Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 153 of 292
Found at i:45419515 original size:93 final size:93
Alignment explanation
Indices: 45419407--45419578 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
45419397 CGCCCATAAG
* *
45419407 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
45419472 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
*
45419500 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCTATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
45419565 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
45419579 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:45419575 original size:46 final size:46
Alignment explanation
Indices: 45419402--45419575 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
45419392 TAACCCGCCC
* *
45419402 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCC
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCT
* * *
45419448 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-T
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCATCT
* *
45419497 -TCA-CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCT
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCT
* *
45419541 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
45419576 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 59 0.56
47 27 0.26
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCT
Found at i:45427017 original size:31 final size:31
Alignment explanation
Indices: 45426968--45427049 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
45426958 TCAATCTCAA
* *
45426968 CATAT-ACTGGGCCAAAGCCTTTGCATTATT
1 CATATCACTAGGCCGAAGCCTTTGCATTATT
* *
45426998 CATGTCACTAGGCCGAAGCCTTTTCATTATT
1 CATATCACTAGGCCGAAGCCTTTGCATTATT
*
45427029 CATATCACTGGGCCGAAGCCT
1 CATATCACTAGGCCGAAGCCT
45427050 CTTACTATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 4 0.09
31 41 0.91
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (31 bp):
CATATCACTAGGCCGAAGCCTTTGCATTATT
Found at i:45427287 original size:25 final size:25
Alignment explanation
Indices: 45427259--45427318 Score: 86
Period size: 26 Copynumber: 2.4 Consensus size: 25
45427249 CTGGAGGCCT
45427259 AGCCTCTTTT-AAAAACTGGGGCAAA
1 AGCC-CTTTTGAAAAACTGGGGCAAA
*
45427284 AGCCCTTTTTGATAAACTGGGGCAAA
1 AGCCC-TTTTGAAAAACTGGGGCAAA
45427310 AGCCCTTTT
1 AGCCCTTTT
45427319 CGGTAAACTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 1 0.03
25 12 0.38
26 19 0.59
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTGAAAAACTGGGGCAAA
Found at i:45427336 original size:25 final size:26
Alignment explanation
Indices: 45427271--45427357 Score: 124
Period size: 26 Copynumber: 3.4 Consensus size: 26
45427261 CCTCTTTTAA
* *
45427271 AAACTGGGGCAAAAGCCCTTTTTGAT
1 AAACTGGGGCAAAAGCCCTTTTCGGT
45427297 AAACTGGGGCAAAAGCCCTTTTCGGT
1 AAACTGGGGCAAAAGCCCTTTTCGGT
* *
45427323 AAACTGGGAC-AAAGTCCTTTTCGGT
1 AAACTGGGGCAAAAGCCCTTTTCGGT
45427348 -AACTGGGGCA
1 AAACTGGGGCA
45427358 TTGCCCTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
24 8 0.15
25 14 0.25
26 33 0.60
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (26 bp):
AAACTGGGGCAAAAGCCCTTTTCGGT
Found at i:45427526 original size:25 final size:25
Alignment explanation
Indices: 45427498--45427545 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
45427488 ATAATTAAAC
* **
45427498 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
45427523 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
45427546 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:45429774 original size:44 final size:45
Alignment explanation
Indices: 45429704--45429809 Score: 180
Period size: 45 Copynumber: 2.4 Consensus size: 45
45429694 ATATCTAATA
45429704 ATAAAAA-TTTCAAATACCAATAATACAGCAAATAATAATAA-TTTC
1 ATAAAAATTTTC-AA-ACCAATAATACAGCAAATAATAATAATTTTC
45429749 ATAAAAATTTTCAAACCAATAATACAGCAAATAATAATAATTTTC
1 ATAAAAATTTTCAAACCAATAATACAGCAAATAATAATAATTTTC
45429794 ATAAAAATTTTCAAAC
1 ATAAAAATTTTCAAAC
45429810 ACACATACAG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
44 26 0.44
45 29 0.49
46 4 0.07
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (45 bp):
ATAAAAATTTTCAAACCAATAATACAGCAAATAATAATAATTTTC
Found at i:45431837 original size:31 final size:30
Alignment explanation
Indices: 45431790--45431877 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 30
45431780 TCAATCTCAA
*
45431790 CATAT-ACTGGGCCGAAGCCTTTGTACTATT
1 CATATCACTCGGCCGAAGCCTTT-TACTATT
* * *
45431820 CATGTCACTCGGTCGAAGCCTTTTCATTATT
1 CATATCACTCGGCCGAAGCCTTTT-ACTATT
*
45431851 CATATCACTGGGCCGAAGCCTTTTACT
1 CATATCACTCGGCCGAAGCCTTTTACT
45431878 GTAAATGATA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 7 0.15
31 41 0.85
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (30 bp):
CATATCACTCGGCCGAAGCCTTTTACTATT
Found at i:45432178 original size:24 final size:25
Alignment explanation
Indices: 45432104--45432189 Score: 120
Period size: 26 Copynumber: 3.4 Consensus size: 25
45432094 AATTGCGGTA
* *
45432104 AAAGCCCTTTTTGATAAACTAGGGC
1 AAAGCCCTTTTCGGTAAACTAGGGC
*
45432129 AAAAGCCCTTTTCGGTAAACTGGGGC
1 -AAAGCCCTTTTCGGTAAACTAGGGC
45432155 AAAGCCCTTTTCGGT-AACTAGGGC
1 AAAGCCCTTTTCGGTAAACTAGGGC
*
45432179 ATAGCCCTTTT
1 AAAGCCCTTTT
45432190 GCACTTCCTC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 18 0.33
25 15 0.27
26 22 0.40
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (25 bp):
AAAGCCCTTTTCGGTAAACTAGGGC
Found at i:45432348 original size:25 final size:25
Alignment explanation
Indices: 45432320--45432367 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
45432310 ATAATTAAAC
* **
45432320 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
45432345 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
45432368 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:45434437 original size:3 final size:3
Alignment explanation
Indices: 45434431--45434455 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45434421 CTACTACTAC
45434431 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
45434456 TTCATAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:45434524 original size:12 final size:12
Alignment explanation
Indices: 45434509--45434533 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45434499 ACAACAAATA
45434509 ATAAAAATTTTC
1 ATAAAAATTTTC
45434521 ATAAAAATTTTC
1 ATAAAAATTTTC
45434533 A
1 A
45434534 AACATACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAAAATTTTC
Found at i:45434659 original size:48 final size:47
Alignment explanation
Indices: 45434600--45434709 Score: 157
Period size: 50 Copynumber: 2.3 Consensus size: 47
45434590 AATTTCATAA
*
45434600 AATTTAAAATATCCGTAATAATAAATATAGTAAAAATTTTCTAGCAGT
1 AATTCAAAATATCC-TAATAATAAATATAGTAAAAATTTTCTAGCAGT
* *
45434648 AATTCAAAATATTTTTCTTATAATAAATATAGTAAAAATTTTCTAGCAGT
1 AATTCAAAATA---TCCTAATAATAAATATAGTAAAAATTTTCTAGCAGT
45434698 AATTCAAAATAT
1 AATTCAAAATAT
45434710 TTTTCTTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
47 1 0.02
48 10 0.18
50 43 0.77
51 2 0.04
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.38
Consensus pattern (47 bp):
AATTCAAAATATCCTAATAATAAATATAGTAAAAATTTTCTAGCAGT
Found at i:45434662 original size:23 final size:23
Alignment explanation
Indices: 45434631--45434712 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 23
45434621 TAAATATAGT
45434631 AAAA-ATTTTCTAGCAGTAATTC
1 AAAATATTTTCTAGCAGTAATTC
* *
45434653 AAAATATTTTTCTTA-TAATAAATAT-
1 AAAATA-TTTTC-TAGCAGT-AAT-TC
*
45434678 AGTAAAAATTTTCTAGCAGTAATTC
1 A--AAATATTTTCTAGCAGTAATTC
45434703 AAAATATTTT
1 AAAATATTTT
45434713 TCTTAAACGG
Statistics
Matches: 45, Mismatches: 6, Indels: 17
0.66 0.09 0.25
Matches are distributed among these distances:
22 4 0.09
23 9 0.20
24 8 0.18
25 12 0.27
26 8 0.18
27 4 0.09
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (23 bp):
AAAATATTTTCTAGCAGTAATTC
Found at i:45434664 original size:24 final size:24
Alignment explanation
Indices: 45434636--45434715 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 24
45434626 ATAGTAAAAA
45434636 TTTTCTAGCAGTAATTCAAAATAT
1 TTTTCTAGCAGTAATTCAAAATAT
* * *
45434660 TTTTCTTA-TAATAAATAT-AGTAAA-AA
1 TTTTC-TAGCAGT-AAT-TCA--AAATAT
45434686 TTTTCTAGCAGTAATTCAAAATAT
1 TTTTCTAGCAGTAATTCAAAATAT
45434710 TTTTCT
1 TTTTCT
45434716 TAAACGGTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
23 3 0.07
24 15 0.36
25 12 0.29
26 9 0.21
27 3 0.07
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (24 bp):
TTTTCTAGCAGTAATTCAAAATAT
Found at i:45434734 original size:50 final size:50
Alignment explanation
Indices: 45434617--45434717 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
45434607 AATATCCGTA
45434617 ATAATAAATATAGTAAAAATTTTCTAGCAGTAATTCAAAATATTTTTCTT
1 ATAATAAATATAGTAAAAATTTTCTAGCAGTAATTCAAAATATTTTTCTT
45434667 ATAATAAATATAGTAAAAATTTTCTAGCAGTAATTCAAAATATTTTTCTT
1 ATAATAAATATAGTAAAAATTTTCTAGCAGTAATTCAAAATATTTTTCTT
45434717 A
1 A
45434718 AACGGTAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (50 bp):
ATAATAAATATAGTAAAAATTTTCTAGCAGTAATTCAAAATATTTTTCTT
Found at i:45436611 original size:31 final size:31
Alignment explanation
Indices: 45436567--45436650 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
45436557 TCAATCTCAA
*
45436567 CATAT-ACTAGGCCGAAGCCTTTGCATTATT
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
* * * *
45436597 TATGTCACTGGGCCGAAGCTTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
45436628 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
45436651 TACTATAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 3 0.07
31 42 0.93
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTGCATTATT
Found at i:45436885 original size:25 final size:25
Alignment explanation
Indices: 45436857--45436916 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
45436847 CTGGAGGCCT
45436857 AGCCTCTTTTAAT-AACTGGGGCAAA
1 AGCC-CTTTTAATCAACTGGGGCAAA
* *
45436882 AGCCCTTTTTGATCAATTGGGGCAAA
1 AGCCC-TTTTAATCAACTGGGGCAAA
45436908 AGCCCTTTT
1 AGCCCTTTT
45436917 CGGTAAACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 1 0.03
25 14 0.45
26 16 0.52
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (25 bp):
AGCCCTTTTAATCAACTGGGGCAAA
Found at i:45436928 original size:26 final size:25
Alignment explanation
Indices: 45436869--45436965 Score: 90
Period size: 26 Copynumber: 3.9 Consensus size: 25
45436859 CCTCTTTTAA
* *
45436869 TAACTGGGGCAAAAGCCCTTTTTGA
1 TAACTGGGGCAAAAGCCCTTTTCGG
*
45436894 TCAATTGGGGCAAAAGCCCTTTTCGG
1 T-AACTGGGGCAAAAGCCCTTTTCGG
** *
45436920 TAAACTGGGG-TGAAGTCCTTTTCGG
1 T-AACTGGGGCAAAAGCCCTTTTCGG
* *
45436945 TAACTAGGGC-ATAGCCCTTTT
1 TAACTGGGGCAAAAGCCCTTTT
45436966 GCACTTCCTC
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
24 15 0.26
25 14 0.24
26 29 0.50
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (25 bp):
TAACTGGGGCAAAAGCCCTTTTCGG
Found at i:45436963 original size:24 final size:25
Alignment explanation
Indices: 45436907--45436965 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
45436897 ATTGGGGCAA
* *
45436907 AAGCCCTTTTCGGTAAACTGGGGTG
1 AAGCCCTTTTCGGTAAACTAGGGTC
*
45436932 AAGTCCTTTTCGGT-AACTAGGG-C
1 AAGCCCTTTTCGGTAAACTAGGGTC
45436955 ATAGCCCTTTT
1 A-AGCCCTTTT
45436966 GCACTTCCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 1 0.03
24 15 0.52
25 13 0.45
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.32
Consensus pattern (25 bp):
AAGCCCTTTTCGGTAAACTAGGGTC
Found at i:45437031 original size:18 final size:19
Alignment explanation
Indices: 45437008--45437045 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
45436998 GCATAAATGA
45437008 ATACATA-ATGTGCATATC
1 ATACATACATGTGCATATC
45437026 ATACATATCATGTGCATATC
1 ATACATA-CATGTGCATATC
45437046 GTATCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
ATACATACATGTGCATATC
Found at i:45439347 original size:12 final size:12
Alignment explanation
Indices: 45439332--45439356 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45439322 ACAGCAAGTA
45439332 ATAAAAATTTTC
1 ATAAAAATTTTC
45439344 ATAAAAATTTTC
1 ATAAAAATTTTC
45439356 A
1 A
45439357 AACATACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAAAATTTTC
Found at i:45452117 original size:31 final size:31
Alignment explanation
Indices: 45452071--45452152 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
45452061 TCAATCTCAA
*
45452071 CATAT-ACTGGGCCGAAGCCTTTGAATTATT
1 CATATCACTAGGCCGAAGCCTTTGAATTATT
* **
45452101 CATGTCACTAGGCCGAAGCCTTTTCATTATT
1 CATATCACTAGGCCGAAGCCTTTGAATTATT
*
45452132 CATATCACTGGGCCGAAGCCT
1 CATATCACTAGGCCGAAGCCT
45452153 CTTACTGTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 4 0.09
31 41 0.91
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (31 bp):
CATATCACTAGGCCGAAGCCTTTGAATTATT
Found at i:45452390 original size:25 final size:26
Alignment explanation
Indices: 45452362--45452446 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 26
45452352 CTGGAGGCCT
*
45452362 AGCCTTTTTTAAT-AACTGGGGCAAA
1 AGCCCTTTTTAATAAACTGGGGCAAA
*
45452387 AGCCCTTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTTAATAAACTGGGGCAAA
*** *
45452413 AGCCCTTTTCGGTAAACTGGGAC-AA
1 AGCCCTTTTTAATAAACTGGGGCAAA
45452438 AGCCCTTTT
1 AGCCCTTTT
45452447 CGGTAACTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
25 22 0.41
26 32 0.59
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTTAATAAACTGGGGCAAA
Found at i:45452447 original size:25 final size:26
Alignment explanation
Indices: 45452375--45452470 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
45452365 CTTTTTTAAT
* *
45452375 AACTGGGGCAAAAGCCCTTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
45452401 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
*
45452427 AACTGGGAC-AAAGCCCTTTTCGGT-
1 AACTGGGGCAAAAGCCCTTTTCGGTA
*
45452451 AACTGGGGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
45452471 GCACTTCCTC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 18 0.28
25 15 0.23
26 32 0.49
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (26 bp):
AACTGGGGCAAAAGCCCTTTTCGGTA
Found at i:45455356 original size:49 final size:49
Alignment explanation
Indices: 45455296--45455833 Score: 928
Period size: 49 Copynumber: 11.1 Consensus size: 49
45455286 TTTGTATGAG
45455296 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
45455345 GTATATATATGTGATAAGGCCTAATGGCCGATGTGA-GAATGTGAAAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
45455393 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
*
45455442 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
* *
45455491 GTGTATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
*
45455540 GTATATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
45455589 GTATATATATGTGATAAGGCCTAATGGCCG-TCGTGATGAATGTGAAAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGAT-GTGATGAATGTGAAAGT
45455638 G--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
* *
45455685 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGAAGAATGTGAAAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
*
45455734 GTATATAAATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
* * *
45455782 G--TATATATGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAAAGT
1 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
45455829 GTATA
1 GTATA
45455834 AATGTGCTAA
Statistics
Matches: 469, Mismatches: 12, Indels: 16
0.94 0.02 0.03
Matches are distributed among these distances:
46 37 0.08
47 50 0.11
48 54 0.12
49 328 0.70
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (49 bp):
GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
Found at i:45455704 original size:194 final size:193
Alignment explanation
Indices: 45455299--45455844 Score: 938
Period size: 194 Copynumber: 2.8 Consensus size: 193
45455289 GTATGAGGTA
45455299 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
45455364 CCTAATGGCCGATGTGA-GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
66 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG-TGTG
45455428 ATGAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
130 ATGAATGTGAAA--GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
45455493 G
193 G
*
45455494 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
*
45455559 CCTAATGGCCGACGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGTCGTG
66 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGT-GTG
45455624 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
130 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* *
45455688 TATATATGTGATAAGGCCTAATGGCCGATGTGAAGAATGTGAAAGTGTATATAAATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
* * *
45455753 CCTAATGGCCGATGTGATGAATGTG-AAGTG--TATATATGTGATAGGGCCGAATGGCCAATGTG
66 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCC-GTGTG
* *
45455815 ATGAATGTGAAAGTGTATAAATGTGCTAAG
130 ATGAATGTGAAAGTGTATATATGTGATAAG
45455845 TCCCGAAGGG
Statistics
Matches: 337, Mismatches: 11, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
191 55 0.16
192 1 0.00
193 5 0.01
194 138 0.41
195 81 0.24
196 57 0.17
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (193 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGTGTGA
TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:45458192 original size:40 final size:40
Alignment explanation
Indices: 45458133--45458373 Score: 412
Period size: 40 Copynumber: 6.0 Consensus size: 40
45458123 AAGTCTCGAC
45458133 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
45458172 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
45458212 GATGTATCCGGGCTACGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
45458252 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
45458292 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * *
45458332 GATGTATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
45458372 GA
1 GA
45458374 CGTGTATTCG
Statistics
Matches: 194, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
39 4 0.02
40 190 0.98
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.24
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:45463433 original size:40 final size:40
Alignment explanation
Indices: 45463306--45463435 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
45463296 ATGCTGGAAA
* *
45463306 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
45463346 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
45463386 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
45463426 TTATATCCGG
1 TTATATCCGG
45463436 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:45471221 original size:39 final size:39
Alignment explanation
Indices: 45471134--45471306 Score: 230
Period size: 40 Copynumber: 4.5 Consensus size: 39
45471124 AACCCAAGTA
* * *
45471134 CCTTCGGATTTAG-CCGGCTATAGCT-ACTCGCTCAAATG
1 CCTTCGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
45471172 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATG
45471212 CCTTCGGACTTAGCCCGGATATAGTAACT-GCACAAATG
1 CCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
45471250 CC-TCGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
45471288 CCTTCGGGACTTAGCCCGG
1 CCTTC-GGACTTAGCCCGG
45471307 TTATCATCCG
Statistics
Matches: 124, Mismatches: 4, Indels: 12
0.89 0.03 0.09
Matches are distributed among these distances:
36 1 0.01
37 23 0.19
38 27 0.22
39 34 0.27
40 39 0.31
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.24
Consensus pattern (39 bp):
CCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:45479244 original size:40 final size:40
Alignment explanation
Indices: 45479174--45479351 Score: 236
Period size: 40 Copynumber: 4.5 Consensus size: 40
45479164 AACCCAAGTA
* * *
45479174 CCTTTGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
45479213 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
45479253 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
45479293 CCTTCGGGACTTAGACCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
45479333 CCTTCGGAACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
45479352 TTATCATCCG
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
39 14 0.11
40 110 0.89
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:45483207 original size:27 final size:26
Alignment explanation
Indices: 45483168--45483278 Score: 123
Period size: 27 Copynumber: 4.1 Consensus size: 26
45483158 GGAAGCGTCT
* *
45483168 TGGTGGCTATGCCACAATTATCTGATT
1 TGGTGGCTCTGCCAC-ATTATCTGATC
*
45483195 TGGTGGCTCTGCCACATATATCTGCTC
1 TGGTGGCTCTGCCACAT-TATCTGATC
*
45483222 TGGTGGCTCTGCCATGATTATCTGTATC
1 TGGTGGCTCTGCCA-CATTATCTG-ATC
* * *
45483250 TGGTGACTCTGTCACATTATCTGTTC
1 TGGTGGCTCTGCCACATTATCTGATC
45483276 TGG
1 TGG
45483279 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.10
27 49 0.68
28 16 0.22
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGATC
Found at i:45483271 original size:54 final size:54
Alignment explanation
Indices: 45483168--45483278 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
45483158 GGAAGCGTCT
* *
45483168 TGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCTGCTC
1 TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGCTC
* ** * *
45483222 TGGTGGCTCTGCCATGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTC
1 TGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGCTC
45483276 TGG
1 TGG
45483279 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
54 32 0.65
55 17 0.35
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGCTC
Found at i:45485987 original size:58 final size:57
Alignment explanation
Indices: 45485880--45485988 Score: 139
Period size: 58 Copynumber: 1.9 Consensus size: 57
45485870 TCCTGTTTCC
* * *
45485880 AACATATGCTCATAAGAGCTTAATTAGGATTACCCGTCTGGGCTAAATCCTATCTAT
1 AACATATGCTCATAAGAGCTTAATCAGGATTACCAGTCTAGGCTAAATCCTATCTAT
* * *
45485937 AACATATGCTCA-AGAGGGTTTAAATCAGGATTACTAGTCTAGGCTAAATCCT
1 AACATATGCTCATA-AGAGCTT-AATCAGGATTACCAGTCTAGGCTAAATCCT
45485989 TTCTGTAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
56 1 0.02
57 17 0.39
58 26 0.59
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (57 bp):
AACATATGCTCATAAGAGCTTAATCAGGATTACCAGTCTAGGCTAAATCCTATCTAT
Found at i:45489250 original size:40 final size:40
Alignment explanation
Indices: 45489205--45489412 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 40
45489195 CGGAATACAA
*
45489205 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* * * *
45489245 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* *
45489285 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* ** * * * *
45489325 CCGGATGTAGTCACTAGCAC-AATTGCCTTCGGGCCTCAAC
1 CCGGATATAACCACTTGCACGAA-TGCCTTCGGGTCTTAGC
** * ** * * *
45489365 CCGGATATAATTACTAGCATAAATGTCTCCGGGACTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
45489405 CCGGATAT
1 CCGGATAT
45489413 CATTCAATTG
Statistics
Matches: 139, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
39 2 0.01
40 135 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:45496487 original size:40 final size:40
Alignment explanation
Indices: 45496442--45496649 Score: 211
Period size: 40 Copynumber: 5.2 Consensus size: 40
45496432 CGGAATACAA
*
45496442 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* * * *
45496482 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* *
45496522 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* ** * * *
45496562 CCGGATGTAGTCACTAGCAC-AATTGCCTTCGGGTCTCAAC
1 CCGGATATAACCACTTGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
45496602 CCGGATATAGTTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
45496642 CCGGATAT
1 CCGGATAT
45496650 CATTCAATTG
Statistics
Matches: 142, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
39 2 0.01
40 138 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:45498017 original size:18 final size:19
Alignment explanation
Indices: 45497996--45498031 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
45497986 AATAAAGAAA
*
45497996 GGAATTAAA-AAGAAAAGG
1 GGAATAAAATAAGAAAAGG
45498014 GGAATAAAATAAGAAAAG
1 GGAATAAAATAAGAAAAG
45498032 AAAAAGGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (19 bp):
GGAATAAAATAAGAAAAGG
Found at i:45499440 original size:59 final size:60
Alignment explanation
Indices: 45499344--45499476 Score: 205
Period size: 59 Copynumber: 2.2 Consensus size: 60
45499334 GACAAGATTG
* * *
45499344 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
* * *
45499404 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
45499463 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
45499477 GATTCACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 52 0.78
60 15 0.22
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (60 bp):
GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
Found at i:45499488 original size:29 final size:29
Alignment explanation
Indices: 45499374--45499476 Score: 188
Period size: 29 Copynumber: 3.5 Consensus size: 29
45499364 AAAATTGTAC
*
45499374 AGCACTAAGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
45499403 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
45499433 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
45499462 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
45499477 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 43 0.60
30 29 0.40
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:45501076 original size:22 final size:20
Alignment explanation
Indices: 45501051--45501102 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
45501041 CTTAAAGTTT
45501051 CTTAATGAAATTCTAATATGAC
1 CTTAATGAAA-TCTAATA-GAC
*
45501073 CTTAAT-ATAATCTCATAGAC
1 CTTAATGA-AATCTAATAGAC
45501093 CTTGAATGAA
1 CTT-AATGAA
45501103 TAATAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 6 0.23
21 11 0.42
22 9 0.35
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
CTTAATGAAATCTAATAGAC
Found at i:45506049 original size:40 final size:40
Alignment explanation
Indices: 45505947--45506130 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
45505937 AAATTGAATG
* * * * *
45505947 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
45505987 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
45506027 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
45506067 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
45506107 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
45506131 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:45507471 original size:19 final size:18
Alignment explanation
Indices: 45507434--45507477 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
45507424 ATACATACAG
45507434 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
45507451 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
45507470 TACTAATT
1 TAATAATT
45507478 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:45511742 original size:19 final size:18
Alignment explanation
Indices: 45511705--45511748 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
45511695 ATACATACAG
45511705 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
45511722 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
45511741 TACTAATT
1 TAATAATT
45511749 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:45518562 original size:28 final size:27
Alignment explanation
Indices: 45518499--45518568 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
45518489 ATAGTGAGTC
45518499 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
45518526 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
45518554 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
45518569 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:45526594 original size:28 final size:27
Alignment explanation
Indices: 45526531--45526600 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
45526521 ATAGTGAGTC
45526531 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
45526558 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
45526586 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
45526601 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:45535059 original size:16 final size:16
Alignment explanation
Indices: 45535027--45535065 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
45535017 GTTGGCATTG
45535027 ATATGTG-ACTCCGAT
1 ATATGTGTACTCCGAT
*
45535042 ATATGTGTACTTCGAT
1 ATATGTGTACTCCGAT
45535058 ATATGTGT
1 ATATGTGT
45535066 GTGAGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (16 bp):
ATATGTGTACTCCGAT
Found at i:45535102 original size:72 final size:72
Alignment explanation
Indices: 45534971--45535121 Score: 205
Period size: 72 Copynumber: 2.1 Consensus size: 72
45534961 CATGGCATCG
*
45534971 ATATGTG-ACTCCAATATATGTGTGCGAGTAAGACCAGGTTTTATACGTTGGCATTGATATGTGA
1 ATATGTGTACTCCAATATATGTGTGCGAGTAAGACCAGGTTTTATACGTTGGCATCGATATGTGA
*
45535035 CTCCGAT
66 CTACGAT
* * * * * **
45535042 ATATGTGTACTTCGATATATGTGTGTGAGTAAGACCATGTTTTCTATTTTGGCATCGATATGTGA
1 ATATGTGTACTCCAATATATGTGTGCGAGTAAGACCAGGTTTTATACGTTGGCATCGATATGTGA
*
45535107 CTATGAT
66 CTACGAT
45535114 ATATGTGT
1 ATATGTGT
45535122 GCGAGCAAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
71 7 0.10
72 62 0.90
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (72 bp):
ATATGTGTACTCCAATATATGTGTGCGAGTAAGACCAGGTTTTATACGTTGGCATCGATATGTGA
CTACGAT
Found at i:45535664 original size:13 final size:13
Alignment explanation
Indices: 45535646--45535670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45535636 GAAATGTTGA
45535646 ATTTTGGTTATGG
1 ATTTTGGTTATGG
45535659 ATTTTGGTTATG
1 ATTTTGGTTATG
45535671 TATAATCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (13 bp):
ATTTTGGTTATGG
Found at i:45537871 original size:48 final size:47
Alignment explanation
Indices: 45537819--45538193 Score: 218
Period size: 48 Copynumber: 7.9 Consensus size: 47
45537809 GCCACATTAT
45537819 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
* * * *
45537866 CGAGAGCTAGTATAAGA-CATGTCTAGGACAT-GCATCGGCCTTGAGA
1 -GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
* *
45537912 TGTA-AGCCAGTGTAAGA-CATGTTTGGGATAT-GCATCGGC--T-ACGA
1 -G-AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GA
* * * * * *
45537956 GATGTGTCAGTGTAAGACCATGTTTGGGAGATGACATCGGCATAT-ATA
1 GA-GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGAGA
* * * * * *
45538004 GAGGTGCCAGTGTAAGACCATGTCTAGGACATGCCATTGGCA-CGAATATGT
1 GA-GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTG---A-GA
* * * ** * * *
45538055 GACAGCTAGTGTAAGACCATGTCTCGGACATGGCATTTGCCTCGATTTCA
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA---GA
* * * *
45538105 -ATAGTCAGTGTAAGACCATGTTTGGGACATGGCATCGAC-TTGATG-
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GA
* * *
45538150 GATGAGCCAGTGTAACACCATATCTGGGACATGGCATCGACATT
1 GA-GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATT
45538194 ATACCCTATG
Statistics
Matches: 258, Mismatches: 49, Indels: 40
0.74 0.14 0.12
Matches are distributed among these distances:
42 1 0.00
43 2 0.01
44 14 0.05
45 13 0.05
46 54 0.21
47 47 0.18
48 56 0.22
49 33 0.13
50 34 0.13
51 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (47 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
Found at i:45537911 original size:46 final size:46
Alignment explanation
Indices: 45537819--45538037 Score: 173
Period size: 46 Copynumber: 4.7 Consensus size: 46
45537809 GCCACATTAT
45537819 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAC
1 GAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGAC
* * * * *
45537867 GAGAGCTAGTATAAGACATGTCTAGGACATGCATCGGCCTTGAGAT
1 GAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAC
* *
45537913 GTA-AGCCAGTGTAAGACATGTTTGGGATATGCATCGGC--T-ACGA-
1 G-AGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGA-GAC
* * * * *
45537956 GATGTGTCAGTGTAAGACCATGTTTGGGAGATGACATCGGCATAT-ATA-
1 GA-GAGCCAGTGTAAGA-CATGTCTGGGACATG-CATCGGCAT-TGAGAC
* *
45538004 GAGGTGCCAGTGTAAGACCATGTCTAGGACATGC
1 GA-GAGCCAGTGTAAGA-CATGTCTGGGACATGC
45538038 CATTGGCACG
Statistics
Matches: 143, Mismatches: 19, Indels: 19
0.79 0.10 0.10
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 14 0.10
45 14 0.10
46 52 0.36
47 15 0.10
48 43 0.30
49 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (46 bp):
GAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAC
Found at i:45544661 original size:58 final size:56
Alignment explanation
Indices: 45544526--45544667 Score: 178
Period size: 57 Copynumber: 2.5 Consensus size: 56
45544516 TGTCATATAA
*
45544526 TAGGATTACCAGTCCAGGCTAAATCCTTAATATAATGTATGCTCAGAGGAGCTCGAT
1 TAGGATTACCAGTCCAGGCTAAATCC-TAATATAATGTATGCTCAGAGGAGCTAGAT
* *
45544583 TAGGATTACCAGTCCAGGCTAAATCCTAATCATAATGTATGCTCGAGAGGTA-TTATAT
1 TAGGATTACCAGTCCAGGCTAAATCCTAAT-ATAATGTATGCTC-AGAGG-AGCTAGAT
* * * *
45544641 TGGGATTACCCGTTCGGGCTAAATCCT
1 TAGGATTACCAGTCCAGGCTAAATCCT
45544668 TTTTCTAACA
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
56 4 0.05
57 39 0.52
58 31 0.41
59 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (56 bp):
TAGGATTACCAGTCCAGGCTAAATCCTAATATAATGTATGCTCAGAGGAGCTAGAT
Found at i:45547808 original size:42 final size:42
Alignment explanation
Indices: 45547710--45547814 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
45547700 ATCGATGCTG
* * * * *
45547710 TATCCTAGATATGGTTTCATACAAAATCTCATTTCGATGCCA
1 TATCCTAGATATGGTTTTACACAAAATCTCATATCAACGCCA
* * * *
45547752 TGTCTTAGACATGGTTTTACACTAAATCTCATATCAACGCCA
1 TATCCTAGATATGGTTTTACACAAAATCTCATATCAACGCCA
* *
45547794 TATCCTAAATATGGTCTTACA
1 TATCCTAGATATGGTTTTACA
45547815 TGATAACACA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.35
Consensus pattern (42 bp):
TATCCTAGATATGGTTTTACACAAAATCTCATATCAACGCCA
Found at i:45557608 original size:16 final size:16
Alignment explanation
Indices: 45557581--45557637 Score: 73
Period size: 16 Copynumber: 3.5 Consensus size: 16
45557571 AGAAAGAGTA
45557581 TGAAAGAAAAAAGAAAG
1 TGAAA-AAAAAAGAAAG
45557598 TGAAAAAAAAAGAGAAG
1 TGAAAAAAAAAGA-AAG
45557615 -GAAAAAGAAAA-AAAG
1 TGAAAAA-AAAAGAAAG
45557630 TGAAAAAA
1 TGAAAAAA
45557638 TGAAAAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.11
16 21 0.57
17 12 0.32
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (16 bp):
TGAAAAAAAAAGAAAG
Found at i:45565376 original size:25 final size:25
Alignment explanation
Indices: 45565342--45565399 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
45565332 TGTGCGGTTG
* **
45565342 ACACAGCCTTGGACGTAGGCGTGTT
1 ACACGGCCTTGGACACAGGCGTGTT
*
45565367 ACACGGCCTTGGACACGGGCGTGTT
1 ACACGGCCTTGGACACAGGCGTGTT
45565392 ACACGGCC
1 ACACGGCC
45565400 GTGTGAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (25 bp):
ACACGGCCTTGGACACAGGCGTGTT
Found at i:45565397 original size:13 final size:13
Alignment explanation
Indices: 45565361--45565403 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
45565351 TGGACGTAGG
45565361 CGTGTTACACGGC
1 CGTGTTACACGGC
* * *
45565374 CTTG-GACACGGG
1 CGTGTTACACGGC
45565386 CGTGTTACACGGC
1 CGTGTTACACGGC
45565399 CGTGT
1 CGTGT
45565404 GAAAATTGCA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.23
Consensus pattern (13 bp):
CGTGTTACACGGC
Found at i:45579664 original size:40 final size:39
Alignment explanation
Indices: 45579605--45579812 Score: 211
Period size: 40 Copynumber: 5.2 Consensus size: 39
45579595 CAGAATACAA
* *
45579605 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA-CACTTGCACAAATGCCTTCGGGTCTTAGC
* *
45579645 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAAC-ACTTGCACAAATGCCTTCGGGTCTTAGC
* *
45579685 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAAC-ACTTGCACAAATGCCTTCGGGTCTTAGC
*** * *
45579725 CCGGATGAGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGAT-ATAACACTTGCACAAAT-GCCTTCGGGTCTTAGC
* * * * *
45579765 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAA-CACTTGCACAAATGCCTTCGGGTCTTAGC
45579805 CCGGATAT
1 CCGGATAT
45579813 CATTCAATTG
Statistics
Matches: 140, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
39 5 0.04
40 131 0.94
41 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACACTTGCACAAATGCCTTCGGGTCTTAGC
Found at i:45579745 original size:80 final size:80
Alignment explanation
Indices: 45579605--45579811 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
45579595 CAGAATACAA
* * *
45579605 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
*
45579669 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAAC
* **
45579685 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGAGGTC-ACTAGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
*
45579749 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
45579765 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
45579812 TCATTCAATT
Statistics
Matches: 109, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 4 0.04
80 102 0.94
81 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAAC
Found at i:45585415 original size:68 final size:70
Alignment explanation
Indices: 45585343--45585540 Score: 285
Period size: 71 Copynumber: 2.8 Consensus size: 70
45585333 ACACCCTGTA
* * * *
45585343 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
45585405 ATAAAT
65 ATAAAT
*
45585411 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
45585476 ATAAAT
65 ATAAAT
* *
45585482 GTAGCTAGGTTGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
45585541 AGACAAATCG
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.03
70 1 0.01
71 92 0.77
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:45585466 original size:71 final size:71
Alignment explanation
Indices: 45585377--45585540 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
45585367 GAGATGTATC
45585377 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
45585442 AGGACA
66 AGGACA
*
45585448 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTTGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
45585513 AGGACA
66 AGGACA
45585519 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
45585541 AGACAAATCG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 92 1.00
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:45592503 original size:2 final size:2
Alignment explanation
Indices: 45592496--45592526 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45592486 TGCAAACATA
45592496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45592527 AATTGATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45601273 original size:25 final size:25
Alignment explanation
Indices: 45601245--45601295 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
45601235 TTATCCAACA
45601245 TGGTATATCATTTCATGCATACATG
1 TGGTATATCATTTCATGCATACATG
45601270 TGGTATATCATTTCATGCATACATG
1 TGGTATATCATTTCATGCATACATG
45601295 T
1 T
45601296 CTATAATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (25 bp):
TGGTATATCATTTCATGCATACATG
Found at i:45604949 original size:9 final size:9
Alignment explanation
Indices: 45604935--45604960 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
45604925 TTGCTTGCTG
45604935 AAGAGAAAT
1 AAGAGAAAT
45604944 AAGAGAAAT
1 AAGAGAAAT
45604953 AAGAGAAA
1 AAGAGAAA
45604961 ATGATGCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (9 bp):
AAGAGAAAT
Found at i:45606131 original size:23 final size:24
Alignment explanation
Indices: 45606105--45606149 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
45606095 ATATCCCAAC
*
45606105 ATGGAGTGTAG-GGTTGGATGGAA
1 ATGGAGTGTAGAGGCTGGATGGAA
*
45606128 ATGGCGTGTAGAGGCTGGATGG
1 ATGGAGTGTAGAGGCTGGATGG
45606150 GTAGGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.22, C:0.04, G:0.49, T:0.24
Consensus pattern (24 bp):
ATGGAGTGTAGAGGCTGGATGGAA
Found at i:45606269 original size:34 final size:34
Alignment explanation
Indices: 45606223--45606290 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
45606213 GCATTTTTGA
*
45606223 CACTGTACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTGTACTGAGAAGGGCTAAGGCCCAAGACTGT
* *
45606256 CACTGATATTGAGAAGGGCTTAGGCCCAAGACTGT
1 CACTG-TACTGAGAAGGGCTAAGGCCCAAGACTGT
45606291 TCAACTATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (34 bp):
CACTGTACTGAGAAGGGCTAAGGCCCAAGACTGT
Found at i:45621252 original size:40 final size:40
Alignment explanation
Indices: 45621189--45621356 Score: 194
Period size: 40 Copynumber: 4.2 Consensus size: 40
45621179 TCTTCAGAAT
** * * *
45621189 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTT
1 TTAGCCCGGATATAATAACTAGCACAAATGCCTTCGGGTC
* * **
45621228 TTAACCCGGATTTGGTAACTAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAATAACTAGCACAAATGCCTTCGGGTC
* * *
45621268 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAATAACTAGCACAAATGCCTTCGGGTC
* * *
45621308 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATAACTAGCACAAATGCCTTCGGGTC
45621348 TTAGCCCGG
1 TTAGCCCGG
45621357 GTATCATTCA
Statistics
Matches: 106, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
39 3 0.03
40 103 0.97
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAATAACTAGCACAAATGCCTTCGGGTC
Found at i:45621329 original size:80 final size:80
Alignment explanation
Indices: 45621189--45621356 Score: 214
Period size: 80 Copynumber: 2.1 Consensus size: 80
45621179 TCTTCAGAAT
* * * **
45621189 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTTTTAACCCGGATTTGGTAACTAGCAC
1 TTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATAACTAGCAC
*
45621253 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGAC
** * *
45621268 TTAGCCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCA
1 TTAGCCCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCGGATATAATAACTAGCA
*
45621332 TAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
45621348 TTAGCCCGG
1 TTAGCCCGG
45621357 GTATCATTCA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
79 4 0.05
80 70 0.92
81 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
TTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATAACTAGCAC
AAATGCCTTCGGGAC
Found at i:45623457 original size:29 final size:29
Alignment explanation
Indices: 45623424--45623480 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
45623414 AAAATCATAT
*
45623424 TTTTGAAAAATTACAATTTTGCCCCAAAC
1 TTTTGAAAAATTACAATTTTACCCCAAAC
* * * *
45623453 TTTTGCATATTTACACTTTTACCCCAAA
1 TTTTGAAAAATTACAATTTTACCCCAAA
45623481 GCTCGTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (29 bp):
TTTTGAAAAATTACAATTTTACCCCAAAC
Found at i:45631862 original size:40 final size:40
Alignment explanation
Indices: 45631813--45632020 Score: 258
Period size: 40 Copynumber: 5.2 Consensus size: 40
45631803 TCTTCGGAAT
* * * *
45631813 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTT
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * ** *
45631852 TTAACCCGGATTTGGTAACTAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* *
45631892 TTAGCCCGGATATAA-CAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
* *
45631932 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* *
45631972 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
45632012 TTAGCCCGG
1 TTAGCCCGG
45632021 GTATCATTCA
Statistics
Matches: 146, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 3 0.02
40 142 0.97
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
Found at i:45636279 original size:48 final size:48
Alignment explanation
Indices: 45636208--45636299 Score: 175
Period size: 48 Copynumber: 1.9 Consensus size: 48
45636198 AGAACAAGAA
45636208 TGATTCTGGAAAATGAAAATTGGTATGATTTTTTGGTTAATTTTTATT
1 TGATTCTGGAAAATGAAAATTGGTATGATTTTTTGGTTAATTTTTATT
*
45636256 TGATTTTGGAAAATGAAAATTGGTATGATTTTTTGGTTAATTTT
1 TGATTCTGGAAAATGAAAATTGGTATGATTTTTTGGTTAATTTT
45636300 GAGTTATATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.29, C:0.01, G:0.20, T:0.50
Consensus pattern (48 bp):
TGATTCTGGAAAATGAAAATTGGTATGATTTTTTGGTTAATTTTTATT
Found at i:45636312 original size:48 final size:48
Alignment explanation
Indices: 45636208--45636313 Score: 169
Period size: 48 Copynumber: 2.2 Consensus size: 48
45636198 AGAACAAGAA
* * *
45636208 TGATTCTGGAAAATGAAAATTGGTATGATTTTTTGGTTAATTTTTATT
1 TGATTTTGGAAAATGAAAATTGGTATGATTTTTTGGTTAATTTTGAGT
45636256 TGATTTTGGAAAATGAAAATTGGTATGATTTTTTGGTTAATTTTGAGT
1 TGATTTTGGAAAATGAAAATTGGTATGATTTTTTGGTTAATTTTGAGT
45636304 T-ATATTTGGA
1 TGAT-TTTGGA
45636314 TTAAATTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 2 0.04
48 52 0.96
ACGTcount: A:0.29, C:0.01, G:0.21, T:0.49
Consensus pattern (48 bp):
TGATTTTGGAAAATGAAAATTGGTATGATTTTTTGGTTAATTTTGAGT
Found at i:45638161 original size:52 final size:51
Alignment explanation
Indices: 45638101--45638208 Score: 128
Period size: 52 Copynumber: 2.1 Consensus size: 51
45638091 AAATGAATAG
*
45638101 AAATGGAGAA-ATGAAAAACATTCAAAAATGATTATGGTTTTCTCCAAAATGA
1 AAATGGAGAACATG-AAAACATTCAAAAATGAATATGGTTTTCT-CAAAATGA
* ** * * *
45638153 AAATGGAGAACATGAAATCATTTGAACATGAATGTGGTTTTCTCAAAATGG
1 AAATGGAGAACATGAAAACATTCAAAAATGAATATGGTTTTCTCAAAATGA
45638204 AAATG
1 AAATG
45638209 AAAACTGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 12 0.25
52 33 0.69
53 3 0.06
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (51 bp):
AAATGGAGAACATGAAAACATTCAAAAATGAATATGGTTTTCTCAAAATGA
Found at i:45639239 original size:46 final size:46
Alignment explanation
Indices: 45639189--45639289 Score: 193
Period size: 46 Copynumber: 2.2 Consensus size: 46
45639179 AATTAGTGGT
45639189 ACACCACATGATGACTACAATATTGTCCAAGTGCATTACTAGTACA
1 ACACCACATGATGACTACAATATTGTCCAAGTGCATTACTAGTACA
*
45639235 ACACCACATGATGACTACAATATTGTCCAAGTGCATTACTAGTACT
1 ACACCACATGATGACTACAATATTGTCCAAGTGCATTACTAGTACA
45639281 ACACCACAT
1 ACACCACAT
45639290 TAAAACATCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (46 bp):
ACACCACATGATGACTACAATATTGTCCAAGTGCATTACTAGTACA
Found at i:45639302 original size:46 final size:46
Alignment explanation
Indices: 45639189--45639304 Score: 162
Period size: 46 Copynumber: 2.5 Consensus size: 46
45639179 AATTAGTGGT
**
45639189 ACACCACATGATGACTACAATATTGTCCAAGTGCATTACTAGTACA
1 ACACCACATGAAAACTACAATATTGTCCAAGTGCATTACTAGTACA
** *
45639235 ACACCACATGATGACTACAATATTGTCCAAGTGCATTACTAGTACT
1 ACACCACATGAAAACTACAATATTGTCCAAGTGCATTACTAGTACA
*
45639281 ACACCACATTAAAAC-ATCAATATT
1 ACACCACATGAAAACTA-CAATATT
45639305 TTTAGTCTTG
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
45 1 0.02
46 64 0.98
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (46 bp):
ACACCACATGAAAACTACAATATTGTCCAAGTGCATTACTAGTACA
Found at i:45642555 original size:37 final size:38
Alignment explanation
Indices: 45642505--45642585 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 38
45642495 ACTTTAATGG
45642505 GAATTC-ATCCAAAGGAATTAAATGGGCTTATTAGGCT
1 GAATTCTATCCAAAGGAATTAAATGGGCTTATTAGGCT
*
45642542 GAATTCTA-CCAAAGGAATTAAATGGGCTTATTGGGCT
1 GAATTCTATCCAAAGGAATTAAATGGGCTTATTAGGCT
*
45642579 AAATTCT
1 GAATTCT
45642586 TACATGATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 40 0.98
38 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.31
Consensus pattern (38 bp):
GAATTCTATCCAAAGGAATTAAATGGGCTTATTAGGCT
Found at i:45646764 original size:14 final size:14
Alignment explanation
Indices: 45646745--45646774 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
45646735 ATCTTTTAGG
45646745 TTGTGGGAATCATC
1 TTGTGGGAATCATC
45646759 TTGTGGGAATCATC
1 TTGTGGGAATCATC
45646773 TT
1 TT
45646775 CAATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (14 bp):
TTGTGGGAATCATC
Found at i:45650391 original size:49 final size:49
Alignment explanation
Indices: 45650280--45650554 Score: 262
Period size: 49 Copynumber: 5.7 Consensus size: 49
45650270 GGGATAAGAT
* * * * * * *
45650280 GCCGACGCCATGTTCCAGACATGGTCTTACACTAG--CTAACACATCAAA
1 GCCGATGCCATGTCCCAGACA-GGTCTTACACTAGCTCTCATATATCGAG
* *
45650328 GTCGATGCCATGTCCCAGACAGGTCTTACACT-GACTTTCATATATCGAG
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTAG-CTCTCATATATCGAG
* * * *
45650377 GCCGATGCCGTGTCCCAGATAGGTCTTACACTGGCTCTCATCTATCG-G
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATCGAG
* * *
45650425 TGTCGATGCCATGTCCCAGATAGGTCTTACACTAGCT-TGCATATCTCGAG
1 -GCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCT-CATATATCGAG
* * * *
45650475 GCCAATG-CATGTCCCAAACATGTCTTACACTAGCTCTCATA-AT-GTG
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATCGAG
*
45650521 GCCGATG-CATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTAGC
45650555 ACACATATCA
Statistics
Matches: 191, Mismatches: 28, Indels: 18
0.81 0.12 0.08
Matches are distributed among these distances:
46 35 0.18
47 12 0.06
48 49 0.26
49 93 0.49
50 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATCGAG
Found at i:45667666 original size:17 final size:17
Alignment explanation
Indices: 45667623--45667677 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
45667613 GTAAATAATA
*
45667623 ATTCAACACTATATTGTAT
1 ATTCAACACTA-ATAG-AT
*
45667642 ATTTAACACTAATAGAT
1 ATTCAACACTAATAGAT
*
45667659 ATTCAACACTAATAAAT
1 ATTCAACACTAATAGAT
45667676 AT
1 AT
45667678 AAACTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 19 0.59
18 3 0.09
19 10 0.31
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (17 bp):
ATTCAACACTAATAGAT
Found at i:45668787 original size:15 final size:16
Alignment explanation
Indices: 45668767--45668800 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
45668757 AATCCTTTTA
*
45668767 AAACTATTATAAT-AT
1 AAACTAATATAATAAT
45668782 AAACTAATATAATAAT
1 AAACTAATATAATAAT
45668798 AAA
1 AAA
45668801 ATTATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
AAACTAATATAATAAT
Found at i:45675028 original size:36 final size:35
Alignment explanation
Indices: 45674972--45675040 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
45674962 ATCCTTGCTG
**
45674972 TTTACTTATTTGAATTGTGTCAAGAATCTTTATGA
1 TTTACTTATTTGAAGGGTGTCAAGAATCTTTATGA
45675007 TTTACTTTATTTGAAGGGTGTCAAGAATCTTTAT
1 TTTAC-TTATTTGAAGGGTGTCAAGAATCTTTAT
45675041 TGTATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.48
Consensus pattern (35 bp):
TTTACTTATTTGAAGGGTGTCAAGAATCTTTATGA
Found at i:45680021 original size:63 final size:63
Alignment explanation
Indices: 45679917--45680036 Score: 204
Period size: 63 Copynumber: 1.9 Consensus size: 63
45679907 CTAAGCCAGT
* * *
45679917 AGATTATCCATCAGATCCATTCAGTAAAAAGCCATATGAAAGAGATTAACCAGGCAAGCTAGC
1 AGATTATCCATCAGATCCATTCAGTAAAAAGCCAAAAGAAAGAGATTAACAAGGCAAGCTAGC
*
45679980 AGATTATCCATCAGATCCATTCAGTAAAAAGCCAAAAGAAAGAGATTTACAAGGCAA
1 AGATTATCCATCAGATCCATTCAGTAAAAAGCCAAAAGAAAGAGATTAACAAGGCAA
45680037 TTTATAGAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (63 bp):
AGATTATCCATCAGATCCATTCAGTAAAAAGCCAAAAGAAAGAGATTAACAAGGCAAGCTAGC
Found at i:45681444 original size:25 final size:25
Alignment explanation
Indices: 45681412--45681461 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
45681402 TCACTTTCCT
45681412 TTCCTTAGCTTTTCCCTCAAATTGG
1 TTCCTTAGCTTTTCCCTCAAATTGG
45681437 TTCCTTAGCTTTTCCCTCAAATTGG
1 TTCCTTAGCTTTTCCCTCAAATTGG
45681462 GGTAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (25 bp):
TTCCTTAGCTTTTCCCTCAAATTGG
Found at i:45685705 original size:1 final size:1
Alignment explanation
Indices: 45685699--45685723 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
45685689 AATCTTAGAC
45685699 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
45685724 CTTTAACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:45686866 original size:13 final size:13
Alignment explanation
Indices: 45686806--45686869 Score: 71
Period size: 13 Copynumber: 5.2 Consensus size: 13
45686796 CGAAATAATT
45686806 AAAGAATATAAAA
1 AAAGAATATAAAA
**
45686819 AATTAAT-TAAAA
1 AAAGAATATAAAA
45686831 AAAGAATATAAAA
1 AAAGAATATAAAA
**
45686844 ATTG-AT-TAAAA
1 AAAGAATATAAAA
45686855 AAAGAATATAAAA
1 AAAGAATATAAAA
45686868 AA
1 AA
45686870 TTATCAATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
11 7 0.17
12 14 0.35
13 19 0.47
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (13 bp):
AAAGAATATAAAA
Found at i:45686883 original size:24 final size:25
Alignment explanation
Indices: 45686806--45686872 Score: 118
Period size: 24 Copynumber: 2.7 Consensus size: 25
45686796 CGAAATAATT
45686806 AAAGAATATAAAAAATTAATTAAAA
1 AAAGAATATAAAAAATTAATTAAAA
*
45686831 AAAGAATAT-AAAAATTGATTAAAA
1 AAAGAATATAAAAAATTAATTAAAA
45686855 AAAGAATATAAAAAATTA
1 AAAGAATATAAAAAATTA
45686873 TCAATTTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
24 23 0.59
25 16 0.41
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (25 bp):
AAAGAATATAAAAAATTAATTAAAA
Found at i:45691467 original size:47 final size:48
Alignment explanation
Indices: 45691279--45691550 Score: 379
Period size: 49 Copynumber: 5.7 Consensus size: 48
45691269 GATTCTACGC
* *
45691279 GATGAATGTGAATGTGTATAAATATGAGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTAT-AATATGTGATAAGGCCTAATGGCCGATGT
*
45691328 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATA-ATATGTGATAAGGCCTAATGGCCGATGT
*
45691377 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATA-ATATGTGATAAGGCCTAATGGCCGATGT
* *
45691426 GATAAATGTGAAAGTGTAT-ATATGTGATAAGGCCTAATGGCCAATGT
1 GATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCGATGT
* * * * * *
45691473 GATGAATGTGAAAGTGTAT-ATATGTGATAGGGTCGAGTGGCCAACGT
1 GATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCGATGT
*
45691520 GATGGATGTGAAAGTGTATAA-ATGTGATAAG
1 GATGAATGTGAAAGTGTATAATATGTGATAAG
45691551 TCCCGAAGGG
Statistics
Matches: 207, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
47 95 0.46
48 2 0.01
49 110 0.53
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (48 bp):
GATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCGATGT
Found at i:45694783 original size:22 final size:22
Alignment explanation
Indices: 45694758--45694810 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
45694748 GCCTAGCAGG
45694758 CTTAGTGCCGGTGTTATTCAAA
1 CTTAGTGCCGGTGTTATTCAAA
* ** **
45694780 CTTATTTTCGGTGTTATTCAGG
1 CTTAGTGCCGGTGTTATTCAAA
45694802 CTTAGTGCC
1 CTTAGTGCC
45694811 TAGCAGGCTT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.42
Consensus pattern (22 bp):
CTTAGTGCCGGTGTTATTCAAA
Found at i:45694917 original size:38 final size:38
Alignment explanation
Indices: 45694790--45694919 Score: 181
Period size: 38 Copynumber: 3.4 Consensus size: 38
45694780 CTTATTTTCG
*
45694790 GTGTTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCA
1 GTGTTATTCAGACTTAGTGCCTAGCAGGCTTAGTGCCA
* *
45694828 GTGTTATTCAGGA-TTAGTGCCTAGTAGGCTTAGTGCTA
1 GTGTTATTCA-GACTTAGTGCCTAGCAGGCTTAGTGCCA
* * *
45694866 GTGTTATTTAGACTTAGTGCCTAGCAGGCTTAGTACCG
1 GTGTTATTCAGACTTAGTGCCTAGCAGGCTTAGTGCCA
*
45694904 GTGTTTTTCAGACTTA
1 GTGTTATTCAGACTTA
45694920 TTACCGGTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
37 2 0.03
38 77 0.96
39 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (38 bp):
GTGTTATTCAGACTTAGTGCCTAGCAGGCTTAGTGCCA
Found at i:45696272 original size:42 final size:43
Alignment explanation
Indices: 45696209--45696315 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 43
45696199 GATTTGAGAT
* * **
45696209 TTACGTGTAAGACCATGTCTGGGACATCGACATCG-TATCTGAA
1 TTACATGTAAGACCATGTCTGGAACAGAGACATCGATA-CTGAA
* * *
45696252 TT-CATGTAAGACCCTTTCTGGAACAGAGGCATCGATACTGAA
1 TTACATGTAAGACCATGTCTGGAACAGAGACATCGATACTGAA
*
45696294 TTACATGTAAGACCACGTCTGG
1 TTACATGTAAGACCATGTCTGG
45696316 GACGTCGGTA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 32 0.62
43 20 0.38
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTGGAACAGAGACATCGATACTGAA
Found at i:45696601 original size:32 final size:32
Alignment explanation
Indices: 45696563--45696629 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
45696553 TGAACTATTC
45696563 TGTGAAATAGCTATGAATTCTTGCTATTGATT
1 TGTGAAATAGCTATGAATTCTTGCTATTGATT
* *
45696595 TGTGAAATGGCTATGAATTCTTGCTGTTGATT
1 TGTGAAATAGCTATGAATTCTTGCTATTGATT
45696627 TGT
1 TGT
45696630 ACTTTATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.45
Consensus pattern (32 bp):
TGTGAAATAGCTATGAATTCTTGCTATTGATT
Found at i:45704408 original size:15 final size:16
Alignment explanation
Indices: 45704388--45704417 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45704378 TGGTGCCTTG
45704388 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
45704403 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
45704418 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:45709301 original size:21 final size:22
Alignment explanation
Indices: 45709259--45709301 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
45709249 ATTGAAATGA
* *
45709259 TAATTTTATTTTTTTATGATAT
1 TAATTTTATTATTTAATGATAT
45709281 TAATTTTATTATTTAAT-ATAT
1 TAATTTTATTATTTAATGATAT
45709302 AAGCTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TAATTTTATTATTTAATGATAT
Found at i:45718919 original size:25 final size:25
Alignment explanation
Indices: 45718890--45718950 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
45718880 CCTTAGCACG
*
45718890 CTCTCTGATTAATAGCACGTTAGTC
1 CTCTCTGATTAATAGCACGTCAGTC
* *
45718915 CTCTCTGATTATTAGCACGTCAGTG
1 CTCTCTGATTAATAGCACGTCAGTC
*
45718940 CTCTCCGATTA
1 CTCTCTGATTA
45718951 GTACATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.36
Consensus pattern (25 bp):
CTCTCTGATTAATAGCACGTCAGTC
Found at i:45720244 original size:22 final size:23
Alignment explanation
Indices: 45720202--45720248 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
45720192 TAACAATTAT
45720202 TAACACACTTAAATGTAGACTAGC
1 TAACACACTTAAA-GTAGACTAGC
45720226 TAACACA-TTAAA-TACGACTAGC
1 TAACACACTTAAAGTA-GACTAGC
45720248 T
1 T
45720249 CAAATATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 8 0.36
23 5 0.23
24 7 0.32
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.26
Consensus pattern (23 bp):
TAACACACTTAAAGTAGACTAGC
Found at i:45727782 original size:28 final size:28
Alignment explanation
Indices: 45727715--45727784 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
45727705 TGGCAGCAGA
45727715 TAACACATATTAAAAACATGTATTAAAC
1 TAACACATATTAAAAACATGTATTAAAC
* * *
45727743 TACCACACATTAATAACATGTATTAAAC
1 TAACACATATTAAAAACATGTATTAAAC
*
45727771 TAAGACATATTAAA
1 TAACACATATTAAA
45727785 CACTTTAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.29
Consensus pattern (28 bp):
TAACACATATTAAAAACATGTATTAAAC
Found at i:45733061 original size:28 final size:28
Alignment explanation
Indices: 45733021--45733078 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
45733011 CTTTCTTTTC
*
45733021 TTTTTTTGTTTTTTATA-ATTTCGAACTT
1 TTTTTTTATTTTTTATATATTTCGAA-TT
45733049 TTTTTTTATTTTTTATATATTTCGAATT
1 TTTTTTTATTTTTTATATATTTCGAATT
45733077 TT
1 TT
45733079 GTACACAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (28 bp):
TTTTTTTATTTTTTATATATTTCGAATT
Found at i:45739509 original size:48 final size:48
Alignment explanation
Indices: 45739439--45739722 Score: 257
Period size: 48 Copynumber: 5.9 Consensus size: 48
45739429 ACAGCCCACC
* * * * * *
45739439 TATGGTCTTACAC-GAAGTCTCATAACGGTGCCGATGCCATGTCCTAGA
1 TATGGTCTTATACGGGA-TCTCATATCGATGCCGATGCCATATCCCAGA
* * * *
45739487 CATGGTCTTATACGGGACCTCATATCGATGCCAATGACATATCCCAGA
1 TATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATATCCCAGA
* * * * * * *
45739535 TATGGTCTTACATGAGATCACATA-CTGATGCCGATGTCATGTCCCAAA
1 TATGGTCTTATACGGGATCTCATATC-GATGCCGATGCCATATCCCAGA
** * * *
45739583 CGTGGTCTTATACGGGATCTCTTATCAATGCCAATGCCATATCCCAGA
1 TATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATATCCCAGA
* * * * * *
45739631 TATGGTCTTACACAGGATCTCATCTCAATGCTGATGCCATATCCTAGA
1 TATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATATCCCAGA
* * *
45739679 TATGGTCTTATACGGGATCTCTTATAGATGCTGATGCCATATCC
1 TATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATATCC
45739723 TATATGTAAC
Statistics
Matches: 186, Mismatches: 47, Indels: 6
0.78 0.20 0.03
Matches are distributed among these distances:
47 1 0.01
48 182 0.98
49 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (48 bp):
TATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATATCCCAGA
Found at i:45739716 original size:96 final size:96
Alignment explanation
Indices: 45739467--45739722 Score: 320
Period size: 96 Copynumber: 2.7 Consensus size: 96
45739457 CTCATAACGG
* * * *
45739467 TGCCGATGCCATGTCCTAGACATGGTCTTATACGGGACCTCATATCGATGCCAATGACATATCCC
1 TGCCGATGCCATGTCCTAGACATGGTCTTATACGGGATCTCTTATAGATGCCAATGCCATATCCC
* *
45739532 AGATATGGTCTTACATGAGATCACATACTGA
66 AGATATGGTCTTACAAGAGATCACATACTAA
* * * *
45739563 TGCCGATGTCATGTCCCAAACGTGGTCTTATACGGGATCTCTTATCA-ATGCCAATGCCATATCC
1 TGCCGATGCCATGTCCTAGACATGGTCTTATACGGGATCTCTTAT-AGATGCCAATGCCATATCC
*
45739627 CAGATATGGTCTTACACAG-GATCTCAT-CTCAA
65 CAGATATGGTCTTACA-AGAGATCACATACT-AA
* * * **
45739659 TGCTGATGCCATATCCTAGATATGGTCTTATACGGGATCTCTTATAGATGCTGATGCCATATCC
1 TGCCGATGCCATGTCCTAGACATGGTCTTATACGGGATCTCTTATAGATGCCAATGCCATATCC
45739723 TATATGTAAC
Statistics
Matches: 136, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
95 3 0.02
96 132 0.97
97 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (96 bp):
TGCCGATGCCATGTCCTAGACATGGTCTTATACGGGATCTCTTATAGATGCCAATGCCATATCCC
AGATATGGTCTTACAAGAGATCACATACTAA
Found at i:45740932 original size:40 final size:42
Alignment explanation
Indices: 45740861--45740958 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 42
45740851 TGAAAGCATT
45740861 GGCACTAAGTGTGCGATTTAAACTAGCTTCGGCTA-TT-A-AA
1 GGCACTAAGTGTGCGA-TTAAACTAGCTTCGGCTAGTTGAGAA
* * *
45740901 GGCACTAAGTGTGCGA-TACGACTTAGTTTCGGCTAGTTGAGAT
1 GGCACTAAGTGTGCGATTA-AAC-TAGCTTCGGCTAGTTGAGAA
45740944 GGCACTAAGTGTGCG
1 GGCACTAAGTGTGCG
45740959 GAATCATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
38 2 0.04
39 2 0.04
40 27 0.54
41 2 0.04
42 1 0.02
43 16 0.32
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (42 bp):
GGCACTAAGTGTGCGATTAAACTAGCTTCGGCTAGTTGAGAA
Found at i:45742486 original size:367 final size:367
Alignment explanation
Indices: 45741813--45742547 Score: 1470
Period size: 367 Copynumber: 2.0 Consensus size: 367
45741803 GTAGGAATGA
45741813 CCCAAAAAGGGGTGGCAAGTTGGCTTAAACTAAGCCTGCATTGTGCCACACGGTCAGGGAATACG
1 CCCAAAAAGGGGTGGCAAGTTGGCTTAAACTAAGCCTGCATTGTGCCACACGGTCAGGGAATACG
45741878 GGCGTGCCTTGTGGCCGTGTATGTAAAGTAGTAACCTCTTAAGATCACATGATTAAGACACATGG
66 GGCGTGCCTTGTGGCCGTGTATGTAAAGTAGTAACCTCTTAAGATCACATGATTAAGACACATGG
45741943 GCGTGTCATATGGCCGTGTGCTTAAGTCAGTAACCAGCTAAGTATCACACAGCCATGGCACAAGG
131 GCGTGTCATATGGCCGTGTGCTTAAGTCAGTAACCAGCTAAGTATCACACAGCCATGGCACAAGG
45742008 CCGTGTCTGTTGGCCTTTTGTAAAAGGTAGTATATATACTCTATTATGGCACGGTTGGATCACAT
196 CCGTGTCTGTTGGCCTTTTGTAAAAGGTAGTATATATACTCTATTATGGCACGGTTGGATCACAT
45742073 GGGCGTGTCTGGTGCTCGTGTAAGGCACACGAGAGTGTGACCTCAACAGAATTGGAAAAATTTTT
261 GGGCGTGTCTGGTGCTCGTGTAAGGCACACGAGAGTGTGACCTCAACAGAATTGGAAAAATTTTT
45742138 CTAAGTTCTGAAAATTCTGAATGTGTTCGGTTTAGTCCCAAC
326 CTAAGTTCTGAAAATTCTGAATGTGTTCGGTTTAGTCCCAAC
45742180 CCCAAAAAGGGGTGGCAAGTTGGCTTAAACTAAGCCTGCATTGTGCCACACGGTCAGGGAATACG
1 CCCAAAAAGGGGTGGCAAGTTGGCTTAAACTAAGCCTGCATTGTGCCACACGGTCAGGGAATACG
45742245 GGCGTGCCTTGTGGCCGTGTATGTAAAGTAGTAACCTCTTAAGATCACATGATTAAGACACATGG
66 GGCGTGCCTTGTGGCCGTGTATGTAAAGTAGTAACCTCTTAAGATCACATGATTAAGACACATGG
45742310 GCGTGTCATATGGCCGTGTGCTTAAGTCAGTAACCAGCTAAGTATCACACAGCCATGGCACAAGG
131 GCGTGTCATATGGCCGTGTGCTTAAGTCAGTAACCAGCTAAGTATCACACAGCCATGGCACAAGG
45742375 CCGTGTCTGTTGGCCTTTTGTAAAAGGTAGTATATATACTCTATTATGGCACGGTTGGATCACAT
196 CCGTGTCTGTTGGCCTTTTGTAAAAGGTAGTATATATACTCTATTATGGCACGGTTGGATCACAT
45742440 GGGCGTGTCTGGTGCTCGTGTAAGGCACACGAGAGTGTGACCTCAACAGAATTGGAAAAATTTTT
261 GGGCGTGTCTGGTGCTCGTGTAAGGCACACGAGAGTGTGACCTCAACAGAATTGGAAAAATTTTT
45742505 CTAAGTTCTGAAAATTCTGAATGTGTTCGGTTTAGTCCCAAC
326 CTAAGTTCTGAAAATTCTGAATGTGTTCGGTTTAGTCCCAAC
45742547 C
1 C
45742548 TCTTCTAAAA
Statistics
Matches: 368, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
367 368 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (367 bp):
CCCAAAAAGGGGTGGCAAGTTGGCTTAAACTAAGCCTGCATTGTGCCACACGGTCAGGGAATACG
GGCGTGCCTTGTGGCCGTGTATGTAAAGTAGTAACCTCTTAAGATCACATGATTAAGACACATGG
GCGTGTCATATGGCCGTGTGCTTAAGTCAGTAACCAGCTAAGTATCACACAGCCATGGCACAAGG
CCGTGTCTGTTGGCCTTTTGTAAAAGGTAGTATATATACTCTATTATGGCACGGTTGGATCACAT
GGGCGTGTCTGGTGCTCGTGTAAGGCACACGAGAGTGTGACCTCAACAGAATTGGAAAAATTTTT
CTAAGTTCTGAAAATTCTGAATGTGTTCGGTTTAGTCCCAAC
Found at i:45743213 original size:13 final size:14
Alignment explanation
Indices: 45743178--45743216 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
45743168 GAAGATATGT
45743178 ATATATTATATATAA
1 ATATATTAT-TATAA
*
45743193 ATAAATTATTAT-A
1 ATATATTATTATAA
45743206 ATATATTATTA
1 ATATATTATTA
45743217 GTAACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTATTATAA
Found at i:45743764 original size:12 final size:13
Alignment explanation
Indices: 45743749--45743789 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
45743739 ATAAAAATTC
*
45743749 AATTAATTAT-TA
1 AATTAATAATGTA
*
45743761 AATTAATGATGT-
1 AATTAATAATGTA
45743773 AATTAATAATGTA
1 AATTAATAATGTA
45743786 AATT
1 AATT
45743790 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
AATTAATAATGTA
Found at i:45747196 original size:28 final size:28
Alignment explanation
Indices: 45747164--45747234 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
45747154 TTGGCAGTAG
45747164 CTAAGACACATTAAAAACATGTACTAAA
1 CTAAGACACATTAAAAACATGTACTAAA
* * *
45747192 CTAAGACACATTAATAACATGTATTAGA
1 CTAAGACACATTAAAAACATGTACTAAA
*
45747220 TTAAGACACATTAAA
1 CTAAGACACATTAAA
45747235 CACTTTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.25
Consensus pattern (28 bp):
CTAAGACACATTAAAAACATGTACTAAA
Found at i:45754622 original size:38 final size:38
Alignment explanation
Indices: 45754576--45754674 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 38
45754566 GAAATCCTTG
*
45754576 TTATAATTATTGTAATTATAATTTACGAT-AGAATATTA
1 TTATAATTATTGTAATTATAATTTACGATCA-AACATTA
* *
45754614 TTATAATTATTGTAATTGA-AATTTTCGGTCAAACATTA
1 TTATAATTATTGTAATT-ATAATTTACGATCAAACATTA
*
45754652 CTATAATTA-TGATAATTATAATT
1 TTATAATTATTG-TAATTATAATT
45754675 ATTATATTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
37 3 0.06
38 48 0.91
39 2 0.04
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.46
Consensus pattern (38 bp):
TTATAATTATTGTAATTATAATTTACGATCAAACATTA
Found at i:45763574 original size:3 final size:3
Alignment explanation
Indices: 45763566--45763614 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
45763556 TGAGTATTGT
45763566 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45763614 A
1 A
45763615 CATATGAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:45765852 original size:32 final size:32
Alignment explanation
Indices: 45765816--45765876 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
45765806 AATAAAATAA
*
45765816 TAAATTTACTTTTTTATTTAATATAAATCAAC
1 TAAATTTACTTTTTAATTTAATATAAATCAAC
45765848 TAAATTTACTTTTTAATTTAATATAAATC
1 TAAATTTACTTTTTAATTTAATATAAATC
45765877 TATTACCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (32 bp):
TAAATTTACTTTTTAATTTAATATAAATCAAC
Found at i:45767479 original size:20 final size:20
Alignment explanation
Indices: 45767444--45767496 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
45767434 TTATGTTGCT
* *
45767444 TAAAATTTT-ATTTGTTTTA
1 TAAAATTTTCTTTTGTTTAA
**
45767463 TATTATTTTCTTTTGTTTAA
1 TAAAATTTTCTTTTGTTTAA
45767483 TAAAATTTTCTTTT
1 TAAAATTTTCTTTT
45767497 CTTTCGTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (20 bp):
TAAAATTTTCTTTTGTTTAA
Found at i:45775912 original size:7 final size:7
Alignment explanation
Indices: 45775900--45775930 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
45775890 TTTATTAGGA
45775900 TTATATT
1 TTATATT
45775907 TTATATT
1 TTATATT
45775914 TTATATT
1 TTATATT
*
45775921 TTATCTT
1 TTATATT
45775928 TTA
1 TTA
45775931 CCTTTTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATATT
Found at i:45779409 original size:13 final size:13
Alignment explanation
Indices: 45779391--45779432 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
45779381 AATTTTAAAT
45779391 TATTTAGAGATAA
1 TATTTAGAGATAA
45779404 TATTTAGA-AT--
1 TATTTAGAGATAA
*
45779414 TATTTAGTGATAA
1 TATTTAGAGATAA
45779427 TATTTA
1 TATTTA
45779433 AAAAAAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TATTTAGAGATAA
Found at i:45779414 original size:23 final size:22
Alignment explanation
Indices: 45779384--45779434 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 22
45779374 ATTTTTAAAT
45779384 TTTAAATTATTTAGAGATAATA
1 TTTAAATTATTTAGAGATAATA
*
45779406 TTTAGAATTATTTAGTGATAATA
1 TTTA-AATTATTTAGAGATAATA
45779429 TTTAAA
1 TTTAAA
45779435 AAAAATCTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (22 bp):
TTTAAATTATTTAGAGATAATA
Found at i:45783849 original size:20 final size:22
Alignment explanation
Indices: 45783804--45783850 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
45783794 GGGTGTTGGT
*
45783804 TTTTAATTTTTATATAATAATG
1 TTTTAATTTTTATATAATAATA
45783826 TTTTAATTTTTATAT-A-AATA
1 TTTTAATTTTTATATAATAATA
45783846 TTTTA
1 TTTTA
45783851 TATTATATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTAATTTTTATATAATAATA
Found at i:45786834 original size:18 final size:19
Alignment explanation
Indices: 45786801--45786836 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
45786791 TCTTAGAGTA
*
45786801 AAATAATGTGTATTAAATC
1 AAATAAAGTGTATTAAATC
45786820 AAATAAAGT-TATTAAAT
1 AAATAAAGTGTATTAAAT
45786837 TTTTGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (19 bp):
AAATAAAGTGTATTAAATC
Found at i:45792045 original size:28 final size:28
Alignment explanation
Indices: 45791977--45792065 Score: 114
Period size: 28 Copynumber: 3.3 Consensus size: 28
45791967 GATATAACAT
*
45791977 TGTGCTAAGTGAAATAAGACCATGGC-A
1 TGTGCTAAGTGAAATAAGTCCATGGCAA
* *
45792004 --T-CTAAATGAAATAAGTCCATGACAA
1 TGTGCTAAGTGAAATAAGTCCATGGCAA
*
45792029 TGTGCTAAGTGAAATAAGTCCATGGCAT
1 TGTGCTAAGTGAAATAAGTCCATGGCAA
45792057 TGTGCTAAG
1 TGTGCTAAG
45792066 CGAGAAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
24 19 0.37
25 2 0.04
27 1 0.02
28 30 0.58
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (28 bp):
TGTGCTAAGTGAAATAAGTCCATGGCAA
Found at i:45792176 original size:51 final size:51
Alignment explanation
Indices: 45792092--45792240 Score: 219
Period size: 51 Copynumber: 2.9 Consensus size: 51
45792082 TGAACCTTAA
* * *
45792092 GAATAAAATAGCTTTGGACACAAGTTTGTTACTATATGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
*
45792143 GAATATAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* * *
45792194 GAATAAAAGAGCTTTGG-CTACAAGGGCGGTACTATGTGAAGGCCACT
1 GAATAAAATAGCTTTGGAC-ACAAGTGTGGTACTATGTGAAGGCCACT
45792241 GTGTAACCGT
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 1 0.01
51 88 0.99
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Found at i:45793219 original size:25 final size:25
Alignment explanation
Indices: 45793185--45793237 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
45793175 ATTATTTACA
*
45793185 TACCAACTTACTAAGCTATAAATCT
1 TACCAACTTACTAAGCTACAAATCT
*
45793210 TACCAACTTACTAAGCTACATATCT
1 TACCAACTTACTAAGCTACAAATCT
45793235 TAC
1 TAC
45793238 TCCTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (25 bp):
TACCAACTTACTAAGCTACAAATCT
Found at i:45797030 original size:48 final size:49
Alignment explanation
Indices: 45796912--45797328 Score: 401
Period size: 48 Copynumber: 8.6 Consensus size: 49
45796902 GGTAAGATGT
* * *
45796912 CGATTCCATG-TCCTAGACATGGTCTTACACTGGCTCT-CATATATCG-GTGC
1 CGATGCCATGTTCC-AGACATGGTCTTACACTAGC-CTACATA-GTCGAG-GC
* *
45796962 CGATACCATGTTCCAAACATGGTCTTACACTAGCCTACA-AGTCGAGGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGCCTACATAGTCGAGGC
* * * ** *
45797010 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTCCATA-TAAATGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGCCTACATAGTCGAGGC
* * * *
45797058 CGATGCCATGTTCCGGACATGGTCTTACACTACCCCACAT-GTCGAGGA
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGCCTACATAGTCGAGGC
* ** *
45797106 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATA-TAAATGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGC-CTACATAGTCGAGGC
* * * *
45797154 CGATGCCATATTCCA-ATCATGGTTTTACACTAGCCCACAT-GTTGAGGC
1 CGATGCCATGTTCCAGA-CATGGTCTTACACTAGCCTACATAGTCGAGGC
* *
45797202 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACAT-GTCGAGGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGCCTACATAGTCGAGGC
* * ** *
45797250 TGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATA-TAAATGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTAGC-CTACATAGTCGAGGC
*
45797298 CGATGCCATGTTCCAAACATGGTCTTACACT
1 CGATGCCATGTTCCAGACATGGTCTTACACT
45797329 GGCTCACATA
Statistics
Matches: 304, Mismatches: 50, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
47 2 0.01
48 262 0.86
49 8 0.03
50 29 0.10
51 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (49 bp):
CGATGCCATGTTCCAGACATGGTCTTACACTAGCCTACATAGTCGAGGC
Found at i:45797088 original size:96 final size:96
Alignment explanation
Indices: 45796912--45797338 Score: 471
Period size: 96 Copynumber: 4.4 Consensus size: 96
45796902 GGTAAGATGT
* * * ** *
45796912 CGATTCCATGTCCTAGACATGGTCTTACACTGGCTCTCATATATCGGTGCCGATACCATGTTCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATA--AATGCCGATGCCATGTTCCA
*
45796977 AACATGGTCTTACACTAGCCTACAAGTCGAGGC
64 AACATGGTCTTACACTAGCCCACAAGTCGAGGC
**
45797010 CGATGCCATGTCCCAGACATGGTCTTACACTAGCT-TCCATATAAATGCCGATGCCATGTTCCGG
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATATAAATGCCGATGCCATGTTCCAA
* * *
45797074 ACATGGTCTTACACTACCCCACATGTCGAGGA
65 ACATGGTCTTACACTAGCCCACAAGTCGAGGC
* *
45797106 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATATTCCAAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAA
* * *
45797171 CATGGTTTTACACTAGCCCACATGTTGAGGC
66 CATGGTCTTACACTAGCCCACAAGTCGAGGC
* * * * * ** * * * *
45797202 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATGTCGAGGCTGATGCCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAA
* * ** *
45797267 CATGGTCTTACACTAGCTCTCATA-TAAATGC
66 CATGGTCTTACACTAGCCCACA-AGTCGAGGC
* * * *
45797298 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATA
45797339 ACCCTAGTAT
Statistics
Matches: 283, Mismatches: 43, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
96 243 0.86
97 2 0.01
98 38 0.13
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (96 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAA
CATGGTCTTACACTAGCCCACAAGTCGAGGC
Found at i:45797182 original size:144 final size:142
Alignment explanation
Indices: 45796962--45797338 Score: 490
Period size: 144 Copynumber: 2.6 Consensus size: 142
45796952 ATATCGGTGC
* * * ** * *
45796962 CGATACCATGTTCCAAACATGGTCTTACACTAGC-CTACA-AGTCGAGGCCGATGCCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATA-TAAATGCCGATGCCATGTTCCA
* * **
45797025 GACATGGTCTTACACTAGCTTC-CATATAAATGCCGATGCCATGTTCCGGACATGGTCTTACACT
64 -ACATGGTCTTACACTAGC-CCACATATAAAGGCCGATGCCATGTTCCAAACATGGTCTTACACT
45797089 ACCCCACATGTCGAGG
127 ACCCCACATGTCGAGG
*
45797105 ACGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATATTCCAA
1 -CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAA
* * ** *
45797170 TCATGGTTTTACACTAGCCCACATGTTGAGGCCGATGCCATGTTCCAAACATGGTCTTACACTAG
65 -CATGGTCTTACACTAGCCCACATATAAAGGCCGATGCCATGTTCCAAACATGGTCTTACACTAC
45797235 CCCACATGTCGAGG
129 CCCACATGTCGAGG
45797249 CTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAA
1 C-GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCC-A
* *
45797314 ACATGGTCTTACACTGGCTCACATA
64 ACATGGTCTTACACTAGCCCACATA
45797339 ACCCTAGTAT
Statistics
Matches: 205, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
143 3 0.01
144 197 0.96
145 5 0.02
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (142 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAC
ATGGTCTTACACTAGCCCACATATAAAGGCCGATGCCATGTTCCAAACATGGTCTTACACTACCC
CACATGTCGAGG
Found at i:45800526 original size:24 final size:27
Alignment explanation
Indices: 45800490--45800558 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 27
45800480 ATATGACATC
*
45800490 GTGCTAAGGGAAATAAGACCATGGC-A
1 GTGCTAAGTGAAATAAGACCATGGCAA
*
45800516 -T-CTAAGTGAAATAAGTCCATGGCAA
1 GTGCTAAGTGAAATAAGACCATGGCAA
45800541 TGTGCTAAGTGAAATAAG
1 -GTGCTAAGTGAAATAAG
45800559 TCCAAGGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 20 0.54
25 2 0.05
27 1 0.03
28 14 0.38
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (27 bp):
GTGCTAAGTGAAATAAGACCATGGCAA
Found at i:45800557 original size:28 final size:27
Alignment explanation
Indices: 45800490--45800578 Score: 103
Period size: 28 Copynumber: 3.3 Consensus size: 27
45800480 ATATGACATC
* *
45800490 GTGCTAAGGGAAATAAGACCATGGCA-
1 GTGCTAAGTGAAATAAGTCCATGGCAT
45800516 -T-CTAAGTGAAATAAGTCCATGGCAAT
1 GTGCTAAGTGAAATAAGTCCATGGC-AT
* *
45800542 GTGCTAAGTGAAATAAGTCCAAGGCTTT
1 GTGCTAAGTGAAATAAGTCCATGGC-AT
45800570 GTGCTAAGT
1 GTGCTAAGT
45800579 CAGAAATTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
24 20 0.37
25 2 0.04
27 1 0.02
28 31 0.57
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.25
Consensus pattern (27 bp):
GTGCTAAGTGAAATAAGTCCATGGCAT
Found at i:45800665 original size:51 final size:51
Alignment explanation
Indices: 45800604--45800773 Score: 277
Period size: 51 Copynumber: 3.3 Consensus size: 51
45800594 TGAACCTTAG
**
45800604 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAATACCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* * ** *
45800655 GAATATAATAGCTTTGAACACAAGTGTGACACTATGTGAAGGTCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
45800706 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
45800757 GAATAAAATAGCTTTGG
1 GAATAAAATAGCTTTGG
45800774 CTAAAAGGGT
Statistics
Matches: 107, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 107 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.31
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Done.