Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 84 of 199
Found at i:25386715 original size:122 final size:122
Alignment explanation
Indices: 25386493--25386715 Score: 311
Period size: 122 Copynumber: 1.8 Consensus size: 122
25386483 TTACCCTTCT
* * *
25386493 AGAGTTTTTCCACAAAGGCGGTCCTTTACATTCAGTACTCGCAACAAAGGCTTTCATGTCTAGAG
1 AGAGTTTTACCACAAAGGCGGTCCTTTACATTCAGTACTCGCAACAAAGGCTTTCATATCCAGAG
* * *
25386558 TTTTGCCACATAGGCGTTTCTTTACATTCACTACTCGCCACAAAGCCTTTCCTATCC
66 TTTTGCCACAAAGGCGTTCCTTTACATTCAATACTCGCCACAAAGCCTTTCCTATCC
* * ** * *
25386615 AGAGTTTTACCACAAAGGTGTTCCTTTACATTCAGTACTCGCCTCAAAGGCTTTCCTATCCAGAT
1 AGAGTTTTACCACAAAGGCGGTCCTTTACATTCAGTACTCGCAACAAAGGCTTTCATATCCAGAG
* * *
25386680 TTTTTCCATAAAGGTGTTCCTTTACATTCAATACTC
66 TTTTGCCACAAAGGCGTTCCTTTACATTCAATACTC
25386716 ACCAAAAAAG
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
122 86 1.00
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.34
Consensus pattern (122 bp):
AGAGTTTTACCACAAAGGCGGTCCTTTACATTCAGTACTCGCAACAAAGGCTTTCATATCCAGAG
TTTTGCCACAAAGGCGTTCCTTTACATTCAATACTCGCCACAAAGCCTTTCCTATCC
Found at i:25386726 original size:33 final size:33
Alignment explanation
Indices: 25386689--25386752 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
25386679 TTTTTTCCAT
* *
25386689 AAAGGTGTTCCTTTACATTCAATACTCACCAAA
1 AAAGGCGTTCATTTACATTCAATACTCACCAAA
*
25386722 AAAGGCGTTCATTTACGTTCAATACTCACCA
1 AAAGGCGTTCATTTACATTCAATACTCACCA
25386753 CAAAGCCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (33 bp):
AAAGGCGTTCATTTACATTCAATACTCACCAAA
Found at i:25391604 original size:20 final size:20
Alignment explanation
Indices: 25391579--25391618 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25391569 GAATTGCTGC
*
25391579 TAAACCATTTCATTACATTT
1 TAAACCAGTTCATTACATTT
*
25391599 TAAACCAGTTCATTGCATTT
1 TAAACCAGTTCATTACATTT
25391619 AGGTTAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (20 bp):
TAAACCAGTTCATTACATTT
Found at i:25393830 original size:28 final size:28
Alignment explanation
Indices: 25393798--25393871 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
25393788 TGGCTATTTC
*
25393798 TGTTAAAGGAATCCTTTACGGCAATCTA
1 TGTTAAAGGAAACCTTTACGGCAATCTA
** ** *
25393826 TGTTATAA-GAAAGCCTTTGTGGTTATTTA
1 TGTTA-AAGGAAA-CCTTTACGGCAATCTA
25393855 TGTTAAAGGAAACCTTT
1 TGTTAAAGGAAACCTTT
25393872 GTGGCTATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 15 0.41
29 22 0.59
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (28 bp):
TGTTAAAGGAAACCTTTACGGCAATCTA
Found at i:25393929 original size:28 final size:28
Alignment explanation
Indices: 25393783--25393935 Score: 146
Period size: 28 Copynumber: 5.4 Consensus size: 28
25393773 ATAAGTAAGT
*
25393783 CTTTGTGGCTATTTCTGTTAAAGGAATC
1 CTTTGTGGCTATTTCTGTTAAAGGAAAC
** * * *
25393811 CTTTACGGCAATCTATGTTATAA-GAAAGC
1 CTTTGTGGCTATTTCTGTTA-AAGGAAA-C
* *
25393840 CTTTGTGGTTATTTATGTTAAAGGAAAC
1 CTTTGTGGCTATTTCTGTTAAAGGAAAC
* * **
25393868 CTTTGTGGCTATCTCTGTAAAAAGGATGC
1 CTTTGTGGCTATTTCTGT-TAAAGGAAAC
* *
25393897 ATTTGTGGTTATTTCTGTTAAAGGAAAC
1 CTTTGTGGCTATTTCTGTTAAAGGAAAC
25393925 CTTTGTGGCTA
1 CTTTGTGGCTA
25393936 ACTATTTTAG
Statistics
Matches: 96, Mismatches: 25, Indels: 8
0.74 0.19 0.06
Matches are distributed among these distances:
28 52 0.54
29 44 0.46
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (28 bp):
CTTTGTGGCTATTTCTGTTAAAGGAAAC
Found at i:25393929 original size:57 final size:57
Alignment explanation
Indices: 25393784--25393940 Score: 197
Period size: 57 Copynumber: 2.8 Consensus size: 57
25393774 TAAGTAAGTC
* * ** * * * *
25393784 TTTGTGGCTATTTCTGTTAAAGGAATCCTTTACGGCAATCTATGTTATAAGAAAGCC
1 TTTGTGGTTATTTCTGTTAAAGGAAACCTTTGTGGCTATCTATGTAAAAAGAAAGCA
* * * *
25393841 TTTGTGGTTATTTATGTTAAAGGAAACCTTTGTGGCTATCTCTGTAAAAAGGATGCA
1 TTTGTGGTTATTTCTGTTAAAGGAAACCTTTGTGGCTATCTATGTAAAAAGAAAGCA
*
25393898 TTTGTGGTTATTTCTGTTAAAGGAAACCTTTGTGGCTAACTAT
1 TTTGTGGTTATTTCTGTTAAAGGAAACCTTTGTGGCTATCTAT
25393941 TTTAGAAAGG
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 85 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (57 bp):
TTTGTGGTTATTTCTGTTAAAGGAAACCTTTGTGGCTATCTATGTAAAAAGAAAGCA
Found at i:25402851 original size:22 final size:22
Alignment explanation
Indices: 25402786--25402851 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
25402776 TTTATTGTTC
*
25402786 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
25402808 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
25402830 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
25402852 CGAGTCCAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:25403468 original size:45 final size:43
Alignment explanation
Indices: 25403362--25403491 Score: 143
Period size: 45 Copynumber: 2.9 Consensus size: 43
25403352 AGACTACTAG
* *
25403362 GATGCCATAGCATCTTTCAACTACTGTCTTAGTCATGTTTACCAT
1 GATGCCATAGCATCTTTCAGCTA-TGTCTTACTCAT-TTTACCAT
*** * *
25403407 GATGCCATAATGTCTTTCAGCCATGGTCTTACTCATTTATATCAT
1 GATGCCATAGCATCTTTCAGCTAT-GTCTTACTCATTT-TACCAT
*
25403452 GATGCCATAGCATCTTTCAGCTATAATCTTACTCATTTTA
1 GATGCCATAGCATCTTTCAGCTAT-GTCTTACTCATTTTA
25403492 AGCACACAAC
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
44 5 0.07
45 65 0.93
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.39
Consensus pattern (43 bp):
GATGCCATAGCATCTTTCAGCTATGTCTTACTCATTTTACCAT
Found at i:25411175 original size:26 final size:26
Alignment explanation
Indices: 25411139--25411192 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
25411129 TTTAGAAAGG
25411139 ACTGAGTCACCAACCTGATATTGCAT
1 ACTGAGTCACCAACCTGATATTGCAT
25411165 ACTGAGTCACCAACCTGATATTGCAT
1 ACTGAGTCACCAACCTGATATTGCAT
25411191 AC
1 AC
25411193 CCCTTCGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (26 bp):
ACTGAGTCACCAACCTGATATTGCAT
Found at i:25420626 original size:23 final size:23
Alignment explanation
Indices: 25420583--25420727 Score: 155
Period size: 23 Copynumber: 6.3 Consensus size: 23
25420573 ATAAGTGCCA
** *
25420583 CACTGATATGTAGTTGAAGCTAC
1 CACTGATATGTAGCCGTAGCTAC
* *
25420606 CATTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGTAGCTAC
* * *
25420629 CACTGAAATGTAGCCGAAACTAC
1 CACTGATATGTAGCCGTAGCTAC
* *
25420652 CACTAATATGTAGTCGTAGCTAC
1 CACTGATATGTAGCCGTAGCTAC
* * **
25420675 CACTGAAATGTAGTCAAAGCTAC
1 CACTGATATGTAGCCGTAGCTAC
*
25420698 CACTGATATATAGCCGTAGCTAC
1 CACTGATATGTAGCCGTAGCTAC
25420721 CACTGAT
1 CACTGAT
25420728 CAATAACACT
Statistics
Matches: 98, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 98 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (23 bp):
CACTGATATGTAGCCGTAGCTAC
Found at i:25420652 original size:46 final size:46
Alignment explanation
Indices: 25420583--25420726 Score: 191
Period size: 46 Copynumber: 3.1 Consensus size: 46
25420573 ATAAGTGCCA
* * * * *
25420583 CACTGATATGTAGTTGAAGCTACCATTGATACGTAGCCGTAGCTAC
1 CACTGAAATGTAGTCGAAACTACCACTGATATGTAGCCGTAGCTAC
* * *
25420629 CACTGAAATGTAGCCGAAACTACCACTAATATGTAGTCGTAGCTAC
1 CACTGAAATGTAGTCGAAACTACCACTGATATGTAGCCGTAGCTAC
*
25420675 CACTGAAATGTAGTC-AAAGCTACCACTGATATATAGCCGTAGCTAC
1 CACTGAAATGTAGTCGAAA-CTACCACTGATATGTAGCCGTAGCTAC
25420721 CACTGA
1 CACTGA
25420727 TCAATAACAC
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 3 0.04
46 82 0.96
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (46 bp):
CACTGAAATGTAGTCGAAACTACCACTGATATGTAGCCGTAGCTAC
Found at i:25420990 original size:18 final size:20
Alignment explanation
Indices: 25420967--25421003 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
25420957 TTCAATAATA
25420967 ATAATTCA-CATAT-CAAAT
1 ATAATTCACCATATACAAAT
25420985 ATAATTCACCATATACAAA
1 ATAATTCACCATATACAAA
25421004 AAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAATTCACCATATACAAAT
Found at i:25433873 original size:25 final size:25
Alignment explanation
Indices: 25433845--25433926 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
25433835 AACTTGTGTG
*
25433845 AGCATACTGATTTATAGCTCGTGAT
1 AGCATACCGATTTATAGCTCGTGAT
* * * *
25433870 AGCATACCAATCTATAGCTCGAGAA
1 AGCATACCGATTTATAGCTCGTGAT
*
25433895 AGCATACCGATTCATAGCTCGT-AT
1 AGCATACCGATTTATAGCTCGTGAT
25433919 GAGCATAC
1 -AGCATAC
25433927 TTGTACATGA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
24 1 0.02
25 45 0.98
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (25 bp):
AGCATACCGATTTATAGCTCGTGAT
Found at i:25448035 original size:24 final size:24
Alignment explanation
Indices: 25447976--25448032 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
25447966 AAATTATCAA
25447976 ATTGGGTTTTAAATATTAATGAGT
1 ATTGGGTTTTAAATATTAATGAGT
25448000 ATTGGGTTTTAAATATTAATGAGT
1 ATTGGGTTTTAAATATTAATGAGT
25448024 -TTGGGTTTT
1 ATTGGGTTTT
25448033 TAAGAGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 9 0.27
24 24 0.73
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (24 bp):
ATTGGGTTTTAAATATTAATGAGT
Found at i:25451451 original size:24 final size:27
Alignment explanation
Indices: 25451414--25451470 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
25451404 TTTTTATTTT
25451414 TATTTTTTAAAATATT-TAAAATAT-TA
1 TATTTTTT-AAATATTATAAAATATATA
*
25451440 TATTTTTT-AATATTATTAAATATATA
1 TATTTTTTAAATATTATAAAATATATA
25451466 TATTT
1 TATTT
25451471 AATTATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 6 0.21
25 7 0.25
26 15 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATTTTTTAAATATTATAAAATATATA
Found at i:25451519 original size:22 final size:22
Alignment explanation
Indices: 25451494--25451537 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25451484 TAGTCATATA
25451494 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
25451516 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
25451538 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:25451640 original size:15 final size:15
Alignment explanation
Indices: 25451620--25451675 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
25451610 ATTCAATATT
25451620 AATATTTTAATAATA
1 AATATTTTAATAATA
*
25451635 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
25451654 AATATATTAATAATA
1 AATATTTTAATAATA
25451669 AAT-TTTT
1 AATATTTT
25451676 TGTAGTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
14 3 0.09
15 13 0.39
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:25452041 original size:28 final size:27
Alignment explanation
Indices: 25452009--25452067 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 27
25451999 ATCTCAAATG
25452009 TATGTTTGTTTCATTGAAAACAACTTT
1 TATGTTTGTTTCATTGAAAACAACTTT
25452036 ATATGTTTGTTTCATTGAAAACAACTTT
1 -TATGTTTGTTTCATTGAAAACAACTTT
25452064 TATG
1 TATG
25452068 AAATATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (27 bp):
TATGTTTGTTTCATTGAAAACAACTTT
Found at i:25455247 original size:14 final size:14
Alignment explanation
Indices: 25455224--25455263 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
25455214 ACAGAAAAGT
*
25455224 AAAACATTTTTCAG
1 AAAACATTTTACAG
* *
25455238 AAATCATTTTACGG
1 AAAACATTTTACAG
25455252 AAAACATTTTAC
1 AAAACATTTTAC
25455264 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:25455247 original size:34 final size:35
Alignment explanation
Indices: 25455189--25455255 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
25455179 CAAACATCAG
* *
25455189 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
25455224 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
25455256 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:25459031 original size:21 final size:19
Alignment explanation
Indices: 25459005--25459059 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
25458995 TTACACGACA
25459005 TTGTGGATAAACCACTCATCG
1 TTGTGGATAAACCAC-C-TCG
*
25459026 TTGTGGATGAACCA-CTCG
1 TTGTGGATAAACCACCTCG
*
25459044 TTGCGGATAAACCACC
1 TTGTGGATAAACCACC
25459060 AGTAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 15 0.50
19 2 0.07
21 13 0.43
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (19 bp):
TTGTGGATAAACCACCTCG
Found at i:25459229 original size:24 final size:23
Alignment explanation
Indices: 25459172--25459239 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
25459162 AGCTGCCAGT
*
25459172 ACAGTGTGG-TTAAACCACTCAA
1 ACAGTGTGGATAAAACCACTCAA
* ** *
25459194 ACAATGAAGATAAAAGCTACTCAA
1 ACAGTGTGGATAAAA-CCACTCAA
25459218 ACAGTGTGGAT-AAACCACTCAA
1 ACAGTGTGGATAAAACCACTCAA
25459240 TAGTACAGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
22 13 0.37
23 7 0.20
24 15 0.43
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (23 bp):
ACAGTGTGGATAAAACCACTCAA
Found at i:25469055 original size:26 final size:26
Alignment explanation
Indices: 25469025--25469076 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
25469015 GGGTCGGTAG
25469025 GTTTACCTAGACCCCTAATTGACTGA
1 GTTTACCTAGACCCCTAATTGACTGA
25469051 GTTTACCTAGACCCCTAATTGACTGA
1 GTTTACCTAGACCCCTAATTGACTGA
25469077 AATGACTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (26 bp):
GTTTACCTAGACCCCTAATTGACTGA
Found at i:25476104 original size:24 final size:23
Alignment explanation
Indices: 25476067--25476144 Score: 81
Period size: 24 Copynumber: 3.5 Consensus size: 23
25476057 TGGTGTGGTT
*
25476067 AAACCACTCAAATGGTGCAGATA
1 AAACTACTCAAATGGTGCAGATA
***
25476090 AAAGCTACTCAAATGGTATGGATA
1 AAA-CTACTCAAATGGTGCAGATA
*
25476114 AAAC-ACTC-AACGGTGCAGAT-
1 AAACTACTCAAATGGTGCAGATA
25476134 AAACTACTCAA
1 AAACTACTCAA
25476145 CTTCCTCCGT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
20 4 0.09
21 12 0.27
22 5 0.11
23 4 0.09
24 19 0.43
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.19
Consensus pattern (23 bp):
AAACTACTCAAATGGTGCAGATA
Found at i:25476106 original size:46 final size:43
Alignment explanation
Indices: 25476056--25476144 Score: 115
Period size: 46 Copynumber: 2.0 Consensus size: 43
25476046 AGTAGCTAGT
* * * *
25476056 ATGGTGTGGTTAAACCACTCAAATGGTGCAGATAAAAGCTACTCAA
1 ATGGTATGGATAAAACACTC-AACGGTGCAGAT-AAA-CTACTCAA
25476102 ATGGTATGGATAAAACACTCAACGGTGCAGATAAACTACTCAA
1 ATGGTATGGATAAAACACTCAACGGTGCAGATAAACTACTCAA
25476145 CTTCCTCCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
43 8 0.21
44 3 0.08
45 11 0.28
46 17 0.44
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (43 bp):
ATGGTATGGATAAAACACTCAACGGTGCAGATAAACTACTCAA
Found at i:25476320 original size:34 final size:35
Alignment explanation
Indices: 25476245--25476320 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 35
25476235 GAACATTACG
*
25476245 GTAGC-AATCATTAAGCTTATAGCAATTCGATTCA
1 GTAGCAAATCATTAAGCTTATAACAATTCGATTCA
* *
25476279 GTGGCAAAT-ATTAAGCTTATAACAGATT-GATTTA
1 GTAGCAAATCATTAAGCTTATAACA-ATTCGATTCA
25476313 GTAGCAAA
1 GTAGCAAA
25476321 AGGCATGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 30 0.83
35 6 0.17
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (35 bp):
GTAGCAAATCATTAAGCTTATAACAATTCGATTCA
Found at i:25479644 original size:22 final size:23
Alignment explanation
Indices: 25479619--25479667 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
25479609 CTTTGGCATG
25479619 AACAGTAAA-ATTCTCTAACATC
1 AACAGTAAATATTCTCTAACATC
* *
25479641 AACAGTAAATATTCTCTAGCATG
1 AACAGTAAATATTCTCTAACATC
25479664 AACA
1 AACA
25479668 CTGAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (23 bp):
AACAGTAAATATTCTCTAACATC
Found at i:25479681 original size:45 final size:44
Alignment explanation
Indices: 25479597--25479682 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 44
25479587 AAGACGAATG
* * * *
25479597 AACAATAAAATTCTTTGGCATGAACAGTAAAATTCTCTAACATC
1 AACAATAAAATTCTCTAGCATGAACACTAAAATTATCTAACATC
*
25479641 AACAGTAAATATTCTCTAGCATGAACACTGAAAA-TATCTAAC
1 AACAATAAA-ATTCTCTAGCATGAACACT-AAAATTATCTAAC
25479683 TGGAACGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 8 0.23
45 23 0.66
46 4 0.11
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (44 bp):
AACAATAAAATTCTCTAGCATGAACACTAAAATTATCTAACATC
Found at i:25506191 original size:22 final size:23
Alignment explanation
Indices: 25506151--25506199 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
25506141 ATATTTACAT
* * *
25506151 AAAAATTAAACTAAGTAAAAGTA
1 AAAAAATAAACTAAATAAAAATA
25506174 AAAAAATAAA-TAAATAAAAATA
1 AAAAAATAAACTAAATAAAAATA
25506196 AAAA
1 AAAA
25506200 CAAAACTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (23 bp):
AAAAAATAAACTAAATAAAAATA
Found at i:25507140 original size:48 final size:45
Alignment explanation
Indices: 25507068--25507164 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 45
25507058 GCACCAAAAG
* * *
25507068 AAAACAAACAAAAAAATAAAAAAATTATATATTGATCAAAGTTTAAA
1 AAAACAAACAAAAAAAAAAAAAAATT-TAGAAT-ATCAAAGTTTAAA
*
25507115 AAAAGCAAA-AAAAAAACAAAAAAAATTTCGAATATCAAAGTTTAAA
1 AAAA-CAAACAAAAAAA-AAAAAAAATTTAGAATATCAAAGTTTAAA
25507161 AAAA
1 AAAA
25507165 TTTCGAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
46 17 0.39
47 14 0.32
48 13 0.30
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (45 bp):
AAAACAAACAAAAAAAAAAAAAAATTTAGAATATCAAAGTTTAAA
Found at i:25540416 original size:11 final size:11
Alignment explanation
Indices: 25540400--25540440 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
25540390 ACGAGATTGT
25540400 AAAAAAATTTG
1 AAAAAAATTTG
*
25540411 AAAAAAATTCG
1 AAAAAAATTTG
*
25540422 AAAAAATTTTG
1 AAAAAAATTTG
25540433 AAAAAAAT
1 AAAAAAAT
25540441 AAAAAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.24
Consensus pattern (11 bp):
AAAAAAATTTG
Found at i:25540447 original size:22 final size:21
Alignment explanation
Indices: 25540400--25540448 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
25540390 ACGAGATTGT
**
25540400 AAAAAAATTTGAAAAAAATTCG
1 AAAAAAATTTGAAAAAAA-TAA
*
25540422 AAAAAATTTTGAAAAAAATAA
1 AAAAAAATTTGAAAAAAATAA
25540443 AAAAAA
1 AAAAAA
25540449 TTAATTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.20
Consensus pattern (21 bp):
AAAAAAATTTGAAAAAAATAA
Found at i:25543586 original size:20 final size:19
Alignment explanation
Indices: 25543557--25543594 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
25543547 AACATTTTCG
*
25543557 ATTCAGCTCATTCGAGCTCA
1 ATTCAACTCATT-GAGCTCA
25543577 ATTCAACTCATTGAGCTC
1 ATTCAACTCATTGAGCTC
25543595 GTTACTAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (19 bp):
ATTCAACTCATTGAGCTCA
Found at i:25550322 original size:15 final size:15
Alignment explanation
Indices: 25550302--25550356 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
25550292 GCTCTCATCA
*
25550302 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
25550317 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
25550332 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
25550346 TTCTTTT-TCTC
1 TTCTTTTCTCTC
25550357 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:25551148 original size:19 final size:19
Alignment explanation
Indices: 25551124--25551173 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
25551114 GTCCAAACTG
25551124 AATTAATTAGACTTAGTTT
1 AATTAATTAGACTTAGTTT
** *
25551143 AATTAATTGAGTTTTATTTT
1 AATTAATT-AGACTTAGTTT
*
25551163 AATTATTTAGA
1 AATTAATTAGA
25551174 TTAATGTTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (19 bp):
AATTAATTAGACTTAGTTT
Found at i:25552046 original size:10 final size:10
Alignment explanation
Indices: 25552031--25552092 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
25552021 TTTGAACCAT
*
25552031 TACCAATTCG
1 TACCAATTCA
*
25552041 TACCAAATACCA
1 TACC-AAT-TCA
*
25552053 TACCATTTCA
1 TACCAATTCA
25552063 TACCAATTCCA
1 TACCAATT-CA
* *
25552074 TACCATTTCG
1 TACCAATTCA
25552084 TACCAATTC
1 TACCAATTC
25552093 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:25552076 original size:21 final size:21
Alignment explanation
Indices: 25552031--25552093 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
25552021 TTTGAACCAT
* *
25552031 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
25552053 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
25552074 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
25552094 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:25552411 original size:14 final size:13
Alignment explanation
Indices: 25552392--25552426 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
25552382 ATAGGTACGT
*
25552392 AAAAAAAAGTTCG
1 AAAAAAAAATTCG
*
25552405 AAAAAAAAATTTG
1 AAAAAAAAATTCG
25552418 AAAAAAAAA
1 AAAAAAAAA
25552427 CAAAAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:25552455 original size:18 final size:17
Alignment explanation
Indices: 25552404--25552475 Score: 82
Period size: 18 Copynumber: 4.5 Consensus size: 17
25552394 AAAAAAGTTC
25552404 GAAAAAAAAATTTGAAA
1 GAAAAAAAAATTTGAAA
*
25552421 -AAAAAACAA----AAA
1 GAAAAAAAAATTTGAAA
*
25552433 CAAAAAAAAATTTCGAAA
1 GAAAAAAAAATTT-GAAA
25552451 GAAAAAAAAATTTGAAA
1 GAAAAAAAAATTTGAAA
25552468 GAAAAAAA
1 GAAAAAAA
25552476 TTGTATACGG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 3 0.07
13 8 0.17
16 8 0.17
17 12 0.26
18 15 0.33
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.12
Consensus pattern (17 bp):
GAAAAAAAAATTTGAAA
Found at i:25568217 original size:10 final size:10
Alignment explanation
Indices: 25568202--25568263 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
25568192 TTTGAACCAT
*
25568202 TACCAATTCG
1 TACCAATTCA
*
25568212 TACCAAATACCA
1 TACC-AAT-TCA
*
25568224 TACCATTTCA
1 TACCAATTCA
25568234 TACCAATTCCA
1 TACCAATT-CA
* *
25568245 TACCATTTCG
1 TACCAATTCA
25568255 TACCAATTC
1 TACCAATTC
25568264 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:25568247 original size:21 final size:21
Alignment explanation
Indices: 25568202--25568264 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
25568192 TTTGAACCAT
* *
25568202 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
25568224 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
25568245 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
25568265 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:25570305 original size:12 final size:12
Alignment explanation
Indices: 25570288--25570329 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
25570278 GAATACAAAC
25570288 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
25570300 TTTTTTTTCGAA
1 TTTTTTTTTGAA
25570312 --TTTTTTTG-A
1 TTTTTTTTTGAA
25570321 TTTTTTTTT
1 TTTTTTTTT
25570330 CAATCTCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 1 0.04
10 7 0.27
11 7 0.27
12 11 0.42
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:25575939 original size:22 final size:23
Alignment explanation
Indices: 25575887--25575952 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
25575877 TATTTGGGAA
* *
25575887 TTGGTATGAAACGGTAA-GGTAT
1 TTGGTACGAAATGGTAATGGTAT
**
25575909 TTGAAACGAAATGGTAATGG-AT
1 TTGGTACGAAATGGTAATGGTAT
*
25575931 TTGGTACGAAAATGGAAATGGT
1 TTGGTACG-AAATGGTAATGGT
25575953 TCAAAAGGCC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.29
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTAT
Found at i:25581283 original size:14 final size:14
Alignment explanation
Indices: 25581253--25581282 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
25581243 CAATTTTTCA
25581253 TTCACTTTTTCTTT
1 TTCACTTTTTCTTT
25581267 TTCATCTTTTTCTTT
1 TTCA-CTTTTTCTTT
25581282 T
1 T
25581283 CTCGCTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCACTTTTTCTTT
Found at i:25581338 original size:19 final size:20
Alignment explanation
Indices: 25581301--25581345 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
25581291 CTTTTCATTC
25581301 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTGAATTTTCTTT
*
25581320 TCTTTTTTT-CATTTGTCTTT
1 TCTTTTTTTGAATTT-TCTTT
25581340 TCTTTT
1 TCTTTT
25581346 GTATTTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 11 0.48
20 8 0.35
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (20 bp):
TCTTTTTTTGAATTTTCTTT
Found at i:25583601 original size:21 final size:22
Alignment explanation
Indices: 25583567--25583618 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
25583557 TATACAATTT
*
25583567 TTTTCTTTTGAAATTTTTTTTG-
1 TTTT-TTTTCAAATTTTTTTTGA
25583589 TTTTTTTTCAAATTTTTTTTGA
1 TTTTTTTTCAAATTTTTTTTGA
*
25583611 ATTTTTTT
1 TTTTTTTT
25583619 ACGTACCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75
Consensus pattern (22 bp):
TTTTTTTTCAAATTTTTTTTGA
Found at i:25584176 original size:13 final size:13
Alignment explanation
Indices: 25584158--25584183 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25584148 ATTGAGTTTA
25584158 AATGTGTCTTAGT
1 AATGTGTCTTAGT
25584171 AATGTGTCTTAGT
1 AATGTGTCTTAGT
25584184 TCATACATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
AATGTGTCTTAGT
Found at i:25585845 original size:13 final size:12
Alignment explanation
Indices: 25585829--25585876 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
25585819 AAAAAAAGGG
25585829 AAAAAAATTCGAAA
1 AAAAAAATTC--AA
*
25585843 AAAAAAATTTTAA
1 AAAAAAA-TTCAA
25585856 AAAAAAATTCAA
1 AAAAAAATTCAA
25585868 AAAAAAATT
1 AAAAAAATT
25585877 TGTATTCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 13 0.42
13 9 0.29
14 7 0.23
15 2 0.06
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:25585846 original size:14 final size:13
Alignment explanation
Indices: 25585829--25585874 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
25585819 AAAAAAAGGG
25585829 AAAAAAATTCGAAA
1 AAAAAAATTC-AAA
**
25585843 AAAAAAATTTTAA
1 AAAAAAATTCAAA
25585856 AAAAAAATTCAAA
1 AAAAAAATTCAAA
25585869 AAAAAA
1 AAAAAA
25585875 TTTGTATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 19 0.68
14 9 0.32
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.17
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:25586886 original size:17 final size:15
Alignment explanation
Indices: 25586866--25586904 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
25586856 GCGAGCGAGA
25586866 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
25586883 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
25586898 AAGATGA
1 AA-ATGA
25586905 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:25608081 original size:21 final size:23
Alignment explanation
Indices: 25608036--25608082 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
25608026 TCACCTGCAA
* *
25608036 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
25608059 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
25608080 TAA
1 TAA
25608083 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:25613148 original size:36 final size:36
Alignment explanation
Indices: 25613078--25613148 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
25613068 CCAAGTGATC
*
25613078 TGGAGAGTGACCAAGCATCGAACCAAAGTAAACGAG
1 TGGAGAGTGACCAAGCATCGAACCAAAGCAAACGAG
* * *
25613114 TGGAGAGTGACCAAGCATCTAACCGAAGCGAACGA
1 TGGAGAGTGACCAAGCATCGAACCAAAGCAAACGA
25613149 TGACGTGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.21, G:0.28, T:0.11
Consensus pattern (36 bp):
TGGAGAGTGACCAAGCATCGAACCAAAGCAAACGAG
Found at i:25614721 original size:20 final size:19
Alignment explanation
Indices: 25614698--25614762 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
25614688 AAGCTCAAAC
25614698 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
25614718 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
25614738 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
25614758 GAGCT
1 GAGCT
25614763 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:25620365 original size:19 final size:18
Alignment explanation
Indices: 25620329--25620368 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25620319 TTTCCACTCG
*
25620329 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
25620347 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
25620366 TTT
1 TTT
25620369 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:25621444 original size:14 final size:13
Alignment explanation
Indices: 25621425--25621461 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
25621415 ACTACCTCTC
25621425 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
25621438 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
25621451 TTTTTTTTTCA
1 TTTTTTTTTCA
25621462 CAACTTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:25621519 original size:12 final size:12
Alignment explanation
Indices: 25621502--25621550 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
25621492 TGGAAACTAG
25621502 TTTTTTTTCGAT
1 TTTTTTTTCGAT
*
25621514 TTTTTTTTTGAATT
1 TTTTTTTTCG-A-T
*
25621528 TTTTTTTTCGAG
1 TTTTTTTTCGAT
25621540 TTTTTTTTCGA
1 TTTTTTTTCGA
25621551 GAAACTACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 20 0.62
13 2 0.06
14 10 0.31
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.73
Consensus pattern (12 bp):
TTTTTTTTCGAT
Found at i:25621520 original size:13 final size:13
Alignment explanation
Indices: 25621502--25621547 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
25621492 TGGAAACTAG
25621502 TTTTTTTTCGATT
1 TTTTTTTTCGATT
25621515 TTTTTTTT-GAATT
1 TTTTTTTTCG-ATT
*
25621528 TTTTTTTTCGAGT
1 TTTTTTTTCGATT
25621541 TTTTTTT
1 TTTTTTT
25621548 CGAGAAACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 1 0.03
13 28 0.93
14 1 0.03
ACGTcount: A:0.09, C:0.04, G:0.09, T:0.78
Consensus pattern (13 bp):
TTTTTTTTCGATT
Found at i:25627296 original size:13 final size:12
Alignment explanation
Indices: 25627257--25627374 Score: 64
Period size: 12 Copynumber: 9.8 Consensus size: 12
25627247 TTTCATCTTC
25627257 TTCTTTTTC-AT
1 TTCTTTTTCAAT
25627268 TTC--TTTCAAT
1 TTCTTTTTCAAT
25627278 TTCTTTTTCAAT
1 TTCTTTTTCAAT
*
25627290 GTTCTTTTCTTCATT
1 -TTC-TTT-TTCAAT
**
25627305 TTCTTTTTCTCT
1 TTCTTTTTCAAT
** **
25627317 CACTTTTTTGAT
1 TTCTTTTTCAAT
**
25627329 TTCTTTTTCTTT
1 TTCTTTTTCAAT
*
25627341 TTCATTTTTC-TT
1 TTC-TTTTTCAAT
**
25627353 TTCTTTTTCTTT
1 TTCTTTTTCAAT
25627365 TTCTTTTTCA
1 TTCTTTTTCA
25627375 CTACAATGTG
Statistics
Matches: 85, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
9 4 0.05
10 5 0.06
11 9 0.11
12 44 0.52
13 12 0.14
14 6 0.07
15 5 0.06
ACGTcount: A:0.08, C:0.19, G:0.02, T:0.71
Consensus pattern (12 bp):
TTCTTTTTCAAT
Found at i:25627312 original size:15 final size:14
Alignment explanation
Indices: 25627243--25627357 Score: 53
Period size: 15 Copynumber: 8.1 Consensus size: 14
25627233 TTTTTCTAAC
*
25627243 TCATTTTCATCTTCT
1 TCATTTTC-TTTTCT
* *
25627258 TCTTTTTCATTTCTT
1 TCATTTTCTTTTC-T
*
25627273 TCAATTTC-TTT-T
1 TCATTTTCTTTTCT
*
25627285 TCAATGTTCTTTTCT
1 TC-ATTTTCTTTTCT
25627300 TCATTTTCTTTTTCT
1 TCATTTTC-TTTTCT
*
25627315 CTCACTTTT-TTGAT-T
1 -TCA-TTTTCTT-TTCT
*
25627330 TCTTTTTC-TTT-T
1 TCATTTTCTTTTCT
25627342 TCATTTTTCTTTTCT
1 TCA-TTTTCTTTTCT
25627357 T
1 T
25627358 TTTCTTTTTC
Statistics
Matches: 76, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
12 7 0.09
13 14 0.18
14 19 0.25
15 28 0.37
16 4 0.05
17 4 0.05
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.69
Consensus pattern (14 bp):
TCATTTTCTTTTCT
Found at i:25627339 original size:30 final size:30
Alignment explanation
Indices: 25627303--25627374 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
25627293 CTTTTCTTCA
25627303 TTTTCTTTTTC-TCTCACTTTT-TTGATTTCT
1 TTTTCTTTTTCATCTCACTTTTCTT--TTTCT
* **
25627333 TTTTCTTTTTCATTTTTCTTTTCTTTTTCT
1 TTTTCTTTTTCATCTCACTTTTCTTTTTCT
25627363 TTTTCTTTTTCA
1 TTTTCTTTTTCA
25627375 CTACAATGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 28 0.76
31 7 0.19
32 2 0.05
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (30 bp):
TTTTCTTTTTCATCTCACTTTTCTTTTTCT
Found at i:25627354 original size:5 final size:6
Alignment explanation
Indices: 25627328--25627373 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
25627318 ACTTTTTTGA
25627328 TTTCTT TTTCTT TTTCATT TTTC-T TTTCTT TTTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
25627374 ACTACAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.13
6 27 0.71
7 6 0.16
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:25628240 original size:18 final size:16
Alignment explanation
Indices: 25628219--25628253 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
25628209 CACTTCTTCT
25628219 TTTTTTTTATACTTTTCG
1 TTTTTTTTA-A-TTTTCG
25628237 TTTTTTTTAATTTTCG
1 TTTTTTTTAATTTTCG
25628253 T
1 T
25628254 AACTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.11, C:0.09, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTTTTTAATTTTCG
Found at i:25636113 original size:23 final size:23
Alignment explanation
Indices: 25636085--25636189 Score: 102
Period size: 23 Copynumber: 4.6 Consensus size: 23
25636075 GGGTTTGTTA
25636085 CGAAATGGTAATGTGATTTGGTT
1 CGAAATGGTAATGTGATTTGGTT
* ** *
25636108 CAAAATGGTAATACGATTTGGTA
1 CGAAATGGTAATGTGATTTGGTT
* * *
25636131 CGAATTGGTAAGGTAATTTGGTT
1 CGAAATGGTAATGTGATTTGGTT
** * *
25636154 CGAAATGGTAATACGATTTAGTA
1 CGAAATGGTAATGTGATTTGGTT
*
25636177 CGAAATGTTAATG
1 CGAAATGGTAATG
25636190 GTTCAAAAAG
Statistics
Matches: 62, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.34
Consensus pattern (23 bp):
CGAAATGGTAATGTGATTTGGTT
Found at i:25636140 original size:46 final size:46
Alignment explanation
Indices: 25636078--25636189 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 46
25636068 CGGTTTTGGG
* *
25636078 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTAATTTGGTTCAAAATGGTAATACGA
* * *
25636124 TTTGGTACGAATTGGTAAGGTAATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTAATTTGGTTCAAAATGGTAATACGA
* *
25636170 TTTAGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
25636190 GTTCAAAAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTAATTTGGTTCAAAATGGTAATACGA
Found at i:25640373 original size:16 final size:15
Alignment explanation
Indices: 25640339--25640389 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
25640329 TTTCAATCAC
25640339 TTTTTCTTTT-TCAT
1 TTTTTCTTTTCTCAT
*
25640353 CTTTTGCTTTTCTCAT
1 -TTTTTCTTTTCTCAT
25640369 TTTTT-TTCATTCTCAT
1 TTTTTCTT--TTCTCAT
25640385 TTTTT
1 TTTTT
25640390 GAATTTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 2 0.06
15 13 0.42
16 16 0.52
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTTCTTTTCTCAT
Found at i:25640405 original size:18 final size:18
Alignment explanation
Indices: 25640384--25640442 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
25640374 TTCATTCTCA
25640384 TTTTTTGAATTTTCTTTC
1 TTTTTTGAATTTTCTTTC
* *
25640402 TTTTTTTCATTTTTCTTT-
1 -TTTTTTGAATTTTCTTTC
* *
25640420 TCTTTTGTATTTTCTTTTC
1 TTTTTTGAATTTTC-TTTC
25640439 TTTT
1 TTTT
25640443 CTTTTTCTCT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
17 10 0.32
18 3 0.10
19 18 0.58
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTTGAATTTTCTTTC
Found at i:25648394 original size:17 final size:17
Alignment explanation
Indices: 25648361--25648394 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25648351 AGACCGTATG
**
25648361 CAATTTTTTTTTCTTTT
1 CAATTTTTTTTGATTTT
25648378 CAATTTTTTTTGATTTT
1 CAATTTTTTTTGATTTT
25648395 TTTTTCGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (17 bp):
CAATTTTTTTTGATTTT
Found at i:25648739 original size:23 final size:23
Alignment explanation
Indices: 25648711--25648815 Score: 111
Period size: 23 Copynumber: 4.6 Consensus size: 23
25648701 GGGTTTGTTA
25648711 CGAAATGGTAATGTGATTTGGTT
1 CGAAATGGTAATGTGATTTGGTT
* ** *
25648734 CAAAATGGTAATACGATTTGGTA
1 CGAAATGGTAATGTGATTTGGTT
* *
25648757 CGAATTGGTAAGGTGATTTGGTT
1 CGAAATGGTAATGTGATTTGGTT
** * *
25648780 CGAAATGGTAATACGATTTAGTA
1 CGAAATGGTAATGTGATTTGGTT
*
25648803 CGAAATGTTAATG
1 CGAAATGGTAATG
25648816 GTTCAAAAAG
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (23 bp):
CGAAATGGTAATGTGATTTGGTT
Found at i:25648766 original size:46 final size:46
Alignment explanation
Indices: 25648704--25648815 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
25648694 CGGTTTTGGG
*
25648704 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* * *
25648750 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* *
25648796 TTTAGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
25648816 GTTCAAAAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
Found at i:25665325 original size:30 final size:30
Alignment explanation
Indices: 25665274--25665332 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
25665264 ACTTTAATAC
*
25665274 GAGCTGAATTAACTTCCATTTCAGCTCAAT
1 GAGCTGAATTAACTTCAATTTCAGCTCAAT
*
25665304 GAGCTCGAATTAGC-TCAATTTCAGCTCAA
1 GAGCT-GAATTAACTTCAATTTCAGCTCAA
25665333 ACATTTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (30 bp):
GAGCTGAATTAACTTCAATTTCAGCTCAAT
Found at i:25666491 original size:22 final size:22
Alignment explanation
Indices: 25666463--25666506 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25666453 TTTTGAACCA
25666463 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
25666485 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
25666507 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:25679677 original size:25 final size:25
Alignment explanation
Indices: 25679584--25679670 Score: 95
Period size: 25 Copynumber: 3.5 Consensus size: 25
25679574 TCCTATATAT
* * *
25679584 GTATGCTCATACGAGCTGTGAATCC
1 GTATGCTCACACGAGCTGTAAATCG
* * *
25679609 GTATGCTCACTCAAGCTGTAGATCG
1 GTATGCTCACACGAGCTGTAAATCG
*
25679634 GTATGCT-ATCACGAGTTGTAAATCG
1 GTATGCTCA-CACGAGCTGTAAATCG
25679659 GTATGCTCACAC
1 GTATGCTCACAC
25679671 TAGTTGTGGG
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
24 1 0.02
25 48 0.96
26 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATCG
Found at i:25683428 original size:15 final size:15
Alignment explanation
Indices: 25683410--25683440 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
25683400 CAAATGAACC
25683410 TTGTAGAGGTGAATG
1 TTGTAGAGGTGAATG
25683425 TTGTAGAGGTGAATG
1 TTGTAGAGGTGAATG
25683440 T
1 T
25683441 ACCGTCAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.39, T:0.35
Consensus pattern (15 bp):
TTGTAGAGGTGAATG
Found at i:25684090 original size:20 final size:19
Alignment explanation
Indices: 25684026--25684090 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
25684016 TATAAACGCA
25684026 AATGAGCTTAAAATGAGCTG
1 AATGAGC-TAAAATGAGCTG
* *
25684046 ATTGAGCTAAGAGTGAGCTTG
1 AATGAGCTAA-AATGAGC-TG
25684067 -ATGAGCTAAAATTGAGCTG
1 AATGAGCTAAAA-TGAGCTG
25684086 AATGA
1 AATGA
25684091 ACTTGAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 6 0.16
20 29 0.78
21 2 0.05
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (19 bp):
AATGAGCTAAAATGAGCTG
Found at i:25689156 original size:20 final size:20
Alignment explanation
Indices: 25689128--25689203 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
25689118 AGCTTATTTT
* *
25689128 TTAGTTCATTCAAGCTCAAA
1 TTAGCTCATTCGAGCTCAAA
*
25689148 TTAGCTCATTCGAGCTCAAG
1 TTAGCTCATTCGAGCTCAAA
*
25689168 TCAGCTCATTCGAGCTC-AA
1 TTAGCTCATTCGAGCTCAAA
*
25689187 TTCAACTCATT-GAGCTC
1 TT-AGCTCATTCGAGCTC
25689204 GTTATTAGCT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
19 8 0.17
20 40 0.83
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (20 bp):
TTAGCTCATTCGAGCTCAAA
Found at i:25689163 original size:10 final size:10
Alignment explanation
Indices: 25689150--25689203 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
25689140 AGCTCAAATT
25689150 AGCTCATTCG
1 AGCTCATTCG
*
25689160 AGCTCAAGTC-
1 AGCTC-ATTCG
25689170 AGCTCATTCG
1 AGCTCATTCG
25689180 AGCTCAATTC-
1 AGCTC-ATTCG
*
25689190 AACTCATT-G
1 AGCTCATTCG
25689199 AGCTC
1 AGCTC
25689204 GTTATTAGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
9 10 0.28
10 19 0.53
11 7 0.19
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (10 bp):
AGCTCATTCG
Found at i:25694104 original size:22 final size:22
Alignment explanation
Indices: 25694052--25694115 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
25694042 TATTTGGGAA
* *
25694052 TTGGTACGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
25694074 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
25694096 TTGGTACGAAATGGAAATGG
1 TTGGTACGAAATGGTAATGG
25694116 TTCAAAAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:25698004 original size:10 final size:10
Alignment explanation
Indices: 25697989--25698026 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
25697979 CCGTATACAA
*
25697989 TTTTTTTCCT
1 TTTTTTTCAT
*
25697999 TTTTTTTCAA
1 TTTTTTTCAT
25698009 TTTTTTT-AT
1 TTTTTTTCAT
25698018 TTTTTTTCA
1 TTTTTTTCA
25698027 CGAGTCTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:25698011 original size:20 final size:19
Alignment explanation
Indices: 25697986--25698026 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
25697976 AGACCGTATA
*
25697986 CAATTTTTTTCCTTTTTTTT
1 CAATTTTTTT-ATTTTTTTT
25698006 CAATTTTTTTATTTTTTTT
1 CAATTTTTTTATTTTTTTT
25698025 CA
1 CA
25698027 CGAGTCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (19 bp):
CAATTTTTTTATTTTTTTT
Found at i:25698346 original size:24 final size:23
Alignment explanation
Indices: 25698292--25698347 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
25698282 GATTAATTAA
**
25698292 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
25698315 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
25698339 GAAATGGTA
1 GAAATGGTA
25698348 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:25701309 original size:12 final size:12
Alignment explanation
Indices: 25701292--25701321 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
25701282 TCAATGAGTT
25701292 ACACGGCCTAGC
1 ACACGGCCTAGC
*
25701304 ACACGGCCTGGC
1 ACACGGCCTAGC
25701316 ACACGG
1 ACACGG
25701322 GCGTGTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:25708892 original size:30 final size:31
Alignment explanation
Indices: 25708853--25708912 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
25708843 GGAGGTGGGA
*
25708853 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
25708884 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
25708913 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:25709144 original size:9 final size:9
Alignment explanation
Indices: 25709127--25709163 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
25709117 TATAGTTTGA
25709127 TATTCGAAT
1 TATTCGAAT
*
25709136 TATTTGAAT
1 TATTCGAAT
*
25709145 TATTCGAGT
1 TATTCGAAT
25709154 TATTCGAAT
1 TATTCGAAT
25709163 T
1 T
25709164 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:25718091 original size:173 final size:173
Alignment explanation
Indices: 25717794--25718143 Score: 583
Period size: 173 Copynumber: 2.0 Consensus size: 173
25717784 TGCCTTCCTA
* * **
25717794 CATCAAATCACAACCTAAACCATTTAAAGGTGTATCGTTGTAAATCACAAATTCTTTACCTGATT
1 CATCAAATCACAACCTAAACCATTTAAAGATGCATCGTTGTAAATCACAAATTCTTTACCCAATT
* * *
25717859 TAGGCTGAACCAAAATTGTGCCTTGGTCAACAGTGCTTTCAACTGTTTAAAACTTTGTTGACATT
66 CAGGCTGAACCAAAATTGTGCCTTGGTCAACAGTGCTTTCAACTGTGTAAAAATTTGTTGACATT
* *
25717924 TCTCAGACTATTCAAATTTGACATCTTTCTGTAATAGTCGTGT
131 TCTCAGACTATTCAAATTTCACATCTTTCTATAATAGTCGTGT
25717967 CATCAAATCACAACCTAAACCATTTAAAGATGCATCGTTGTAAATCACAAATTCTTTACCCAATT
1 CATCAAATCACAACCTAAACCATTTAAAGATGCATCGTTGTAAATCACAAATTCTTTACCCAATT
* * *
25718032 CAGGTTGAACCAAAATTGTGTCTTGGTCAATAGTGCTTTCAACTGTGTAAAAATTTGTTGACATT
66 CAGGCTGAACCAAAATTGTGCCTTGGTCAACAGTGCTTTCAACTGTGTAAAAATTTGTTGACATT
*
25718097 TCTTAGACTATTCAAATTTCACATCTTTCTATAATAGTCGTGT
131 TCTCAGACTATTCAAATTTCACATCTTTCTATAATAGTCGTGT
25718140 CATC
1 CATC
25718144 GGTGTAGCTA
Statistics
Matches: 164, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
173 164 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (173 bp):
CATCAAATCACAACCTAAACCATTTAAAGATGCATCGTTGTAAATCACAAATTCTTTACCCAATT
CAGGCTGAACCAAAATTGTGCCTTGGTCAACAGTGCTTTCAACTGTGTAAAAATTTGTTGACATT
TCTCAGACTATTCAAATTTCACATCTTTCTATAATAGTCGTGT
Found at i:25739982 original size:17 final size:16
Alignment explanation
Indices: 25739953--25739988 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
25739943 CTATATCAGC
25739953 AAAAATTTCAAAAATT
1 AAAAATTTCAAAAATT
*
25739969 AAAAATTATTAAAAATT
1 AAAAATT-TCAAAAATT
25739986 AAA
1 AAA
25739989 TTCTAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATTTCAAAAATT
Found at i:25740369 original size:11 final size:11
Alignment explanation
Indices: 25740353--25740377 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25740343 TTAATTAGAT
25740353 AATTTATTAAA
1 AATTTATTAAA
25740364 AATTTATTAAA
1 AATTTATTAAA
25740375 AAT
1 AAT
25740378 AAAAAATAGA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTATTAAA
Found at i:25744373 original size:13 final size:13
Alignment explanation
Indices: 25744355--25744402 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
25744345 GTAGTTTCTC
*
25744355 AAAAAAAAACTCG
1 AAAAAAAAATTCG
25744368 AAAAAAAAATTTC-
1 AAAAAAAAA-TTCG
25744381 AAAAAAAAATTCG
1 AAAAAAAAATTCG
25744394 AAAAAAAAA
1 AAAAAAAAA
25744403 ACTAGTTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 3 0.09
13 27 0.84
14 2 0.06
ACGTcount: A:0.75, C:0.08, G:0.04, T:0.12
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:25744387 original size:26 final size:26
Alignment explanation
Indices: 25744353--25744402 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
25744343 TAGTAGTTTC
25744353 TCAAAAAAAAACTCGAAAAAAAAATT
1 TCAAAAAAAAACTCGAAAAAAAAATT
*
25744379 TCAAAAAAAAATTCGAAAAAAAAA
1 TCAAAAAAAAACTCGAAAAAAAAA
25744403 ACTAGTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.72, C:0.10, G:0.04, T:0.14
Consensus pattern (26 bp):
TCAAAAAAAAACTCGAAAAAAAAATT
Found at i:25744462 original size:13 final size:14
Alignment explanation
Indices: 25744441--25744480 Score: 66
Period size: 12 Copynumber: 3.0 Consensus size: 14
25744431 GGATATCAAG
25744441 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
25744455 TT-TG-AAAAAAAA
1 TTGTGAAAAAAAAA
25744467 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
25744481 GAGAGAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.42
13 4 0.17
14 10 0.42
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:25744464 original size:12 final size:13
Alignment explanation
Indices: 25744441--25744479 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
25744431 GGATATCAAG
25744441 TTGTGAAAAAAAAA
1 TTGTG-AAAAAAAA
25744455 TT-TGAAAAAAAA
1 TTGTGAAAAAAAA
25744467 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
25744480 AGAGAGAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.42
13 12 0.50
14 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:25762200 original size:26 final size:26
Alignment explanation
Indices: 25762171--25762224 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
25762161 GATTGAAAAA
25762171 GTAAAAGTAATCAAATCTTGTTATGG
1 GTAAAAGTAATCAAATCTTGTTATGG
25762197 GTAAAAGTAATCAAATCTTGTTATGG
1 GTAAAAGTAATCAAATCTTGTTATGG
25762223 GT
1 GT
25762225 GATTAGCTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.35
Consensus pattern (26 bp):
GTAAAAGTAATCAAATCTTGTTATGG
Found at i:25764701 original size:27 final size:27
Alignment explanation
Indices: 25764644--25764823 Score: 236
Period size: 27 Copynumber: 6.6 Consensus size: 27
25764634 TTAGAGTTTG
* * *
25764644 CCACAAAAGGCTTTCCTTTCATATTACG
1 CCAC-AAAGGCTTTTCTTCCATATTACA
* * *
25764672 CCACAAACGATTTTCTTCCATATTACG
1 CCACAAAGGCTTTTCTTCCATATTACA
**
25764699 CCACAAACACTTTTCTTCCATATTACA
1 CCACAAAGGCTTTTCTTCCATATTACA
25764726 CCACAAAGGCTTTTCTTCCATATTACA
1 CCACAAAGGCTTTTCTTCCATATTACA
* **
25764753 CCACAAAGGCTTTTCTTTCATATTATG
1 CCACAAAGGCTTTTCTTCCATATTACA
25764780 CCACAAAGGCTTTTACTT-CATATTACA
1 CCACAAAGGCTTTT-CTTCCATATTACA
25764807 CCACAAAGGCTTTTCTT
1 CCACAAAGGCTTTTCTT
25764824 TCTTGATGTG
Statistics
Matches: 137, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
26 3 0.02
27 127 0.93
28 7 0.05
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.34
Consensus pattern (27 bp):
CCACAAAGGCTTTTCTTCCATATTACA
Found at i:25768979 original size:46 final size:46
Alignment explanation
Indices: 25768919--25769006 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
25768909 AAAAGTGTAG
* *
25768919 TGTGGGCATTAGCCCATTATAGT-ATCAAAATCAGAAATAGAATACA
1 TGTGGGCATAAGCCCAATATAGTGA-CAAAATCAGAAATAGAATACA
* * *
25768965 TGTGGGCCTAAGCCCAATATAGTGACAGAATCAGTAATAGAA
1 TGTGGGCATAAGCCCAATATAGTGACAAAATCAGAAATAGAA
25769007 ATGCAACAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
46 35 0.97
47 1 0.03
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (46 bp):
TGTGGGCATAAGCCCAATATAGTGACAAAATCAGAAATAGAATACA
Found at i:25769192 original size:22 final size:22
Alignment explanation
Indices: 25769138--25769202 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
25769128 TGCCAGTGAT
25769138 CAGAATGGCTAAGAGCCATAAA
1 CAGAATGGCTAAGAGCCATAAA
* * * *
25769160 TAGGATAGCTATA-AGCTATAAA
1 CAGAATGGCTA-AGAGCCATAAA
**
25769182 CAGAATGGCTACTAGCCATAA
1 CAGAATGGCTAAGAGCCATAA
25769203 GTACAGTAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (22 bp):
CAGAATGGCTAAGAGCCATAAA
Found at i:25769248 original size:32 final size:32
Alignment explanation
Indices: 25769195--25769303 Score: 114
Period size: 32 Copynumber: 3.4 Consensus size: 32
25769185 AATGGCTACT
* * *
25769195 AGCCATAAGTA-CAGTAATATGATTGGCACAA
1 AGCCATCAGTAGCAATAATATGATCGGCACAA
* * *
25769226 AGCCATCAGTAGCAATGATATGACCGGCACAT
1 AGCCATCAGTAGCAATAATATGATCGGCACAA
* **
25769258 AGCC-TACAGTAACGGTAATATGATCGGCACAA
1 AGCCAT-CAGTAGCAATAATATGATCGGCACAA
25769290 AGCCATCAGTAGCA
1 AGCCATCAGTAGCA
25769304 TCGCAGTAAA
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
31 11 0.18
32 49 0.80
33 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (32 bp):
AGCCATCAGTAGCAATAATATGATCGGCACAA
Found at i:25769578 original size:24 final size:24
Alignment explanation
Indices: 25769472--25769581 Score: 139
Period size: 24 Copynumber: 4.6 Consensus size: 24
25769462 CCATGCTCAG
**
25769472 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
***
25769496 AATCAGTCATACCAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
*
25769520 AATTAGTCATTTAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* *
25769544 AATCAGTCATTTACATCACGGACA
1 AATCAGTCATTTAAATCACAGACA
*
25769568 AATCAATCATTTAA
1 AATCAGTCATTTAA
25769582 CCTCGAGGGG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:25769732 original size:27 final size:26
Alignment explanation
Indices: 25769654--25769739 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
25769644 TGTATTACAG
* *
25769654 TCATTTTA-CCTATAGGGCCATCACGT
1 TCATTTTACCCTATAGGG-CATTACGA
* *
25769680 TCATTTTACCCTACAAGGGCAGTACGA
1 TCATTTTACCCTA-TAGGGCATTACGA
25769707 TCATTTTACCCTATAGGAGCATTACGA
1 TCATTTTACCCTATAGG-GCATTACGA
*
25769734 TAATTT
1 TCATTT
25769740 ACAAATATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
26 11 0.22
27 35 0.70
28 4 0.08
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (26 bp):
TCATTTTACCCTATAGGGCATTACGA
Found at i:25770132 original size:19 final size:17
Alignment explanation
Indices: 25770092--25770134 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
25770082 TTTATCCATG
25770092 TGGCCCACAAGCCCACT
1 TGGCCCACAAGCCCACT
* *
25770109 CGGCCCACACAGCCCATTT
1 TGGCCCACA-AGCCCA-CT
25770128 TGGCCCA
1 TGGCCCA
25770135 ATGAGGCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 6 0.29
19 7 0.33
ACGTcount: A:0.21, C:0.47, G:0.19, T:0.14
Consensus pattern (17 bp):
TGGCCCACAAGCCCACT
Found at i:25774958 original size:24 final size:24
Alignment explanation
Indices: 25774926--25774975 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
25774916 TGTACTAATT
25774926 GAAGACATATTTA-AACAATGTATTA
1 GAAGACATATTTATAA-AAT-TATTA
25774951 GAAG-CATATTTATAAAATTATTA
1 GAAGACATATTTATAAAATTATTA
25774974 GA
1 GA
25774976 CCCAAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 7 0.29
24 11 0.46
25 6 0.25
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (24 bp):
GAAGACATATTTATAAAATTATTA
Found at i:25776630 original size:12 final size:12
Alignment explanation
Indices: 25776597--25776677 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
25776587 TTTCCACTCG
25776597 ATTT-TTTTTCA
1 ATTTCTTTTTCA
** *
25776608 AGCTCTCTTTCA
1 ATTTCTTTTTCA
25776620 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
25776633 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
25776646 --TTCTCTTTCA
1 ATTTCTTTTTCA
25776656 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
25776668 ATCTCTTTTT
1 ATTTCTTTTT
25776678 TTCTTTTCAC
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 2 0.04
12 31 0.58
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.23, G:0.01, T:0.63
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:25776638 original size:21 final size:20
Alignment explanation
Indices: 25776612--25776667 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
25776602 TTTTCAAGCT
25776612 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
25776633 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
25776648 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
25776668 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:25776658 original size:36 final size:36
Alignment explanation
Indices: 25776611--25776679 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
25776601 TTTTTCAAGC
*
25776611 TCTCTTTCAATTTCTTTTTCCA-CTCTTTCTTTTTCT
1 TCTCTTTCAATTTCTTTTTCAATCTCTTT-TTTTTCT
25776647 TCTCTTTCAATTTCTTTTTCAATCTCTTTTTTT
1 TCTCTTTCAATTTCTTTTTCAATCTCTTTTTTT
25776680 CTTTTCACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 25 0.81
37 6 0.19
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (36 bp):
TCTCTTTCAATTTCTTTTTCAATCTCTTTTTTTTCT
Found at i:25777920 original size:11 final size:11
Alignment explanation
Indices: 25777904--25777954 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
25777894 CAAAATAAAC
25777904 TTTTTTTTGAA
1 TTTTTTTTGAA
*
25777915 TTTTTTTTCAAAA
1 TTTTTTTT--GAA
25777928 TTTATTTTTG-A
1 TTT-TTTTTGAA
25777939 -TTTTTTTGAA
1 TTTTTTTTGAA
25777949 TTTTTT
1 TTTTTT
25777955 CTCATAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
9 6 0.18
10 3 0.09
11 14 0.42
13 5 0.15
14 5 0.15
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:25783810 original size:19 final size:19
Alignment explanation
Indices: 25783788--25783849 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
25783778 CCCTAATCGC
25783788 ACTTACGTGCCCTTGTTGT
1 ACTTACGTGCCCTTGTTGT
* * *
25783807 ACTT-CGGTACCCTTGATCGC
1 ACTTAC-GTGCCCTTG-TTGT
* *
25783827 ACTTACGTGCCCCTATTGT
1 ACTTACGTGCCCTTGTTGT
25783846 ACTT
1 ACTT
25783850 CAATACCCCT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.03
19 18 0.56
20 12 0.38
21 1 0.03
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.37
Consensus pattern (19 bp):
ACTTACGTGCCCTTGTTGT
Found at i:25783837 original size:39 final size:39
Alignment explanation
Indices: 25783776--25783953 Score: 180
Period size: 39 Copynumber: 4.6 Consensus size: 39
25783766 AATTATTGGC
* **
25783776 ACCCCTAATCGCACTTACGTGCCCTTGTTGTACTTCGGT
1 ACCCCTAATCGCACTTACGTGCCCCTGTTGTACTTCAAT
* * *
25783815 ACCCTTGATCGCACTTACGTGCCCCTATTGTACTTCAAT
1 ACCCCTAATCGCACTTACGTGCCCCTGTTGTACTTCAAT
* *
25783854 ACCCCTAATCGCACTTACGTACCCCTGTTGTAC-TCAAC
1 ACCCCTAATCGCACTTACGTGCCCCTGTTGTACTTCAAT
* * * * *
25783892 ACCACTGATCGAACTTACGAT-CCCCTATTGTACTTCGAT
1 ACCCCTAATCGCACTTACG-TGCCCCTGTTGTACTTCAAT
* * * *
25783931 ACTCCTAATAGAACTTTCGTGCC
1 ACCCCTAATCGCACTTACGTGCC
25783954 GTGGTTACGT
Statistics
Matches: 114, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
38 32 0.28
39 82 0.72
ACGTcount: A:0.22, C:0.34, G:0.13, T:0.31
Consensus pattern (39 bp):
ACCCCTAATCGCACTTACGTGCCCCTGTTGTACTTCAAT
Found at i:25783917 original size:38 final size:38
Alignment explanation
Indices: 25783820--25783925 Score: 133
Period size: 38 Copynumber: 2.8 Consensus size: 38
25783810 TCGGTACCCT
* * *
25783820 TGATCGCACTTACGTGCCCCTATTGTACTTCAATACCCC
1 TGATCGCACTTACGTACCCCTATTGTAC-TCAACACCAC
* *
25783859 TAATCGCACTTACGTACCCCTGTTGTACTCAACACCAC
1 TGATCGCACTTACGTACCCCTATTGTACTCAACACCAC
*
25783897 TGATCGAACTTACG-ATCCCCTATTGTACT
1 TGATCGCACTTACGTA-CCCCTATTGTACT
25783926 TCGATACTCC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 1 0.02
38 32 0.55
39 25 0.43
ACGTcount: A:0.24, C:0.34, G:0.12, T:0.30
Consensus pattern (38 bp):
TGATCGCACTTACGTACCCCTATTGTACTCAACACCAC
Found at i:25783938 original size:77 final size:78
Alignment explanation
Indices: 25783776--25783939 Score: 217
Period size: 77 Copynumber: 2.1 Consensus size: 78
25783766 AATTATTGGC
* * *** *
25783776 ACCCCTAATCGCACTTACGTGCCCTTGTTGTACTTCGGTACCCTTGATCGCACTTACGTGCCCCT
1 ACCCCTAATCGCACTTACGTACCCCTGTTGTACTTCAACACCCTTGATCGAACTTACGTGCCCCT
25783841 ATTGTACTTCAAT
66 ATTGTACTTCAAT
25783854 ACCCCTAATCGCACTTACGTACCCCTGTTGTAC-TCAACACCAC-TGATCGAACTTACGAT-CCC
1 ACCCCTAATCGCACTTACGTACCCCTGTTGTACTTCAACACC-CTTGATCGAACTTACG-TGCCC
*
25783916 CTATTGTACTTCGAT
64 CTATTGTACTTCAAT
*
25783931 ACTCCTAAT
1 ACCCCTAAT
25783940 AGAACTTTCG
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
77 43 0.57
78 33 0.43
ACGTcount: A:0.22, C:0.34, G:0.13, T:0.31
Consensus pattern (78 bp):
ACCCCTAATCGCACTTACGTACCCCTGTTGTACTTCAACACCCTTGATCGAACTTACGTGCCCCT
ATTGTACTTCAAT
Found at i:25789543 original size:24 final size:24
Alignment explanation
Indices: 25789511--25789559 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
25789501 CATGAAAACT
25789511 TAGTTTAGGCTTATGTTTTTTAGC
1 TAGTTTAGGCTTATGTTTTTTAGC
25789535 TAGTTTAGGCTTATGTTTTTTAGC
1 TAGTTTAGGCTTATGTTTTTTAGC
25789559 T
1 T
25789560 GATTATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.55
Consensus pattern (24 bp):
TAGTTTAGGCTTATGTTTTTTAGC
Found at i:25790455 original size:37 final size:37
Alignment explanation
Indices: 25790401--25790514 Score: 185
Period size: 37 Copynumber: 3.0 Consensus size: 37
25790391 AACATGTTTT
25790401 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTA
*
25790438 TGAGTATTGTGGA-ATATGCTTGAATGTTATGTCATTTTA
1 TGAGTATTGT-GATATATGCTTGAATGTTATGTGA--TTA
25790477 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTA
25790514 T
1 T
25790515 ATGTGTATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
37 34 0.48
38 4 0.06
39 33 0.46
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (37 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTA
Found at i:25790494 original size:39 final size:39
Alignment explanation
Indices: 25790397--25790522 Score: 188
Period size: 39 Copynumber: 3.3 Consensus size: 39
25790387 TCTAAACATG
25790397 TTTT-TGAGTATTGTGATATATGCTTGAATGTTATGTGA
1 TTTTATGAGTATTGTGATATATGCTTGAATGTTATGTGA
*
25790435 --TTATGAGTATTGTGGA-ATATGCTTGAATGTTATGTCA
1 TTTTATGAGTATTGT-GATATATGCTTGAATGTTATGTGA
25790472 TTTTATGAGTATTGTGATATATGCTTGAATGTTATGTGA
1 TTTTATGAGTATTGTGATATATGCTTGAATGTTATGTGA
* *
25790511 TTATATGTGTAT
1 TTTTATGAGTAT
25790523 ATGCTTAAAT
Statistics
Matches: 79, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
36 2 0.03
37 30 0.38
38 4 0.05
39 43 0.54
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.48
Consensus pattern (39 bp):
TTTTATGAGTATTGTGATATATGCTTGAATGTTATGTGA
Found at i:25790524 original size:31 final size:33
Alignment explanation
Indices: 25790484--25790545 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
25790474 TTATGAGTAT
* *
25790484 TGTGATATATGCTTGAATGT-TATGTGATTATA
1 TGTGATATATGCTTAAATGTAAATGTGATTATA
25790516 TGTG-TATATGCTTAAATGTAAATGTGATTA
1 TGTGATATATGCTTAAATGTAAATGTGATTA
25790546 CGATGTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.45
Consensus pattern (33 bp):
TGTGATATATGCTTAAATGTAAATGTGATTATA
Found at i:25797823 original size:20 final size:20
Alignment explanation
Indices: 25797800--25797853 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25797790 AGTTTTTCCC
*
25797800 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
25797820 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
25797840 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
25797854 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:25797835 original size:30 final size:30
Alignment explanation
Indices: 25797800--25797873 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
25797790 AGTTTTTCCC
25797800 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
25797830 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
25797860 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
25797874 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:25797863 original size:20 final size:20
Alignment explanation
Indices: 25797800--25797864 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
25797790 AGTTTTTCCC
* * * *
25797800 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
25797820 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
25797839 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
25797860 AGCTC
1 AGCTC
25797865 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:25799504 original size:13 final size:13
Alignment explanation
Indices: 25799486--25799510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25799476 AAAAAAGAAG
25799486 AAATTCAGAAAAA
1 AAATTCAGAAAAA
25799499 AAATTCAGAAAA
1 AAATTCAGAAAA
25799511 TTACAAAAAT
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:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (13 bp):
AAATTCAGAAAAA
Found at i:25800596 original size:12 final size:12
Alignment explanation
Indices: 25800575--25800713 Score: 52
Period size: 12 Copynumber: 11.6 Consensus size: 12
25800565 AGAAAAGGAG
*
25800575 AAAGAGATTGAA
1 AAAGAAATTGAA
25800587 AAAGAAATTG--
1 AAAGAAATTGAA
**
25800597 AAAGAAA-ACAA
1 AAAGAAATTGAA
**
25800608 AAAGAAAACGAA
1 AAAGAAATTGAA
**
25800620 AAAGAAAAAGAA
1 AAAGAAATTGAA
** *
25800632 ATTGCAAA-AGAA
1 AAAG-AAATTGAA
*
25800644 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
25800656 AAAGTGAGAGAA
1 AAAGAAATTGAA
* *
25800668 AAACAAAATGAAGA
1 AAAGAAATTG-A-A
25800682 AAAGAAAATTGAA
1 AAAG-AAATTGAA
25800695 AAAGAAATTGAA
1 AAAGAAATTGAA
*
25800707 AATGAAA
1 AAAGAAA
25800714 AAAAATTGAA
Statistics
Matches: 96, Mismatches: 23, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
10 7 0.07
11 10 0.10
12 60 0.62
13 9 0.09
14 5 0.05
15 5 0.05
ACGTcount: A:0.68, C:0.04, G:0.18, T:0.10
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:25800627 original size:18 final size:18
Alignment explanation
Indices: 25800601--25800659 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
25800591 AAATTGAAAG
* *
25800601 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* *
25800619 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
25800637 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
25800655 AAAAG
1 AAAAG
25800660 TGAGAGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:25800629 original size:6 final size:6
Alignment explanation
Indices: 25800597--25800733 Score: 71
Period size: 6 Copynumber: 22.7 Consensus size: 6
25800587 AAAGAAATTG
* * ** *
25800597 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * * *
25800644 AAAGAA ATCGAA AAAGTG AGAGAA AAACAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
** * **
25800695 AAAGAA ATTGAA AATGAA AAA-AA ATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG
25800734 CGAAAAAAGA
Statistics
Matches: 93, Mismatches: 34, Indels: 9
0.68 0.25 0.07
Matches are distributed among these distances:
5 6 0.06
6 76 0.82
7 7 0.08
8 4 0.04
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.09
Consensus pattern (6 bp):
AAAGAA
Found at i:25800657 original size:69 final size:71
Alignment explanation
Indices: 25800566--25800730 Score: 177
Period size: 69 Copynumber: 2.4 Consensus size: 71
25800556 CATTGAGCGA
* * *
25800566 GAAAAGGAGAAAGAGATTGAAAAAGAAATTGAAAG-AAAAC-AAA-AAGAAAACGAAAA-AGAAA
1 GAAAATGAAAAAGAAATTGAAAAAGAAA-TGAAAGAAAAACAAAAGAAGAAAA-GAAAATAGAAA
25800627 AAGAAATT
64 AAGAAATT
* * *
25800635 GCAAAA-GAAAAAGAAATCGAAAAAG---TGAGAGAAAAACAAAATGAAGAAAAGAAAATTGAAA
1 G-AAAATGAAAAAGAAATTGAAAAAGAAATGAAAGAAAAACAAAA-GAAGAAAAGAAAATAGAAA
25800696 AAGAAATT
64 AAGAAATT
25800704 GAAAATGAAAAA-AAATTGAAAAAGAAA
1 GAAAATGAAAAAGAAATTGAAAAAGAAA
25800731 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
65 5 0.06
66 5 0.06
67 3 0.04
68 20 0.25
69 43 0.54
70 4 0.05
ACGTcount: A:0.68, C:0.03, G:0.19, T:0.10
Consensus pattern (71 bp):
GAAAATGAAAAAGAAATTGAAAAAGAAATGAAAGAAAAACAAAAGAAGAAAAGAAAATAGAAAAA
GAAATT
Found at i:25800785 original size:33 final size:33
Alignment explanation
Indices: 25800748--25800810 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
25800738 AAAAGAAATT
25800748 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
25800781 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
25800811 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Done.