Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 54 of 186
Found at i:16647397 original size:23 final size:23
Alignment explanation
Indices: 16647371--16647417 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
16647361 ACACTTCTTA
*
16647371 TAAATAATATATTTTTTCATTAC
1 TAAATAATATATTTTGTCATTAC
16647394 TAAATAATATATTTTGTCATTAC
1 TAAATAATATATTTTGTCATTAC
16647417 T
1 T
16647418 TTTAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (23 bp):
TAAATAATATATTTTGTCATTAC
Found at i:16648837 original size:44 final size:44
Alignment explanation
Indices: 16648774--16648858 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
16648764 TGATCAATGG
16648774 TAGAACACAAAAAGTGGAATATGAAGCTTTATCTACTATCTATT
1 TAGAACACAAAAAGTGGAATATGAAGCTTTATCTACTATCTATT
16648818 TAGAACACAAAAAGTGGAATATGAAGCTTTATCTACTATCT
1 TAGAACACAAAAAGTGGAATATGAAGCTTTATCTACTATCT
16648859 GTTTTCATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (44 bp):
TAGAACACAAAAAGTGGAATATGAAGCTTTATCTACTATCTATT
Found at i:16671390 original size:27 final size:26
Alignment explanation
Indices: 16671360--16671424 Score: 60
Period size: 27 Copynumber: 2.4 Consensus size: 26
16671350 TATCAAAGAT
16671360 TTTATTGATTAAAAATATATATATT-TA
1 TTTATT-ATTAAAAATAT-TATATTATA
* **
16671387 TTTAATAATTAAGTATATTATATTATA
1 TTT-ATTATTAAAAATATTATATTATA
16671414 TTATATTATTA
1 TT-TATTATTA
16671425 TTATATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
26 6 0.19
27 22 0.71
28 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (26 bp):
TTTATTATTAAAAATATTATATTATA
Found at i:16671410 original size:5 final size:5
Alignment explanation
Indices: 16671400--16671430 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
16671390 AATAATTAAG
16671400 TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TA-TAT TATAT
16671431 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:16671500 original size:31 final size:30
Alignment explanation
Indices: 16671465--16671525 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
16671455 GAAACATAAT
*
16671465 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
16671496 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
16671526 AATAAGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:16673125 original size:39 final size:38
Alignment explanation
Indices: 16673077--16673152 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 38
16673067 TACCAGGTAC
*
16673077 CAACTTTACTTCG-GCTAGGCCGATGAGACACTGGGTGT
1 CAACTTTACTTCGAACTA-GCCGATGAGACACTGGGTGT
* *
16673115 CAACTATTACTTCGAACTATCCGATGAGGCACTGGGTG
1 CAACT-TTACTTCGAACTAGCCGATGAGACACTGGGTG
16673153 CCATATTGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 5 0.15
39 25 0.76
40 3 0.09
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (38 bp):
CAACTTTACTTCGAACTAGCCGATGAGACACTGGGTGT
Found at i:16678837 original size:13 final size:13
Alignment explanation
Indices: 16678786--16678837 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
16678776 AATAAACCGC
*
16678786 TAATAAAATCAAT
1 TAATCAAATCAAT
*
16678799 TAATCAAATTAAT
1 TAATCAAATCAAT
*
16678812 TAATAAAATCAAT
1 TAATCAAATCAAT
*
16678825 TAATCAAACCAAT
1 TAATCAAATCAAT
16678838 CGCCGCAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATCAAATCAAT
Found at i:16684992 original size:52 final size:51
Alignment explanation
Indices: 16684931--16685079 Score: 154
Period size: 52 Copynumber: 2.9 Consensus size: 51
16684921 ACATCATACT
* * * * *
16684931 GATGCCATAGCCCAGCCATGGTATTATATGAGAGTACATATCACAATGCACC
1 GATG-CATAGCCCAGCTATGGTCTTATACGAGAGCACAAATCACAATGCACC
* * * *
16684983 GATGTCATAGCCCAGCTTTGGTCTTATACGGGTGCACAAATCACAATGTACC
1 GATG-CATAGCCCAGCTATGGTCTTATACGAGAGCACAAATCACAATGCACC
* * * *
16685035 AATGCTATAGCCCAGCTATGGTCTTATACGGGTGCACATATCACA
1 GATGC-ATAGCCCAGCTATGGTCTTATACGAGAGCACAAATCACA
16685080 TCTATTCCGT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
51 1 0.01
52 82 0.99
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (51 bp):
GATGCATAGCCCAGCTATGGTCTTATACGAGAGCACAAATCACAATGCACC
Found at i:16686677 original size:24 final size:24
Alignment explanation
Indices: 16686648--16686814 Score: 99
Period size: 24 Copynumber: 6.8 Consensus size: 24
16686638 CTGTATAATG
*
16686648 GGAAGCTCATAAGAGCCATAATTA
1 GGAAGCTCAGAAGAGCCATAATTA
* * **
16686672 GGAAGCTCATACGAGCCAATAA-CG
1 GGAAGCTCAGAAGAGCC-ATAATTA
*
16686696 GGTAGCTTC-GAAGAGCCATTAATTA
1 GGAAGC-TCAGAAGAGCCA-TAATTA
* * *
16686721 GAAAGCTCGGAATAGCCAT-ATTA
1 GGAAGCTCAGAAGAGCCATAATTA
* * *
16686744 GGAAGCTCCGAAGAGTCATTAATCA
1 GGAAGCTCAGAAGAGCCA-TAATTA
* **
16686769 GGAAGCTCTCA-AAGAGCCTTTAATCG
1 GGAAG--CTCAGAAGAGCC-ATAATTA
*
16686795 GGAAGCTCCGAAGAGCCATA
1 GGAAGCTCAGAAGAGCCATA
16686815 TATCGGGACG
Statistics
Matches: 110, Mismatches: 22, Indels: 22
0.71 0.14 0.14
Matches are distributed among these distances:
23 19 0.17
24 39 0.35
25 33 0.30
26 16 0.15
27 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (24 bp):
GGAAGCTCAGAAGAGCCATAATTA
Found at i:16686791 original size:26 final size:25
Alignment explanation
Indices: 16686648--16686813 Score: 124
Period size: 25 Copynumber: 6.8 Consensus size: 25
16686638 CTGTATAATG
** *
16686648 GGAAGCTCATAAGAGCCA-TAATTA
1 GGAAGCTCCGAAGAGCCATTAATCA
** * * *
16686672 GGAAGCTCATACGAGCCAATAA-CG
1 GGAAGCTCCGAAGAGCCATTAATCA
* * *
16686696 GGTAGCTTCGAAGAGCCATTAATTA
1 GGAAGCTCCGAAGAGCCATTAATCA
* * * *
16686721 GAAAGCTCGGAATAGCCA-T-ATTA
1 GGAAGCTCCGAAGAGCCATTAATCA
*
16686744 GGAAGCTCCGAAGAGTCATTAATCA
1 GGAAGCTCCGAAGAGCCATTAATCA
* * *
16686769 GGAAGCTCTCAAAGAGCCTTTAATCG
1 GGAAGCTC-CGAAGAGCCATTAATCA
16686795 GGAAGCTCCGAAGAGCCAT
1 GGAAGCTCCGAAGAGCCAT
16686814 ATATCGGGAC
Statistics
Matches: 110, Mismatches: 27, Indels: 9
0.75 0.18 0.06
Matches are distributed among these distances:
23 18 0.16
24 35 0.32
25 36 0.33
26 21 0.19
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (25 bp):
GGAAGCTCCGAAGAGCCATTAATCA
Found at i:16693879 original size:14 final size:14
Alignment explanation
Indices: 16693860--16693895 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
16693850 TTGTTTCATT
*
16693860 AAAAATTATTTTTG
1 AAAAATGATTTTTG
16693874 AAAAATGATTTTTG
1 AAAAATGATTTTTG
*
16693888 GAAAATGA
1 AAAAATGA
16693896 CTTGTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (14 bp):
AAAAATGATTTTTG
Found at i:16695381 original size:13 final size:14
Alignment explanation
Indices: 16695365--16695399 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
16695355 GAAACAGGGG
16695365 AAAGAAAGAA-GAA
1 AAAGAAAGAACGAA
*
16695378 AAAGAGAGAACGAA
1 AAAGAAAGAACGAA
16695392 AAAGAAAG
1 AAAGAAAG
16695400 GGGGAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAACGAA
Found at i:16697289 original size:6 final size:5
Alignment explanation
Indices: 16697259--16697288 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
16697249 GCCCTCTGTG
16697259 AAAAT AAAAT AAAAT AAAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
16697289 ACACAGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:16701726 original size:6 final size:5
Alignment explanation
Indices: 16701696--16701725 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
16701686 CCAATTTGTG
16701696 AAAAT AAAAT AAAAT AAAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
16701726 ACACACAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:16703966 original size:52 final size:48
Alignment explanation
Indices: 16703947--16704149 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
16703937 TGACAAGTGG
* *
16703947 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
16703993 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
16704045 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
16704091 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
16704137 AAAGTGATAAGTG
1 AAAGTGATAAGTG
16704150 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:16704001 original size:98 final size:98
Alignment explanation
Indices: 16703881--16704149 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
16703871 TTTGAGTACT
*
16703881 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
16703946 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
16703979 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
16704044 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
16704077 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
16704142 GATAAGTG
65 GAAAAGTG
16704150 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:16704157 original size:37 final size:37
Alignment explanation
Indices: 16704113--16704258 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
16704103 GATAGCTTTA
*
16704113 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
16704150 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
16704187 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
16704224 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
16704259 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:16721894 original size:14 final size:14
Alignment explanation
Indices: 16721875--16721965 Score: 51
Period size: 14 Copynumber: 6.5 Consensus size: 14
16721865 GTTCATTTGA
* *
16721875 ATTCATAGATACAT
1 ATTCATACATACAG
*
16721889 ATTCATACATGCAG
1 ATTCATACATACAG
* *
16721903 ATTCATAAATGC-G
1 ATTCATACATACAG
**
16721916 AATTCATACAT-GTG
1 -ATTCATACATACAG
* *
16721930 AATTCATAGATACAA
1 -ATTCATACATACAG
* *
16721945 ATTCATACATGCGG
1 ATTCATACATACAG
16721959 ATTCATA
1 ATTCATA
16721966 GATATAATCC
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
13 1 0.02
14 59 0.98
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (14 bp):
ATTCATACATACAG
Found at i:16721920 original size:28 final size:28
Alignment explanation
Indices: 16721875--16721992 Score: 105
Period size: 28 Copynumber: 4.2 Consensus size: 28
16721865 GTTCATTTGA
* *
16721875 ATTCATAGATACATATTCATACATGCAG
1 ATTCATAAATACAAATTCATACATGCAG
* * *
16721903 ATTCATAAATGCGAATTCATACATG-TG
1 ATTCATAAATACAAATTCATACATGCAG
* *
16721930 AATTCATAGATACAAATTCATACATGCGG
1 -ATTCATAAATACAAATTCATACATGCAG
* * * * *
16721959 ATTCATAGATA-TAATCCATAAATGTAG
1 ATTCATAAATACAAATTCATACATGCAG
16721986 ATTCATA
1 ATTCATA
16721993 CATGTGAATT
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
27 19 0.26
28 54 0.73
29 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (28 bp):
ATTCATAAATACAAATTCATACATGCAG
Found at i:16721997 original size:14 final size:14
Alignment explanation
Indices: 16721889--16721997 Score: 62
Period size: 14 Copynumber: 7.9 Consensus size: 14
16721879 ATAGATACAT
*
16721889 ATTCATACATGCAG
1 ATTCATACATGTAG
* *
16721903 ATTCATAAATG-CG
1 ATTCATACATGTAG
16721916 AATTCATACATGT-G
1 -ATTCATACATGTAG
* ** *
16721930 AATTCATAGATACAA
1 -ATTCATACATGTAG
**
16721945 ATTCATACATGCGG
1 ATTCATACATGTAG
* *
16721959 ATTCATAGATATA-
1 ATTCATACATGTAG
* *
16721972 ATCCATAAATGTAG
1 ATTCATACATGTAG
16721986 ATTCATACATGT
1 ATTCATACATGT
16721998 GAATTGATAG
Statistics
Matches: 71, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
13 11 0.15
14 60 0.85
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (14 bp):
ATTCATACATGTAG
Found at i:16729597 original size:48 final size:48
Alignment explanation
Indices: 16729503--16729598 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
16729493 CAATAATTAT
** *
16729503 ACATAACATATAACACATACAGAGTTATATCAACTTGCTCTTTTCAAA
1 ACATAACATATAACACATACAGAGCCATATCAACTTACTCTTTTCAAA
*
16729551 ACATAACATATATCACATACAGAGCCATA-CTAACTTACT-TTATTCAAA
1 ACATAACATATAACACATACAGAGCCATATC-AACTTACTCTT-TTCAAA
16729599 TTCTTTCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 3 0.07
48 39 0.93
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (48 bp):
ACATAACATATAACACATACAGAGCCATATCAACTTACTCTTTTCAAA
Found at i:16734373 original size:138 final size:136
Alignment explanation
Indices: 16733950--16734507 Score: 828
Period size: 138 Copynumber: 4.0 Consensus size: 136
16733940 AGAAAAATGG
*
16733950 ATTATATTCTTTCCAAAAGAATATTGATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATT-AATTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
* *
16734015 ATAACTTTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTT
65 ATAAC-GTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
16734080 ATATATATTA
129 ATATA-A-TA
16734090 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAA-TTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
* *
16734155 ATAAATGTTTATATTAATTAAATTCAGTAAAATATATACGATTAATATTTTGTATGAATCAAATT
65 AT-AACGTTTATATTAA-TAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
* *
16734220 TATATATTA
128 CATATAATA
* * **
16734229 ATTATATTCTTTTCAAAAGAATACTAATTTCAATGTCTTTTATATTTTGACTAAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTC-ATGTCTTTTATATTTTGACCGAAATTAATTAAT
* * *
16734294 ATAACGATTTATATGAATAAATTCAGTAATATATATAGAATTAATATTTTGTATGAATCAAATTC
65 ATAACG-TTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
16734359 ATATAATA
129 ATATAATA
* *
16734367 AATATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTT-CATGTCTTTTATATTTTGACCGAAATTAATTAAT
* * * *
16734432 ATAACCCTTTATATCAATAAACTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
65 ATAA-CGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
*
16734497 ATATATTA
129 ATATAATA
16734505 ATT
1 ATT
16734508 TTATCTATGT
Statistics
Matches: 383, Mismatches: 28, Indels: 16
0.90 0.07 0.04
Matches are distributed among these distances:
138 183 0.48
139 72 0.19
140 74 0.19
141 54 0.14
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (136 bp):
ATTATATTCTTTCCAAAAGAATATTAATTTCATGTCTTTTATATTTTGACCGAAATTAATTAATA
TAACGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCAT
ATAATA
Found at i:16736400 original size:45 final size:45
Alignment explanation
Indices: 16736351--16736481 Score: 163
Period size: 45 Copynumber: 2.9 Consensus size: 45
16736341 TCCTGTTTGC
* * *
16736351 CATGATGTCATATCATCTTTCAGCCATGGTCTTACTAATTTATAT
1 CATGATGTCATAGCATCTTTCAGCTATGGTCTTACTCATTTATAT
* * * * ** *
16736396 CATGACGCCATAGCATCTTTTAGCTATGGTCGTACTCATCCATGT
1 CATGATGTCATAGCATCTTTCAGCTATGGTCTTACTCATTTATAT
*
16736441 CATGATGTCATAGCATCTTTCAGCTATGGCCTTACTCATTT
1 CATGATGTCATAGCATCTTTCAGCTATGGTCTTACTCATTT
16736482 CAGGCTATAG
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (45 bp):
CATGATGTCATAGCATCTTTCAGCTATGGTCTTACTCATTTATAT
Found at i:16738644 original size:21 final size:21
Alignment explanation
Indices: 16738610--16738654 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
16738600 ATTTGAATTG
16738610 ATTGTCTTTTTGTTCAAATCA
1 ATTGTCTTTTTGTTCAAATCA
**
16738631 ATTGT-TTTTCTGTTTGAATCA
1 ATTGTCTTTT-TGTTCAAATCA
16738652 ATT
1 ATT
16738655 CATTTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (21 bp):
ATTGTCTTTTTGTTCAAATCA
Found at i:16738686 original size:41 final size:42
Alignment explanation
Indices: 16738616--16738697 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
16738606 ATTGATTGTC
* * *
16738616 TTTTTGTTCAAATCAATTGTTTTTCTGTTTGAA-TCAATTCAT
1 TTTTTGTTCAAACCAATTCTTTGTCTGTTT-AACTCAATTCAT
*
16738658 TTTTTGTTTAAACCAATTCTTTGT-TGTTTAACTCAATTCA
1 TTTTTGTTCAAACCAATTCTTTGTCTGTTTAACTCAATTCA
16738698 AACTCCAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.06
41 13 0.37
42 20 0.57
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (42 bp):
TTTTTGTTCAAACCAATTCTTTGTCTGTTTAACTCAATTCAT
Found at i:16738694 original size:20 final size:21
Alignment explanation
Indices: 16738616--16738696 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
16738606 ATTGATTGTC
* *
16738616 TTTTTGTTCAAA-TCAATTGT
1 TTTTTGTTTAAACTCAATTCT
*
16738636 TTTTCTGTTTGAA-TCAATTCAT
1 TTTT-TGTTTAAACTCAATTC-T
16738658 TTTTTGTTTAAAC-CAATTCT
1 TTTTTGTTTAAACTCAATTCT
*
16738678 TTGTTGTTT-AACTCAATTC
1 TTTTTGTTTAAACTCAATTC
16738697 AAACTCCAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 3 0.06
20 19 0.37
21 25 0.48
22 5 0.10
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.54
Consensus pattern (21 bp):
TTTTTGTTTAAACTCAATTCT
Found at i:16740200 original size:23 final size:23
Alignment explanation
Indices: 16740174--16740217 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
16740164 ATATGATGAG
* *
16740174 ATATTTTTTTATTTATAAAAATA
1 ATATTTGTTGATTTATAAAAATA
*
16740197 ATATTTGTTGATTTCTAAAAA
1 ATATTTGTTGATTTATAAAAA
16740218 AAACTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
ATATTTGTTGATTTATAAAAATA
Found at i:16746789 original size:44 final size:43
Alignment explanation
Indices: 16746725--16746811 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 43
16746715 AATCTGATTG
* *
16746725 TTGTTTTATCTATTTTCTGATTGATGCAAATATTGTTGATGTA
1 TTGTTTTATCTATTTCCTGATTGATGCAAATATTCTTGATGTA
*
16746768 TTGTTTTATTCTATTTCCTGATTGATGCAAATTTTCTTGATGTA
1 TTGTTTTA-TCTATTTCCTGATTGATGCAAATATTCTTGATGTA
16746812 GACTGATTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 8 0.20
44 32 0.80
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.54
Consensus pattern (43 bp):
TTGTTTTATCTATTTCCTGATTGATGCAAATATTCTTGATGTA
Found at i:16749012 original size:3 final size:3
Alignment explanation
Indices: 16749004--16749041 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16748994 TTGTAAATGT
16749004 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
16749042 GTATGTAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:16756559 original size:2 final size:2
Alignment explanation
Indices: 16756552--16756582 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16756542 TATGTTGCAT
16756552 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16756583 TTTTACATAG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16757260 original size:31 final size:31
Alignment explanation
Indices: 16757216--16757287 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
16757206 GATAGTTCGG
* *
16757216 AAGTGTATGAATCAAACTAATACAAAATGAT
1 AAGTATATTAATCAAACTAATACAAAATGAT
16757247 AAGTATATTAATCAAACTAATACAAAATGAT
1 AAGTATATTAATCAAACTAATACAAAATGAT
16757278 AAGTATATTA
1 AAGTATATTA
16757288 CTGAGTATCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (31 bp):
AAGTATATTAATCAAACTAATACAAAATGAT
Found at i:16759463 original size:12 final size:12
Alignment explanation
Indices: 16759446--16759487 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
16759436 TTTCGTTAGC
16759446 AAAAAAAAGGAA
1 AAAAAAAAGGAA
16759458 AAAAAAAA-GAA
1 AAAAAAAAGGAA
16759469 GAAAAAAAAGGAA
1 -AAAAAAAAGGAA
16759482 AAAAAA
1 AAAAAA
16759488 GATGAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.11
12 22 0.79
13 3 0.11
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGGAA
Found at i:16760380 original size:3 final size:3
Alignment explanation
Indices: 16760372--16760396 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16760362 AGATATTTAC
16760372 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
16760397 CAATTAATTG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16760571 original size:19 final size:20
Alignment explanation
Indices: 16760523--16760573 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
16760513 TTAATTTAGT
* *
16760523 AAATGAAAGAAATAAATAAT
1 AAATAAAAGAAATAAATAAC
16760543 AAATAAAAGAAATAAA-AAC
1 AAATAAAAGAAATAAATAAC
16760562 AAGA-AAAAGAAA
1 AA-ATAAAAGAAA
16760574 CAGAGAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (20 bp):
AAATAAAAGAAATAAATAAC
Found at i:16767843 original size:5 final size:5
Alignment explanation
Indices: 16767833--16767891 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
16767823 AAATAAAAAC
* *
16767833 AAGAA AAGAA ACAGAG AAGAA ACGAA ATAG-A AAG-A AAGAAA GAAGAA
1 AAGAA AAGAA A-AGAA AAGAA AAGAA A-AGAA AAGAA AAG-AA -AAGAA
16767880 AAGAA AAGAA AA
1 AAGAA AAGAA AA
16767892 AAGAGAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
4 6 0.13
5 28 0.62
6 8 0.18
7 3 0.07
ACGTcount: A:0.73, C:0.03, G:0.22, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:16767866 original size:26 final size:25
Alignment explanation
Indices: 16767837--16767890 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
16767827 AAAAACAAGA
* *
16767837 AAAGAAACAGAGAAGAAACGAAATAG
1 AAAGAAACAAAGAAGAAAAGAAA-AG
*
16767863 AAAGAAAGAAAGAAGAAAAGAAAAG
1 AAAGAAACAAAGAAGAAAAGAAAAG
16767888 AAA
1 AAA
16767891 AAAGAGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.72, C:0.04, G:0.22, T:0.02
Consensus pattern (25 bp):
AAAGAAACAAAGAAGAAAAGAAAAG
Found at i:16767898 original size:26 final size:26
Alignment explanation
Indices: 16767847--16767899 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
16767837 AAAGAAACAG
* *
16767847 AGAAGAAACGAAATAGAAAGAAAGAA
1 AGAAGAAAAGAAATAGAAAAAAAGAA
16767873 AGAAGAAAAGAAA-AGAAAAAAGAGAA
1 AGAAGAAAAGAAATAGAAAAAA-AGAA
16767899 A
1 A
16767900 TTAGGGTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (26 bp):
AGAAGAAAAGAAATAGAAAAAAAGAA
Found at i:16769800 original size:20 final size:20
Alignment explanation
Indices: 16769775--16769812 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16769765 GCCCCACGGG
16769775 CAGGCCACACGGGCATGTCC
1 CAGGCCACACGGGCATGTCC
*
16769795 CAGGCCATACGGGCATGT
1 CAGGCCACACGGGCATGT
16769813 GCCCCTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.34, G:0.32, T:0.13
Consensus pattern (20 bp):
CAGGCCACACGGGCATGTCC
Found at i:16772956 original size:43 final size:43
Alignment explanation
Indices: 16772891--16772981 Score: 148
Period size: 43 Copynumber: 2.1 Consensus size: 43
16772881 TTCGTGAGAT
*
16772891 ATGTG-GCATCCGAGCTCGTTGAGTGGTCCGAGTTCATTATGG
1 ATGTGAGCATCCGAGCTCATTGAGTGGTCCGAGTTCATTATGG
* *
16772933 GTGTGAGCATCCGAGCTCATTGAGTGGTCCGAGTTCATTGTGG
1 ATGTGAGCATCCGAGCTCATTGAGTGGTCCGAGTTCATTATGG
16772976 ATGTGA
1 ATGTGA
16772982 TGCCTGTGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 4 0.09
43 40 0.91
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.31
Consensus pattern (43 bp):
ATGTGAGCATCCGAGCTCATTGAGTGGTCCGAGTTCATTATGG
Found at i:16773541 original size:12 final size:12
Alignment explanation
Indices: 16773524--16773556 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
16773514 AAAATTATGG
16773524 AAATTGAATTAT
1 AAATTGAATTAT
16773536 AAATTGAATTAT
1 AAATTGAATTAT
16773548 AAATTGAAT
1 AAATTGAAT
16773557 AAGATATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (12 bp):
AAATTGAATTAT
Found at i:16776278 original size:21 final size:22
Alignment explanation
Indices: 16776252--16776308 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
16776242 CCGGGCATAT
16776252 GTCTTGAGAGATGATAAGC-AA
1 GTCTTGAGAGATGATAAGCAAA
* * *
16776273 GTCTTGAGACATGGTAGGCAAA
1 GTCTTGAGAGATGATAAGCAAA
*
16776295 GTCTCGAGAGATGA
1 GTCTTGAGAGATGA
16776309 CATTAGAGTC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.23
Consensus pattern (22 bp):
GTCTTGAGAGATGATAAGCAAA
Found at i:16784934 original size:33 final size:34
Alignment explanation
Indices: 16784883--16784947 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
16784873 CCACACCGTA
*
16784883 ACTATATAGGGCTAAGGCCCAGACTA-TACTGTT
1 ACTAAATAGGGCTAAGGCCCAGACTATTACTGTT
*
16784916 ACTAAATAGGGCTTAGGCCCAGACTATTACTG
1 ACTAAATAGGGCTAAGGCCCAGACTATTACTG
16784948 CATGCATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 24 0.83
34 5 0.17
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (34 bp):
ACTAAATAGGGCTAAGGCCCAGACTATTACTGTT
Found at i:16785935 original size:29 final size:31
Alignment explanation
Indices: 16785893--16785958 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
16785883 GTGAAAATGT
*
16785893 AAAT-TATGGATTAAATTGTGAAAT-ATGAA
1 AAATATATGGATTAAAATGTGAAATAATGAA
16785922 AAATATATGG-TTAAAATGTGAAATAAATGAA
1 AAATATATGGATTAAAATGTGAAAT-AATGAA
16785953 AAATAT
1 AAATAT
16785959 GGGCTGATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 17 0.52
30 5 0.15
31 11 0.33
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (31 bp):
AAATATATGGATTAAAATGTGAAATAATGAA
Found at i:16785959 original size:29 final size:30
Alignment explanation
Indices: 16785887--16785960 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
16785877 TTTTTAGTGA
* * *
16785887 AAATGTAAATTATGGATTAAATTGTGAAAT
1 AAATGAAAAATATGGATTAAAATGTGAAAT
16785917 --ATGAAAAATATATGG-TTAAAATGTGAAAT
1 AAATG-AAAA-ATATGGATTAAAATGTGAAAT
16785946 AAATGAAAAATATGG
1 AAATGAAAAATATGG
16785961 GCTGATATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 3 0.08
29 22 0.59
30 9 0.24
31 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (30 bp):
AAATGAAAAATATGGATTAAAATGTGAAAT
Found at i:16788535 original size:17 final size:17
Alignment explanation
Indices: 16788496--16788538 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
16788486 ACAAAAATGG
*
16788496 ATAGAAATGGAAAAGTT
1 ATAGAAATGGAAAAATT
*
16788513 AAAGAAATGGAGAAAATT
1 ATAGAAATGGA-AAAATT
16788531 -TAGAAATG
1 ATAGAAATG
16788539 AATGTGGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (17 bp):
ATAGAAATGGAAAAATT
Found at i:16788851 original size:54 final size:54
Alignment explanation
Indices: 16788787--16788896 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
16788777 TATTTGGGAA
*
16788787 ATAGAAAAATAAATATTGGGTTGGATCGAATTATAAAGTACTAGTTAAAAGTCC
1 ATAGAAAAATAAATATCGGGTTGGATCGAATTATAAAGTACTAGTTAAAAGTCC
*
16788841 ATAGAAAAATAAATATCGGGTTGGATCGAATTATGAAGTACTAGTTAAAAGTCC
1 ATAGAAAAATAAATATCGGGTTGGATCGAATTATAAAGTACTAGTTAAAAGTCC
16788895 AT
1 AT
16788897 GAAGTACTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (54 bp):
ATAGAAAAATAAATATCGGGTTGGATCGAATTATAAAGTACTAGTTAAAAGTCC
Found at i:16790319 original size:19 final size:19
Alignment explanation
Indices: 16790291--16790327 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16790281 ACAAAACCCG
16790291 ATAAACGATAATGCCTGAA
1 ATAAACGATAATGCCTGAA
* *
16790310 ATAAATGATAATGTCTGA
1 ATAAACGATAATGCCTGA
16790328 TAGATGATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (19 bp):
ATAAACGATAATGCCTGAA
Found at i:16797911 original size:65 final size:65
Alignment explanation
Indices: 16797835--16797967 Score: 248
Period size: 65 Copynumber: 2.0 Consensus size: 65
16797825 AATATTTAAT
*
16797835 TATTTTTTTGACAAGAATTTAACCAAATTTGCTTGAATTTAAGTAGAATTGGGTATGAAAAAGTA
1 TATTTTTTTGACAAGAATTTAACCAAATTTGCATGAATTTAAGTAGAATTGGGTATGAAAAAGTA
*
16797900 TATTTTTTTGACAAGAATTTAACCGAATTTGCATGAATTTAAGTAGAATTGGGTATGAAAAAGTA
1 TATTTTTTTGACAAGAATTTAACCAAATTTGCATGAATTTAAGTAGAATTGGGTATGAAAAAGTA
16797965 TAT
1 TAT
16797968 AAATTTTTGT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (65 bp):
TATTTTTTTGACAAGAATTTAACCAAATTTGCATGAATTTAAGTAGAATTGGGTATGAAAAAGTA
Found at i:16802906 original size:17 final size:19
Alignment explanation
Indices: 16802884--16802921 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
16802874 TTTCTGTTGG
16802884 TGACATT-TC-CAACTCTT
1 TGACATTGTCACAACTCTT
16802901 TGACATTGGTCACAACTCTT
1 TGACATT-GTCACAACTCTT
16802921 T
1 T
16802922 ATATATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (19 bp):
TGACATTGTCACAACTCTT
Found at i:16805266 original size:34 final size:34
Alignment explanation
Indices: 16805215--16805283 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
16805205 AAATTACAAA
* * * *
16805215 ATCAGCAGGTAATATAAATTTATCTTCACGTACC
1 ATCAGCAGGAAAGATAAACTTATCTACACGTACC
16805249 ATCAGCAGGAAAGATAAACTTATCTACACGTACC
1 ATCAGCAGGAAAGATAAACTTATCTACACGTACC
16805283 A
1 A
16805284 ATATGTCCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (34 bp):
ATCAGCAGGAAAGATAAACTTATCTACACGTACC
Found at i:16813953 original size:46 final size:46
Alignment explanation
Indices: 16813888--16814206 Score: 471
Period size: 46 Copynumber: 7.0 Consensus size: 46
16813878 TTATCTTTGA
* * * * * *
16813888 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
16813934 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
16813980 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGCATATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* * * ** *
16814026 TAGGTTGCCATGGTATCTTTCAACCGTGGTCTTATTC-TTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
16814071 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
16814117 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
16814163 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
16814207 TTCAGAGAGC
Statistics
Matches: 247, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
45 43 0.17
46 204 0.83
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:16814000 original size:25 final size:25
Alignment explanation
Indices: 16813972--16814047 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
16813962 GTCTTACACA
16813972 TTTCATATCATGTTGCCATGGTATC
1 TTTCATATCATGTTGCCATGGTATC
* * * * *
16813997 TTTCA-ACCATG--GTC-TTGCATA
1 TTTCATATCATGTTGCCATGGTATC
* *
16814018 TTTCATATTAGGTTGCCATGGTATC
1 TTTCATATCATGTTGCCATGGTATC
16814043 TTTCA
1 TTTCA
16814048 ACCGTGGTCT
Statistics
Matches: 35, Mismatches: 12, Indels: 8
0.64 0.22 0.15
Matches are distributed among these distances:
21 9 0.26
22 5 0.14
24 7 0.20
25 14 0.40
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (25 bp):
TTTCATATCATGTTGCCATGGTATC
Found at i:16814116 original size:137 final size:137
Alignment explanation
Indices: 16813893--16814204 Score: 509
Period size: 137 Copynumber: 2.3 Consensus size: 137
16813883 TTTGACATGA
* * * *
16813893 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCTGTCACGTTGCCATGGTATCTTTCAAC
* *
16813958 CATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTGCATATTTCA
65 CATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
*
16814023 TATTAGGT
130 TATCAGGT
* *
16814031 TGCCATGGTATCTTTCAACCGTGGTCTTATTC-TTTCATGTCACGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTC-TGTCACGTTGCCATGGTATCTTTCAAC
16814095 CATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
65 CATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
16814160 TATCAGGT
130 TATCAGGT
*
16814168 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTC
16814205 ATTTCAGAGA
Statistics
Matches: 160, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
136 4 0.03
137 125 0.78
138 31 0.19
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (137 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCTGTCACGTTGCCATGGTATCTTTCAACC
ATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
ATCAGGT
Found at i:16816361 original size:3 final size:3
Alignment explanation
Indices: 16816347--16816395 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
16816337 TTTTATACTA
*
16816347 AAT AATT AAT AAT AA- AAT AAT AAT GA- AAT AAT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16816390 AA- AAT A
1 AAT AAT A
16816396 TCTCATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:16816369 original size:11 final size:11
Alignment explanation
Indices: 16816353--16816391 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
16816343 ACTAAATAAT
16816353 TAATAATAAAA
1 TAATAATAAAA
*
16816364 TAATAATGAAA
1 TAATAATAAAA
16816375 TAATAATAAAA
1 TAATAATAAAA
16816386 TAATAA
1 TAATAA
16816392 AATATCTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:16816378 original size:19 final size:19
Alignment explanation
Indices: 16816354--16816395 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
16816344 CTAAATAATT
*
16816354 AATAATAAAATAATAATGA
1 AATAATAAAATAATAATAA
16816373 AATAATAATAA-AATAATAA
1 AATAATAA-AATAATAATAA
16816392 AATA
1 AATA
16816396 TCTCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAATAAAATAATAATAA
Found at i:16816418 original size:20 final size:21
Alignment explanation
Indices: 16816365--16816440 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
16816355 ATAATAAAAT
* *
16816365 AATAATGAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
16816384 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
16816405 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
16816426 TAATCATAAAATATC
1 -AATAATAAAATATC
16816441 ATCAACATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 11 0.24
20 12 0.27
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:16822945 original size:42 final size:42
Alignment explanation
Indices: 16822898--16822986 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
16822888 GACGTCGAGA
* * *
16822898 GAGCACCAGCATCGTTAACACTCACGACGTCTACTTTTTATG
1 GAGCACCAGCATCGTCAACACTCACGACGCCTACTTTCTATG
* *
16822940 GAGCACCAGCGTTGTCAACACTCACGACGCCTACTTTCTATG
1 GAGCACCAGCATCGTCAACACTCACGACGCCTACTTTCTATG
16822982 GAGCA
1 GAGCA
16822987 TGGTGAACGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (42 bp):
GAGCACCAGCATCGTCAACACTCACGACGCCTACTTTCTATG
Found at i:16824706 original size:14 final size:14
Alignment explanation
Indices: 16824687--16824716 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
16824677 TTCTTAAAAA
16824687 ATATATATATACAT
1 ATATATATATACAT
16824701 ATATATATATACAT
1 ATATATATATACAT
16824715 AT
1 AT
16824717 TAGTAGTAGT
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATATATACAT
Found at i:16824957 original size:8 final size:8
Alignment explanation
Indices: 16824944--16824986 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
16824934 AGTGGTGGAG
16824944 ATACATGT
1 ATACATGT
*
16824952 ATACATAT
1 ATACATGT
*
16824960 ATACATAT
1 ATACATGT
*
16824968 ATATATGT
1 ATACATGT
*
16824976 ATATATGT
1 ATACATGT
16824984 ATA
1 ATA
16824987 TATATACATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (8 bp):
ATACATGT
Found at i:16824965 original size:16 final size:15
Alignment explanation
Indices: 16824944--16824995 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
16824934 AGTGGTGGAG
16824944 ATACATGTATACATAT
1 ATACATGTATA-ATAT
* *
16824960 ATACATATATATATGT
1 ATACATGTATA-ATAT
*
16824976 ATATATGTAT-ATAT
1 ATACATGTATAATAT
16824990 ATACAT
1 ATACAT
16824996 ATTAGTAGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 8 0.28
16 21 0.72
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (15 bp):
ATACATGTATAATAT
Found at i:16825205 original size:281 final size:281
Alignment explanation
Indices: 16824687--16825226 Score: 1053
Period size: 281 Copynumber: 1.9 Consensus size: 281
16824677 TTCTTAAAAA
16824687 ATATATATATACATATATATATATACATATTAGTAGTAGTGATCTTCTGAGCTAAAGAAGTTAAA
1 ATATATATATACATATATATATATACATATTAGTAGTAGTGATCTTCTGAGCTAAAGAAGTTAAA
16824752 TTCCATTTTTTGAAAAAAAGCTCTGTTGTATGCAATTGATGACTAGTCATTTTTCTAGTTAGGTA
66 TTCCATTTTTTGAAAAAAAGCTCTGTTGTATGCAATTGATGACTAGTCATTTTTCTAGTTAGGTA
16824817 ATTTTTCAATTCAATCTCGATTCTAACCCTTCCTATTAGCTTGTGACCATAACCTCTAACCAAAG
131 ATTTTTCAATTCAATCTCGATTCTAACCCTTCCTATTAGCTTGTGACCATAACCTCTAACCAAAG
16824882 CCACATTACAACCCTCTAAAGACATTTTGATTGATGTTTCATCTCAATTTATAGTGGTGGAGATA
196 CCACATTACAACCCTCTAAAGACATTTTGATTGATGTTTCATCTCAATTTATAGTGGTGGAGATA
16824947 CATGTATACATATATACATAT
261 CATGTATACATATATACATAT
* * *
16824968 ATATATGTATATATGTATATATATACATATTAGTAGTAGTGATCTTCTGAGCTAAAGAAGTTAAA
1 ATATATATATACATATATATATATACATATTAGTAGTAGTGATCTTCTGAGCTAAAGAAGTTAAA
16825033 TTCCATTTTTTGAAAAAAAGCTCTGTTGTATGCAATTGATGACTAGTCATTTTTCTAGTTAGGTA
66 TTCCATTTTTTGAAAAAAAGCTCTGTTGTATGCAATTGATGACTAGTCATTTTTCTAGTTAGGTA
16825098 ATTTTTCAATTCAATCTCGATTCTAACCCTTCCTATTAGCTTGTGACCATAACCTCTAACCAAAG
131 ATTTTTCAATTCAATCTCGATTCTAACCCTTCCTATTAGCTTGTGACCATAACCTCTAACCAAAG
16825163 CCACATTACAACCCTCTAAAGACATTTTGATTGATGTTTCATCTCAATTTATAGTGGTGGAGAT
196 CCACATTACAACCCTCTAAAGACATTTTGATTGATGTTTCATCTCAATTTATAGTGGTGGAGAT
16825227 TTGATTTTCA
Statistics
Matches: 256, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
281 256 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (281 bp):
ATATATATATACATATATATATATACATATTAGTAGTAGTGATCTTCTGAGCTAAAGAAGTTAAA
TTCCATTTTTTGAAAAAAAGCTCTGTTGTATGCAATTGATGACTAGTCATTTTTCTAGTTAGGTA
ATTTTTCAATTCAATCTCGATTCTAACCCTTCCTATTAGCTTGTGACCATAACCTCTAACCAAAG
CCACATTACAACCCTCTAAAGACATTTTGATTGATGTTTCATCTCAATTTATAGTGGTGGAGATA
CATGTATACATATATACATAT
Found at i:16832622 original size:26 final size:27
Alignment explanation
Indices: 16832571--16832627 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
16832561 AGGTCGTTAT
*
16832571 ATGACCGTAATGCCCCTGTAGAGTAAA
1 ATGACAGTAATGCCCCTGTAGAGTAAA
*
16832598 ATGACAGTAATG-CCCTGTAGGGTAAA
1 ATGACAGTAATGCCCCTGTAGAGTAAA
16832624 ATGA
1 ATGA
16832628 TCGAGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (27 bp):
ATGACAGTAATGCCCCTGTAGAGTAAA
Found at i:16832647 original size:39 final size:40
Alignment explanation
Indices: 16832591--16832667 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
16832581 TGCCCCTGTA
* *
16832591 GAGTAAAATGACAGTAATG-CCCTGTAGGGTAAAATGATC
1 GAGTAAAATAACAGTAATGTCCCAGTAGGGTAAAATGATC
*
16832630 GAGTAAAATAACTGTAATGTCCCAGTAGGGTAAAATGA
1 GAGTAAAATAACAGTAATGTCCCAGTAGGGTAAAATGA
16832668 CCATAACGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 17 0.50
40 17 0.50
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (40 bp):
GAGTAAAATAACAGTAATGTCCCAGTAGGGTAAAATGATC
Found at i:16832713 original size:26 final size:27
Alignment explanation
Indices: 16832632--16832720 Score: 110
Period size: 27 Copynumber: 3.3 Consensus size: 27
16832622 AAATGATCGA
* * * *
16832632 GTAAAATAACTGTAATGTCCCAGTAGG
1 GTAAAATGACAGTAATGCCCCTGTAGG
*
16832659 GTAAAATGACCA-TAACGCCCCTGTAGG
1 GTAAAATGA-CAGTAATGCCCCTGTAGG
16832686 GTAAAATGACAGTAATG-CCCTGTAGG
1 GTAAAATGACAGTAATGCCCCTGTAGG
16832712 GTAAAATGA
1 GTAAAATGA
16832721 TCGAGTGAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 20 0.37
27 33 0.61
28 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (27 bp):
GTAAAATGACAGTAATGCCCCTGTAGG
Found at i:16832732 original size:93 final size:93
Alignment explanation
Indices: 16832571--16832814 Score: 391
Period size: 93 Copynumber: 2.6 Consensus size: 93
16832561 AGGTCGTTAT
* * *
16832571 ATGACCGTAATGCCCCTGTAGAGTAAAATGACAGTAATGCCCTGTAGGGTAAAATGATCGAGTAA
1 ATGACCATAACGCCCCTGTAGGGTAAAATGACAGTAATGCCCTGTAGGGTAAAATGATCGAGTAA
16832636 AATAACTGTAATGTCCCAGTAGGGTAAA
66 AATAACTGTAATGTCCCAGTAGGGTAAA
*
16832664 ATGACCATAACGCCCCTGTAGGGTAAAATGACAGTAATGCCCTGTAGGGTAAAATGATCGAGTGA
1 ATGACCATAACGCCCCTGTAGGGTAAAATGACAGTAATGCCCTGTAGGGTAAAATGATCGAGTAA
*
16832729 AATAACTGTAATGTCCCTGTAGGGTAAA
66 AATAACTGTAATGTCCCAGTAGGGTAAA
* **
16832757 ATGACCATAACGCCCCTGTAGGGTAAAATGACCA-TAATACCCCTGTACAGTAAAATGA
1 ATGACCATAACGCCCCTGTAGGGTAAAATGA-CAGTAAT-GCCCTGTAGGGTAAAATGA
16832815 CTATTATGCC
Statistics
Matches: 141, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
93 123 0.87
94 18 0.13
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (93 bp):
ATGACCATAACGCCCCTGTAGGGTAAAATGACAGTAATGCCCTGTAGGGTAAAATGATCGAGTAA
AATAACTGTAATGTCCCAGTAGGGTAAA
Found at i:16832773 original size:27 final size:27
Alignment explanation
Indices: 16832743--16832815 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
16832733 ACTGTAATGT
*
16832743 CCCTGTAGGGTAAAATGACCATAACGC
1 CCCTGTAGGGTAAAATGACCATAACAC
*
16832770 CCCTGTAGGGTAAAATGACCATAATAC
1 CCCTGTAGGGTAAAATGACCATAACAC
**
16832797 CCCTGTACAGTAAAATGAC
1 CCCTGTAGGGTAAAATGAC
16832816 TATTATGCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (27 bp):
CCCTGTAGGGTAAAATGACCATAACAC
Found at i:16840799 original size:26 final size:26
Alignment explanation
Indices: 16840770--16840877 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
16840760 TGGTACAAAT
16840770 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
16840796 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16840822 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
16840848 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16840874 TGAT
1 TGAT
16840878 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:16850293 original size:51 final size:50
Alignment explanation
Indices: 16850222--16850381 Score: 212
Period size: 51 Copynumber: 3.2 Consensus size: 50
16850212 CTGATCACAT
* *
16850222 TTATCACTTGTCACTGATCAGGTAAGTGTAGCTAAAGCTCCCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
* * *
16850273 TTATCACTTGTCACTGATCAGATAAGAGTAGCTGAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
* * * *
16850323 TTGTCACTTATCATTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
*
16850374 TTGTCACT
1 TTATCACT
16850382 GATCAGAAGT
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 43 0.45
51 53 0.55
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
Found at i:16860141 original size:36 final size:37
Alignment explanation
Indices: 16860092--16860180 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 37
16860082 TATTTACATA
* * * *
16860092 TCACTTTTTAATATATTAAGTAAATATCATTT-CATG
1 TCACGTTTCAATATATCAAGTAAATATCATTTCCAAG
* *
16860128 TCATGTTTCAATATATCAAGTAAATATCTTTTCCAAG
1 TCACGTTTCAATATATCAAGTAAATATCATTTCCAAG
16860165 TCACGTTTCAATATAT
1 TCACGTTTCAATATAT
16860181 ATACTGGTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 27 0.60
37 18 0.40
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.44
Consensus pattern (37 bp):
TCACGTTTCAATATATCAAGTAAATATCATTTCCAAG
Found at i:16861942 original size:17 final size:17
Alignment explanation
Indices: 16861916--16861948 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
16861906 CTTCTTTCTC
16861916 TTTTTCCTTTGCTTTTTA
1 TTTTTCCTTT-CTTTTTA
16861934 TTTTT-CTTTCTTTTT
1 TTTTTCCTTTCTTTTT
16861949 CGTTTGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTCCTTTCTTTTTA
Found at i:16861949 original size:28 final size:28
Alignment explanation
Indices: 16861914--16861974 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
16861904 TTCTTCTTTC
16861914 TCTTTTTCCTTTGCTTTT-TATTTTTCTT
1 TCTTTTTCCTTTGCTTTTCTA-TTTTCTT
* * *
16861942 TCTTTTTCGTTTGGTTTTCTATTTTGTT
1 TCTTTTTCCTTTGCTTTTCTATTTTCTT
16861970 TCTTT
1 TCTTT
16861975 CTTTATTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.03, C:0.15, G:0.08, T:0.74
Consensus pattern (28 bp):
TCTTTTTCCTTTGCTTTTCTATTTTCTT
Found at i:16862013 original size:7 final size:7
Alignment explanation
Indices: 16862003--16862028 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16861993 TTATTATATA
16862003 ATATAAT
1 ATATAAT
16862010 ATATAAT
1 ATATAAT
16862017 ATATAAT
1 ATATAAT
16862024 ATATA
1 ATATA
16862029 TTTATGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:16862068 original size:12 final size:12
Alignment explanation
Indices: 16862051--16862075 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16862041 CAGTAAGAAT
16862051 ATATATATAATA
1 ATATATATAATA
16862063 ATATATATAATA
1 ATATATATAATA
16862075 A
1 A
16862076 AATAATAAAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATAATA
Found at i:16862086 original size:12 final size:15
Alignment explanation
Indices: 16862048--16862079 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16862038 AAACAGTAAG
16862048 AATATATAT-ATAAT
1 AATATATATAATAAT
16862062 AATATATATAATAA-
1 AATATATATAATAAT
16862076 AATA
1 AATA
16862080 ATAAATATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATATATAATAAT
Found at i:16865972 original size:18 final size:18
Alignment explanation
Indices: 16865949--16866034 Score: 91
Period size: 18 Copynumber: 4.7 Consensus size: 18
16865939 GAACGATTAT
* *
16865949 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAATCAA
* *
16865967 TTATTCGGTAAAAATCAA
1 TTATTCAGTAACAATCAA
* * *
16865985 TTATTCAATAATAATCAG
1 TTATTCAGTAACAATCAA
*
16866003 TTATTCAGTAACAATTAAA
1 TTATTCAGTAACAA-TCAA
16866022 TTATTCAGTAACA
1 TTATTCAGTAACA
16866035 GTCGATCTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
18 40 0.73
19 15 0.27
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:16865990 original size:36 final size:37
Alignment explanation
Indices: 16865949--16866037 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 37
16865939 GAACGATTAT
* *
16865949 TTATTCAGTAACAGTCAGTTATTCGGTAA-AAATCAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAAATAAA
* * * *
16865985 TTATTCAATAATAATCAGTTATTCAGTAACAATTAAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAAATAAA
16866022 TTATTCAGTAACAGTC
1 TTATTCAGTAACAGTC
16866038 GATCTTTCCA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 25 0.58
37 18 0.42
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (37 bp):
TTATTCAGTAACAGTCAGTTATTCAGTAACAAATAAA
Found at i:16866242 original size:47 final size:47
Alignment explanation
Indices: 16866173--16866278 Score: 187
Period size: 47 Copynumber: 2.3 Consensus size: 47
16866163 ACAATAGCAA
*
16866173 TACGGTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAG
1 TACGGTACACAGAGTACCTCATCGGAACAAATCCGAAACAGTAACAG
16866220 TACGGTACACAGAGTACCTCATCGGAACAAATCCGAAACAGTAACAG
1 TACGGTACACAGAGTACCTCATCGGAACAAATCCGAAACAGTAACAG
16866267 TAACGGTA-ACAG
1 T-ACGGTACACAG
16866279 TAACAATATC
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
47 51 0.89
48 6 0.11
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (47 bp):
TACGGTACACAGAGTACCTCATCGGAACAAATCCGAAACAGTAACAG
Found at i:16866267 original size:53 final size:52
Alignment explanation
Indices: 16866156--16866270 Score: 159
Period size: 47 Copynumber: 2.3 Consensus size: 52
16866146 CCAAAACAGT
* *
16866156 AACAGTAACAATAGCAATACGGTACACAGAGTACCTCATCGGAACAAATCCG
1 AACAGTAACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCG
*
16866208 ----G-AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCG
1 AACAGTAACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCG
16866255 AAACAGTAACAGTAAC
1 -AACAGTAACAGTAAC
16866271 GGTAACAGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
47 43 0.80
48 1 0.02
52 1 0.02
53 9 0.17
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (52 bp):
AACAGTAACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCG
Found at i:16866326 original size:12 final size:12
Alignment explanation
Indices: 16866309--16866333 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16866299 AGTTCCGAAT
16866309 CGGTAACAGTAA
1 CGGTAACAGTAA
16866321 CGGTAACAGTAA
1 CGGTAACAGTAA
16866333 C
1 C
16866334 AGTAGTCGGC
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:16868121 original size:31 final size:32
Alignment explanation
Indices: 16868065--16868127 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
16868055 CACACTTGTC
*
16868065 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
16868097 ATAATATAA-ATATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
16868128 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:16872888 original size:18 final size:18
Alignment explanation
Indices: 16872865--16872950 Score: 91
Period size: 18 Copynumber: 4.7 Consensus size: 18
16872855 GAACGATTAT
* *
16872865 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAATCAA
*
16872883 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAA
** * *
16872901 TTATTCAAAAATAATCAG
1 TTATTCAGTAACAATCAA
*
16872919 TTATTCAGTAACAATTAAA
1 TTATTCAGTAACAA-TCAA
16872938 TTATTCAGTAACA
1 TTATTCAGTAACA
16872951 GTCGATCTTT
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
18 39 0.72
19 15 0.28
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:16872906 original size:36 final size:37
Alignment explanation
Indices: 16872865--16872953 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 37
16872855 GAACGATTAT
* *
16872865 TTATTCAGTAACAGTCAGTTATTCGGTAACAA-TCAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATTAAA
** * *
16872901 TTATTCAAAAATAATCAGTTATTCAGTAACAATTAAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATTAAA
16872938 TTATTCAGTAACAGTC
1 TTATTCAGTAACAGTC
16872954 GATCTTTCCA
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
36 27 0.64
37 15 0.36
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (37 bp):
TTATTCAGTAACAGTCAGTTATTCAGTAACAATTAAA
Found at i:16877553 original size:21 final size:20
Alignment explanation
Indices: 16877508--16877553 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
16877498 TTGTTGGAAT
16877508 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
16877527 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
16877548 GGTTGA
1 GGTTGA
16877554 TTGCATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:16883552 original size:22 final size:22
Alignment explanation
Indices: 16883527--16883571 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
16883517 TTTATATGTA
16883527 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
* *
16883549 TTAATTTATATCTAATTTAATT
1 TTAATTCATATATAATTTAATT
16883571 T
1 T
16883572 GGGTTAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:16891372 original size:22 final size:22
Alignment explanation
Indices: 16891347--16891389 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
16891337 TTCAAATGTA
*
16891347 GTGTTATTCAAGCTTATTGCCG
1 GTGTTATTCAAGCTTAGTGCCG
16891369 GTGTTATTCAAGCTTAGTGCC
1 GTGTTATTCAAGCTTAGTGCC
16891390 TAGCAGGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (22 bp):
GTGTTATTCAAGCTTAGTGCCG
Found at i:16891387 original size:38 final size:38
Alignment explanation
Indices: 16891358--16891475 Score: 148
Period size: 38 Copynumber: 3.1 Consensus size: 38
16891348 TGTTATTCAA
* * *
16891358 GCTTATTGCCGGTGTTATTCAAGCTTAGTGCCTAGCAG
1 GCTTAGTGCCGGTGTTATTCAGGCTTAGTGCCTATCAG
* *
16891396 GATTAGTGCCGGTTTTATTCAGGCTTAGTGCCTAGT-AG
1 GCTTAGTGCCGGTGTTATTCAGGCTTAGTGCCTA-TCAG
* * *
16891434 GCTTAGTGTCGGTGTTATTCAGGCTTAGTGCTTAGCAG
1 GCTTAGTGCCGGTGTTATTCAGGCTTAGTGCCTATCAG
16891472 GCTT
1 GCTT
16891476 TGAGCTTGTG
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
38 68 1.00
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.36
Consensus pattern (38 bp):
GCTTAGTGCCGGTGTTATTCAGGCTTAGTGCCTATCAG
Found at i:16891423 original size:22 final size:21
Alignment explanation
Indices: 16891350--16891464 Score: 70
Period size: 22 Copynumber: 5.8 Consensus size: 21
16891340 AAATGTAGTG
* *
16891350 TTATTCAAGCTTATTGCCGGT
1 TTATTCAGGCTTAGTGCCGGT
*
16891371 GTTATTCAAGCTTAGTGCC---
1 -TTATTCAGGCTTAGTGCCGGT
* *
16891390 -TA-GCAGGATTAGTGCCGGTT
1 TTATTCAGGCTTAGTGCCGG-T
16891410 TTATTCAGGCTTAGTGCC---
1 TTATTCAGGCTTAGTGCCGGT
* *
16891428 -TAGT-AGGCTTAGTGTCGGT
1 TTATTCAGGCTTAGTGCCGGT
16891447 GTTATTCAGGCTTAGTGC
1 -TTATTCAGGCTTAGTGC
16891465 TTAGCAGGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 24
0.68 0.10 0.23
Matches are distributed among these distances:
16 22 0.31
17 5 0.07
21 5 0.07
22 39 0.55
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.37
Consensus pattern (21 bp):
TTATTCAGGCTTAGTGCCGGT
Found at i:16899719 original size:92 final size:92
Alignment explanation
Indices: 16899562--16899782 Score: 316
Period size: 92 Copynumber: 2.4 Consensus size: 92
16899552 TTTGACATGA
* * * * * *
16899562 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGAATCTTTCAAC
* ** *
16899627 CATGGTCTTATTCATTTCATGTCACGC
66 CATGGCCTTACACATTTCATATCACGC
* *
16899654 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGTCATGTTGCCATGGAATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGAATCTTTCAAC
*
16899719 CATGGCCTTACACATTTCATATCAGGC
66 CATGGCCTTACACATTTCATATCACGC
*
16899746 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTC
16899783 ATATCAGAGA
Statistics
Matches: 113, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 113 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.39
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGAATCTTTCAAC
CATGGCCTTACACATTTCATATCACGC
Found at i:16899782 original size:46 final size:46
Alignment explanation
Indices: 16899562--16899789 Score: 269
Period size: 46 Copynumber: 5.0 Consensus size: 46
16899552 TTTGACATGA
* * * * *
16899562 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCAGGC
* *
16899608 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGC
* * ** * *
16899654 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGC
* * * *
16899700 TGCCATGGAATCTTTCAACCATGGCCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGC
* *
16899746 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAG
16899790 AGAGCACACT
Statistics
Matches: 158, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 4 0.03
46 154 0.97
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGC
Found at i:16901083 original size:18 final size:20
Alignment explanation
Indices: 16901068--16901104 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16901058 TAATAATAAA
*
16901068 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
16901088 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
16901105 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:16903461 original size:23 final size:23
Alignment explanation
Indices: 16903435--16903511 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
16903425 AATGATGTGT
16903435 GAAAGATTGTTAAGCTATAAGTG
1 GAAAGATTGTTAAGCTATAAGTG
* **
16903458 GAAA-TTATGATTACTCATAAATAACGT-
1 GAAAGAT-TG-TTAAGC-T--ATAA-GTG
16903485 GAAAGATTGTTAAGCTATAAGTG
1 GAAAGATTGTTAAGCTATAAGTG
16903508 GAAA
1 GAAA
16903512 TTATGATTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
22 3 0.08
23 14 0.35
24 4 0.10
25 2 0.05
26 4 0.10
27 10 0.25
28 3 0.08
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (23 bp):
GAAAGATTGTTAAGCTATAAGTG
Found at i:16903481 original size:27 final size:27
Alignment explanation
Indices: 16903451--16903531 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
16903441 TTGTTAAGCT
16903451 ATAAGTGGAAATTATGATTACTCATAA
1 ATAAGTGGAAATTATGATTACTCATAA
* **
16903478 ATAACGT-GAAA-GATTG-TTAAGC-T--
1 ATAA-GTGGAAATTA-TGATTACTCATAA
16903501 ATAAGTGGAAATTATGATTACTCATAA
1 ATAAGTGGAAATTATGATTACTCATAA
16903528 ATAA
1 ATAA
16903532 CGTGCATGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
22 2 0.05
23 10 0.25
24 5 0.12
25 2 0.05
26 5 0.12
27 14 0.35
28 2 0.05
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.32
Consensus pattern (27 bp):
ATAAGTGGAAATTATGATTACTCATAA
Found at i:16903492 original size:50 final size:50
Alignment explanation
Indices: 16903433--16903535 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
16903423 CAAATGATGT
16903433 GTGAAAGATTGTTAAGCTATAAGTGGAAATTATGATTACTCATAAATAAC
1 GTGAAAGATTGTTAAGCTATAAGTGGAAATTATGATTACTCATAAATAAC
16903483 GTGAAAGATTGTTAAGCTATAAGTGGAAATTATGATTACTCATAAATAAC
1 GTGAAAGATTGTTAAGCTATAAGTGGAAATTATGATTACTCATAAATAAC
16903533 GTG
1 GTG
16903536 CATGTTGTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (50 bp):
GTGAAAGATTGTTAAGCTATAAGTGGAAATTATGATTACTCATAAATAAC
Found at i:16919138 original size:5 final size:5
Alignment explanation
Indices: 16919124--16919200 Score: 147
Period size: 5 Copynumber: 15.6 Consensus size: 5
16919114 TAATTCCAAC
16919124 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
16919173 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
16919201 TATCATTATC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
4 4 0.06
5 68 0.94
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:16925084 original size:20 final size:20
Alignment explanation
Indices: 16925056--16925094 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16925046 AATTTAATGG
*
16925056 TACTGATACTATCATACTAA
1 TACTAATACTATCATACTAA
16925076 TACTAATACTATCATACTA
1 TACTAATACTATCATACTA
16925095 TTCCACATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.36
Consensus pattern (20 bp):
TACTAATACTATCATACTAA
Found at i:16934155 original size:121 final size:122
Alignment explanation
Indices: 16934000--16934225 Score: 303
Period size: 124 Copynumber: 1.9 Consensus size: 122
16933990 GTAAAAAAAA
* *
16934000 TTTGGTTCTGGCTTCTTACGGCCGGCACCAGAGACTTTTTTCGTGTCCCAATGC-A-TTTTTTTT
1 TTTGGTTCTGCCTTCTAACGGCCGGCACCAGAGACTTTTTTCGTGTCCCAATGCAATTTTTTTTT
* * * * * *
16934063 ATTTTTCTACATTGATTGTCGGCACCAGACCAGTAATTTTTAAAAACAATTTTTTTT
66 ACTTTTCTACACTGATGGCCGACACCAAACCAGTAATTTTTAAAAACAATTTTTTTT
* * * *
16934120 TTTGGTTCTAGCCTTCTAATGGCTGGTACCAGAGACTTTTTTCGTGTCCTAATGCAATTTTTTTT
1 TTTGGTTCT-GCCTTCTAACGGCCGGCACCAGAGACTTTTTTCGTGTCCCAATGCAA-TTTTTTT
*
16934185 TTACTTTTCTACACTGATGGCCTACACCAAACCAGTAATTT
64 TTACTTTTCTACACTGATGGCCGACACCAAACCAGTAATTT
16934226 AAAAAAATTA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
120 9 0.10
121 39 0.44
122 1 0.01
124 40 0.45
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (122 bp):
TTTGGTTCTGCCTTCTAACGGCCGGCACCAGAGACTTTTTTCGTGTCCCAATGCAATTTTTTTTT
ACTTTTCTACACTGATGGCCGACACCAAACCAGTAATTTTTAAAAACAATTTTTTTT
Found at i:16934284 original size:45 final size:45
Alignment explanation
Indices: 16934233--16934324 Score: 141
Period size: 45 Copynumber: 2.0 Consensus size: 45
16934223 TTTAAAAAAA
* *
16934233 TTACTAGTGTATTGCCGGCCATTAGAAGGTCAGAA-CTATTTTTTT
1 TTACTAGTGTAGTGCCGGCCATTAGAAGGCCAGAATC-ATTTTTTT
*
16934278 TTACTAGTGTGGTGCCGGCCATTAGAAGGCCAGAATCATTTTTTT
1 TTACTAGTGTAGTGCCGGCCATTAGAAGGCCAGAATCATTTTTTT
16934323 TT
1 TT
16934325 TATTTTTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (45 bp):
TTACTAGTGTAGTGCCGGCCATTAGAAGGCCAGAATCATTTTTTT
Found at i:16936301 original size:3 final size:3
Alignment explanation
Indices: 16936293--16936318 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16936283 TCTTAATCTA
16936293 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
16936319 AAGAACCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16936535 original size:23 final size:24
Alignment explanation
Indices: 16936491--16936536 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
16936481 AGATATAATC
* **
16936491 AAAATCTATAATAAAATTGTTAAA
1 AAAATCTAAAATAAAAAGGTTAAA
16936515 AAAAT-TAAAATAAAAAGGTTAA
1 AAAATCTAAAATAAAAAGGTTAA
16936537 TTGTACAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (24 bp):
AAAATCTAAAATAAAAAGGTTAAA
Found at i:16942032 original size:14 final size:15
Alignment explanation
Indices: 16942013--16942049 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
16942003 ATAATTTAAA
16942013 ATATAATAATAAT-G
1 ATATAATAATAATAG
16942027 ATATAAT-ATAATAG
1 ATATAATAATAATAG
*
16942041 TTATAATAA
1 ATATAATAA
16942050 ATAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 14 0.70
15 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
ATATAATAATAATAG
Found at i:16942140 original size:4 final size:4
Alignment explanation
Indices: 16942103--16942133 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
16942093 CGAACAGAAC
16942103 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
16942134 AAGAAAGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:16945622 original size:46 final size:44
Alignment explanation
Indices: 16945563--16945677 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
16945553 ACAGGACAGA
* *
16945563 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
16945609 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
16945653 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
16945678 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:16945658 original size:44 final size:45
Alignment explanation
Indices: 16945563--16945696 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
16945553 ACAGGACAGA
* *
16945563 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
16945609 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
16945653 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
16945697 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:16950720 original size:5 final size:5
Alignment explanation
Indices: 16950710--16950781 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
16950700 TGTTAAAAAA
* *
16950710 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
16950756 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
16950782 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 32 0.57
6 11 0.20
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:16950763 original size:19 final size:19
Alignment explanation
Indices: 16950739--16950781 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
16950729 ATTATGTTTT
16950739 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
16950758 TATATTATATTATATTATA
1 TATATTATATTATATTATA
16950777 TATAT
1 TATAT
16950782 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:16950814 original size:18 final size:19
Alignment explanation
Indices: 16950786--16950825 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
16950776 ATATATACAT
*
16950786 AAAACAAAAGAAAGAATAG
1 AAAACAAAAGAAAGAAAAG
16950805 AAAA-AAAAGAAAGAAAAG
1 AAAACAAAAGAAAGAAAAG
16950823 AAA
1 AAA
16950826 CAGAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAACAAAAGAAAGAAAAG
Found at i:16951788 original size:44 final size:44
Alignment explanation
Indices: 16951695--16951828 Score: 144
Period size: 44 Copynumber: 3.0 Consensus size: 44
16951685 ACAGGACAGA
* *
16951695 ACAGAAATGAGCCATGTAAGTCCAGTTTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCA-TTTA-AAATATGGCATTGGAG
* *
16951741 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCAT-TTAAAATATGGCATTGGAG
* ** *
16951785 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCAT-TTAAA-ATATGGCATTGG
16951829 CAGGATATTG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
44 37 0.50
45 2 0.03
46 35 0.47
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATTTAAAATATGGCATTGGAG
Found at i:16959001 original size:50 final size:50
Alignment explanation
Indices: 16958921--16959025 Score: 192
Period size: 50 Copynumber: 2.1 Consensus size: 50
16958911 TTGGCTTAAA
* *
16958921 TAAGACTTGAAACATGATATTTGTCAATATGTATGGGTATGTGTTATGGT
1 TAAGGCTTGAAACATGATATTTGTCAATATGTATAGGTATGTGTTATGGT
16958971 TAAGGCTTGAAACATGATATTTGTCAATATGTATAGGTATGTGTTATGGT
1 TAAGGCTTGAAACATGATATTTGTCAATATGTATAGGTATGTGTTATGGT
16959021 TAAGG
1 TAAGG
16959026 TAGGTGAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (50 bp):
TAAGGCTTGAAACATGATATTTGTCAATATGTATAGGTATGTGTTATGGT
Found at i:16959478 original size:33 final size:33
Alignment explanation
Indices: 16959440--16959502 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
16959430 TTCTGATATG
* *
16959440 ATATGACATTTTGATATGATATATGCTTCTGAA
1 ATATGACATTCTAATATGATATATGCTTCTGAA
* *
16959473 ATATGACATTCTAATATTATATATGTTTCT
1 ATATGACATTCTAATATGATATATGCTTCT
16959503 AGTGATGCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (33 bp):
ATATGACATTCTAATATGATATATGCTTCTGAA
Found at i:16959752 original size:28 final size:28
Alignment explanation
Indices: 16959698--16959752 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
16959688 ACGGTTTGAA
*
16959698 TTATTTTTAACTAAGTTTTCTGTATTTT
1 TTATTTTTAACTAAGTTTTCTGGATTTT
16959726 TTATTTTTAGACTAAGTTTTC-GGATTT
1 TTATTTTTA-ACTAAGTTTTCTGGATTT
16959753 GATTTTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.60
Consensus pattern (28 bp):
TTATTTTTAACTAAGTTTTCTGGATTTT
Found at i:16971023 original size:13 final size:13
Alignment explanation
Indices: 16971005--16971033 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16970995 GTTAGTCTGT
16971005 TACTGTTTTGTTA
1 TACTGTTTTGTTA
16971018 TACTGTTTTGTTA
1 TACTGTTTTGTTA
16971031 TAC
1 TAC
16971034 AGGCTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.10, G:0.14, T:0.59
Consensus pattern (13 bp):
TACTGTTTTGTTA
Found at i:16974923 original size:32 final size:31
Alignment explanation
Indices: 16974828--16974969 Score: 108
Period size: 32 Copynumber: 4.5 Consensus size: 31
16974818 TGGGAGACCT
* * *
16974828 ATTAAAATTTTCAAAAATTTTAGGA-GTTTT
1 ATTAAAATTTTCAAAAATTTTAGAAGGTATA
* **
16974858 ATGAAAATTTTCAAAAATTTTA-AGAGAACATA
1 ATTAAAATTTTCAAAAATTTTAGA-AG-GTATA
*
16974890 ATTAAAATTTTCAAAAAGTATTAGAAGGTATA
1 ATTAAAATTTTCAAAAA-TTTTAGAAGGTATA
* * * * * *
16974922 ATTAGACTTTTAAAAAATTTGAGAGGGTCTA
1 ATTAAAATTTTCAAAAATTTTAGAAGGTATA
*
16974953 ATTAAAACTTTTTAAAA
1 ATTAAAA-TTTTCAAAA
16974970 GCCTTAAAGG
Statistics
Matches: 86, Mismatches: 20, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
30 22 0.26
31 15 0.17
32 42 0.49
33 6 0.07
34 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.37
Consensus pattern (31 bp):
ATTAAAATTTTCAAAAATTTTAGAAGGTATA
Found at i:16980324 original size:24 final size:24
Alignment explanation
Indices: 16980297--16980348 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16980287 TTAGTAAGTC
*
16980297 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
16980321 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
16980345 AAAT
1 AAAT
16980349 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:16982294 original size:24 final size:24
Alignment explanation
Indices: 16982267--16982318 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16982257 TTAGTAAGTC
*
16982267 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
16982291 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
16982315 AAAT
1 AAAT
16982319 TTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:16995332 original size:21 final size:20
Alignment explanation
Indices: 16995308--16995371 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
16995298 TAGCCTTCGG
16995308 GCTTCCGTCTAGCACTTATGT
1 GCTTCCGT-TAGCACTTATGT
* * *
16995329 GCTTCAGTTAGC-CTT-CGG
1 GCTTCCGTTAGCACTTATGT
16995347 GCTTCCGTTTAGCACTTATGT
1 GCTTCCG-TTAGCACTTATGT
16995368 GCTT
1 GCTT
16995372 GAGCTAGACT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 7 0.21
21 12 0.35
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (20 bp):
GCTTCCGTTAGCACTTATGT
Found at i:16995333 original size:39 final size:39
Alignment explanation
Indices: 16995290--16995390 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
16995280 ACTCTGGTGA
16995290 GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
*
16995329 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
* * *
16995368 GCTTGAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
16995391 AGATCACGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.13, C:0.27, G:0.25, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
Found at i:17002202 original size:9 final size:9
Alignment explanation
Indices: 17002185--17002219 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
17002175 GAATTTCGAG
17002185 TTCGAATAA
1 TTCGAATAA
17002194 CTT-GAATAA
1 -TTCGAATAA
17002203 TTCGAATAA
1 TTCGAATAA
17002212 TTCGAATA
1 TTCGAATA
17002220 TCAAACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 2 0.08
9 20 0.83
10 2 0.08
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (9 bp):
TTCGAATAA
Found at i:17003197 original size:5 final size:5
Alignment explanation
Indices: 17003187--17003212 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17003177 AAACAAATAT
17003187 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
17003213 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:17003679 original size:33 final size:33
Alignment explanation
Indices: 17003612--17003679 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
17003602 TCAAGGCCGC
* *
17003612 CATCATAGTCTCAATGGCATCAGCCTTACCAGT
1 CATCATAGCCTCAATGGCATCAGCCCTACCAGT
* *
17003645 CATCATAGCCTCAATGGCATCATCCCTACTAGT
1 CATCATAGCCTCAATGGCATCAGCCCTACCAGT
17003678 CA
1 CA
17003680 GCTTTTCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.26
Consensus pattern (33 bp):
CATCATAGCCTCAATGGCATCAGCCCTACCAGT
Done.