Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 10 of 79
Found at i:3449158 original size:51 final size:51
Alignment explanation
Indices: 3449103--3449210 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 51
3449093 ATAGGTGTCA
* * * * *
3449103 TGACACTGAGGGTAGAATACTCCAATGTCATGATACTAACTTTTGGTGTTG
1 TGACACTGAGGGCAAAATACTCCAATGTCACGACACTAACTTGTGGTGTTG
*
3449154 TGACACTGAGGGCAAAATACTTCAATGTCACGACACTAACTTGTGGTGTTG
1 TGACACTGAGGGCAAAATACTCCAATGTCACGACACTAACTTGTGGTGTTG
3449205 TGACAC
1 TGACAC
3449211 CTTAGATAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (51 bp):
TGACACTGAGGGCAAAATACTCCAATGTCACGACACTAACTTGTGGTGTTG
Found at i:3449957 original size:5 final size:6
Alignment explanation
Indices: 3449943--3449967 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3449933 TTGAGTGACT
3449943 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
3449968 TTAGATAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:3456062 original size:124 final size:123
Alignment explanation
Indices: 3455917--3456163 Score: 413
Period size: 124 Copynumber: 2.0 Consensus size: 123
3455907 ATAGTTTGTC
* *
3455917 ACAATATTCATACATTGGTAAATTTGTGGAAAAATTTGCAATGCAAGTTGCTAAGAAAGGTACAT
1 ACAATATTCATACATTCGTAAAGTTGTGGAAAAATTTGCAATGCAAGTTGCTAAGAAAGGTACAT
* *
3455982 AAAGATTTATACTATGATGAGAACTTTCTTTAAGAGATTGTCATGAGACAATGGAAGAA
66 AAAGATTTATAATATGATGAGAACTTTCTTTAAGAGA-TGTCATAAGACAATGGAAGAA
*
3456041 ACAATATTCATACATTCGTAAAGTTGTGGAAAAATTTGCAATGTAAGTTGCTAAGAAAGGTACAT
1 ACAATATTCATACATTCGTAAAGTTGTGGAAAAATTTGCAATGCAAGTTGCTAAGAAAGGTACAT
* * *
3456106 AATGTTTTATAATATGATGAGAACTTTCTTTAGGAGATGTCATAAGACAATGGAAGAA
66 AAAGATTTATAATATGATGAGAACTTTCTTTAAGAGATGTCATAAGACAATGGAAGAA
3456164 TGAAAGTGTA
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
123 20 0.17
124 95 0.83
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (123 bp):
ACAATATTCATACATTCGTAAAGTTGTGGAAAAATTTGCAATGCAAGTTGCTAAGAAAGGTACAT
AAAGATTTATAATATGATGAGAACTTTCTTTAAGAGATGTCATAAGACAATGGAAGAA
Found at i:3456230 original size:2 final size:2
Alignment explanation
Indices: 3456223--3456250 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3456213 GCGAACAACC
3456223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3456251 TATTCAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3458207 original size:22 final size:22
Alignment explanation
Indices: 3458179--3458225 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3458169 TGCTAAAGGT
3458179 CAACACCATACAGGAATGTCAA
1 CAACACCATACAGGAATGTCAA
*
3458201 CAACACCATACGGGAATGTCAA
1 CAACACCATACAGGAATGTCAA
3458223 CAA
1 CAA
3458226 GTCCTTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.13
Consensus pattern (22 bp):
CAACACCATACAGGAATGTCAA
Found at i:3466975 original size:10 final size:10
Alignment explanation
Indices: 3466962--3467007 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
3466952 ACGAACAAAT
3466962 ATAAATATAA
1 ATAAATATAA
3466972 ATAATTATATAA
1 ATAA--ATATAA
3466984 ATAAATA-AA
1 ATAAATATAA
3466993 ATAAAT-TAA
1 ATAAATATAA
3467002 TATAAA
1 -ATAAA
3467008 CAAATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 10 0.31
10 12 0.38
12 10 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAAATATAA
Found at i:3468199 original size:623 final size:625
Alignment explanation
Indices: 3467002--3468250 Score: 2484
Period size: 623 Copynumber: 2.0 Consensus size: 625
3466992 AATAAATTAA
3467002 TATAAACAAATATTTATATTTATTTAAAACATCATATTTGAAAACAATTAAATAAACAAGATTTT
1 TATAAACAAATATTTATATTTATTTAAAACATCATATTTGAAAACAATTAAATAAACAAGATTTT
3467067 GGAAAACCAAGAATCGAGTTTTACTAGATGTTGAGGTTTGTTTCCATAGTTTCCTTAAAATAAAT
66 GGAAAACCAAGAATCGAGTTTTACTAGATGTTGAGGTTTGTTTCCATAGTTTCCTTAAAATAAAT
3467132 TTGGCCGCTCTTATGATACTTAGAAAAACGTTGGTTGATTGTCTCTTAGGATACAACAACAAAAT
131 TTGGCCGCTCTTATGATACTTAGAAAAACGTTGGTTGATTGTCTCTTAGGATACAACAACAAAAT
3467197 GATCGCGGCAGTAGTACCTTTGCAGTGATCAACGAACAAACTTTACCTTCTTCTATCACCAAAAC
196 GATCGCGGCAGTAGTACCTTTGCAGTGATCAACGAACAAACTTTACCTTCTTCTATCACCAAAAC
3467262 GTTTGAAAGCTTTGGAGGAAATGAAAAGAATTTTTTAGAGTGAAAATTCATTATTTTTGTGTGTA
261 GTTTGAAAGCTTTGGAGGAAATGAAAAGAATTTTTTAGAGTGAAAATTCATTATTTTTGTGTGTA
3467327 TGTAAAGAATTCTGCCGCTTTTATAGGTATTCAATATGGAGGAATTTTAGAAATTTTCATAAATA
326 TGTAAAGAATTCTGCCGCTTTTATAGGTATTCAATATGGAGGAATTTTAGAAATTTTCATAAATA
3467392 AAGATACAAATATTTCCATTAAAGGAGCCTTTAAATCAATTTGAATAAAATCAAATCGAGACATT
391 AAGATACAAATATTTCCATTAAAGGAGCCTTTAAATCAATTTGAATAAAATCAAATCGAGACATT
3467457 TTTCCTTTTAATACAGATTTTGTTTAATATCTGTTGAGAAAAATAAAATATATATTGGGCTAAAA
456 TTTCCTTTTAATACAGATTTTGTTTAATATCTGTTGAGAAAAATAAAATATATATTGGGCTAAAA
3467522 TATCCAGAAACTCTTTTTGGGTCAAACTAGTCCAAAGATTTCACGTCACCCATATTGTGCAAGTG
521 TATCCAGAAACTCTTTTTGGGTCAAACTAGTCCAAAGATTTCACGTCACCCATATTGTGCAAGTG
3467587 CACCTTCAACCCCGATGGGTTTCGACTTGCACCCTATGCG
586 CACCTTCAACCCCGATGGGTTTCGACTTGCACCCTATGCG
3467627 TATAAAC-AA-ATTTATATTTATTTAAAACATCATATTTGAAAACAATTAAATAAACAAGATTTT
1 TATAAACAAATATTTATATTTATTTAAAACATCATATTTGAAAACAATTAAATAAACAAGATTTT
3467690 GGAAAACCAAGAATCGAGTTTTACTAGATGTTGAGGTTTGTTTCCATAGTTTCCTTAAAATAAAT
66 GGAAAACCAAGAATCGAGTTTTACTAGATGTTGAGGTTTGTTTCCATAGTTTCCTTAAAATAAAT
3467755 TTGGCCGCTCTTATGATACTTAGAAAAACGTTGGTTGATTGTCTCTTAGGATACAACAACAAAAT
131 TTGGCCGCTCTTATGATACTTAGAAAAACGTTGGTTGATTGTCTCTTAGGATACAACAACAAAAT
3467820 GATCGCGGCAGTAGTACCTTTGCAGTGATCAACGAACAAACTTTACCTTCTTCTATCACCAAAAC
196 GATCGCGGCAGTAGTACCTTTGCAGTGATCAACGAACAAACTTTACCTTCTTCTATCACCAAAAC
3467885 GTTTGAAAGCTTTGGAGGAAATGAAAAGAATTTTTTAGAGTGAAAATTCATTATTTTTGTGTGTA
261 GTTTGAAAGCTTTGGAGGAAATGAAAAGAATTTTTTAGAGTGAAAATTCATTATTTTTGTGTGTA
3467950 TGTAAAGAATTCTGCCGCTTTTATAGGTATTCAATATGGAGGAATTTTAGAAATTTTCATAAATA
326 TGTAAAGAATTCTGCCGCTTTTATAGGTATTCAATATGGAGGAATTTTAGAAATTTTCATAAATA
3468015 AAGATACAAATATTTCCATTAAAGGAGCCTTTAAATCAATTTGAATAAAATCAAATCGAGACATT
391 AAGATACAAATATTTCCATTAAAGGAGCCTTTAAATCAATTTGAATAAAATCAAATCGAGACATT
3468080 TTTCCTTTTAATACAGATTTTGTTTAATATCTGTTGAGAAAAATAAAATATATATTGGGCTAAAA
456 TTTCCTTTTAATACAGATTTTGTTTAATATCTGTTGAGAAAAATAAAATATATATTGGGCTAAAA
3468145 TATCCAGAAACTCTTTTTGGGTCAAACTAGTCCAAAGATTTCACGTCACCCATATTGTGCAAGTG
521 TATCCAGAAACTCTTTTTGGGTCAAACTAGTCCAAAGATTTCACGTCACCCATATTGTGCAAGTG
3468210 CACCTTCAACCCCGATGGGTTTCGACTTGCACCCTATGCG
586 CACCTTCAACCCCGATGGGTTTCGACTTGCACCCTATGCG
3468250 T
1 T
3468251 GAAATAAGGT
Statistics
Matches: 624, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
623 615 0.99
624 2 0.00
625 7 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (625 bp):
TATAAACAAATATTTATATTTATTTAAAACATCATATTTGAAAACAATTAAATAAACAAGATTTT
GGAAAACCAAGAATCGAGTTTTACTAGATGTTGAGGTTTGTTTCCATAGTTTCCTTAAAATAAAT
TTGGCCGCTCTTATGATACTTAGAAAAACGTTGGTTGATTGTCTCTTAGGATACAACAACAAAAT
GATCGCGGCAGTAGTACCTTTGCAGTGATCAACGAACAAACTTTACCTTCTTCTATCACCAAAAC
GTTTGAAAGCTTTGGAGGAAATGAAAAGAATTTTTTAGAGTGAAAATTCATTATTTTTGTGTGTA
TGTAAAGAATTCTGCCGCTTTTATAGGTATTCAATATGGAGGAATTTTAGAAATTTTCATAAATA
AAGATACAAATATTTCCATTAAAGGAGCCTTTAAATCAATTTGAATAAAATCAAATCGAGACATT
TTTCCTTTTAATACAGATTTTGTTTAATATCTGTTGAGAAAAATAAAATATATATTGGGCTAAAA
TATCCAGAAACTCTTTTTGGGTCAAACTAGTCCAAAGATTTCACGTCACCCATATTGTGCAAGTG
CACCTTCAACCCCGATGGGTTTCGACTTGCACCCTATGCG
Found at i:3472974 original size:17 final size:18
Alignment explanation
Indices: 3472935--3472982 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
3472925 AAATTCAATC
* *
3472935 CCCTTTTTCTGATTGTAA
1 CCCTTTTTCTAACTGTAA
3472953 CCCTTTTTCTAACTGTAA
1 CCCTTTTTCTAACTGTAA
3472971 -CCTTTTCTCTAA
1 CCCTTTT-TCTAA
3472983 TACCAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.19, C:0.27, G:0.06, T:0.48
Consensus pattern (18 bp):
CCCTTTTTCTAACTGTAA
Found at i:3475265 original size:31 final size:31
Alignment explanation
Indices: 3475225--3475289 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
3475215 TAAAAGATAA
3475225 AATAATCTCATAAATTTTAGTATTA-TCTCAT
1 AATAATCTCATAAATTTTAGTATTACT-TCAT
* *
3475256 AATATTCTCATAATTTTTAGTATTACTTCAT
1 AATAATCTCATAAATTTTAGTATTACTTCAT
3475287 AAT
1 AAT
3475290 TATTTGTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (31 bp):
AATAATCTCATAAATTTTAGTATTACTTCAT
Found at i:3476015 original size:22 final size:23
Alignment explanation
Indices: 3475988--3476034 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
3475978 TCTTCAAGTC
*
3475988 TTTTGGTATTTCCT-TAATATTT
1 TTTTGGTATTCCCTCTAATATTT
3476010 TTTTGGTATTCCCTCGTAATATTT
1 TTTTGGTATTCCCTC-TAATATTT
3476034 T
1 T
3476035 ATTCTTCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
24 9 0.41
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.60
Consensus pattern (23 bp):
TTTTGGTATTCCCTCTAATATTT
Found at i:3476106 original size:20 final size:20
Alignment explanation
Indices: 3476058--3476130 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
3476048 TTTTCTCCTG
* * *
3476058 ATAATTTTTTGGTACTCCCTA
1 ATAA-TTTTTGGCATTCCCTC
* *
3476079 ATATTTTTTGGCA-TCTTCTC
1 ATAATTTTTGGCATTC-CCTC
* *
3476099 ATAATTTTTTGTATTCCCTC
1 ATAATTTTTGGCATTCCCTC
3476119 ATAATTTTTGGC
1 ATAATTTTTGGC
3476131 GTGCTGTTGA
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
19 2 0.05
20 33 0.82
21 5 0.12
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.52
Consensus pattern (20 bp):
ATAATTTTTGGCATTCCCTC
Found at i:3476722 original size:107 final size:107
Alignment explanation
Indices: 3476536--3476848 Score: 457
Period size: 115 Copynumber: 2.9 Consensus size: 107
3476526 AAGATGTAAG
* * * *
3476536 AGGATATTTAGCCATTCGGTCCAACGAG-AAATCGAAACCCAGCACATTAAGGCACGTTTTCTCG
1 AGGATATTTGGCTATTTGGTCAAACGAGAAAATCGAAACCCAGCACATTAAGGCACGTTTTCTCG
3476600 AATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTAAA
66 AATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTAAA
* * *
3476642 AGGATATTTGGCTATTTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACATTTTCTCG
1 AGGATATTTGGCTATTTGGTCAAACGAGAAAATCGAAACCCAGCACATTAAGGCACGTTTTCTCG
* *
3476707 AATTTCCAAATGCAAAACATTGTCTTATTTTAAAATTTTAAAATTTTAAA
66 AATTTCCAAACGCAAAACATTG-C----CTT---ATTTTAAAATTTTAAA
*
3476757 AGGATATTTGGCTATTTGGTCAAACGAGAAAATCGAAACCCAGCACATTAAGGCACGTTTCCTCG
1 AGGATATTTGGCTATTTGGTCAAACGAGAAAATCGAAACCCAGCACATTAAGGCACGTTTTCTCG
3476822 AATTTCCAAACGCAAAACATTGCCTTA
66 AATTTCCAAACGCAAAACATTGCCTTA
3476849 AAAAATTAAA
Statistics
Matches: 184, Mismatches: 14, Indels: 17
0.86 0.07 0.08
Matches are distributed among these distances:
106 24 0.13
107 56 0.30
108 1 0.01
110 2 0.01
112 2 0.01
114 1 0.01
115 98 0.53
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (107 bp):
AGGATATTTGGCTATTTGGTCAAACGAGAAAATCGAAACCCAGCACATTAAGGCACGTTTTCTCG
AATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTAAA
Found at i:3476746 original size:8 final size:8
Alignment explanation
Indices: 3476733--3476757 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3476723 ACATTGTCTT
3476733 ATTTTAAA
1 ATTTTAAA
3476741 ATTTTAAA
1 ATTTTAAA
3476749 ATTTTAAA
1 ATTTTAAA
3476757 A
1 A
3476758 GGATATTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:3478931 original size:18 final size:18
Alignment explanation
Indices: 3478890--3478931 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3478880 CTCTCTCATG
* *
3478890 ATTTTTGGTTTTATCGTG
1 ATTTTTGGTATTATCGTC
3478908 ATTTTTGGTATT-TCGTC
1 ATTTTTGGTATTATCGTC
3478925 ATGTTTT
1 AT-TTTT
3478932 TTTTGGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.12, C:0.07, G:0.19, T:0.62
Consensus pattern (18 bp):
ATTTTTGGTATTATCGTC
Found at i:3478956 original size:22 final size:22
Alignment explanation
Indices: 3478909--3478957 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
3478899 TTTATCGTGA
* *
3478909 TTTTTGGTATTTCGTCATGTTT
1 TTTTTGGTATTTCGTCATCTTC
*
3478931 TTTTTGGTATTTTC-TCTTCTTC
1 TTTTTGGTA-TTTCGTCATCTTC
3478953 TTTTT
1 TTTTT
3478958 TTTCATAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.69
Consensus pattern (22 bp):
TTTTTGGTATTTCGTCATCTTC
Found at i:3479042 original size:20 final size:19
Alignment explanation
Indices: 3479019--3479076 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
3479009 TTTATATCCT
*
3479019 CTCATAATTTTTTGTACTTC
1 CTCAT-ATTTTTAGTACTTC
*
3479039 CTCATATTTTGTAGTATTTC
1 CTCATATTTT-TAGTACTTC
*
3479059 CTCATGATTTTTGGTACT
1 CTCAT-ATTTTTAGTACT
3479077 CTACCTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.16
20 22 0.69
21 5 0.16
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.53
Consensus pattern (19 bp):
CTCATATTTTTAGTACTTC
Found at i:3479231 original size:20 final size:21
Alignment explanation
Indices: 3479194--3479233 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3479184 TATTCCCTCT
*
3479194 CCCTCGTATATTTTTGGTACC
1 CCCTCGTATATTTCTGGTACC
3479215 CCCTCGTA-ATTTCTGGTAC
1 CCCTCGTATATTTCTGGTAC
3479234 TTCATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.40
Consensus pattern (21 bp):
CCCTCGTATATTTCTGGTACC
Found at i:3480737 original size:15 final size:15
Alignment explanation
Indices: 3480717--3480754 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3480707 TTAATTAATA
*
3480717 AAAATATTTAAAAAT
1 AAAATATTTAAAAAC
*
3480732 AAAATA-TTAATAAC
1 AAAATATTTAAAAAC
3480746 AAAATATTT
1 AAAATATTT
3480755 CAACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATATTTAAAAAC
Found at i:3483426 original size:24 final size:25
Alignment explanation
Indices: 3483383--3483435 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
3483373 CGTCATTGCA
3483383 TTATATTAAATTTGGAATTTTATTT
1 TTATATTAAATTTGGAATTTTATTT
* * *
3483408 TTATATTTATTTTGG-ATTTTTTTT
1 TTATATTAAATTTGGAATTTTATTT
3483432 TTAT
1 TTAT
3483436 TCATATGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.68
Consensus pattern (25 bp):
TTATATTAAATTTGGAATTTTATTT
Found at i:3484118 original size:29 final size:29
Alignment explanation
Indices: 3484084--3484141 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
3484074 TTAGAGGGAC
*
3484084 TGAATTAAATTAGTCCATT-TACTATTAAA
1 TGAATTAAATTAAT-CATTGTACTATTAAA
*
3484113 TGAATTAATTTAATCATTGTACTATTAAA
1 TGAATTAAATTAATCATTGTACTATTAAA
3484142 GAAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (29 bp):
TGAATTAAATTAATCATTGTACTATTAAA
Found at i:3493997 original size:31 final size:31
Alignment explanation
Indices: 3493949--3494007 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
3493939 AAATAATCAT
*
3493949 TAAATTATTCGAAAGTTTTCATTCAAGTCAC
1 TAAACTATTCGAAAGTTTTCATTCAAGTCAC
* * *
3493980 TAAACTATTTGAAAGTTTTTATTTAAGT
1 TAAACTATTCGAAAGTTTTCATTCAAGT
3494008 TATTACGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (31 bp):
TAAACTATTCGAAAGTTTTCATTCAAGTCAC
Found at i:3507177 original size:229 final size:230
Alignment explanation
Indices: 3506768--3507227 Score: 904
Period size: 229 Copynumber: 2.0 Consensus size: 230
3506758 GTTCAAATCT
3506768 TGTTGGTAACAATTTTGAATATTTTTTGTACTTGTTGCTATTGATGTAATATTGAAGAGTTAATT
1 TGTTGGTAACAATTTTGAATATTTTTTGTACTTGTTGCTATTGATGTAATATTGAAGAGTTAATT
*
3506833 GATTAAAAAAAATAAATACAAATACAAAAAGATTCAAAATTTATTTTTTCAAAATACCAAAAAAG
66 GATTAAAAAAAATAAATACAAATACAAAAAAATTCAAAATTTATTTTTTCAAAATACCAAAAAAG
3506898 CCCTATATTTTTAAATTTTATCGAAATGGGCCCGGTATTTTATTTTTTTTACTGTTGGGTACTGT
131 CCCTATATTTTTAAATTTTATCGAAATGGGCCCGGTATTTTATTTTTTTTACTGTTGGGTACTGT
3506963 AACACCCCTTAACCGTATCCAACACCGGAATAGGG
196 AACACCCCTTAACCGTATCCAACACCGGAATAGGG
3506998 TGTTGGTAAC-ATTTTGAATATTTTTTGTACTTGTTGCTATTGATGTAATATTGAAGAGTTAATT
1 TGTTGGTAACAATTTTGAATATTTTTTGTACTTGTTGCTATTGATGTAATATTGAAGAGTTAATT
3507062 GATTAAAAAAAATAAATACAAATACAAAAAAATTCAAAATTTATTTTTTCAAAATACCAAAAAAG
66 GATTAAAAAAAATAAATACAAATACAAAAAAATTCAAAATTTATTTTTTCAAAATACCAAAAAAG
3507127 CCCTATATTTTTAAATTTTATCGAAATGGGCCCGGTATTTTATTTTTTTTACTGTTGGGTACTGT
131 CCCTATATTTTTAAATTTTATCGAAATGGGCCCGGTATTTTATTTTTTTTACTGTTGGGTACTGT
3507192 AACACCCCTTAACCGTATCCAACACCGGAATAGGG
196 AACACCCCTTAACCGTATCCAACACCGGAATAGGG
3507227 T
1 T
3507228 ACGAGGCATT
Statistics
Matches: 229, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
229 219 0.96
230 10 0.04
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Consensus pattern (230 bp):
TGTTGGTAACAATTTTGAATATTTTTTGTACTTGTTGCTATTGATGTAATATTGAAGAGTTAATT
GATTAAAAAAAATAAATACAAATACAAAAAAATTCAAAATTTATTTTTTCAAAATACCAAAAAAG
CCCTATATTTTTAAATTTTATCGAAATGGGCCCGGTATTTTATTTTTTTTACTGTTGGGTACTGT
AACACCCCTTAACCGTATCCAACACCGGAATAGGG
Found at i:3511214 original size:228 final size:228
Alignment explanation
Indices: 3510805--3511215 Score: 513
Period size: 228 Copynumber: 1.8 Consensus size: 228
3510795 CGTAAACGAA
* *
3510805 AAACGCCGGAACATTTGAAACTGAAACGCAACGTTTCATCTTGAGCTATAGCGCCTTTAGTGGCG
1 AAACGCCGAAAAATTTGAAACTGAAACGCAACGTTTCATCTTGAGCTATAGCGCCTTTAGTGGCG
** * * ** * * * * *
3510870 CTTAGCTGAAAACGCCGCTATATATCAGCTTTTCGTGATGCTATTCCTGAATCGCCTCAAATATT
66 CTTAGCCCAAAACGCCGCTATAGATCAACTTTTAATGACGCTATTCCTGAAGCGCCGCAAAAAAT
* * * *
3510935 TTGAACAAAACGCATCGTTCGGGTTTGACGTATAAAGGCATTGGTGGCGCTTACCAGAAAACGCC
131 TTGAACAAAACGCATCGTTCGGGCTTCACGTATAAAGGCATTAGCGGCGCTTACCAGAAAACGCC
3511000 GCTATATCCCATAAATAGTGGCGTTTAACTAAC
196 GCTATATCCCATAAATAGTGGCGTTTAACTAAC
* * *
3511033 AAACGCCGAAAAATTTTAAACTGAAACTCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGTGGCG
1 AAACGCCGAAAAATTTGAAACTGAAACGCAACGTTTCATCTTGAGCTATAGCGCCTTTAGTGGCG
* * *
3511098 CTTA-CCCATAAACGCCGCTATAGATCAACTTTTAATGGCGCT-TCTGCTTAAGCGCCGCAAAAA
66 CTTAGCCCA-AAACGCCGCTATAGATCAACTTTTAATGACGCTAT-TCCTGAAGCGCCGCAAAAA
* * * * **
3511161 ATTTGACCAAAACGTATTGTTTC-GGCTTCACGTATAGATTCATTAGCGGCGCTTA
129 ATTTGAACAAAACGCATCG-TTCGGGCTTCACGTATAAAGGCATTAGCGGCGCTTA
3511216 TTTGGAAACA
Statistics
Matches: 151, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
227 3 0.02
228 145 0.96
229 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (228 bp):
AAACGCCGAAAAATTTGAAACTGAAACGCAACGTTTCATCTTGAGCTATAGCGCCTTTAGTGGCG
CTTAGCCCAAAACGCCGCTATAGATCAACTTTTAATGACGCTATTCCTGAAGCGCCGCAAAAAAT
TTGAACAAAACGCATCGTTCGGGCTTCACGTATAAAGGCATTAGCGGCGCTTACCAGAAAACGCC
GCTATATCCCATAAATAGTGGCGTTTAACTAAC
Found at i:3511575 original size:13 final size:14
Alignment explanation
Indices: 3511557--3511597 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
3511547 TTTCTAAAGA
3511557 TATGGTTTAGGA-T
1 TATGGTTTAGGACT
*
3511570 TATGGTTTATGACT
1 TATGGTTTAGGACT
*
3511584 TACGGTTTA-GACT
1 TATGGTTTAGGACT
3511597 T
1 T
3511598 TAGGGGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (14 bp):
TATGGTTTAGGACT
Found at i:3511724 original size:8 final size:8
Alignment explanation
Indices: 3511711--3511737 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3511701 TTTGGATTTT
3511711 GTGGTTTG
1 GTGGTTTG
3511719 GTGGTTTG
1 GTGGTTTG
3511727 GTGGTTTG
1 GTGGTTTG
3511735 GTG
1 GTG
3511738 TTTTATGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (8 bp):
GTGGTTTG
Found at i:3511780 original size:21 final size:21
Alignment explanation
Indices: 3511755--3511831 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
3511745 GTCAATTGAC
3511755 GGGTTTAGGGTTTAAGTTTTA
1 GGGTTTAGGGTTTAAGTTTTA
* * * * *
3511776 TGGTTTGGGGTTTGAGGTGTA
1 GGGTTTAGGGTTTAAGTTTTA
* *
3511797 GGGTTAAGGGTTTATAG-TTTG
1 GGGTTTAGGGTTTA-AGTTTTA
*
3511818 GGGTTTAGGATTTA
1 GGGTTTAGGGTTTA
3511832 CAATTAATTA
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
21 40 0.95
22 2 0.05
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (21 bp):
GGGTTTAGGGTTTAAGTTTTA
Found at i:3512014 original size:15 final size:16
Alignment explanation
Indices: 3511982--3512020 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3511972 GATATTCTAG
3511982 ATTAATATAAATGAAA
1 ATTAATATAAATGAAA
3511998 A-TAATATAAAT-ATAA
1 ATTAATATAAATGA-AA
3512013 ATTAATAT
1 ATTAATAT
3512021 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 13 0.62
16 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTAATATAAATGAAA
Found at i:3512272 original size:16 final size:16
Alignment explanation
Indices: 3512251--3512306 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
3512241 CAAAAGTAAT
3512251 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
3512267 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
* * *
3512283 GAAATAAATA-AATAAA
1 TAAA-AGATACAATTAA
3512299 TAAAAGAT
1 TAAAAGAT
3512307 GTGAGATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 27 0.79
17 4 0.12
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.23
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:3515068 original size:20 final size:18
Alignment explanation
Indices: 3515027--3515078 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
3515017 TGTAATGTCA
*
3515027 ATAAATATTT-AAAAAT-
1 ATAAAAATTTAAAAAATC
3515043 -TAAAAATATATAAAAAATC
1 ATAAAAAT-T-TAAAAAATC
3515062 ATAAAAATTTAAAAAAT
1 ATAAAAATTTAAAAAAT
3515079 AACATGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 6 0.20
16 1 0.03
17 1 0.03
18 14 0.47
19 1 0.03
20 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATTTAAAAAATC
Found at i:3515881 original size:373 final size:374
Alignment explanation
Indices: 3515196--3515943 Score: 1489
Period size: 373 Copynumber: 2.0 Consensus size: 374
3515186 TAATGGTTAA
3515196 ATTCGATTCTTTATAGAAGTTTAAGCGTCAAACTTAACTAAAAGAAAAAGGGTCAAATTGATAAA
1 ATTCGATTCTTTATAGAAGTTTAAGCGTCAAACTTAACTAAAAGAAAAAGGGTCAAATTGATAAA
3515261 AAGAATATAAACATTAAGGGATAAATTTTTCATTATGCCTATTAGTTATTAATGGATTAATTATT
66 AAGAATATAAACATTAAGGGATAAATTTTTCATTATGCCTATTAGTTATTAATGGATTAATTATT
3515326 ACTACCCTATGTAAAACTTTTATAAATAGAATTACGTTGCTCCCGAATTTTTTTTAAAAAAATTG
131 ACTACCCTATGTAAAACTTTTATAAATAGAATTACGTTGCTCCCGAATTTTTTTTAAAAAAATTG
3515391 GTTTAAAATTGAAGTACTATTGTTAAAAATTGTTTTTAAGAAGTTAAAATTTTGATCTTAGATAT
196 GTTTAAAATTGAAGTACTATTGTTAAAAATTGTTTTTAAGAAGTTAAAATTTTGATCTTAGATAT
3515456 AATGTTGAAAAGTAAATATATATATTTAAATGACATTTAAATTCAATGTTTCAATAAAAATATGA
261 AATGTTGAAAAGTAAATATATATATTTAAATGACATTTAAATTCAATGTTTCAATAAAAATATGA
3515521 GAAAATTATTTATTTTAATTTATTACTAATTTTTTGATA-CTGAAATAT
326 GAAAATTATTTATTTTAATTTATTACTAATTTTTTGATAGCTGAAATAT
3515569 ATTCGATTCTTTATAGAAGTTTAAGCGTCAAACTTAACTAAAAGAAAAAGGGTCAAATTGATAAA
1 ATTCGATTCTTTATAGAAGTTTAAGCGTCAAACTTAACTAAAAGAAAAAGGGTCAAATTGATAAA
3515634 AAGAATATAAACATTAAGGGATAAATTTTTCATTATGCCTATTAGTTATTAATGGATTAATTATT
66 AAGAATATAAACATTAAGGGATAAATTTTTCATTATGCCTATTAGTTATTAATGGATTAATTATT
3515699 ACTACCCTATGTAAAACTTTTATAAATAGAATTACGTTGCTCCCGAATTTTTTTTAAAAAAATTG
131 ACTACCCTATGTAAAACTTTTATAAATAGAATTACGTTGCTCCCGAATTTTTTTTAAAAAAATTG
3515764 GTTTAAAATTGAAGTACTATTGTTAAAAATTGTTTTTAAGAAGTTAAAATTTTGATCTTAGATAT
196 GTTTAAAATTGAAGTACTATTGTTAAAAATTGTTTTTAAGAAGTTAAAATTTTGATCTTAGATAT
3515829 AATGTTGAAAAGTAAATATATATATTTAAATGACATTTAAATTCAATGTTTCAATAAAAATATGA
261 AATGTTGAAAAGTAAATATATATATTTAAATGACATTTAAATTCAATGTTTCAATAAAAATATGA
3515894 GAAAATTATTTATTTTAATTTATTACTAATTTTTTGATAGCTGAAATAT
326 GAAAATTATTTATTTTAATTTATTACTAATTTTTTGATAGCTGAAATAT
3515943 A
1 A
3515944 AAGTTTAAGT
Statistics
Matches: 374, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
373 364 0.97
374 10 0.03
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.40
Consensus pattern (374 bp):
ATTCGATTCTTTATAGAAGTTTAAGCGTCAAACTTAACTAAAAGAAAAAGGGTCAAATTGATAAA
AAGAATATAAACATTAAGGGATAAATTTTTCATTATGCCTATTAGTTATTAATGGATTAATTATT
ACTACCCTATGTAAAACTTTTATAAATAGAATTACGTTGCTCCCGAATTTTTTTTAAAAAAATTG
GTTTAAAATTGAAGTACTATTGTTAAAAATTGTTTTTAAGAAGTTAAAATTTTGATCTTAGATAT
AATGTTGAAAAGTAAATATATATATTTAAATGACATTTAAATTCAATGTTTCAATAAAAATATGA
GAAAATTATTTATTTTAATTTATTACTAATTTTTTGATAGCTGAAATAT
Found at i:3516016 original size:19 final size:20
Alignment explanation
Indices: 3515984--3516021 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3515974 AAATTTTTAA
* *
3515984 TTTAATTATATAAATTATAT
1 TTTAACTATATAAAATATAT
3516004 TTTAACTAT-TAAAATATA
1 TTTAACTATATAAAATATA
3516022 ATTATCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAACTATATAAAATATAT
Found at i:3517828 original size:15 final size:15
Alignment explanation
Indices: 3517796--3517835 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
3517786 ACAGAAAAGT
*
3517796 AAAA-CATTTT-CTA
1 AAAATCATTTTACGA
3517809 AAAATCATTTTACGA
1 AAAATCATTTTACGA
3517824 AAAAT-ATTTTAC
1 AAAATCATTTTAC
3517836 TTGCAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 13 0.54
15 7 0.29
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (15 bp):
AAAATCATTTTACGA
Found at i:3518144 original size:17 final size:18
Alignment explanation
Indices: 3518110--3518147 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3518100 AGTGAAAGAA
*
3518110 AAAAATGTATAATTATAAT
1 AAAAATATATAA-TATAAT
3518129 AAAAATATATAA-ATAAT
1 AAAAATATATAATATAAT
3518146 AA
1 AA
3518148 CTAATAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAAATATATAATATAAT
Found at i:3518152 original size:7 final size:7
Alignment explanation
Indices: 3518137--3518168 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3518127 ATAAAAATAT
*
3518137 ATAAATA
1 ATAACTA
3518144 ATAACTA
1 ATAACTA
3518151 ATAACTA
1 ATAACTA
3518158 ATAACTA
1 ATAACTA
3518165 ATAA
1 ATAA
3518169 ATAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAACTA
Found at i:3518154 original size:14 final size:14
Alignment explanation
Indices: 3518137--3518184 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
3518127 ATAAAAATAT
3518137 ATAAATAATAACTA
1 ATAAATAATAACTA
*
3518151 ATAACTAATAACTA
1 ATAAATAATAACTA
*
3518165 ATAAATAA-AAATA
1 ATAAATAATAACTA
3518178 A-AAATAA
1 ATAAATAA
3518185 ATAGATAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
12 6 0.19
13 5 0.16
14 20 0.65
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (14 bp):
ATAAATAATAACTA
Found at i:3527303 original size:21 final size:21
Alignment explanation
Indices: 3527251--3527345 Score: 75
Period size: 21 Copynumber: 4.5 Consensus size: 21
3527241 ATTTAACTCA
* * *
3527251 TATGAGTTTCCGTTCAGCCCT
1 TATGGGTTTCTGTTCAACCCT
* * * *
3527272 TTTGAGCTTCTGTTTAACCCT
1 TATGGGTTTCTGTTCAACCCT
* *
3527293 TATGGGTTTCTGTTCAGCTCT
1 TATGGGTTTCTGTTCAACCCT
* *
3527314 TACGAGCTTTC-GTTCAACCCT
1 TATG-GGTTTCTGTTCAACCCT
3527335 TATGGGTTTCT
1 TATGGGTTTCT
3527346 ATTTAGCTTT
Statistics
Matches: 55, Mismatches: 17, Indels: 4
0.72 0.22 0.05
Matches are distributed among these distances:
20 5 0.09
21 45 0.82
22 5 0.09
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (21 bp):
TATGGGTTTCTGTTCAACCCT
Found at i:3527345 original size:42 final size:42
Alignment explanation
Indices: 3527251--3527371 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
3527241 ATTTAACTCA
* * ** *
3527251 TATGAGTTTCCGTTCAGCCCTTTTGAGCTTCTGTTTAACCCT
1 TATGGGTTTCTGTTCAGCCCTTACGAGCTTCTGTTCAACCCT
*
3527293 TATGGGTTTCTGTTCAGCTCTTACGAGCTT-TCGTTCAACCCT
1 TATGGGTTTCTGTTCAGCCCTTACGAGCTTCT-GTTCAACCCT
* * * *
3527335 TATGGGTTTCTATTTAG-CTTTCATGAGCTTCTGTTCA
1 TATGGGTTTCTGTTCAGCCCTT-ACGAGCTTCTGTTCA
3527372 GCCTTCGGGC
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
41 3 0.05
42 61 0.94
43 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (42 bp):
TATGGGTTTCTGTTCAGCCCTTACGAGCTTCTGTTCAACCCT
Found at i:3530483 original size:9 final size:9
Alignment explanation
Indices: 3530458--3530547 Score: 62
Period size: 10 Copynumber: 9.8 Consensus size: 9
3530448 TTAAAAATGA
*
3530458 TATAAAATT
1 TATAAAAAT
3530467 TATAAAAAAT
1 TAT-AAAAAT
*
3530477 AATAAAAACT
1 TATAAAAA-T
*
3530487 TATAAATAT
1 TATAAAAAT
3530496 TATAAAAA-
1 TATAAAAAT
3530504 TATAAAAAT
1 TATAAAAAT
3530513 CTAGT--AAAT
1 -TA-TAAAAAT
*
3530522 TCTAATAAAT
1 TATAA-AAAT
3530532 TAT-AAAAT
1 TATAAAAAT
3530540 TAATAAAA
1 T-ATAAAA
3530548 CATGTTTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
7 1 0.02
8 14 0.22
9 23 0.36
10 25 0.39
11 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (9 bp):
TATAAAAAT
Found at i:3530512 original size:19 final size:19
Alignment explanation
Indices: 3530449--3530512 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
3530439 CTAAAGATAT
*
3530449 TAAAAATGA-TATAAAATTTA
1 TAAAAAT-ATTATAAAA-ATA
*
3530469 TAAAAA-ATAATAAAAACT-
1 TAAAAATATTATAAAAA-TA
*
3530487 TATAAATATTATAAAAATA
1 TAAAAATATTATAAAAATA
3530506 TAAAAAT
1 TAAAAAT
3530513 CTAGTAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
18 7 0.20
19 22 0.63
20 6 0.17
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAAATATTATAAAAATA
Found at i:3531063 original size:15 final size:14
Alignment explanation
Indices: 3531043--3531078 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
3531033 AAAATTGGAG
3531043 ATAAAAATTTTAAAA
1 ATAAAAA-TTTAAAA
*
3531058 ATAAAAATTTATAA
1 ATAAAAATTTAAAA
3531072 ATAAAAA
1 ATAAAAA
3531079 GGAGAGGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAAAATTTAAAA
Found at i:3531199 original size:8 final size:9
Alignment explanation
Indices: 3531182--3531260 Score: 63
Period size: 9 Copynumber: 8.4 Consensus size: 9
3531172 AAATGATTAT
*
3531182 TTTTTAAAA
1 TTTTTATAA
3531191 TTTTTA-AA
1 TTTTTATAA
3531199 TTTTTATAA
1 TTTTTATAA
*
3531208 CTTTTATAA
1 TTTTTATAA
*
3531217 TTTCTATATACC
1 TTT-T-TATA-A
*
3531229 TTATTATAA
1 TTTTTATAA
3531238 TTTTTAT-A
1 TTTTTATAA
3531246 TTATTTATAAA
1 TT-TTTAT-AA
3531257 TTTT
1 TTTT
3531261 GGGAAATTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
8 11 0.19
9 29 0.51
10 7 0.12
11 8 0.14
12 2 0.04
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3531212 original size:18 final size:19
Alignment explanation
Indices: 3531182--3531245 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 19
3531172 AAATGATTAT
*
3531182 TTTTTA-AAATTTTTA-AA
1 TTTTTATAACTTTTTATAA
3531199 TTTTTATAAC-TTTTATAA
1 TTTTTATAACTTTTTATAA
* *
3531217 TTTCTATATACCTTATTATAA
1 TTT-T-TATAACTTTTTATAA
3531238 TTTTTATA
1 TTTTTATA
3531246 TTATTTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 11 0.28
18 7 0.18
19 5 0.13
20 6 0.15
21 10 0.26
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTTATAACTTTTTATAA
Found at i:3531253 original size:21 final size:21
Alignment explanation
Indices: 3531197--3531246 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3531187 AAAATTTTTA
3531197 AATTTTTATA-A-CTT-TTAT
1 AATTTTTATATACCTTATTAT
*
3531215 AATTTCTATATACCTTATTAT
1 AATTTTTATATACCTTATTAT
3531236 AATTTTTATAT
1 AATTTTTATAT
3531247 TATTTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 1 0.04
20 3 0.11
21 14 0.52
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTTTTATATACCTTATTAT
Found at i:3531255 original size:18 final size:18
Alignment explanation
Indices: 3531193--3531260 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
3531183 TTTTAAAATT
*
3531193 TTTA-AATTTTTATAACT-
1 TTTATAATTTTTAT-ATTA
3531210 TTTATAATTTCTATATACCTTA
1 TTTATAATTT-T-TATA--TTA
3531232 -TTATAATTTTTATATTA
1 TTTATAATTTTTATATTA
3531249 TTTATAAATTTT
1 TTTAT-AATTTT
3531261 GGGAAATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
17 7 0.17
18 9 0.21
19 12 0.29
20 4 0.10
21 10 0.24
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATAATTTTTATATTA
Found at i:3531292 original size:11 final size:10
Alignment explanation
Indices: 3531180--3531293 Score: 53
Period size: 9 Copynumber: 11.7 Consensus size: 10
3531170 TTAAATGATT
3531180 ATTTTT-TAA
1 ATTTTTATAA
*
3531189 AATTTT-TAA
1 ATTTTTATAA
3531198 ATTTTTAT-A
1 ATTTTTATAA
*
3531207 ACTTTTAT-A
1 ATTTTTATAA
*
3531216 ATTTCTATATAC
1 ATTT-T-TATAA
* *
3531228 CTTATTAT-A
1 ATTTTTATAA
3531237 ATTTTTAT--
1 ATTTTTATAA
3531245 ATTATTTATAA
1 ATT-TTTATAA
***
3531256 ATTTTGGGAA
1 ATTTTTATAA
3531266 ATTTTTTATAA
1 A-TTTTTATAA
*
3531277 GTTTTTATAA
1 ATTTTTATAA
*
3531287 AATTTTA
1 ATTTTTA
3531294 AATACATTTC
Statistics
Matches: 78, Mismatches: 19, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
8 3 0.04
9 36 0.46
10 24 0.31
11 13 0.17
12 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:3531392 original size:20 final size:20
Alignment explanation
Indices: 3531367--3531412 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3531357 TTATTTTTTA
*
3531367 TTTTTAAGGACTTTTATAAG
1 TTTTTAAGAACTTTTATAAG
* *
3531387 TTTTTAAGAATTTTTATACG
1 TTTTTAAGAACTTTTATAAG
3531407 TTTTTA
1 TTTTTA
3531413 TAAAAATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (20 bp):
TTTTTAAGAACTTTTATAAG
Found at i:3531477 original size:105 final size:106
Alignment explanation
Indices: 3531354--3531570 Score: 418
Period size: 105 Copynumber: 2.1 Consensus size: 106
3531344 TTTAAAGGGT
3531354 ATATTATTTTTTATTTTTAAGGACTTTTATAAGTTTTTAAGAATTTTTATACGTTTTTATAAAAA
1 ATATTATTTTTTATTTTTAAGGACTTTTATAAGTTTTTAAGAATTTTTATACGTTTTTATAAAAA
3531419 TAGATTAAATAAATTGTCATTTTTATCATTTTTATG-GAAA
66 TAGATTAAATAAATTGTCATTTTTATCATTTTTATGAGAAA
*
3531459 ATATTATTTTTTATTTTTAATGACTTTTATAAGTTTTTAAGAATTTTTATACGTTTTTATAAAAA
1 ATATTATTTTTTATTTTTAAGGACTTTTATAAGTTTTTAAGAATTTTTATACGTTTTTATAAAAA
3531524 TAGATTAAATAAATTGTCATTTTTATCATTTTTATGAGAAA
66 TAGATTAAATAAATTGTCATTTTTATCATTTTTATGAGAAA
3531565 ATATTA
1 ATATTA
3531571 AATTAAATCA
Statistics
Matches: 110, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
105 100 0.91
106 10 0.09
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (106 bp):
ATATTATTTTTTATTTTTAAGGACTTTTATAAGTTTTTAAGAATTTTTATACGTTTTTATAAAAA
TAGATTAAATAAATTGTCATTTTTATCATTTTTATGAGAAA
Found at i:3531497 original size:20 final size:20
Alignment explanation
Indices: 3531472--3531517 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3531462 TTATTTTTTA
3531472 TTTTTAATG-ACTTTTATAAG
1 TTTTTAA-GAACTTTTATAAG
* *
3531492 TTTTTAAGAATTTTTATACG
1 TTTTTAAGAACTTTTATAAG
3531512 TTTTTA
1 TTTTTA
3531518 TAAAAATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (20 bp):
TTTTTAAGAACTTTTATAAG
Found at i:3531571 original size:40 final size:41
Alignment explanation
Indices: 3531501--3531578 Score: 99
Period size: 40 Copynumber: 1.9 Consensus size: 41
3531491 GTTTTTAAGA
*
3531501 ATTTTTATACGTTTTTATAAAAATAGATTAAA-TAAATTGTC
1 ATTTTTATACATTTTTATAAAAATA-ATTAAATTAAATTGTC
3531542 ATTTTTAT-CATTTTTATGAGAAAAT-ATTAAATTAAAT
1 ATTTTTATACATTTTTAT-A-AAAATAATTAAATTAAAT
3531579 CAAGAATTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
40 14 0.42
41 14 0.42
42 5 0.15
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (41 bp):
ATTTTTATACATTTTTATAAAAATAATTAAATTAAATTGTC
Found at i:3546199 original size:15 final size:15
Alignment explanation
Indices: 3546163--3546199 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3546153 AGTTATAATT
3546163 ATAATAATAAAAGAA
1 ATAATAATAAAAGAA
3546178 A-ACATAATAAAAGAA
1 ATA-ATAATAAAAGAA
3546193 ATAATAA
1 ATAATAA
3546200 GAAAGTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 18 0.90
16 1 0.05
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (15 bp):
ATAATAATAAAAGAA
Found at i:3548722 original size:51 final size:50
Alignment explanation
Indices: 3548633--3548730 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
3548623 TAGTGTAAAA
* *
3548633 TTTAAATTTATTATTCTATTTAAAAAAATGTTTATGTATATTTATATATT
1 TTTAAATTTATTATTATATTTAAAAAAATATTTATGTATATTTATATATT
*** * *
3548683 TTTAAATTTATTATTATATTTTTTGAAAATATTTGTGTATTTTTATAT
1 TTTAAATTTATTATTATA-TTTAAAAAAATATTTATGTATATTTATAT
3548731 GTTTATTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 17 0.43
51 23 0.57
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (50 bp):
TTTAAATTTATTATTATATTTAAAAAAATATTTATGTATATTTATATATT
Found at i:3554450 original size:26 final size:25
Alignment explanation
Indices: 3554411--3554460 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
3554401 ATTATTTTAT
* *
3554411 TTTAGTTTTTTATTCAAAATTTTTTG
1 TTTAGTTATATATT-AAAATTTTTTG
*
3554437 TTTAGTTATATATTACAATTTTTT
1 TTTAGTTATATATTAAAATTTTTT
3554461 TAAAGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (25 bp):
TTTAGTTATATATTAAAATTTTTTG
Found at i:3554546 original size:21 final size:20
Alignment explanation
Indices: 3554516--3554564 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
3554506 TAAACCTTAA
**
3554516 AAAT-AAAAATAATGTAATT
1 AAATAAAAAATAAACTAATT
3554535 AGAATAAAAAATAAACTAATT
1 A-AATAAAAAATAAACTAATT
3554556 AAATAAAAA
1 AAATAAAAA
3554565 TGGATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 11 0.42
21 14 0.54
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
AAATAAAAAATAAACTAATT
Found at i:3559448 original size:14 final size:15
Alignment explanation
Indices: 3559429--3559460 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3559419 GTGGTTATAG
3559429 TTAAAATA-ATAAAA
1 TTAAAATAGATAAAA
3559443 TTAAAATAGATAAAA
1 TTAAAATAGATAAAA
3559458 TTA
1 TTA
3559461 TGATGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
TTAAAATAGATAAAA
Found at i:3562694 original size:30 final size:30
Alignment explanation
Indices: 3562660--3562911 Score: 201
Period size: 30 Copynumber: 8.4 Consensus size: 30
3562650 ATGGTTGACA
* *
3562660 CATCCCTTTTCGTAATTTGATAACCGAAGC
1 CATCCCTTTTCATAATTTGATAGCCGAAGC
* * *
3562690 CATCCCTTTTCATAATTTGATGGTCGTCA-C
1 CATCCCTTTTCATAATTTGATAGCCG-AAGC
* * ** * *
3562720 CATCCATTTTTATTGTTTGATGGTCGTCAA--
1 CATCCCTTTTCATAATTTGATAGCCG--AAGC
*
3562750 CATCCCTTTTCATAATTTGATAGCCAAAGC
1 CATCCCTTTTCATAATTTGATAGCCGAAGC
*
3562780 CATCCCTTTTCATAGA-TCGATAGCCGAAGC
1 CATCCCTTTTCATA-ATTTGATAGCCGAAGC
* ** *
3562810 CATCCCTTTTCATAGTACGATAGCCAAAGC
1 CATCCCTTTTCATAATTTGATAGCCGAAGC
* * * *
3562840 CATCCCTTTTCATAATTTTATGGTCGTCA-C
1 CATCCCTTTTCATAATTTGATAGCCG-AAGC
* *
3562870 AATCCCTTTTCATTA-TTGATAGCCGAAGC
1 CATCCCTTTTCATAATTTGATAGCCGAAGC
*
3562899 TATCCCTTTTCAT
1 CATCCCTTTTCAT
3562912 TCGTCAATGA
Statistics
Matches: 176, Mismatches: 38, Indels: 17
0.76 0.16 0.07
Matches are distributed among these distances:
28 3 0.02
29 20 0.11
30 149 0.85
31 4 0.02
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.37
Consensus pattern (30 bp):
CATCCCTTTTCATAATTTGATAGCCGAAGC
Found at i:3573000 original size:26 final size:26
Alignment explanation
Indices: 3572964--3573026 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
3572954 TCAATAGTGC
3572964 TCACACGAGCTGTGAAATGGGTCTGT
1 TCACACGAGCTGTGAAATGGGTCTGT
3572990 TCACACGAGCTGTGAAATGGGTCTGT
1 TCACACGAGCTGTGAAATGGGTCTGT
*
3573016 TTACACGAGCT
1 TCACACGAGCT
3573027 ATGGGTCAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (26 bp):
TCACACGAGCTGTGAAATGGGTCTGT
Found at i:3576349 original size:26 final size:28
Alignment explanation
Indices: 3576306--3576357 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
3576296 AAAAAATAAA
3576306 AAAAATAGAAAAACGAAAAAAAAACAGC
1 AAAAATAGAAAAACGAAAAAAAAACAGC
* *
3576334 AAAAATAG-TAAA-GAAAAAACAACA
1 AAAAATAGAAAAACGAAAAAAAAACA
3576358 AATTTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 3 0.14
28 8 0.36
ACGTcount: A:0.75, C:0.10, G:0.10, T:0.06
Consensus pattern (28 bp):
AAAAATAGAAAAACGAAAAAAAAACAGC
Found at i:3587406 original size:43 final size:42
Alignment explanation
Indices: 3587345--3587449 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
3587335 TTTATGGTTT
3587345 CTCTTACGAGCTTCCGTTCAACCCTTATGGGGTTTCTGTTCAG
1 CTCTTACGAGCTTCCGTTCAACCCTTAT-GGGTTTCTGTTCAG
*
3587388 CTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAG
1 CTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTCAG
* * * *
3587430 TTCTCATGAGCTTCTGTTCA
1 CTCTTACGAGCTTCCGTTCA
3587450 GCCTTCGAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 29 0.51
43 28 0.49
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (42 bp):
CTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTCAG
Found at i:3587414 original size:21 final size:21
Alignment explanation
Indices: 3587347--3587414 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
3587337 TATGGTTTCT
3587347 CTTACGAGCTTCCGTTCAACC
1 CTTACGAGCTTCCGTTCAACC
* * * * * *
3587368 CTTATGGGGTTTCTGTTCAGCT
1 CTTA-CGAGCTTCCGTTCAACC
3587390 CTTACGAGCTTCCGTTCAACC
1 CTTACGAGCTTCCGTTCAACC
3587411 CTTA
1 CTTA
3587415 TGGGTTTCTG
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (21 bp):
CTTACGAGCTTCCGTTCAACC
Found at i:3592421 original size:21 final size:21
Alignment explanation
Indices: 3592395--3592435 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3592385 TTTAACTGAG
3592395 CTCGTGTCACGAGTCACTAAT
1 CTCGTGTCACGAGTCACTAAT
3592416 CTCGTGTCACGAGTCACTAA
1 CTCGTGTCACGAGTCACTAA
3592436 AAATCAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (21 bp):
CTCGTGTCACGAGTCACTAAT
Found at i:3594596 original size:31 final size:31
Alignment explanation
Indices: 3594561--3594619 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3594551 ACACAATGAT
3594561 TTAAATGAAAAATTTTGATTAGTTCAGTTAC
1 TTAAATGAAAAATTTTGATTAGTTCAGTTAC
* *
3594592 TTAAATGTAAACTTTTGATTAGTTCAGT
1 TTAAATGAAAAATTTTGATTAGTTCAGT
3594620 GATTACTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (31 bp):
TTAAATGAAAAATTTTGATTAGTTCAGTTAC
Found at i:3608276 original size:33 final size:33
Alignment explanation
Indices: 3608231--3608298 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
3608221 ATTTGTCCAG
3608231 GTATGTTCCGTACTCCGTTAATTTTGATGATAC
1 GTATGTTCCGTACTCCGTTAATTTTGATGATAC
*
3608264 GTATGTTTCGTACTCCGTTAATTTTGATGATAC
1 GTATGTTCCGTACTCCGTTAATTTTGATGATAC
3608297 GT
1 GT
3608299 CCTTGTGTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (33 bp):
GTATGTTCCGTACTCCGTTAATTTTGATGATAC
Found at i:3610273 original size:26 final size:26
Alignment explanation
Indices: 3610227--3610276 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3610217 ACCTAAGTCC
*
3610227 ATAACAGTAATAGATATCAGAATCAA
1 ATAACAGTAATAGACATCAGAATCAA
*
3610253 ATAACAGT-TTAGACATACAGAATC
1 ATAACAGTAATAGACAT-CAGAATC
3610277 CTATCCCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (26 bp):
ATAACAGTAATAGACATCAGAATCAA
Found at i:3611420 original size:5 final size:5
Alignment explanation
Indices: 3611410--3611442 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
3611400 AAAAGGGGAA
3611410 AAATT AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAA
3611443 ACTATACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:3611479 original size:7 final size:7
Alignment explanation
Indices: 3611466--3611506 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
3611456 CTCACTCCCC
3611466 CACTAAT
1 CACTAAT
*
3611473 AACTAAT
1 CACTAAT
3611480 CACTAAT
1 CACTAAT
3611487 CACTAAT
1 CACTAAT
3611494 CACTAAT
1 CACTAAT
3611501 CACTAA
1 CACTAA
3611507 CAGTCTTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (7 bp):
CACTAAT
Found at i:3612684 original size:3 final size:3
Alignment explanation
Indices: 3612676--3612716 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3612666 CTAGAAAAAT
*
3612676 GAA GAA GAA GAA GAA GAA GAA TAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3612717 TAATTGGGCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:3615712 original size:17 final size:16
Alignment explanation
Indices: 3615692--3615749 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
3615682 ATGAAATGTT
3615692 AATAATTTAAATTTTGA
1 AATAATTTAAA-TTTGA
*
3615709 AATATTTTAAATTTGA
1 AATAATTTAAATTTGA
* *
3615725 AATTATAT-AA-TT-A
1 AATAATTTAAATTTGA
3615738 AATAATTTAAAT
1 AATAATTTAAAT
3615750 AATTCGAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 2 0.06
16 10 0.30
17 10 0.30
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AATAATTTAAATTTGA
Found at i:3615723 original size:16 final size:17
Alignment explanation
Indices: 3615692--3615727 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3615682 ATGAAATGTT
3615692 AATAATTTAAATTTTGA
1 AATAATTTAAATTTTGA
*
3615709 AATATTTTAAA-TTTGA
1 AATAATTTAAATTTTGA
3615725 AAT
1 AAT
3615728 TATATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
AATAATTTAAATTTTGA
Found at i:3615994 original size:31 final size:31
Alignment explanation
Indices: 3615946--3616023 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
3615936 TCAATCCATC
*
3615946 TAATTAAAAAAAATCAAAATAATGGTTGTACG
1 TAATT-AAACAAATCAAAATAATGGTTGTACG
3615978 TAATTAAACAAATCAAAATAATGGTTGTACG
1 TAATTAAACAAATCAAAATAATGGTTGTACG
3616009 TAATTAAACAAATCA
1 TAATTAAACAAATCA
3616024 TGTTATTCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 40 0.89
32 5 0.11
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.28
Consensus pattern (31 bp):
TAATTAAACAAATCAAAATAATGGTTGTACG
Found at i:3617455 original size:21 final size:22
Alignment explanation
Indices: 3617431--3617473 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3617421 TTTGGTTAAC
3617431 AAGT-TTGAGGA-TAGAATATGT
1 AAGTATTGAGGACTA-AATATGT
3617452 AAGTATTGAGGACTAAATATGT
1 AAGTATTGAGGACTAAATATGT
3617474 TATTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 14 0.70
23 2 0.10
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.33
Consensus pattern (22 bp):
AAGTATTGAGGACTAAATATGT
Found at i:3618694 original size:300 final size:301
Alignment explanation
Indices: 3618152--3618752 Score: 1195
Period size: 300 Copynumber: 2.0 Consensus size: 301
3618142 TTGCCTCTTA
3618152 CTCTCATTGAATAGTACACATATGTTTATTTGTACGAATATTAAAATATTGTGTTAACCTTGGGG
1 CTCTCATTGAATAGTACACATATGTTTATTTGTACGAATATTAAAATATTGTGTTAACCTTGGGG
3618217 AGTCAACATGATCAGGATGAATTTACTTTTAAATCAGTGATTCTTTCACGACATAGTAATTATTT
66 AGTCAACATGATCAGGATGAATTTACTTTTAAATCAGTGATTCTTTCACGACATAGTAATTATTT
3618282 TATTTATTTACGTTTATTTTTCCTATCAAATTCAAAGAAAATTTGAATTTAAAACTCTATTTATC
131 TATTTATTTACGTTTATTTTTCCTATCAAATTCAAAGAAAATTTGAATTTAAAACTCTATTTATC
3618347 TAGTAAAATTTTGTATATTATGGACAGATTGTTGTTATATGCCTATCTATAATATATATTTATAA
196 TAGTAAAATTTTGTATATTATGGACAGATTGTTGTTATATGCCTATCTATAATATATATTTATAA
3618412 TAATTCTATTTGTCTGTTAAAATTTTGCAT-TTATGGAAAG
261 TAATTCTATTTGTCTGTTAAAATTTTGCATGTTATGGAAAG
3618452 CTCTCATTGAATAGTACACATATGTTTATTTGTACGAATATTAAAATATTGTGTTAACCTTGGGG
1 CTCTCATTGAATAGTACACATATGTTTATTTGTACGAATATTAAAATATTGTGTTAACCTTGGGG
3618517 AGTCAACATGATCAGGATGAATTTACTTTTAAATCAGTGATTCTTTCACGACATAGTAATTATTT
66 AGTCAACATGATCAGGATGAATTTACTTTTAAATCAGTGATTCTTTCACGACATAGTAATTATTT
3618582 TATTTATTTACGTTTATTTTTCCTATCAAATTCAAAGAAAATTTGAATTTAAAACTCTATTTATC
131 TATTTATTTACGTTTATTTTTCCTATCAAATTCAAAGAAAATTTGAATTTAAAACTCTATTTATC
3618647 TAGTAAAATTTTGTATATTATGGACAGATTGTTGTTATATGCCTATCTATAATATATATTTATAA
196 TAGTAAAATTTTGTATATTATGGACAGATTGTTGTTATATGCCTATCTATAATATATATTTATAA
3618712 TAATTCTATTTGTCTGTTAAAATTTTGCATGTTATGGAAAG
261 TAATTCTATTTGTCTGTTAAAATTTTGCATGTTATGGAAAG
3618753 GCCGTTATTA
Statistics
Matches: 300, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
300 290 0.97
301 10 0.03
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (301 bp):
CTCTCATTGAATAGTACACATATGTTTATTTGTACGAATATTAAAATATTGTGTTAACCTTGGGG
AGTCAACATGATCAGGATGAATTTACTTTTAAATCAGTGATTCTTTCACGACATAGTAATTATTT
TATTTATTTACGTTTATTTTTCCTATCAAATTCAAAGAAAATTTGAATTTAAAACTCTATTTATC
TAGTAAAATTTTGTATATTATGGACAGATTGTTGTTATATGCCTATCTATAATATATATTTATAA
TAATTCTATTTGTCTGTTAAAATTTTGCATGTTATGGAAAG
Found at i:3618764 original size:79 final size:80
Alignment explanation
Indices: 3618637--3618794 Score: 176
Period size: 79 Copynumber: 2.0 Consensus size: 80
3618627 AATTTAAAAC
* * ** * * *
3618637 TCTATTTATCTAGTAAAATTTTGTATATTATGGACAGATTGTTGTTATATGCCTATCTATAATAT
1 TCTATTTATCTAGTAAAATTTTGCATATTATGGAAAGACCGTTATTATATACCAATCTATAATAT
*
3618702 ATATTTATA-ATAAT
66 ATATATATATATAAT
* * * * *
3618716 TCTATTTGTCT-GTTAAAATTTTGCATGTTATGGAAAGGCCGTTATTATATATCAATTTATAATA
1 TCTATTTATCTAG-TAAAATTTTGCATATTATGGAAAGACCGTTATTATATACCAATCTATAATA
3618780 TATATATATATATAA
65 TATATATATATATAA
3618795 GCATGAATTT
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
78 1 0.02
79 59 0.92
80 4 0.06
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.47
Consensus pattern (80 bp):
TCTATTTATCTAGTAAAATTTTGCATATTATGGAAAGACCGTTATTATATACCAATCTATAATAT
ATATATATATATAAT
Found at i:3624074 original size:5 final size:5
Alignment explanation
Indices: 3624060--3624099 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
3624050 AGTTGACTCG
* *
3624060 TTTT- TTTTA TTTTA TGTTA CTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
3624100 CCTTTATTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:3631506 original size:17 final size:17
Alignment explanation
Indices: 3631484--3631521 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3631474 TTTAAGTCGT
**
3631484 AAAAAAATGATGAAATG
1 AAAAAAATGAAAAAATG
3631501 AAAAAAATGAAAAAATG
1 AAAAAAATGAAAAAATG
3631518 AAAA
1 AAAA
3631522 TGAAAAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (17 bp):
AAAAAAATGAAAAAATG
Found at i:3632919 original size:88 final size:88
Alignment explanation
Indices: 3632765--3632952 Score: 259
Period size: 88 Copynumber: 2.1 Consensus size: 88
3632755 GAAACCATAA
* * * * * *
3632765 AGCCTTATCTCCCTGAGTAGCAGTAGAGTAGGTTGAAAATAGCAGATCTTGTCTTTATGCATTGG
1 AGCCTTATCTCCATGAGCAGCAATAGAGTAGGTTGAAAATAGCAGATCTTGCCTTCATGCACTGG
* *
3632830 CAGCGAAGTAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGACACC
* * * *
3632853 AGCCTTGTCTCCATGAGCAGCAATAGAGTAGGTTGAAAATGGCAGATCTTGCCTTCCTGTACTGG
1 AGCCTTATCTCCATGAGCAGCAATAGAGTAGGTTGAAAATAGCAGATCTTGCCTTCATGCACTGG
3632918 CAGCGAAGCAGATCGAAGACACC
66 CAGCGAAGCAGATCGAAGACACC
*
3632941 AGTCTTATCTCC
1 AGCCTTATCTCC
3632953 TTGACGTTGC
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (88 bp):
AGCCTTATCTCCATGAGCAGCAATAGAGTAGGTTGAAAATAGCAGATCTTGCCTTCATGCACTGG
CAGCGAAGCAGATCGAAGACACC
Found at i:3633176 original size:50 final size:50
Alignment explanation
Indices: 3633021--3633561 Score: 275
Period size: 50 Copynumber: 10.9 Consensus size: 50
3633011 ACAGTGGAAC
* * * * * * **
3633021 AGATTGAAGCTACGATGGCGGATCTAGTTTCCCCGACATTGCAAT-TTAA
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCGGCATTGCAATGAAAA
* * ** *** ** * * *
3633070 ATATTGAAGCCACAACGGTGAATCTTACTTCCTTAGCGGTGCAGTGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCGGCATTGCAATGAAAA
* * * *
3633120 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGGCATTGCAATGAAAA
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCGGCATTGCAATGAAAA
* * * ** * * *
3633170 AGATTGAAGCCACAACAGCGAATCTTACTTT-CCTGGCGGTGCAGTGGAAT
1 AGATTGAAGCCACAACGGCGAATCTT-GTTTCCCCGGCATTGCAATGAAAA
* * * * * *
3633220 AGATTGAAGCTACAATGGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCGGCATTGCAATGAAAA
** * ** * * * *
3633270 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAAT
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCGGCATTGCAATGAAAA
* * * *
3633320 AGATTGAAGCCACGACGGTGAATCTTGTTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCGGCATTGCAATGAAAA
* * ** * * * *
3633370 AGATTGAAGCCACAACGGCAAATCTTACTTT-CTTGGCAGTGTAGTTG-AAC
1 AGATTGAAGCCACAACGGCGAATCTT-GTTTCCCCGGCATTGCA-ATGAAAA
* * * * * * * *
3633420 AGATTGAAGCTACGATGGCGGATCTTGTTT-CTCGACATTGCAATTAAAT
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCGGCATTGCAATGAAAA
* * * * ** * *
3633469 AGATTGAAGCCATAACGGCGAATCTTATCTCCCTGGCGGTGCAGT-AGAAT
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCGGCATTGCAATGA-AAA
* * * * * *
3633519 AGATTAAAGTCACGACAGCGAATCTTGTTTCCCTGACATTGCA
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCGGCATTGCA
3633562 GTTAAACAAA
Statistics
Matches: 347, Mismatches: 137, Indels: 15
0.70 0.27 0.03
Matches are distributed among these distances:
48 1 0.00
49 69 0.20
50 270 0.78
51 7 0.02
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCGGCATTGCAATGAAAA
Found at i:3633231 original size:100 final size:100
Alignment explanation
Indices: 3632977--3633577 Score: 780
Period size: 100 Copynumber: 6.0 Consensus size: 100
3632967 GAATAGAATA
* * *
3632977 AAGCCACAGCGGCGAATCTTACTTCCCTGGCGGTACAGTGGAACAGATTGAAGCTACGATGGCGG
1 AAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGG
* * *
3633042 ATCTAGTTTCCCCGACATTGCAATT-TAAATATTG
66 ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTG
* * *
3633076 AAGCCACAACGGTGAATCTTACTTCCTTAGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGG
1 AAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGG
* * *
3633141 ATCTGGTTTCCCCGGCATTGCAATGAAAAAGATTG
66 ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTG
* * * * *
3633176 AAGCCACAACAGCGAATCTTACTTTCCTGGCGGTGCAGTGGAATAGATTGAAGCTACAATGGCGG
1 AAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGG
*
3633241 ATCTGGTTTCCCCGACATTGCAATTAAAAAGATTG
66 ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTG
* * * * *
3633276 AAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCCACGACGGTGA
1 AAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGG
3633341 ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTG
66 ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTG
* * * * * * *
3633376 AAGCCACAACGGCAAATCTTACTTTCTTGGCAGTGTAGTTGAACAGATTGAAGCTACGATGGCGG
1 AAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGG
* *
3633441 ATCTTGTTT-CTCGACATTGCAATTAAATAGATTG
66 ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTG
* * * * *
3633475 AAGCCATAACGGCGAATCTTA-TCTCCCTGGCGGTGCAGTAGAATAGATTAAAG-TCACGACAGC
1 AAGCCACAACGGCGAATCTTACT-TCCCTGGCGGTGCAGTGGAACAGATTGAAGCT-ACGACGGC
* * *
3633538 GAATCTTGTTTCCCTGACATTGCAGTTAAACAA-ATTG
64 GGATCTTGTTTCCCCGACATTGCAATTAAA-AAGATTG
3633575 AAG
1 AAG
3633578 AAAATAATCC
Statistics
Matches: 439, Mismatches: 58, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
98 2 0.00
99 162 0.37
100 274 0.62
101 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (100 bp):
AAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGG
ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTG
Found at i:3633548 original size:199 final size:199
Alignment explanation
Indices: 3632977--3633577 Score: 834
Period size: 199 Copynumber: 3.0 Consensus size: 199
3632967 GAATAGAATA
* * *
3632977 AAGCCACAGCGGCGAATCTTACTTCCCTGGCGGTACAGTGGAACAGATTGAAGCTACGATGGCGG
1 AAGCCACAACGGCGAATCTTACTTTCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGATGGCGG
* * *
3633042 ATCTAGTTTCCCCGACATTGCAATTTAAAT--ATTGAAGCCACAACGGTGAATCTTACTTCCTTA
66 ATCTAGTTTCCCCGACATTGCAA-TTAAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTG
* * * * *
3633105 GCGGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGGCATTGCAATGAAAA
130 GCGGTGCAGTGGAATAGATTGAAGC-ACGACGGCGAATCTTGTTTCCCCGACATTGCAATTAAAA
3633170 AGATTG
194 AGATTG
* * *
3633176 AAGCCACAACAGCGAATCTTACTTTCCTGGCGGTGCAGTGGAATAGATTGAAGCTACAATGGCGG
1 AAGCCACAACGGCGAATCTTACTTTCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGATGGCGG
* *
3633241 ATCTGGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGG
66 ATCTAGTTTCCCCGACATTGCAATTAAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGG
* *
3633306 CGGTGTAGTGGAATAGATTGAAGCCACGACGGTGAATCTTGTTTCCCCGACATTGCAATTAAAAA
131 CGGTGCAGTGGAATAGATTGAAG-CACGACGGCGAATCTTGTTTCCCCGACATTGCAATTAAAAA
3633371 GATTG
195 GATTG
* * * * *
3633376 AAGCCACAACGGCAAATCTTACTTTCTTGGCAGTGTAGTTGAACAGATTGAAGCTACGATGGCGG
1 AAGCCACAACGGCGAATCTTACTTTCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGATGGCGG
* * *
3633441 ATCTTGTTT-CTCGACATTGCAATTAAATAGATTGAAGCCATAACGGCGAATCTTA-TCTCCCTG
66 ATCTAGTTTCCCCGACATTGCAATTAAATAGATTGAAGCCACAACGGCGAATCTTACT-TCCCTG
* * * * *
3633504 GCGGTGCAGTAGAATAGATTAAAGTCACGACAGCGAATCTTGTTTCCCTGACATTGCAGTTAAAC
130 GCGGTGCAGTGGAATAGATTGAAG-CACGACGGCGAATCTTGTTTCCCCGACATTGCAATTAAA-
3633569 AA-ATTG
193 AAGATTG
3633575 AAG
1 AAG
3633578 AAAATAATCC
Statistics
Matches: 359, Mismatches: 38, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
198 6 0.02
199 193 0.54
200 159 0.44
201 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (199 bp):
AAGCCACAACGGCGAATCTTACTTTCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGATGGCGG
ATCTAGTTTCCCCGACATTGCAATTAAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGG
CGGTGCAGTGGAATAGATTGAAGCACGACGGCGAATCTTGTTTCCCCGACATTGCAATTAAAAAG
ATTG
Found at i:3636536 original size:19 final size:19
Alignment explanation
Indices: 3636503--3636549 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
3636493 GCTTTCGATG
*
3636503 AAAATA-TTATCTGAAGT-T
1 AAAATATTTTTCTGAA-TAT
3636521 AAAATATTTTTCTGAATAT
1 AAAATATTTTTCTGAATAT
3636540 AAAAT-TTTTT
1 AAAATATTTTT
3636550 GTTTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (19 bp):
AAAATATTTTTCTGAATAT
Found at i:3640033 original size:3 final size:3
Alignment explanation
Indices: 3640025--3640070 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3640015 AAGTCCCTAC
3640025 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3640071 TTCTCAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3643317 original size:14 final size:15
Alignment explanation
Indices: 3643293--3643321 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3643283 GAACTTTTAC
3643293 AAATTCGAATTTATT
1 AAATTCGAATTTATT
3643308 AAATTC-AATTTATT
1 AAATTCGAATTTATT
3643322 TTGGAAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (15 bp):
AAATTCGAATTTATT
Found at i:3646596 original size:29 final size:29
Alignment explanation
Indices: 3646554--3646613 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
3646544 GTAAACAATA
3646554 ATGCACTTGTGATTAGATTTAGATGTTGG
1 ATGCACTTGTGATTAGATTTAGATGTTGG
3646583 ATGCACTTGTGATTAGATTTAGATGTTGG
1 ATGCACTTGTGATTAGATTTAGATGTTGG
3646612 AT
1 AT
3646614 CCCAACTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.42
Consensus pattern (29 bp):
ATGCACTTGTGATTAGATTTAGATGTTGG
Found at i:3656867 original size:50 final size:50
Alignment explanation
Indices: 3656804--3656982 Score: 241
Period size: 50 Copynumber: 3.6 Consensus size: 50
3656794 CAATGTCATA
* * * * * *
3656804 TCCCAGATATGGTCTTACATGAGAGTTCTCATATTGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGAGACTTCTCATCTCGGTGCCAACGCCATG
** * *
3656854 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGAGACTTCTCATCTCGGTGCCAACGCCATG
* * *
3656904 TCCCAGACATGGTCTTACATGAGACCTCTTATCTCGATGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGAGACTTCTCATCTCGGTGCCAACGCCATG
3656954 TCCCAGACATGGTCTTACATGAGACTTCT
1 TCCCAGACATGGTCTTACATGAGACTTCT
3656983 TTACCCAAAT
Statistics
Matches: 113, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 113 1.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGAGACTTCTCATCTCGGTGCCAACGCCATG
Found at i:3658791 original size:17 final size:15
Alignment explanation
Indices: 3658764--3658803 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
3658754 ATTAGAAATA
3658764 TGAAAAATTGAAAGGG
1 TGAAAAATTG-AAGGG
3658780 TGAAAAACTTGAAGGG
1 TGAAAAA-TTGAAGGG
*
3658796 TGGAAAAT
1 TGAAAAAT
3658804 ATAAAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.82
17 3 0.14
ACGTcount: A:0.47, C:0.03, G:0.30, T:0.20
Consensus pattern (15 bp):
TGAAAAATTGAAGGG
Found at i:3659751 original size:18 final size:18
Alignment explanation
Indices: 3659730--3659764 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3659720 TAATATTATA
3659730 AAATAAAATAATTATTTC
1 AAATAAAATAATTATTTC
* *
3659748 AAATACAATTATTATTT
1 AAATAAAATAATTATTT
3659765 TTATATGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAAAATAATTATTTC
Found at i:3663917 original size:24 final size:24
Alignment explanation
Indices: 3663889--3663939 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3663879 TAACATTATA
3663889 AATGGAGATGGATTAAATTATCCC
1 AATGGAGATGGATTAAATTATCCC
3663913 AATGGAGATGGATTAAATTATCCC
1 AATGGAGATGGATTAAATTATCCC
3663937 AAT
1 AAT
3663940 TTAAAGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (24 bp):
AATGGAGATGGATTAAATTATCCC
Found at i:3672467 original size:40 final size:40
Alignment explanation
Indices: 3672394--3672531 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 40
3672384 AACATACTAG
* * * *
3672394 TTTGGCACCCAGTGCCTCATTGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGTTAATCCGAAGTAATAA
* *
3672434 TTTGACACCCAGTGTCTCATCGGTTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGTTAATCCGAAGTAATAA
* * * * *
3672472 -TTGGCACCCAGTGCCTTATCGAATTAATCAGAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCG-GTTAATCCGAAGTAATAA
* * *
3672512 ATTGACACCTAGTGTCTCAT
1 TTTGACACCCAGTGCCTCAT
3672532 AGACTCGAAG
Statistics
Matches: 77, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 18 0.23
38 12 0.16
39 1 0.01
40 31 0.40
41 15 0.19
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGTTAATCCGAAGTAATAA
Found at i:3673376 original size:6 final size:6
Alignment explanation
Indices: 3673350--3673404 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
3673340 TAACTTTGTA
*
3673350 TCTTTC TCCTTTCC TTCTTTC TCTTTC TCTTTT TCTTTC T-TTT- TCTTTC
1 TCTTTC T-CTTT-C -TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC
*
3673399 TATTTC
1 TCTTTC
3673405 GTTTAACCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
4 1 0.02
5 6 0.15
6 23 0.56
7 5 0.12
8 5 0.12
9 1 0.02
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (6 bp):
TCTTTC
Found at i:3673389 original size:22 final size:21
Alignment explanation
Indices: 3673350--3673399 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
3673340 TAACTTTGTA
3673350 TCTTTCTCCTTTCCTTCTTTC
1 TCTTTCTCCTTTCCTTCTTTC
* * *
3673371 TCTTTCTCTTTTTCTTTCTTTT
1 TCTTTCTC-CTTTCCTTCTTTC
3673393 TCTTTCT
1 TCTTTCT
3673400 ATTTCGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TCTTTCTCCTTTCCTTCTTTC
Found at i:3673390 original size:10 final size:10
Alignment explanation
Indices: 3673364--3673428 Score: 53
Period size: 10 Copynumber: 6.2 Consensus size: 10
3673354 TCTCCTTTCC
*
3673364 TTCTTTCTCT
1 TTCTTTCTTT
3673374 TTC--TCTTT
1 TTCTTTCTTT
3673382 TTCTTTCTTT
1 TTCTTTCTTT
*
3673392 TTCTTTCTAT
1 TTCTTTCTTT
3673402 TTCGTTTAACCTTT
1 TTC-TTT---CTTT
3673416 TGTCTTTCTTT
1 T-TCTTTCTTT
3673427 TT
1 TT
3673429 GTTCTTTCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
8 7 0.16
10 21 0.47
11 8 0.18
14 7 0.16
15 2 0.04
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.71
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:3673430 original size:12 final size:12
Alignment explanation
Indices: 3673371--3673443 Score: 55
Period size: 12 Copynumber: 6.1 Consensus size: 12
3673361 TCCTTCTTTC
3673371 TCTTTCTCTTTT-
1 TCTTTCT-TTTTG
3673383 TCTTTC-TTTT-
1 TCTTTCTTTTTG
*
3673393 TCTTTCTATTTCG
1 TCTTTCT-TTTTG
* *
3673406 T-TTAACCTTTTG
1 TCTT-TCTTTTTG
3673418 TCTTTCTTTTTG
1 TCTTTCTTTTTG
3673430 TTCTTTCTTTTTG
1 -TCTTTCTTTTTG
3673443 T
1 T
3673444 TGCTTTTATT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
10 10 0.20
12 23 0.47
13 16 0.33
ACGTcount: A:0.04, C:0.19, G:0.05, T:0.71
Consensus pattern (12 bp):
TCTTTCTTTTTG
Found at i:3673436 original size:13 final size:13
Alignment explanation
Indices: 3673413--3673449 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
3673403 TCGTTTAACC
3673413 TTTTG-TCTTTCT
1 TTTTGTTCTTTCT
3673425 TTTTGTTCTTTCT
1 TTTTGTTCTTTCT
3673438 TTTTGTTGCTTT
1 TTTTGTT-CTTT
3673450 TATTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.22
13 14 0.61
14 4 0.17
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.76
Consensus pattern (13 bp):
TTTTGTTCTTTCT
Found at i:3673523 original size:8 final size:8
Alignment explanation
Indices: 3673467--3673532 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 8
3673457 TATATTTACT
3673467 TATTATAA
1 TATTATAA
3673475 TA-TATAA
1 TATTATAA
3673482 TATGATATATA
1 TAT--TATA-A
3673493 TATT-TAA
1 TATTATAA
*
3673500 TAAT-TAA
1 TATTATAA
* *
3673507 GA-AATAA
1 TATTATAA
3673514 TATTATAA
1 TATTATAA
3673522 TATTATAA
1 TATTATAA
3673530 TAT
1 TAT
3673533 ATACTTTAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 19 0.40
8 19 0.40
9 1 0.02
10 4 0.09
11 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (8 bp):
TATTATAA
Found at i:3692910 original size:15 final size:15
Alignment explanation
Indices: 3692886--3692940 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
3692876 AATGTTTTTG
*
3692886 TACATTTTATTACCA
1 TACATATTATTACCA
*
3692901 TACATATTATT-TCA
1 TACATATTATTACCA
* *
3692915 TACATTTTATTACCG
1 TACATATTATTACCA
3692930 TACATATTATT
1 TACATATTATT
3692941 TCATGTGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 12 0.36
15 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.02, T:0.49
Consensus pattern (15 bp):
TACATATTATTACCA
Found at i:3692918 original size:14 final size:14
Alignment explanation
Indices: 3692899--3692944 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3692889 ATTTTATTAC
3692899 CATACATATTATTT
1 CATACATATTATTT
* *
3692913 CATACATTTTATTAC
1 CATACATATTATT-T
*
3692928 CGTACATATTATTT
1 CATACATATTATTT
3692942 CAT
1 CAT
3692945 GTGTTATTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (14 bp):
CATACATATTATTT
Found at i:3692919 original size:29 final size:29
Alignment explanation
Indices: 3692886--3692944 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3692876 AATGTTTTTG
3692886 TACATTTTATTACCATACATATTATTTCA
1 TACATTTTATTACCATACATATTATTTCA
*
3692915 TACATTTTATTACCGTACATATTATTTCA
1 TACATTTTATTACCATACATATTATTTCA
3692944 T
1 T
3692945 GTGTTATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (29 bp):
TACATTTTATTACCATACATATTATTTCA
Found at i:3695944 original size:30 final size:30
Alignment explanation
Indices: 3695910--3695967 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3695900 CAGCAAATAC
*
3695910 TAGAAGTGGAAGAGGAAATCGAAGAAGAAG
1 TAGAAGTAGAAGAGGAAATCGAAGAAGAAG
* *
3695940 TAGAAGTAGAAGAGGAATTTGAAGAAGA
1 TAGAAGTAGAAGAGGAAATCGAAGAAGA
3695968 GGAGGAGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.34, T:0.14
Consensus pattern (30 bp):
TAGAAGTAGAAGAGGAAATCGAAGAAGAAG
Found at i:3695972 original size:3 final size:3
Alignment explanation
Indices: 3695966--3696000 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3695956 ATTTGAAGAA
3695966 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
3696001 AGATGACGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:3696983 original size:27 final size:27
Alignment explanation
Indices: 3696932--3696989 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
3696922 GCCTGCTGGA
* *
3696932 GCTGGGTTCAACCATGGTGTTGCTGCT
1 GCTGGGTTCAACCATGGAGTGGCTGCT
* *
3696959 GCTGGGTTTAACCCTGGAGTGGCTGCT
1 GCTGGGTTCAACCATGGAGTGGCTGCT
3696986 GCTG
1 GCTG
3696990 CACCGGGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.10, C:0.22, G:0.36, T:0.31
Consensus pattern (27 bp):
GCTGGGTTCAACCATGGAGTGGCTGCT
Found at i:3700722 original size:14 final size:14
Alignment explanation
Indices: 3700703--3700735 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3700693 TAAAAATAAA
3700703 ATAAAATTAAAAAT
1 ATAAAATTAAAAAT
3700717 ATAAAATTAAAAAT
1 ATAAAATTAAAAAT
*
3700731 TTAAA
1 ATAAA
3700736 TGAGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAATTAAAAAT
Found at i:3709540 original size:13 final size:13
Alignment explanation
Indices: 3709522--3709548 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3709512 ACCCACCCCC
3709522 CCAAAAAAAAAAA
1 CCAAAAAAAAAAA
3709535 CCAAAAAAAAAAA
1 CCAAAAAAAAAAA
3709548 C
1 C
3709549 GTTGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (13 bp):
CCAAAAAAAAAAA
Found at i:3711151 original size:29 final size:30
Alignment explanation
Indices: 3711118--3711175 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
3711108 ATAAATTTGA
* *
3711118 AATTTAATCTCCCTACTTTT-ATTTTTAAG
1 AATTTAATCACCCTACTTTTCAATTTTAAG
* *
3711147 AATTTAGTCACTCTACTTTTCAATTTTAA
1 AATTTAATCACCCTACTTTTCAATTTTAA
3711176 AAATCCAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.50
Consensus pattern (30 bp):
AATTTAATCACCCTACTTTTCAATTTTAAG
Found at i:3711703 original size:14 final size:14
Alignment explanation
Indices: 3711684--3711710 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3711674 AAAATTATTT
3711684 TAAAAATTAAATTA
1 TAAAAATTAAATTA
3711698 TAAAAATTAAATT
1 TAAAAATTAAATT
3711711 TCAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAAATTAAATTA
Found at i:3714727 original size:16 final size:16
Alignment explanation
Indices: 3714706--3714755 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
3714696 NNNNNNNNNN
*
3714706 TATTAAATATTTTTTA
1 TATTAATTATTTTTTA
*
3714722 TATTAATTATTTTTAA
1 TATTAATTATTTTTTA
3714738 TA-TAATTATTTTTT-
1 TATTAATTATTTTTTA
3714752 TATT
1 TATT
3714756 CGTGTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 2 0.07
15 12 0.40
16 16 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTAATTATTTTTTA
Found at i:3714736 original size:15 final size:15
Alignment explanation
Indices: 3714706--3714755 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3714696 NNNNNNNNNN
*
3714706 TATTAAATATTTTTTA
1 TATTAATTA-TTTTTA
3714722 TATTAATTATTTTTA
1 TATTAATTATTTTTA
*
3714737 -ATATAATTATTTTTT
1 TAT-TAATTATTTTTA
3714752 TATT
1 TATT
3714756 CGTGTTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 2 0.07
15 18 0.60
16 10 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTAATTATTTTTA
Found at i:3724593 original size:11 final size:12
Alignment explanation
Indices: 3724573--3724601 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3724563 TTTTATTTTA
3724573 TTTTATAAAATT
1 TTTTATAAAATT
3724585 TTTTA-AAAATT
1 TTTTATAAAATT
3724596 TTTTAT
1 TTTTAT
3724602 TTTTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTATAAAATT
Found at i:3724786 original size:21 final size:20
Alignment explanation
Indices: 3724742--3724786 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
3724732 CAATATTTTT
* *
3724742 TTTAAAAAATAAAGACTAAT
1 TTTAAAAAATAAAAACTAAA
*
3724762 TTTAAAAAATTAAAAAGTAAA
1 TTTAAAAAA-TAAAAACTAAA
3724783 TTTA
1 TTTA
3724787 TTAATATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
TTTAAAAAATAAAAACTAAA
Found at i:3725936 original size:2 final size:2
Alignment explanation
Indices: 3725929--3725970 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3725919 TAAACAATAA
*
3725929 CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3725971 ACACTAGTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3730622 original size:33 final size:31
Alignment explanation
Indices: 3730543--3730622 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 31
3730533 TTATTTAGAA
3730543 ATAATAAAAACATAAA-ATATTTTTATATTTT
1 ATAATAAAAA-ATAAATATATTTTTATATTTT
**
3730574 ATAACT-AAATTTAAATATATTTTTTTATTATTTT
1 ATAA-TAAAAAATAAATATA--TTTTTA-TATTTT
3730608 -TAATAAAAAATAAAT
1 ATAATAAAAAATAAAT
3730623 CATTTGAGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
30 4 0.10
31 10 0.26
32 2 0.05
33 17 0.44
34 6 0.15
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (31 bp):
ATAATAAAAAATAAATATATTTTTATATTTT
Found at i:3733529 original size:11 final size:11
Alignment explanation
Indices: 3733515--3733567 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
3733505 ATTTTTTTAA
3733515 TTTTAAAATAT
1 TTTTAAAATAT
3733526 TTTTAAAATACT
1 TTTTAAAATA-T
**
3733538 TTTTTTAAT-T
1 TTTTAAAATAT
*
3733548 TTTTTAAA-AT
1 TTTTAAAATAT
3733558 TTTTAAAATA
1 TTTTAAAATA
3733568 AAAATAGGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 16 0.46
11 11 0.31
12 8 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3733560 original size:32 final size:31
Alignment explanation
Indices: 3733506--3733567 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
3733496 TTTTTTTTAA
3733506 TTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAAATATTTTTAAAATAC
*
3733537 TTTTTTTAATTTTTTTAAA-ATTTTTAAAATA
1 TTTTTTTAA--TTTTAAAATATTTTTAAAATA
3733568 AAAATAGGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.32
32 12 0.43
33 7 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:3736678 original size:26 final size:26
Alignment explanation
Indices: 3736649--3736721 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
3736639 CCCGATATAT
3736649 GGCTCTTCGTAAGCTTCCCGATTAAA
1 GGCTCTTCGTAAGCTTCCCGATTAAA
* * *
3736675 GGCTCTTTGTAAGCTTCTCG-TTAAT
1 GGCTCTTCGTAAGCTTCCCGATTAAA
* *
3736700 GGCTCTCCG-GAGCTTCCC-ATTA
1 GGCTCTTCGTAAGCTTCCCGATTA
3736722 CATGGCTCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 10 0.26
25 11 0.28
26 18 0.46
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (26 bp):
GGCTCTTCGTAAGCTTCCCGATTAAA
Found at i:3743137 original size:41 final size:41
Alignment explanation
Indices: 3743091--3743178 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 41
3743081 GATAAGTCAC
3743091 ATGTCATATTTCAAGATTTAATATGATTAATTATGTGTTAT
1 ATGTCATATTTCAAGATTTAATATGATTAATTATGTGTTAT
*
3743132 ATGTCATATTTCAAGATTTAATATGATTACTTATGTGTTAT
1 ATGTCATATTTCAAGATTTAATATGATTAATTATGTGTTAT
3743173 AT-TCAT
1 ATGTCAT
3743179 GTTTTGATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 4 0.09
41 42 0.91
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (41 bp):
ATGTCATATTTCAAGATTTAATATGATTAATTATGTGTTAT
Found at i:3744350 original size:16 final size:16
Alignment explanation
Indices: 3744331--3744364 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3744321 ATGTTCTTTA
*
3744331 TTTTTATTTCTTTTCT
1 TTTTTATCTCTTTTCT
*
3744347 TTTTTCTCTCTTTTCT
1 TTTTTATCTCTTTTCT
3744363 TT
1 TT
3744365 GAGATATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTATCTCTTTTCT
Found at i:3748700 original size:19 final size:20
Alignment explanation
Indices: 3748658--3748700 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3748648 TCATGCTTGC
* *
3748658 TATTTACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
3748678 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
3748696 TATTC
1 TATTC
3748701 CACAATCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:3748899 original size:38 final size:37
Alignment explanation
Indices: 3748827--3748959 Score: 106
Period size: 38 Copynumber: 3.5 Consensus size: 37
3748817 ACCAGATTGG
* * * *
3748827 CACCCAGTGCCTCATCGGATAGTTCGAAGCAAAGTTGA
1 CACCCAGTGTCTCATCGGCTAGCT-GAAGTAAAGTTGA
3748865 CACCCAGTGTCTCATCGGCCTAGCTGAAGTAAAG-TGA
1 CACCCAGTGTCTCATCGG-CTAGCTGAAGTAAAGTTGA
* * * * * *
3748902 TACCCAGTATCTCATCGAATCTATCCGAAGTAAAATAGTGA
1 CACCCAGTGTCTCATCG--GCTAGCTGAAGTAAAGT--TGA
*
3748943 CACCTAGTGTCTCATCG
1 CACCCAGTGTCTCATCG
3748960 ACTCGACGTC
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
37 18 0.24
38 37 0.49
39 4 0.05
41 17 0.22
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (37 bp):
CACCCAGTGTCTCATCGGCTAGCTGAAGTAAAGTTGA
Found at i:3750161 original size:29 final size:29
Alignment explanation
Indices: 3750119--3750175 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
3750109 GTCTTTTCTT
*
3750119 AATTTATTTCATAATATAATAATATAATC
1 AATTTATTTCATAATATAATAAAATAATC
3750148 AATTTAATTT-ATAATATAATAAAATAAT
1 AATTT-ATTTCATAATATAATAAAATAAT
3750176 AATAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
AATTTATTTCATAATATAATAAAATAATC
Found at i:3750184 original size:29 final size:30
Alignment explanation
Indices: 3750124--3750184 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
3750114 TTCTTAATTT
* *
3750124 ATTTCATAATATAATAATATAATCAATTTA
1 ATTTCATAATATAATAAAATAATCAATATA
3750154 ATTT-ATAATATAATAAAATAAT-AATAATA
1 ATTTCATAATATAATAAAATAATCAAT-ATA
3750183 AT
1 AT
3750185 AATATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 3 0.11
29 21 0.75
30 4 0.14
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
ATTTCATAATATAATAAAATAATCAATATA
Found at i:3750196 original size:37 final size:37
Alignment explanation
Indices: 3750129--3750200 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
3750119 AATTTATTTC
* *
3750129 ATAATATAATAATATAATCAATTTAATTTATAATATA
1 ATAAAATAATAATATAATCAATATAATTTATAATATA
*
3750166 ATAAAATAATAATAATAAT-AATATATTTTATAATA
1 ATAAAATAATAAT-ATAATCAATATAATTTATAATA
3750201 AAACAATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 26 0.84
38 5 0.16
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (37 bp):
ATAAAATAATAATATAATCAATATAATTTATAATATA
Found at i:3750198 original size:32 final size:33
Alignment explanation
Indices: 3750117--3750212 Score: 97
Period size: 32 Copynumber: 2.9 Consensus size: 33
3750107 TTGTCTTTTC
* *
3750117 TTAATTTATTTCATAATATAATAATATAATCAA
1 TTAATTTATTTTATAATAAAATAATATAATCAA
**
3750150 TTTAATTTATAATATAATAAAATAATAATAAT-AA
1 -TTAATTTATTTTATAATAAAATAAT-ATAATCAA
* *
3750184 -TAATATATTTTATAATAAAACAATCATAA
1 TTAATTTATTTTATAATAAAATAAT-ATAA
3750213 AAATTAAAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
32 24 0.46
34 23 0.44
35 5 0.10
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (33 bp):
TTAATTTATTTTATAATAAAATAATATAATCAA
Done.