1 TTAATATGAAATTTAATTTAATATTTATCTAGATA
2803113 ATATTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (35 bp):
TTAATATGAAATTTAATTTAATATTTATCTAGATA
Found at i:2803255 original size:13 final size:13
Alignment explanation
Indices: 2803239--2803270 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2803229 AAGTAGAGAG
2803239 AAAATTATTTGAA
1 AAAATTATTTGAA
*
2803252 AAAATTATTTTAA
1 AAAATTATTTGAA
2803265 AAAATT
1 AAAATT
2803271 TCTAGAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
AAAATTATTTGAA
Found at i:2803680 original size:38 final size:37
Alignment explanation
Indices: 2803632--2803725 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 37
2803622 CAGTCATTTC
* * * *
2803632 GAAGATTTGAAATGTTGAACAAATCTTCCCTCTATCTT
1 GAAGCTTTGAAGTGTTGAA-AAATCTTCCCACCATCTT
* * * *
2803670 GATGCTTTGAAGTGTTAGGAGAATCTTGCCACCATCTT
1 GAAGCTTTGAAGTGTT-GAAAAATCTTCCCACCATCTT
2803708 GAAGCTTTGAAGTGTTGA
1 GAAGCTTTGAAGTGTTGA
2803726 GTGAATCTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
37 1 0.02
38 42 0.93
39 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (37 bp):
GAAGCTTTGAAGTGTTGAAAAATCTTCCCACCATCTT
Found at i:2803732 original size:38 final size:37
Alignment explanation
Indices: 2803665--2803746 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 37
2803655 TCTTCCCTCT
*
2803665 ATCTTGATGCTTTGAAGTGTTAGGAGAATCTTGCCACC
1 ATCTTGAAGCTTTGAAGTGTTAGGAGAATCTT-CCACC
*
2803703 ATCTTGAAGCTTTGAAGTGTT-GAGTGAATCTTCCACC
1 ATCTTGAAGCTTTGAAGTGTTAG-GAGAATCTTCCACC
*
2803740 ATATTGA
1 ATCTTGA
2803747 TATTCTACTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 12 0.30
38 28 0.70
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (37 bp):
ATCTTGAAGCTTTGAAGTGTTAGGAGAATCTTCCACC
Found at i:2809810 original size:21 final size:21
Alignment explanation
Indices: 2809784--2809824 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2809774 AGACAAGCGA
* *
2809784 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2809805 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2809825 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2816316 original size:32 final size:32
Alignment explanation
Indices: 2816263--2816328 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
2816253 TAATGTAACA
2816263 TAGCTGCTAAGAATTCAGGGTTTAAATAAGTT
1 TAGCTGCTAAGAATTCAGGGTTTAAATAAGTT
**
2816295 TAGCTGCTATA-AATTTGGGGTTTAAATAAGTT
1 TAGCTGCTA-AGAATTCAGGGTTTAAATAAGTT
2816327 TA
1 TA
2816329 TTCATGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (32 bp):
TAGCTGCTAAGAATTCAGGGTTTAAATAAGTT
Found at i:2822467 original size:6 final size:6
Alignment explanation
Indices: 2822456--2822498 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
2822446 TGTGTTGTTG
2822456 TGTCTT TGTCTT TGTCTT TGTCTT TGTCTT TGTCTT TGTCTT T
1 TGTCTT TGTCTT TGTCTT TGTCTT TGTCTT TGTCTT TGTCTT T
2822499 CACTTTCTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.67
Consensus pattern (6 bp):
TGTCTT
Found at i:2822504 original size:18 final size:18
Alignment explanation
Indices: 2822465--2822504 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2822455 GTGTCTTTGT
**
2822465 CTTTGTCTTTGTCTTTGT
1 CTTTGTCTTTGTCTTTCA
2822483 CTTTGTCTTTGTCTTTCA
1 CTTTGTCTTTGTCTTTCA
2822501 CTTT
1 CTTT
2822505 CTGACTCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.20, G:0.12, T:0.65
Consensus pattern (18 bp):
CTTTGTCTTTGTCTTTCA
Found at i:2824638 original size:28 final size:29
Alignment explanation
Indices: 2824606--2824665 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
2824596 CACAATTCTC
*
2824606 TATAACACT-AAAAAAAGAGTAAATAAGT
1 TATAACAATAAAAAAAAGAGTAAATAAGT
2824634 TATAACAATAGAAAAAAAGAGTAAATAAGT
1 TATAACAATA-AAAAAAAGAGTAAATAAGT
2824664 TA
1 TA
2824666 ATTTTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 8 0.28
30 21 0.72
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.22
Consensus pattern (29 bp):
TATAACAATAAAAAAAAGAGTAAATAAGT
Found at i:2826097 original size:97 final size:97
Alignment explanation
Indices: 2825925--2826119 Score: 302
Period size: 97 Copynumber: 2.0 Consensus size: 97
2825915 TATGCGGGTG
** * *
2825925 ACAAGTGATGCTCATTCCATCAATATAAATTACCTGTTCAAAAGTAGTGGTTCATGTGTTCTCTA
1 ACAAGTGATGCTCATTCCATCAATATAAATTACCTACTCAAAAGTAGCGGTTCACGTGTTCTCTA
2825990 GGTACTGGTTGAATAGTACTATTAATGGAGGT
66 GGTACTGGTTGAATAGTACTATTAATGGAGGT
** *
2826022 ACAAGTGATGCTTGTTCCATCAATATAAATTGCCTACTCAAAAGTAGCGGTTCACGTGTTCTCTA
1 ACAAGTGATGCTCATTCCATCAATATAAATTACCTACTCAAAAGTAGCGGTTCACGTGTTCTCTA
*
2826087 GGTA-TGGGTTGAATAGTACTATTAGTGGAGGT
66 GGTACT-GGTTGAATAGTACTATTAATGGAGGT
2826119 A
1 A
2826120 TGTTGATGGA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
96 1 0.01
97 88 0.99
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (97 bp):
ACAAGTGATGCTCATTCCATCAATATAAATTACCTACTCAAAAGTAGCGGTTCACGTGTTCTCTA
GGTACTGGTTGAATAGTACTATTAATGGAGGT
Found at i:2834158 original size:20 final size:19
Alignment explanation
Indices: 2834133--2834178 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
2834123 GTCATGTGAA
*
2834133 AAAAAATTATAAAAAGTTAT
1 AAAAAATCATAAAAA-TTAT
*
2834153 AAAAAATCGTAAAAATTAT
1 AAAAAATCATAAAAATTAT
*
2834172 GAAAAAT
1 AAAAAAT
2834179 ATTTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (19 bp):
AAAAAATCATAAAAATTAT
Found at i:2834278 original size:21 final size:21
Alignment explanation
Indices: 2834236--2834280 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2834226 AAAAAATTAT
* *
2834236 AAAATTTTATAAAGTCGTAAG
1 AAAATTATATAAAATCGTAAG
2834257 AAAATTATATAAAAT-GTAAAG
1 AAAATTATATAAAATCGT-AAG
2834278 AAA
1 AAA
2834281 CATAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (21 bp):
AAAATTATATAAAATCGTAAG
Found at i:2834310 original size:21 final size:21
Alignment explanation
Indices: 2834252--2834311 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 21
2834242 TTATAAAGTC
*
2834252 GTAAGAAAATTATATAAAA-T-
1 GTAAAAAAATTATA-AAAATTA
* *
2834272 GTAAAGAAA-CAT-AAAATTA
1 GTAAAAAAATTATAAAAATTA
2834291 GTAAAAAAATTATAAAAATTA
1 GTAAAAAAATTATAAAAATTA
2834312 TCGTACAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
17 4 0.13
18 1 0.03
19 10 0.32
20 9 0.29
21 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (21 bp):
GTAAAAAAATTATAAAAATTA
Found at i:2834800 original size:53 final size:54
Alignment explanation
Indices: 2834719--2834829 Score: 170
Period size: 53 Copynumber: 2.1 Consensus size: 54
2834709 AATGTTTTTT
* * *
2834719 TTTTCTTTTTCATTTTAGAATAAACTTTGGCATAATTATTTTCAAATCCCTTGA
1 TTTTCTTTTTCATTTTAAAATAAACTTTGACATAAATATTTTCAAATCCCTTGA
* *
2834773 TTTT-TTTTTCCTTTTAAAATAAACTTTGATATAAATATTTTCAAATCCCTTGA
1 TTTTCTTTTTCATTTTAAAATAAACTTTGACATAAATATTTTCAAATCCCTTGA
2834826 TTTT
1 TTTT
2834830 GATTAAAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
53 48 0.92
54 4 0.08
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (54 bp):
TTTTCTTTTTCATTTTAAAATAAACTTTGACATAAATATTTTCAAATCCCTTGA
Done.