Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 8 of 145
Found at i:3497813 original size:22 final size:24
Alignment explanation
Indices: 3497775--3497823 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
3497765 GTGTATATGT
*
3497775 ATATGTATTTACTAAAA-TA-AAA
1 ATATGTATGTACTAAAAGTATAAA
3497797 ATATGTATGTA-TAAAAAGTATAAA
1 ATATGTATGTACT-AAAAGTATAAA
3497821 ATA
1 ATA
3497824 CAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 2 0.09
24 6 0.26
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
ATATGTATGTACTAAAAGTATAAA
Found at i:3498932 original size:20 final size:21
Alignment explanation
Indices: 3498907--3498946 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3498897 AAACAAGTAA
3498907 AAAATAAA-AAAATAAAAAGG
1 AAAATAAAGAAAATAAAAAGG
*
3498927 AAAATAAAGAAGATAAAAAG
1 AAAATAAAGAAAATAAAAAG
3498947 CGAATCGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (21 bp):
AAAATAAAGAAAATAAAAAGG
Found at i:3499749 original size:31 final size:31
Alignment explanation
Indices: 3499692--3499750 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
3499682 AAAAATCGAT
* *
3499692 TCTTTTTAAAAGGTTAATAATTAAATTTGAC
1 TCTTTTTAAAACGTTAATAATCAAATTTGAC
* *
3499723 TCTTTTTAAAACGTTGATCATCAAATTT
1 TCTTTTTAAAACGTTAATAATCAAATTT
3499751 AGCTCAAAAA
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:0.08, T:0.46
Consensus pattern (31 bp):
TCTTTTTAAAACGTTAATAATCAAATTTGAC
Found at i:3503312 original size:25 final size:24
Alignment explanation
Indices: 3503245--3503312 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
3503235 ATGAAAATGT
*
3503245 TATTGTATAAATAAAATTA-CAAA
1 TATTGTAAAAATAAAATTATCAAA
* * * *
3503268 TA-TATAAAAATGGAATTTATGAATA
1 TATTGTAAAAAT-AAAATTATCAA-A
3503293 TATTGTAAAAATAAAATTAT
1 TATTGTAAAAATAAAATTAT
3503313 AAAAATGTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 7 0.21
23 7 0.21
24 2 0.06
25 9 0.27
26 8 0.24
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (24 bp):
TATTGTAAAAATAAAATTATCAAA
Found at i:3503403 original size:21 final size:21
Alignment explanation
Indices: 3503373--3503412 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3503363 TAATTGAATA
* *
3503373 AATAATAATACATGATAAAGG
1 AATAAAAATACATAATAAAGG
3503394 AATAAAAATACATAATAAA
1 AATAAAAATACATAATAAA
3503413 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (21 bp):
AATAAAAATACATAATAAAGG
Found at i:3503477 original size:12 final size:12
Alignment explanation
Indices: 3503461--3503496 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3503451 AATAACATCT
3503461 ATAATAATAGTA
1 ATAATAATAGTA
*
3503473 GTAATAATAGTA
1 ATAATAATAGTA
3503485 ATAATAATAGTA
1 ATAATAATAGTA
3503497 TTATAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:3518867 original size:4 final size:4
Alignment explanation
Indices: 3518858--3518908 Score: 93
Period size: 4 Copynumber: 12.8 Consensus size: 4
3518848 ATATACTCCT
*
3518858 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC CTAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3518906 ATA
1 ATA
3518909 TATATATCGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:3527441 original size:17 final size:16
Alignment explanation
Indices: 3527412--3527447 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
3527402 TTATAAAAAT
3527412 AATAATTAATTACGAA
1 AATAATTAATTACGAA
*
3527428 AATAGATTATTTACGAA
1 AATA-ATTAATTACGAA
3527445 AAT
1 AAT
3527448 GAGTTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (16 bp):
AATAATTAATTACGAA
Found at i:3532045 original size:14 final size:14
Alignment explanation
Indices: 3532003--3532046 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3531993 ACGTTTGCGA
*
3532003 ATAAAAT-AAATAA
1 ATAAAATAAAATAT
3532016 ATAAAAATAAACATAT
1 AT-AAAATAAA-ATAT
3532032 ATAAAATAAAATAT
1 ATAAAATAAAATAT
3532046 A
1 A
3532047 AATAGAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.07
14 10 0.37
15 10 0.37
16 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (14 bp):
ATAAAATAAAATAT
Found at i:3537677 original size:26 final size:25
Alignment explanation
Indices: 3537632--3537680 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
3537622 ATATCTCTAT
*
3537632 TTTCCATATTTGTTATTCTATTTCC
1 TTTCCATATTTGTTACTCTATTTCC
3537657 TTTCCTATATTTGATT-CTCTATTT
1 TTTCC-ATATTTG-TTACTCTATTT
3537681 TCAACAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 14 0.67
27 2 0.10
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTCCATATTTGTTACTCTATTTCC
Found at i:3537709 original size:84 final size:85
Alignment explanation
Indices: 3537568--3537736 Score: 252
Period size: 84 Copynumber: 2.0 Consensus size: 85
3537558 TATTACACTC
* * *
3537568 TTTCCTTTTCTATATTTGATTCTCTATTTTCCATAAAATATTAAATTTCCTTTCATATCTCTATT
1 TTTCCTTTCCTATATTTGATTCTCTATTTTCAACAAAATATTAAATTTCCTTTCATATCTCTATT
* *
3537633 TTCCATAT-TTGTTATTCTA
66 GTACATATATTGTTATTCTA
*
3537652 TTTCCTTTCCTATATTTGATTCTCTATTTTCAACAAAATATTCAA-TTCTCTTTCATATCTCTAT
1 TTTCCTTTCCTATATTTGATTCTCTATTTTCAACAAAATATTAAATTTC-CTTTCATATCTCTAT
3537716 TGTACATATAGTTGTTATTCT
65 TGTACATATA-TTGTTATTCT
3537737 CTTGCATTTC
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 3 0.04
84 63 0.83
86 10 0.13
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.54
Consensus pattern (85 bp):
TTTCCTTTCCTATATTTGATTCTCTATTTTCAACAAAATATTAAATTTCCTTTCATATCTCTATT
GTACATATATTGTTATTCTA
Found at i:3539133 original size:42 final size:42
Alignment explanation
Indices: 3539074--3539299 Score: 281
Period size: 42 Copynumber: 5.3 Consensus size: 42
3539064 CTATAGAATG
* * * * *
3539074 TGACCTTTAGCTGCGCTTTTCCACAAATGACAATAAAGAACA
1 TGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAAAGAACA
*
3539116 TGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGAACA
1 TGACCTTTAGCGGCGC-TTTCCCACAAACGCCACTAAAGAACA
* * *
3539159 TGATCTTTAGCGGCGCTGTCCCACAAACGCCGCTAAAGAACA
1 TGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAAAGAACA
*** *
3539201 TGACCTTTAGCGGCGCTTTCCCACAAACGCGGTTAAAAAACA
1 TGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAAAGAACA
* ** *
3539243 TGACTTTTAGCGGTACTTTCCCTACAAACGCCACTACAGAACA
1 TGACCTTTAGCGGCGCTTTCCC-ACAAACGCCACTAAAGAACA
3539286 TGACCTTTAGCGGC
1 TGACCTTTAGCGGC
3539300 ATTTGTGGAA
Statistics
Matches: 157, Mismatches: 25, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
42 94 0.60
43 63 0.40
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (42 bp):
TGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAAAGAACA
Found at i:3539207 original size:85 final size:85
Alignment explanation
Indices: 3539107--3539299 Score: 264
Period size: 85 Copynumber: 2.3 Consensus size: 85
3539097 CAAATGACAA
* *
3539107 TAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGAACATGA-TCTTTAGCG
1 TAAAGAACATGACCTTTAGCGGCGC-TTTCCCACAAACGCCACTAAAAAACATGACT-TTTAGCG
* *
3539171 GCGCTGTCCC-ACAAACGCCGC
64 GCACTGTCCCTACAAACGCCAC
*** *
3539192 TAAAGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCGGTTAAAAAACATGACTTTTAGCGGT
1 TAAAGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAAAAAACATGACTTTTAGCGGC
*
3539257 ACTTTCCCTACAAACGCCAC
66 ACTGTCCCTACAAACGCCAC
*
3539277 TACAGAACATGACCTTTAGCGGC
1 TAAAGAACATGACCTTTAGCGGC
3539300 ATTTGTGGAA
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
84 38 0.40
85 58 0.60
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (85 bp):
TAAAGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAAAAAACATGACTTTTAGCGGC
ACTGTCCCTACAAACGCCAC
Found at i:3548900 original size:9 final size:9
Alignment explanation
Indices: 3548852--3548980 Score: 61
Period size: 9 Copynumber: 14.6 Consensus size: 9
3548842 ATCCAAAGTT
3548852 TTATGTAAG
1 TTATGTAAG
*
3548861 TTATGATATG
1 TTATG-TAAG
* * *
3548871 ATATAT-AT
1 TTATGTAAG
3548879 TTATGT-A-
1 TTATGTAAG
3548886 TTATGTAAG
1 TTATGTAAG
3548895 TTATGTAAG
1 TTATGTAAG
*
3548904 TTATGATATG
1 TTATG-TAAG
* * *
3548914 ATATAT-AT
1 TTATGTAAG
*
3548922 TTTTGTAAG
1 TTATGTAAG
*
3548931 TTACGTAAG
1 TTATGTAAG
*
3548940 TTATGATATG
1 TTATG-TAAG
* * *
3548950 ATATAT-AC
1 TTATGTAAG
3548958 TTATGTAAG
1 TTATGTAAG
*
3548967 TTATGTAAA
1 TTATGTAAG
3548976 TTATG
1 TTATG
3548981 AAATTTGAAC
Statistics
Matches: 85, Mismatches: 28, Indels: 14
0.67 0.22 0.11
Matches are distributed among these distances:
7 6 0.07
8 13 0.15
9 48 0.56
10 18 0.21
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:3548902 original size:43 final size:42
Alignment explanation
Indices: 3548852--3548980 Score: 162
Period size: 36 Copynumber: 3.1 Consensus size: 42
3548842 ATCCAAAGTT
3548852 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
1 TTATGTAAGTTATGATATGATATATA-TTATGTATTATGTAAG
3548895 TTATGTAAGTTATGATATG--ATATA-TAT-T-TT-TGTAAG
1 TTATGTAAGTTATGATATGATATATATTATGTATTATGTAAG
* *
3548931 TTACGTAAGTTATGATATGATATATACTTATGTAAGTTATGTAAA
1 TTATGTAAGTTATGATATGATATATA-TTATGT-A-TTATGTAAG
3548976 TTATG
1 TTATG
3548981 AAATTTGAAC
Statistics
Matches: 74, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
36 24 0.32
37 2 0.03
38 6 0.08
39 3 0.04
40 3 0.04
41 6 0.08
43 19 0.26
44 2 0.03
45 9 0.12
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (42 bp):
TTATGTAAGTTATGATATGATATATATTATGTATTATGTAAG
Found at i:3553611 original size:631 final size:631
Alignment explanation
Indices: 3552408--3553670 Score: 2526
Period size: 631 Copynumber: 2.0 Consensus size: 631
3552398 TGAAATAATA
3552408 AAATTTGAGCTAATAGAGACAAAATCAGAAAATAAAGGACTTCTAAATGCAATAAAAAAGGAAGC
1 AAATTTGAGCTAATAGAGACAAAATCAGAAAATAAAGGACTTCTAAATGCAATAAAAAAGGAAGC
3552473 TGGATGACAGATAACAGATAACAGGTAATAGTGTAAAAGTTTTTTTCTACTCTGTAGGAGTTGCT
66 TGGATGACAGATAACAGATAACAGGTAATAGTGTAAAAGTTTTTTTCTACTCTGTAGGAGTTGCT
3552538 CGGTCAACCTGAATTCGACTAAATTTAAAATAATTTTACAATTTAGACTAAATGTCACCAAAATT
131 CGGTCAACCTGAATTCGACTAAATTTAAAATAATTTTACAATTTAGACTAAATGTCACCAAAATT
3552603 ATTATTTAAATTTAATTATAAAAATAGTTTTTAACATTTTAAATAGTACAAACAAAACTCAAGCC
196 ATTATTTAAATTTAATTATAAAAATAGTTTTTAACATTTTAAATAGTACAAACAAAACTCAAGCC
3552668 ATGTACATCTACTGTTGATAGATATTTGAGTTTAAAATAGAAAAGCTTAACAAAAGGTGTAGAGA
261 ATGTACATCTACTGTTGATAGATATTTGAGTTTAAAATAGAAAAGCTTAACAAAAGGTGTAGAGA
3552733 AATCACAGCTCTAGCAATTACAACATTACTAACCTGAAGTCACTGAGAAAAGCGTATAAAAATGG
326 AATCACAGCTCTAGCAATTACAACATTACTAACCTGAAGTCACTGAGAAAAGCGTATAAAAATGG
3552798 AAAAAATAATCAGTACTCAAAGCTGTAAGCATGTGCTTCTAGTAAAACACCAGCTTTTTATGCTG
391 AAAAAATAATCAGTACTCAAAGCTGTAAGCATGTGCTTCTAGTAAAACACCAGCTTTTTATGCTG
3552863 CATAGAAAACTAAATATTCAAACACAACACATCTAAACTTCTGATTATTTGGATCAATATGGAAA
456 CATAGAAAACTAAATATTCAAACACAACACATCTAAACTTCTGATTATTTGGATCAATATGGAAA
3552928 TGGAACTCTTCACTCAAGCATTAACAATGACAGTAAACAATATTTGAAATGACAACCTTGCTGTA
521 TGGAACTCTTCACTCAAGCATTAACAATGACAGTAAACAATATTTGAAATGACAACCTTGCTGTA
3552993 ATTGAACACCATATTAAGCTCCCAAACATTCTGGAAGCACTTGTCC
586 ATTGAACACCATATTAAGCTCCCAAACATTCTGGAAGCACTTGTCC
3553039 AAATTTGAGCTAATAGAGACAAAATCAGAAAATAAAGGACTTCTAAATGCAATAAAAAAGGAAGC
1 AAATTTGAGCTAATAGAGACAAAATCAGAAAATAAAGGACTTCTAAATGCAATAAAAAAGGAAGC
3553104 TGGATGACAGATAACAGATAACAGGTAATAGTGTAAAAGTTTTTTTCTACTCTGTAGGAGTTGCT
66 TGGATGACAGATAACAGATAACAGGTAATAGTGTAAAAGTTTTTTTCTACTCTGTAGGAGTTGCT
3553169 CGGTCAACCTGAATTCGACTAAATTTAAAATAATTTTACAATTTAGACTAAATGTCACCAAAATT
131 CGGTCAACCTGAATTCGACTAAATTTAAAATAATTTTACAATTTAGACTAAATGTCACCAAAATT
3553234 ATTATTTAAATTTAATTATAAAAATAGTTTTTAACATTTTAAATAGTACAAACAAAACTCAAGCC
196 ATTATTTAAATTTAATTATAAAAATAGTTTTTAACATTTTAAATAGTACAAACAAAACTCAAGCC
3553299 ATGTACATCTACTGTTGATAGATATTTGAGTTTAAAATAGAAAAGCTTAACAAAAGGTGTAGAGA
261 ATGTACATCTACTGTTGATAGATATTTGAGTTTAAAATAGAAAAGCTTAACAAAAGGTGTAGAGA
3553364 AATCACAGCTCTAGCAATTACAACATTACTAACCTGAAGTCACTGAGAAAAGCGTATAAAAATGG
326 AATCACAGCTCTAGCAATTACAACATTACTAACCTGAAGTCACTGAGAAAAGCGTATAAAAATGG
3553429 AAAAAATAATCAGTACTCAAAGCTGTAAGCATGTGCTTCTAGTAAAACACCAGCTTTTTATGCTG
391 AAAAAATAATCAGTACTCAAAGCTGTAAGCATGTGCTTCTAGTAAAACACCAGCTTTTTATGCTG
3553494 CATAGAAAACTAAATATTCAAACACAACACATCTAAACTTCTGATTATTTGGATCAATATGGAAA
456 CATAGAAAACTAAATATTCAAACACAACACATCTAAACTTCTGATTATTTGGATCAATATGGAAA
3553559 TGGAACTCTTCACTCAAGCATTAACAATGACAGTAAACAATATTTGAAATGACAACCTTGCTGTA
521 TGGAACTCTTCACTCAAGCATTAACAATGACAGTAAACAATATTTGAAATGACAACCTTGCTGTA
3553624 ATTGAACACCATATTAAGCTCCCAAACATTCTGGAAGCACTTGTCC
586 ATTGAACACCATATTAAGCTCCCAAACATTCTGGAAGCACTTGTCC
3553670 A
1 A
3553671 GCGTTTCCAC
Statistics
Matches: 632, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
631 632 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.29
Consensus pattern (631 bp):
AAATTTGAGCTAATAGAGACAAAATCAGAAAATAAAGGACTTCTAAATGCAATAAAAAAGGAAGC
TGGATGACAGATAACAGATAACAGGTAATAGTGTAAAAGTTTTTTTCTACTCTGTAGGAGTTGCT
CGGTCAACCTGAATTCGACTAAATTTAAAATAATTTTACAATTTAGACTAAATGTCACCAAAATT
ATTATTTAAATTTAATTATAAAAATAGTTTTTAACATTTTAAATAGTACAAACAAAACTCAAGCC
ATGTACATCTACTGTTGATAGATATTTGAGTTTAAAATAGAAAAGCTTAACAAAAGGTGTAGAGA
AATCACAGCTCTAGCAATTACAACATTACTAACCTGAAGTCACTGAGAAAAGCGTATAAAAATGG
AAAAAATAATCAGTACTCAAAGCTGTAAGCATGTGCTTCTAGTAAAACACCAGCTTTTTATGCTG
CATAGAAAACTAAATATTCAAACACAACACATCTAAACTTCTGATTATTTGGATCAATATGGAAA
TGGAACTCTTCACTCAAGCATTAACAATGACAGTAAACAATATTTGAAATGACAACCTTGCTGTA
ATTGAACACCATATTAAGCTCCCAAACATTCTGGAAGCACTTGTCC
Found at i:3557863 original size:178 final size:173
Alignment explanation
Indices: 3557518--3557868 Score: 612
Period size: 178 Copynumber: 2.0 Consensus size: 173
3557508 CTAATTCATC
*
3557518 CCTTCTCTGTATTGAACTCCAAAATCCATTGTCTTGGATCTCTAACTCTTTTTCTCGAAATTTCT
1 CCTTCTCTGTATTGAACTCCAAAATCCATTGTCTTGGATCTATAACTCTTTTTCTCGAAATTTCT
3557583 TCATGATAAAGTCTTGAACGAATAAGTTGAGCTTTGACTTCAACTATTTGGATTTGGATCTCGTG
66 TCATGATAAAGTCTTGAACGAATAAGTTGAGCTTTGACTTCAACTATTTGGATTTGGATCTCGTG
3557648 ATTGGGCCTTGAGGGAATTTAAGCCCATCTCCATCATAAACTT
131 ATTGGGCCTTGAGGGAATTTAAGCCCATCTCCATCATAAACTT
* *
3557691 CCTTGCTCTGTATTGAATTCCAAAATCCATTGTCTTGGATCTATATCTCTTTTTCTCGAAATTTC
1 CCTT-CTCTGTATTGAACTCCAAAATCCATTGTCTTGGATCTATAACTCTTTTTCTCGAAATTTC
*
3557756 TTCATGATAAAGTCTTGAACGAATATATAAGTTGAGCTTTGACTTCAACTGTTTGGATTTGGATC
65 TTCATGATAAAGTCTTGAACG---A-ATAAGTTGAGCTTTGACTTCAACTATTTGGATTTGGATC
*
3557821 TTGTGATTGGGCCTTGAGGGAATTTAAGCCCATCTCCATCATAAACTT
126 TCGTGATTGGGCCTTGAGGGAATTTAAGCCCATCTCCATCATAAACTT
3557869 TGAATTGGAT
Statistics
Matches: 168, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
173 4 0.02
174 78 0.46
177 1 0.01
178 85 0.51
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (173 bp):
CCTTCTCTGTATTGAACTCCAAAATCCATTGTCTTGGATCTATAACTCTTTTTCTCGAAATTTCT
TCATGATAAAGTCTTGAACGAATAAGTTGAGCTTTGACTTCAACTATTTGGATTTGGATCTCGTG
ATTGGGCCTTGAGGGAATTTAAGCCCATCTCCATCATAAACTT
Found at i:3566408 original size:28 final size:28
Alignment explanation
Indices: 3566368--3566425 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
3566358 TGATTCAAAC
*
3566368 TTTCAAGTTTGACTTGATCAACCAGATT
1 TTTCAAGTTTGACTTGATCAACCAAATT
3566396 TTTCAAGTTTGACTTGATCAACCAAATT
1 TTTCAAGTTTGACTTGATCAACCAAATT
3566424 TT
1 TT
3566426 AACATGCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (28 bp):
TTTCAAGTTTGACTTGATCAACCAAATT
Found at i:3568477 original size:13 final size:13
Alignment explanation
Indices: 3568459--3568488 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3568449 AATATTTATA
*
3568459 AAAGATCGAACCC
1 AAAGATCAAACCC
3568472 AAAGATCAAACCC
1 AAAGATCAAACCC
3568485 AAAG
1 AAAG
3568489 GAAAAGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.27, G:0.13, T:0.07
Consensus pattern (13 bp):
AAAGATCAAACCC
Found at i:3569069 original size:19 final size:18
Alignment explanation
Indices: 3569041--3569076 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3569031 AAGCAGCTAT
3569041 AAAAGTAAAACTTAAGAA
1 AAAAGTAAAACTTAAGAA
*
3569059 AAAATGTAAAAGTTAAGA
1 AAAA-GTAAAACTTAAGA
3569077 TTTTAATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.64, C:0.03, G:0.14, T:0.19
Consensus pattern (18 bp):
AAAAGTAAAACTTAAGAA
Found at i:3569394 original size:11 final size:11
Alignment explanation
Indices: 3569378--3569421 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
3569368 CTAAGTGCAG
3569378 AGAAAACCTAA
1 AGAAAACCTAA
*
3569389 AGAAAACCTAG
1 AGAAAACCTAA
* *
3569400 AGAAAACTTAG
1 AGAAAACCTAA
3569411 AGAAAA-CTAA
1 AGAAAACCTAA
3569421 A
1 A
3569422 CCTAAACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 3 0.10
11 26 0.90
ACGTcount: A:0.61, C:0.14, G:0.14, T:0.11
Consensus pattern (11 bp):
AGAAAACCTAA
Found at i:3569404 original size:22 final size:22
Alignment explanation
Indices: 3569376--3569417 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3569366 ACCTAAGTGC
3569376 AGAGAAAACCTAAAGAAAACCT
1 AGAGAAAACCTAAAGAAAACCT
* *
3569398 AGAGAAAACTTAGAGAAAAC
1 AGAGAAAACCTAAAGAAAAC
3569418 TAAACCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.14, G:0.17, T:0.10
Consensus pattern (22 bp):
AGAGAAAACCTAAAGAAAACCT
Found at i:3572880 original size:12 final size:12
Alignment explanation
Indices: 3572861--3572889 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3572851 TATGATTAAA
3572861 AATA-TTATCTT
1 AATATTTATCTT
3572872 AATATTTATCTT
1 AATATTTATCTT
3572884 AATATT
1 AATATT
3572890 AATTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (12 bp):
AATATTTATCTT
Found at i:3581456 original size:20 final size:20
Alignment explanation
Indices: 3581431--3581470 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3581421 TTTATTTTTA
3581431 CAAAATCTACATA-AAAATTT
1 CAAAATCTA-ATATAAAATTT
*
3581451 CAAAATGTAATATAAAATTT
1 CAAAATCTAATATAAAATTT
3581471 ACCTCGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (20 bp):
CAAAATCTAATATAAAATTT
Found at i:3583005 original size:29 final size:26
Alignment explanation
Indices: 3582959--3583016 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 26
3582949 GATTTCGGGG
3582959 AAAACGGCCCATTCCGGTAAATAATTAA
1 AAAACGGCCCATTCCGGTAAAT--TTAA
* *
3582987 AAAACCGGCCTATTTCGGTAAATTTAA
1 AAAA-CGGCCCATTCCGGTAAATTTAA
3583014 AAA
1 AAA
3583017 GAAAAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (26 bp):
AAAACGGCCCATTCCGGTAAATTTAA
Found at i:3588484 original size:17 final size:18
Alignment explanation
Indices: 3588448--3588485 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3588438 ATTGCTTTTC
* *
3588448 AAAAGTGTTTTTGGGCCA
1 AAAAGTGCTTTTGAGCCA
3588466 AAAAGTGCTTTTGAG-CA
1 AAAAGTGCTTTTGAGCCA
3588483 AAA
1 AAA
3588486 GCTAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (18 bp):
AAAAGTGCTTTTGAGCCA
Found at i:3588594 original size:18 final size:18
Alignment explanation
Indices: 3588568--3588604 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3588558 TTAGCAATGC
3588568 TTTTATCCAAAAAGTGTT
1 TTTTATCCAAAAAGTGTT
*
3588586 TTTTGTCCAAAAAGTGTT
1 TTTTATCCAAAAAGTGTT
3588604 T
1 T
3588605 ATTAGAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
TTTTATCCAAAAAGTGTT
Found at i:3589980 original size:13 final size:13
Alignment explanation
Indices: 3589958--3590001 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
3589948 TTTAACAATA
*
3589958 CTTTTGAAAAGTG
1 CTTTTAAAAAGTG
3589971 CTTTTAAAAAGTG
1 CTTTTAAAAAGTG
*
3589984 -TTGTGAAAAAGTG
1 CTT-TTAAAAAGTG
3589997 CTTTT
1 CTTTT
3590002 TATAAGTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (13 bp):
CTTTTAAAAAGTG
Found at i:3590019 original size:26 final size:26
Alignment explanation
Indices: 3589948--3590019 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
3589938 TTAGGGCTAG
*
3589948 TTTAACAA-TACTTTTGAAAAGTGCT
1 TTTAAAAAGTACTTTTGAAAAGTGCT
* *
3589973 TTTAAAAAGT-GTTGTGAAAAAGTGCT
1 TTTAAAAAGTACTTTTG-AAAAGTGCT
* *
3589999 TTTTATAAGTACTTTTGAAAA
1 TTTAAAAAGTACTTTTGAAAA
3590020 TTTTTGAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
25 11 0.30
26 22 0.59
27 4 0.11
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (26 bp):
TTTAAAAAGTACTTTTGAAAAGTGCT
Found at i:3593692 original size:3 final size:3
Alignment explanation
Indices: 3593684--3593723 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3593674 TAACCAATTT
3593684 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3593724 ACAATACTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3594899 original size:10 final size:10
Alignment explanation
Indices: 3594886--3594914 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3594876 AAGTGATCAC
3594886 TTTCCTCTCG
1 TTTCCTCTCG
3594896 TTTCCTCTCG
1 TTTCCTCTCG
3594906 TTTCCTCTC
1 TTTCCTCTC
3594915 CTAATCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.07, T:0.52
Consensus pattern (10 bp):
TTTCCTCTCG
Found at i:3597024 original size:7 final size:7
Alignment explanation
Indices: 3597012--3597040 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3597002 GAAGAATTGT
3597012 AGTTTGC
1 AGTTTGC
3597019 AGTTTGC
1 AGTTTGC
3597026 AGTTTGC
1 AGTTTGC
3597033 AGTTTGC
1 AGTTTGC
3597040 A
1 A
3597041 CCTAGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (7 bp):
AGTTTGC
Found at i:3605646 original size:2 final size:2
Alignment explanation
Indices: 3605639--3605673 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3605629 GCAGCAGCTA
3605639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3605674 CCTTGAATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3605755 original size:45 final size:46
Alignment explanation
Indices: 3605694--3605786 Score: 179
Period size: 45 Copynumber: 2.0 Consensus size: 46
3605684 GACAGTAACC
3605694 CTCTTTTCAGCTTCACAATTAAGCTAAAGAGAAAAGACAGTAATTG
1 CTCTTTTCAGCTTCACAATTAAGCTAAAGAGAAAAGACAGTAATTG
3605740 CTCTTTTCAGC-TCACAATTAAGCTAAAGAGAAAAGACAGTAATTG
1 CTCTTTTCAGCTTCACAATTAAGCTAAAGAGAAAAGACAGTAATTG
3605785 CT
1 CT
3605787 GTACAATTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 36 0.77
46 11 0.23
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (46 bp):
CTCTTTTCAGCTTCACAATTAAGCTAAAGAGAAAAGACAGTAATTG
Found at i:3613916 original size:131 final size:132
Alignment explanation
Indices: 3613765--3614034 Score: 515
Period size: 131 Copynumber: 2.1 Consensus size: 132
3613755 TAATAGAACA
3613765 ATATATATATACATGTACAATATTCAATAATATGATACATATGTAAGCACTTACGTGTGTGTATA
1 ATATATATATACATGTACAATATTCAATAATATGATACATATGTAAGCACTTACGTGTGTGTATA
*
3613830 TATATATTATAAGCATAAAATGTTAATAATTATAGAAGAATATTTGTTTTATAGTACAATCTCAT
66 TATATATTATAAGCATAAAATGTTAATAAATATAGAAGAATATTTGTTTTATAGTACAATCTCAT
3613895 AT
131 AT
*
3613897 ATTTATATATACA-GTACAATATTCAATAATATGATACATATGTAAGCACTTACGTGTGTGTATA
1 ATATATATATACATGTACAATATTCAATAATATGATACATATGTAAGCACTTACGTGTGTGTATA
3613961 TATATATTATAAGCATAAAATGTTAATAAATATAGAAGAATATTTGTTTTATAGTACAATCTCAT
66 TATATATTATAAGCATAAAATGTTAATAAATATAGAAGAATATTTGTTTTATAGTACAATCTCAT
3614026 AT
131 AT
3614028 ATATATA
1 ATATATA
3614035 NNNNNNNNNN
Statistics
Matches: 135, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
131 123 0.91
132 12 0.09
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (132 bp):
ATATATATATACATGTACAATATTCAATAATATGATACATATGTAAGCACTTACGTGTGTGTATA
TATATATTATAAGCATAAAATGTTAATAAATATAGAAGAATATTTGTTTTATAGTACAATCTCAT
AT
Found at i:3614029 original size:68 final size:68
Alignment explanation
Indices: 3613826--3614034 Score: 181
Period size: 65 Copynumber: 3.1 Consensus size: 68
3613816 TACGTGTGTG
*
3613826 TATATATATATTATAAGCATAAAATGTTAATAATTATAGAAGAATATTTGTTTTATAGTACAATC
1 TATATATATATTATAAGCATAAAATGTTAATAAATATAGAAGAATATTTGTTTTATAGTACAATC
3613891 TCA
66 TCA
* * * * *
3613894 TATATTTATA-TAT-A-CAGTACAATATTCAAT-AATAT-GATA-CATA--TG---TA-AGCACT
1 TATATATATATTATAAGCA-TAAAATGTT-AATAAATATAGA-AGAATATTTGTTTTATAGTAC-
* * **
3613947 TACGTGTGTG
62 -A-ATCT-CA
3613957 TATATATATATTATAAGCATAAAATGTTAATAAATATAGAAGAATATTTGTTTTATAGTACAATC
1 TATATATATATTATAAGCATAAAATGTTAATAAATATAGAAGAATATTTGTTTTATAGTACAATC
3614022 TCA
66 TCA
3614025 TATATATATA
1 TATATATATA
3614035 NNNNNNNNNN
Statistics
Matches: 103, Mismatches: 19, Indels: 38
0.64 0.12 0.24
Matches are distributed among these distances:
59 4 0.04
60 2 0.02
61 1 0.01
62 2 0.02
63 11 0.11
64 6 0.06
65 21 0.20
66 20 0.19
67 6 0.06
68 21 0.20
69 2 0.02
70 1 0.01
71 2 0.02
72 4 0.04
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (68 bp):
TATATATATATTATAAGCATAAAATGTTAATAAATATAGAAGAATATTTGTTTTATAGTACAATC
TCA
Found at i:3617618 original size:2 final size:2
Alignment explanation
Indices: 3617611--3617638 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3617601 GTACAATCTC
3617611 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
3617639 TAAAAAGCCA
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:3617982 original size:21 final size:24
Alignment explanation
Indices: 3617931--3617987 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 24
3617921 AATTGATGTG
3617931 AACTTTTGTAGTACATAAATCAAACAA
1 AACTTTTGTAGTACATAAATC--AC-A
3617958 AACTTTTGTAGTACATAAA-C-C-
1 AACTTTTGTAGTACATAAATCACA
3617979 AACTTTTGT
1 AACTTTTGT
3617988 GAATAAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 9 0.30
23 1 0.03
26 1 0.03
27 19 0.63
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (24 bp):
AACTTTTGTAGTACATAAATCACA
Found at i:3625476 original size:25 final size:25
Alignment explanation
Indices: 3625441--3625516 Score: 109
Period size: 25 Copynumber: 3.0 Consensus size: 25
3625431 CAAAGTCCCG
3625441 ATTCACAGCTCGTGTGAGCAA-TAT
1 ATTCACAGCTCGTGTGAGCAATTAT
* *
3625465 ATTTCACAGCTCATGTTAGCAATTAT
1 A-TTCACAGCTCGTGTGAGCAATTAT
3625491 ATTCACAGCTCGTGTGAGCAAATTAT
1 ATTCACAGCTCGTGTGAGC-AATTAT
3625517 GTCATGTGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.02
25 34 0.76
26 10 0.22
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (25 bp):
ATTCACAGCTCGTGTGAGCAATTAT
Found at i:3627431 original size:15 final size:15
Alignment explanation
Indices: 3627413--3627446 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3627403 GTTGTTCGAG
3627413 AATAGCTATGTCCAA
1 AATAGCTATGTCCAA
* *
3627428 AATAGTTATGTTCAA
1 AATAGCTATGTCCAA
3627443 AATA
1 AATA
3627447 TGATTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
AATAGCTATGTCCAA
Found at i:3627720 original size:15 final size:16
Alignment explanation
Indices: 3627686--3627732 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
3627676 CAGTTATTCG
*
3627686 GAACAACCTCAATATTGA
1 GAACAA-CTC-ATGTTGA
3627704 GAACAACT-ATGTTGA
1 GAACAACTCATGTTGA
3627719 GAACAACTCATGTT
1 GAACAACTCATGTT
3627733 TGGAACAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 14 0.52
16 5 0.19
17 2 0.07
18 6 0.22
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (16 bp):
GAACAACTCATGTTGA
Found at i:3634243 original size:24 final size:24
Alignment explanation
Indices: 3634188--3634244 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
3634178 GTTACATAAA
* *
3634188 AATTCAAAATACTAATTCAAAAAT
1 AATTTAAAATAATAATTCAAAAAT
** *
3634212 AAGATAAAATAATAATTCAAAATT
1 AATTTAAAATAATAATTCAAAAAT
3634236 AATTTAAAA
1 AATTTAAAA
3634245 CTAAGATAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (24 bp):
AATTTAAAATAATAATTCAAAAAT
Found at i:3634250 original size:35 final size:37
Alignment explanation
Indices: 3634183--3634258 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
3634173 AGATAGTTAC
3634183 ATAAAAATTCAAAATACTAATTCAAAAATAAGATAA-A
1 ATAAAAATTCAAAATA-TAATTCAAAAATAAGATAATA
* * *
3634220 ATAATAATTCAAAAT-TAATTTAAAACTAAGATAATA
1 ATAAAAATTCAAAATATAATTCAAAAATAAGATAATA
3634256 ATA
1 ATA
3634259 GCTAATCTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 17 0.49
36 4 0.11
37 14 0.40
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.29
Consensus pattern (37 bp):
ATAAAAATTCAAAATATAATTCAAAAATAAGATAATA
Found at i:3636480 original size:28 final size:29
Alignment explanation
Indices: 3636422--3636486 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
3636412 TTATAAAAGT
*
3636422 TATATATATTATATAAAGAAATACGTATA
1 TATATATACTATATAAAGAAATACGTATA
* *
3636451 TATATATACTATAT-AAGAAATGCGTGTA
1 TATATATACTATATAAAGAAATACGTATA
*
3636479 TAAATATA
1 TATATATA
3636487 GAAATAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (29 bp):
TATATATACTATATAAAGAAATACGTATA
Found at i:3638123 original size:28 final size:28
Alignment explanation
Indices: 3638073--3638126 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3638063 AACTCAACCT
**
3638073 TTCTCTTCCCTTTTTTTTTTCTTTTCCA
1 TTCTCTTCCCTTTTTTAGTTCTTTTCCA
3638101 TTCT-TTCCCTTTTATTAGTTCTTTTC
1 TTCTCTTCCCTTTT-TTAGTTCTTTTC
3638127 TTCAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.67
Consensus pattern (28 bp):
TTCTCTTCCCTTTTTTAGTTCTTTTCCA
Found at i:3645489 original size:17 final size:18
Alignment explanation
Indices: 3645459--3645494 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3645449 GTATAAATAC
3645459 GTATATATAAAATATAAG
1 GTATATATAAAATATAAG
3645477 GTATATA-AAAATATAAG
1 GTATATATAAAATATAAG
3645494 G
1 G
3645495 GATAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (18 bp):
GTATATATAAAATATAAG
Found at i:3653504 original size:20 final size:20
Alignment explanation
Indices: 3653479--3653518 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3653469 TAAAGGTCTT
*
3653479 TAATGCATATGATGCGATGC
1 TAATGCATATGATACGATGC
3653499 TAATGCATATGATACGATGC
1 TAATGCATATGATACGATGC
3653519 ATGAGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (20 bp):
TAATGCATATGATACGATGC
Found at i:3657214 original size:17 final size:18
Alignment explanation
Indices: 3657184--3657219 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3657174 GTATAAATAC
3657184 GTATATATAAAATATAAG
1 GTATATATAAAATATAAG
3657202 GTATATA-AAAATATAAG
1 GTATATATAAAATATAAG
3657219 G
1 G
3657220 GATAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (18 bp):
GTATATATAAAATATAAG
Found at i:3657966 original size:16 final size:16
Alignment explanation
Indices: 3657945--3657976 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3657935 CTAGCGTCCT
3657945 CGCGCCGCCGCCGCAA
1 CGCGCCGCCGCCGCAA
*
3657961 CGCGCCTCCGCCGCAA
1 CGCGCCGCCGCCGCAA
3657977 TATCACCGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.56, G:0.28, T:0.03
Consensus pattern (16 bp):
CGCGCCGCCGCCGCAA
Found at i:3673276 original size:31 final size:31
Alignment explanation
Indices: 3673209--3673274 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
3673199 TTAATAAAAG
*
3673209 TAAAATTGTACTTTAATCTCCTTAAAAATTA
1 TAAAATTGTAATTTAATCTCCTTAAAAATTA
* *
3673240 TAAAATTTTAATTTAATC-CTTTAAAAATTA
1 TAAAATTGTAATTTAATCTCCTTAAAAATTA
3673270 TAAAA
1 TAAAA
3673275 ATATAGGCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (31 bp):
TAAAATTGTAATTTAATCTCCTTAAAAATTA
Found at i:3674682 original size:17 final size:17
Alignment explanation
Indices: 3674660--3674708 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
3674650 CAAAAAGTTT
*
3674660 AAAAATACATATATAAA
1 AAAAATATATATATAAA
* **
3674677 AAAAATGTATATATTTA
1 AAAAATATATATATAAA
3674694 AAAAATATATATATA
1 AAAAATATATATATA
3674709 CGTATAAGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAAATATATATATAAA
Found at i:3674695 original size:19 final size:19
Alignment explanation
Indices: 3674668--3674708 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3674658 TTAAAAATAC
*
3674668 ATATATAAAAAAAATGTAT
1 ATATATAAAAAAAATATAT
* *
3674687 ATATTTAAAAAATATATAT
1 ATATATAAAAAAAATATAT
3674706 ATA
1 ATA
3674709 CGTATAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATATATAAAAAAAATATAT
Found at i:3674733 original size:3 final size:3
Alignment explanation
Indices: 3674725--3674768 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
3674715 AGAATATAGA
* *
3674725 AAT AAT AAT AAT AAT CAT AAT AAT AAAT AAT -AT AAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
3674769 ATATTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3674769 original size:18 final size:19
Alignment explanation
Indices: 3674725--3674771 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
3674715 AGAATATAGA
* *
3674725 AATAAT-AATAATAATCAT
1 AATAATAAATAATAATAAC
3674743 AATAATAAATAAT-ATAAC
1 AATAATAAATAATAATAAC
3674761 AATAATAAATA
1 AATAATAAATA
3674772 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAATAAATAATAATAAC
Found at i:3675202 original size:13 final size:14
Alignment explanation
Indices: 3675184--3675213 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3675174 AAGCCGAATG
3675184 AAAG-AAAAAAATA
1 AAAGAAAAAAAATA
3675197 AAAGAAAAAAAATA
1 AAAGAAAAAAAATA
3675211 AAA
1 AAA
3675214 CGTTTCTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAGAAAAAAAATA
Found at i:3676381 original size:44 final size:45
Alignment explanation
Indices: 3676304--3676421 Score: 168
Period size: 44 Copynumber: 2.6 Consensus size: 45
3676294 AAGACTTGTA
3676304 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
* *
3676349 TCTTTGATCTACTTCA-CGCCAGTA-GGTGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAGTATGG-GAAGACAAGATCTGCTT
* * *
3676393 TCTTCAATCTACTCCACCACTAGTATGGG
1 TCTTCGATCTACTTCACCACCAGTATGGG
3676422 GAGATAGAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
43 2 0.03
44 37 0.59
45 22 0.35
46 2 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (45 bp):
TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
Found at i:3676665 original size:100 final size:98
Alignment explanation
Indices: 3676561--3676783 Score: 266
Period size: 100 Copynumber: 2.3 Consensus size: 98
3676551 TGGGGAAACC
* * ** * * ** *
3676561 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACCACACCGTCAGGGAAGTAAGATCCGCCGTCGTG
1 AGATCCGCCGTTGTGGCTTCAATCTGTTAAACCACAACATCAGGGAAACAAGATCCGCCGT-GTA
* *
3676626 GCTTCAACCTGCTCCGCTGCACTGGTAAGGAAGTA
65 GCTTCAA-CTGCTCCGCTGCACTGCTAAAGAAGTA
* * * *
3676661 AGATCCGCCGTTGTGGCTTCAATCTTTTAAATCGCAATATCAGGGAAACAAGATCCGCCGTGTAG
1 AGATCCGCCGTTGTGGCTTCAATCTGTTAAACCACAACATCAGGGAAACAAGATCCGCCGTGTAG
* *
3676726 CTTCAACTGTTCCGCTGCATTGCTAAAGAAGTA
66 CTTCAACTGCTCCGCTGCACTGCTAAAGAAGTA
*
3676759 AGATCTGCCGTTGTGGCTTCAATCT
1 AGATCCGCCGTTGTGGCTTCAATCT
3676784 TTTCAGTTTT
Statistics
Matches: 105, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
98 47 0.45
99 9 0.09
100 49 0.47
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (98 bp):
AGATCCGCCGTTGTGGCTTCAATCTGTTAAACCACAACATCAGGGAAACAAGATCCGCCGTGTAG
CTTCAACTGCTCCGCTGCACTGCTAAAGAAGTA
Found at i:3676774 original size:98 final size:100
Alignment explanation
Indices: 3676600--3676786 Score: 288
Period size: 98 Copynumber: 1.9 Consensus size: 100
3676590 CACCACACCG
** * * *
3676600 TCAGGGAAGTAAGATCCGCCGTCGTGGCTTCAACCTGCTCCGCTGCACTGGTAAGGAAGTAAGAT
1 TCAGGGAAACAAGATCCGCCGTCGTAGCTTCAACCTGCTCCGCTGCACTGCTAAAGAAGTAAGAT
3676665 CCGCCGTTGTGGCTTCAATCTTTTAAATCGCAATA
66 CCGCCGTTGTGGCTTCAATCTTTTAAATCGCAATA
* *
3676700 TCAGGGAAACAAGATCCGCCGT-GTAGCTTCAA-CTGTTCCGCTGCATTGCTAAAGAAGTAAGAT
1 TCAGGGAAACAAGATCCGCCGTCGTAGCTTCAACCTGCTCCGCTGCACTGCTAAAGAAGTAAGAT
*
3676763 CTGCCGTTGTGGCTTCAATCTTTT
66 CCGCCGTTGTGGCTTCAATCTTTT
3676787 CAGTTTTCAA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
98 50 0.63
99 9 0.11
100 20 0.25
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (100 bp):
TCAGGGAAACAAGATCCGCCGTCGTAGCTTCAACCTGCTCCGCTGCACTGCTAAAGAAGTAAGAT
CCGCCGTTGTGGCTTCAATCTTTTAAATCGCAATA
Found at i:3684670 original size:20 final size:20
Alignment explanation
Indices: 3684645--3684684 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3684635 TAAAGGTCCT
*
3684645 TAATGCATATGATGTGATGC
1 TAATGCATATGATGCGATGC
3684665 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
3684685 ATGAGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:3688418 original size:3 final size:3
Alignment explanation
Indices: 3688410--3688453 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
3688400 AGAATATAGA
* *
3688410 AAT AAT AAT AAT AAT CAT AAT AAT AAAT AAT -AT AAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
3688454 ATATTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3688454 original size:18 final size:19
Alignment explanation
Indices: 3688410--3688456 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
3688400 AGAATATAGA
* *
3688410 AATAAT-AATAATAATCAT
1 AATAATAAATAATAATAAC
3688428 AATAATAAATAAT-ATAAC
1 AATAATAAATAATAATAAC
3688446 AATAATAAATA
1 AATAATAAATA
3688457 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAATAAATAATAATAAC
Found at i:3688891 original size:13 final size:13
Alignment explanation
Indices: 3688873--3688897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3688863 CGAATGAAAG
3688873 AAAAAAATAAAAT
1 AAAAAAATAAAAT
3688886 AAAAAAATAAAA
1 AAAAAAATAAAA
3688898 CGTTTCTCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:3690230 original size:30 final size:30
Alignment explanation
Indices: 3690196--3690407 Score: 424
Period size: 30 Copynumber: 7.1 Consensus size: 30
3690186 AATTAAGGTT
3690196 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
3690226 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
3690256 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
3690286 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
3690316 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
3690346 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
3690376 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
3690406 TG
1 TG
3690408 TAGTAGTCTA
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 182 1.00
ACGTcount: A:0.20, C:0.07, G:0.37, T:0.37
Consensus pattern (30 bp):
TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
Found at i:3692837 original size:22 final size:23
Alignment explanation
Indices: 3692808--3692858 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
3692798 AATTTATTTT
* *
3692808 ATAA-TAAGATGATAT-TTTATA
1 ATAATTAAGATCATATATATATA
3692829 ATAATTAAGATCATATATATATA
1 ATAATTAAGATCATATATATATA
3692852 A-AATTAA
1 ATAATTAA
3692859 TGATAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 16 0.62
23 6 0.23
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (23 bp):
ATAATTAAGATCATATATATATA
Found at i:3697067 original size:29 final size:29
Alignment explanation
Indices: 3697035--3697091 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3697025 AATCATCATC
* *
3697035 TCAAACATAAGTGACTAAAATGTAACATT
1 TCAAACATAAATAACTAAAATGTAACATT
3697064 TCAAACATAAATAACTAAAATGTAACAT
1 TCAAACATAAATAACTAAAATGTAACAT
3697092 AATGTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (29 bp):
TCAAACATAAATAACTAAAATGTAACATT
Found at i:3700372 original size:6 final size:6
Alignment explanation
Indices: 3700361--3700411 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
3700351 GGAGGAAAAT
3700361 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAA-G
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
3700408 AGAA
1 AGAA
3700412 TGAAAAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 40 0.89
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:3716269 original size:2 final size:2
Alignment explanation
Indices: 3716264--3716292 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3716254 ACACATGCAT
3716264 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3716293 TCTGTACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3723144 original size:17 final size:17
Alignment explanation
Indices: 3723122--3723155 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3723112 AAGGAGGACT
3723122 ATAATAAT-ATAATCATA
1 ATAATAATCAT-ATCATA
3723139 ATAATAATCATATCATA
1 ATAATAATCATATCATA
3723156 GGAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAATCATATCATA
Found at i:3723468 original size:37 final size:36
Alignment explanation
Indices: 3723393--3723501 Score: 85
Period size: 37 Copynumber: 2.9 Consensus size: 36
3723383 AATAAAGGCA
* **
3723393 AAAAGAAAAATAAAAAAATAAAAATGAATACACGAC
1 AAAAGAAAAATAAAAAAATAAAAATGAATAAAAAAC
* *
3723429 AAAAGAAAGAATAAAAAAATTTAAAAT-ATTAAAAAAC
1 AAAAGAAA-AATAAAAAAA-TAAAAATGAATAAAAAAC
* *
3723466 AAAGAAGTAATAACTAAATAAAATAAAAATAAATAA
1 -AA-AAG-AA-AAATAAA-AAAATAAAAATGAATAA
3723502 TCTAGGAAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
36 8 0.14
37 16 0.28
38 8 0.14
39 3 0.05
40 13 0.23
41 9 0.16
ACGTcount: A:0.72, C:0.05, G:0.06, T:0.17
Consensus pattern (36 bp):
AAAAGAAAAATAAAAAAATAAAAATGAATAAAAAAC
Found at i:3724132 original size:89 final size:89
Alignment explanation
Indices: 3724018--3724316 Score: 445
Period size: 89 Copynumber: 3.4 Consensus size: 89
3724008 GTGGATCCTA
3724018 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
3724083 AGATAAGATTTATAGCTTTAATCT
66 AGATAAGATTTATAGCTTTAATCT
* *
3724107 GCTCTACTGCAATTTCAGAGAGATAATATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
3724172 AGATAAGATTTATAGCTTTAATCT
66 AGATAAGATTTATAGCTTTAATCT
* * * ** * *
3724196 GCTCTACTACAATTTCAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
* * *
3724261 AGATAAGATTTGTATCTTCAATCT
66 AGATAAGATTTATAGCTTTAATCT
* * * * *
3724285 ACTCCACTGCCACTTCAGGGAGATAATATTTG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTG
3724317 TAACTTATAG
Statistics
Matches: 191, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 191 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (89 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
AGATAAGATTTATAGCTTTAATCT
Found at i:3724317 original size:44 final size:44
Alignment explanation
Indices: 3724018--3724318 Score: 341
Period size: 44 Copynumber: 6.8 Consensus size: 44
3724008 GTGGATCCTA
* *
3724018 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATAT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCT
** * * * *
3724063 TTTCTACTGCAACTTCATGGAGATAAGATTTATAGCTTTAATCT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCT
* * * *
3724107 GCTCTACTGCAATTTCAGAGAGATAATATTTGCTATCTTCAATAT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCT
** * * * *
3724152 TTTCTACTGCAACTTCATGGAGATAAGATTTATAGCTTTAATCT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCT
* * *
3724196 GCTCTACTACAATTTCAGAGAGATAAGATTTGCTATCTTCAATCT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCT
*
3724241 GCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCT
* * * *
3724285 ACTCCACTGCCACTTCAGGGAGATAATATTTGTA
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTGTA
3724319 ACTTATAGCT
Statistics
Matches: 210, Mismatches: 44, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
44 111 0.53
45 99 0.47
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (44 bp):
GCTCTACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCT
Found at i:3726543 original size:44 final size:44
Alignment explanation
Indices: 3726480--3726716 Score: 465
Period size: 44 Copynumber: 5.4 Consensus size: 44
3726470 GGCTGTTACA
3726480 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
3726524 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
3726568 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
3726612 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
3726656 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
*
3726700 AGTGACAAGTGACAAGT
1 AGTGACAAGTGATAAGT
3726717 GATAAGTAGT
Statistics
Matches: 192, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 192 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
Found at i:3727500 original size:45 final size:45
Alignment explanation
Indices: 3727409--3727506 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
3727399 GGGTAAGGGG
* **
3727409 TGTTACACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAATC
1 TGTTACACTGCAACTTCAGGGAAATAAGATTAGCTATCACTAATC
* * * * *
3727454 TGTTACACTGCAACTTTAGGGAGATAAGATTAGGTTTCACTGATC
1 TGTTACACTGCAACTTCAGGGAAATAAGATTAGCTATCACTAATC
3727499 TGTTACAC
1 TGTTACAC
3727507 CATTCTCTAG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (45 bp):
TGTTACACTGCAACTTCAGGGAAATAAGATTAGCTATCACTAATC
Found at i:3729874 original size:24 final size:22
Alignment explanation
Indices: 3729831--3729875 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
3729821 ACTATTTTTT
3729831 TACTGTTTGCTTTTGTTTCTGC
1 TACTGTTTGCTTTTGTTTCTGC
*
3729853 TACTGTTTCTCTTGTTGTTTCTG
1 TACTGTTT-GCTT-TTGTTTCTG
3729876 TGTTCCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 3 0.15
24 9 0.45
ACGTcount: A:0.04, C:0.18, G:0.18, T:0.60
Consensus pattern (22 bp):
TACTGTTTGCTTTTGTTTCTGC
Found at i:3741068 original size:16 final size:16
Alignment explanation
Indices: 3741047--3741077 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3741037 TGCCATTTCG
3741047 GAATTTCCTTTTTCAT
1 GAATTTCCTTTTTCAT
3741063 GAATTTCCTTTTTCA
1 GAATTTCCTTTTTCA
3741078 GATAGTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (16 bp):
GAATTTCCTTTTTCAT
Found at i:3742269 original size:25 final size:27
Alignment explanation
Indices: 3742234--3742283 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
3742224 TTTTAAATGT
3742234 GATTATAAAAAA-TAA-TTAAAATAAA
1 GATTATAAAAAATTAATTTAAAATAAA
*
3742259 GATTATTAAAAATTAATTTAAAATA
1 GATTATAAAAAATTAATTTAAAATA
3742284 TGACAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 3 0.14
27 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (27 bp):
GATTATAAAAAATTAATTTAAAATAAA
Found at i:3742275 original size:26 final size:26
Alignment explanation
Indices: 3742234--3742283 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
3742224 TTTTAAATGT
3742234 GATTATAAAAAATAA-TTAAAATAAA
1 GATTATAAAAAATAATTTAAAATAAA
*
3742259 GATTATTAAAAATTAATTTAAAATA
1 GATTA-TAAAAAATAATTTAAAATA
3742284 TGACAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 9 0.41
27 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (26 bp):
GATTATAAAAAATAATTTAAAATAAA
Found at i:3742985 original size:27 final size:28
Alignment explanation
Indices: 3742955--3743014 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
3742945 TTCTTCCTTG
3742955 TTTTTAAAAC-AAAAACGAAATAGATTT
1 TTTTTAAAACAAAAAACGAAATAGATTT
*
3742982 TTTTTAAAACAGAAAAATGAAATAGATTT
1 TTTTTAAAACA-AAAAACGAAATAGATTT
3743011 TTTT
1 TTTT
3743015 GTTTTAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 10 0.33
29 20 0.67
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.38
Consensus pattern (28 bp):
TTTTTAAAACAAAAAACGAAATAGATTT
Found at i:3743472 original size:23 final size:21
Alignment explanation
Indices: 3743442--3743494 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
3743432 CCTTAGCCTC
3743442 TCCATTTTTACTTTTTTCCATTT
1 TCCATTTTTA-TTTTTTCCA-TT
*
3743465 TCCATTTTTTATTTTTTTCATT
1 TCCA-TTTTTATTTTTTCCATT
3743487 T-CATTTTT
1 TCCATTTTT
3743495 TTACGACTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.18
21 2 0.07
22 3 0.11
23 12 0.43
24 6 0.21
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (21 bp):
TCCATTTTTATTTTTTCCATT
Found at i:3743982 original size:1 final size:1
Alignment explanation
Indices: 3743968--3744072 Score: 57
Period size: 1 Copynumber: 105.0 Consensus size: 1
3743958 CCGGTAGAGG
* * * * * * * * * * *
3743968 TTTTTGTTTCTTTTTGTTTTTATTTTTTTGTTCTTGTTTTTTGTTCTTTTCTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * *
3744033 TTTCTTTTCTTTTCTTTTCTTTTCTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3744073 GGAATTGAAT
Statistics
Matches: 70, Mismatches: 34, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.01, C:0.10, G:0.05, T:0.84
Consensus pattern (1 bp):
T
Found at i:3743983 original size:10 final size:9
Alignment explanation
Indices: 3743968--3744072 Score: 83
Period size: 9 Copynumber: 11.6 Consensus size: 9
3743958 CCGGTAGAGG
*
3743968 TTTTTGTTT
1 TTTTTCTTT
*
3743977 CTTTTTGTTT
1 -TTTTTCTTT
*
3743987 TTATT-TTT
1 TTTTTCTTT
*
3743995 TTGTTCTTGT
1 TTTTTCTT-T
*
3744005 TTTTT-GTT
1 TTTTTCTTT
*
3744013 CTTTTCTTT
1 TTTTTCTTT
3744022 TTTTT-TCTT
1 TTTTTCT-TT
3744031 TTTTTCTTT
1 TTTTTCTTT
3744040 TCTTTTCTTT
1 T-TTTTCTTT
3744050 TCTTTTC-TT
1 T-TTTTCTTT
3744059 TTTTTCTTT
1 TTTTTCTTT
3744068 TTTTT
1 TTTTT
3744073 GGAATTGAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 15
0.79 0.07 0.15
Matches are distributed among these distances:
8 18 0.22
9 33 0.41
10 30 0.37
ACGTcount: A:0.01, C:0.10, G:0.05, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:3743997 original size:14 final size:13
Alignment explanation
Indices: 3743978--3744072 Score: 75
Period size: 13 Copynumber: 7.1 Consensus size: 13
3743968 TTTTTGTTTC
3743978 TTTTTGTTTTTATT
1 TTTTTGTTTTT-TT
* *
3743992 TTTTTGTTCTTGT
1 TTTTTGTTTTTTT
*
3744005 TTTTTGTTCTTTTC
1 TTTTTGTT-TTTTT
*
3744019 TTTTT-TTTTCTT
1 TTTTTGTTTTTTT
*
3744031 TTTTTCTTTTCTTT
1 TTTTTGTTTT-TTT
* *
3744045 TCTTTTCTTTTCTT
1 T-TTTTGTTTTTTT
*
3744059 TTTTTCTTTTTTT
1 TTTTTGTTTTTTT
3744072 T
1 T
3744073 GGAATTGAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
12 8 0.12
13 27 0.40
14 23 0.34
15 9 0.13
ACGTcount: A:0.01, C:0.11, G:0.04, T:0.84
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:3744021 original size:5 final size:5
Alignment explanation
Indices: 3744011--3744072 Score: 80
Period size: 5 Copynumber: 13.4 Consensus size: 5
3744001 TTGTTTTTTG
*
3744011 TTCTT TTCTT TTTTT TTC-T TT-TT TTCTT TTCTT TTCTT TTCTT TTC-T
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
3744058 TT-TT TTCTT TT-TT TT
1 TTCTT TTCTT TTCTT TT
3744073 GGAATTGAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
4 16 0.31
5 35 0.69
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTCTT
Found at i:3744023 original size:28 final size:26
Alignment explanation
Indices: 3743968--3744063 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 26
3743958 CCGGTAGAGG
*
3743968 TTTTTGTTTCTTTTTGTT-TTTAT-TTT
1 TTTTTCTTT-TTTTTGTTCTTT-TCTTT
3743994 TTTGTTCTTGTTTTTTGTTCTTTTCTTTT
1 TTT-TTCTT-TTTTTTGTTCTTTTC-TTT
*
3744023 TTTTTCTTTTTTTCTTTTCTTTTCTTT
1 TTTTTCTTTTTTT-TGTTCTTTTCTTT
3744050 TCTTTTCTTTTTTT
1 T-TTTTCTTTTTTT
3744064 CTTTTTTTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
26 3 0.05
27 22 0.36
28 30 0.49
29 6 0.10
ACGTcount: A:0.01, C:0.10, G:0.05, T:0.83
Consensus pattern (26 bp):
TTTTTCTTTTTTTTGTTCTTTTCTTT
Found at i:3744032 original size:23 final size:23
Alignment explanation
Indices: 3744006--3744072 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
3743996 TGTTCTTGTT
*
3744006 TTTTGTTCTTTTCTTTTTTTTTC
1 TTTTCTTCTTTTCTTTTTTTTTC
* *
3744029 TTTTTTTCTTTTCTTTTCTTTTC
1 TTTTCTTCTTTTCTTTTTTTTTC
*
3744052 TTTTCTTTTTTTCTTTTTTTT
1 TTTTCTTCTTTTCTTTTTTTT
3744073 GGAATTGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.00, C:0.13, G:0.01, T:0.85
Consensus pattern (23 bp):
TTTTCTTCTTTTCTTTTTTTTTC
Found at i:3744064 original size:28 final size:28
Alignment explanation
Indices: 3743998--3744072 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 28
3743988 TATTTTTTTG
* *
3743998 TTCTTGTTTTT-TGTTCTTTTCTTTTTTT
1 TTCTT-TTTTTCTTTTCTTTTCTTTTCTT
3744026 TTCTTTTTTTCTTTTCTTTTCTTTTCTT
1 TTCTTTTTTTCTTTTCTTTTCTTTTCTT
3744054 TTCTTTTTTTCTTTT-TTTT
1 TTCTTTTTTTCTTTTCTTTT
3744073 GGAATTGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 9 0.20
28 35 0.80
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (28 bp):
TTCTTTTTTTCTTTTCTTTTCTTTTCTT
Found at i:3749815 original size:44 final size:44
Alignment explanation
Indices: 3749698--3749944 Score: 135
Period size: 44 Copynumber: 5.7 Consensus size: 44
3749688 ACTTGATGCG
*
3749698 ATCTACTCTACTGCAACTTTAGAGAGATAAGATCTGGATGTTTTA
1 ATCTACTCTACTGCAACTTCA-AGAGATAAGATCTGGATGTTTTA
** * * * * * *
3749743 ATCCGCTCCACTACAACTTCAGGGAGATAGGAT-T-GATTTCTTTT
1 ATCTACTCTACTGCAACTTCA-AGAGATAAGATCTGGATGT-TTTA
* *
3749787 ATCTACTCTACTGCAACTTCAAGCAGATAAGA-CTGTATG---TG
1 ATCTACTCTACTGCAACTTCAAG-AGATAAGATCTGGATGTTTTA
* *
3749828 ATCTGCTCT-CTGCAACTTCAGAGAGATAAGATAT--ATGGTTTTA
1 ATCTACTCTACTGCAACTTCA-AGAGATAAGATCTGGAT-GTTTTA
** * * *
3749871 ATCCGCTCCACTGCAACTTCAGGAAGAT-AGAAT-TGGATG---TG
1 ATCTACTCTACTGCAACTTCAAG-AGATAAG-ATCTGGATGTTTTA
* *
3749912 ATCTACTCTACTGTAACTTTAGAGAGATAAGAT
1 ATCTACTCTACTGCAACTTCA-AGAGATAAGAT
3749945 TTGTGGTTTT
Statistics
Matches: 154, Mismatches: 31, Indels: 38
0.69 0.14 0.17
Matches are distributed among these distances:
39 2 0.01
40 20 0.13
41 35 0.23
42 3 0.02
43 17 0.11
44 47 0.31
45 30 0.19
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (44 bp):
ATCTACTCTACTGCAACTTCAAGAGATAAGATCTGGATGTTTTA
Found at i:3749955 original size:85 final size:85
Alignment explanation
Indices: 3749796--3749985 Score: 240
Period size: 85 Copynumber: 2.2 Consensus size: 85
3749786 TATCTACTCT
* * * *
3749796 ACTGCAACTTCAAGCAGATA-AGACTGTATGTGATCTGCTCTCTGCAACTTCAGAGAGATAAGAT
1 ACTGCAACTTCAGGAAGATAGAGACTGGATGTGATCTACTCTCTGCAACTTCAGAGAGATAAGAT
*
3749860 ATATGGTTTTAATCCGCTCC
66 ATATGGTTTTAACCCGCTCC
* * *
3749880 ACTGCAACTTCAGGAAGATAGA-ATTGGATGTGATCTACTCTACTGTAACTTTAGAGAGATAAGA
1 ACTGCAACTTCAGGAAGATAGAGACTGGATGTGATCTACTCT-CTGCAACTTCAGAGAGATAAGA
* *
3749944 TTTGTGGTTTTAACCCGCTCC
65 TATATGGTTTTAACCCGCTCC
* * *
3749965 ACTACAACTTTAGGGAGATAG
1 ACTGCAACTTCAGGAAGATAG
3749986 GATCATTGGC
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
84 34 0.37
85 57 0.63
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (85 bp):
ACTGCAACTTCAGGAAGATAGAGACTGGATGTGATCTACTCTCTGCAACTTCAGAGAGATAAGAT
ATATGGTTTTAACCCGCTCC
Found at i:3750129 original size:50 final size:50
Alignment explanation
Indices: 3750064--3750654 Score: 233
Period size: 50 Copynumber: 11.8 Consensus size: 50
3750054 ATTGCAATGT
** *
3750064 CGGGGAAACAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCAC
1 CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
* * * ** ** ** *
3750114 CAGAGAAGTAAGATTCGCCATT-GTTTCTTCAATCTGTTTAACTACAATGT
1 CGGGGAAGTAAGATTCACC-TTCGTAGCTTCAATCTGTTCCACTACACCGC
** * *
3750164 CGGGGAAACAAGATTCGA-CATCCTAGCTTCAATCTGTTCCACTACACCGC
1 CGGGGAAGTAAGATTC-ACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
** * * * ** * ** *
3750214 CGGGGAAGTAAGATTTGTCGTT-ATAGCTTCAATCTATTTAACTGCAATGT
1 CGGGGAAGTAAGA-TTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
** * * *
3750264 CGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTTCACTACACCGC
1 CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
** * * * * * * ** ** *
3750314 TAGAGAAGTAAGACTCGCCGTT-GTGGCTTCAATTTATTTAACTACAATGT
1 CGGGGAAGTAAGATTCACC-TTCGTAGCTTCAATCTGTTCCACTACACCGC
* ** * * *
3750364 CGTGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGC
1 CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
* * * * * ** * ** *
3750414 CAGGGAAGTAAGATTC-GCTGTTGTGGCTTCAATCTTTTTAACTGCAATGT
1 CGGGGAAGTAAGATTCACCT-TCGTAGCTTCAATCTGTTCCACTACACCGC
** * * *
3750464 CGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCATTACACCGC
1 CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
* ** * * * ** ** ** *
3750514 CAGGGAAGTAAGATTC-GTTATTGTGGCTTCAATCTTTTTAACTGTAATGT
1 CGGGGAAGTAAGATTCACCT-TCGTAGCTTCAATCTGTTCCACTACACCGC
** * * * * *
3750564 CGGGGAAACAAGATTCGCCGTCGTAGATTCAATCTATTCCACTACACTGC
1 CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
** * * *
3750614 TAGGGAAGTAAGATTCACCGTT-GTGGTTTCAATCTATTCCA
1 CGGGGAAGTAAGATTCACC-TTCGTAGCTTCAATCTGTTCCA
3750655 TTGTAATGCC
Statistics
Matches: 374, Mismatches: 154, Indels: 26
0.68 0.28 0.05
Matches are distributed among these distances:
49 7 0.02
50 359 0.96
51 8 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (50 bp):
CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
Found at i:3750662 original size:100 final size:100
Alignment explanation
Indices: 3750044--3750651 Score: 838
Period size: 100 Copynumber: 6.1 Consensus size: 100
3750034 TGCCATCTTT
* * * *
3750044 AATCTGTTTAATTGCAATGTCGGGGAAACAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
* * * **
3750109 ACCACCAGAGAAGTAAGATTCGCCATTGTTTCTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
* * * *
3750144 AATCTGTTTAACTACAATGTCGGGGAAACAAGATTCGACATCCTAGCTTCAATCTGTTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
* * * * *
3750209 ACCGCCGGGGAAGTAAGATTTGTCGTTATAGCTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
*
3750244 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTTCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
* * *
3750309 ACCGCTAGAGAAGTAAGACTCGCCGTTGTGGCTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
* * * * *
3750344 AATTTATTTAACTACAATGTCGTGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
*
3750409 ACCGCCAGGGAAGTAAGATTCGCTGTTGTGGCTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
* *
3750444 AATCTTTTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCATTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
***
3750509 ACCGCCAGGGAAGTAAGATTCGTTATTGTGGCTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
* * * * *
3750544 AATCTTTTTAACTGTAATGTCGGGGAAACAAGATTCGCCGTCGTAGATTCAATCTATTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
* * * *
3750609 ACTGCTAGGGAAGTAAGATTCACCGTTGTGGTTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
3750644 AATCTATT
1 AATCTATT
3750652 CCATTGTAAT
Statistics
Matches: 448, Mismatches: 60, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 448 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (100 bp):
AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
Found at i:3751014 original size:88 final size:88
Alignment explanation
Indices: 3750849--3751191 Score: 463
Period size: 88 Copynumber: 3.9 Consensus size: 88
3750839 TAAGACTGGT
* ** * * *
3750849 GTCTTCGATCTGCTTCATTGCCAGTACAGGAAGGCAAGATCTGCCATTTTTCAACCTACTCCACT
1 GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA-TTTTCAACCTACTCCACT
*
3750914 GCTGCTCAGGGAGACAAGGCT-AG
65 ACTGCTCAGGGAGACAAGGCTGAG
* * * * *
3750937 TATCTTCAATCTACTTTGCTGCCAATACAGGAAAACAAGATCTTCTATTTTCAACCTACTCCACT
1 -GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACT
* *
3751002 GCTGCTCAGGGAGATAAGGCTGAG
65 ACTGCTCAGGGAGACAAGGCTGAG
* **
3751026 GTCTTCGATCTACTTCACTGTGAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
1 GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
* *
3751091 CTGCTCAAGGAGACAAGACTGAG
66 CTGCTCAGGGAGACAAGGCTGAG
* *
3751114 GTCTTCGATCTACTTCGCTGCCAATACATGAAGACAAGATTTGCTATTTTCAACCTACTCCACTA
1 GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
*
3751179 CTGCTTAGGGAGA
66 CTGCTCAGGGAGA
3751192 TAGGATTTAT
Statistics
Matches: 222, Mismatches: 31, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
88 185 0.83
89 37 0.17
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (88 bp):
GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
CTGCTCAGGGAGACAAGGCTGAG
Found at i:3754247 original size:22 final size:23
Alignment explanation
Indices: 3754209--3754251 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
3754199 AAAGAATCAT
3754209 AAAAATTATAGACAAAATTTATG
1 AAAAATTATAGACAAAATTTATG
3754232 AAAAAGTTATA-A-AAAATTTA
1 AAAAA-TTATAGACAAAATTTA
3754252 AAATTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (23 bp):
AAAAATTATAGACAAAATTTATG
Found at i:3754410 original size:11 final size:12
Alignment explanation
Indices: 3754389--3754425 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
3754379 TAAATTTAAA
3754389 TTTTTATAACTT
1 TTTTTATAACTT
3754401 TTTTTA-AACTT
1 TTTTTATAACTT
*
3754412 TGTTTATAA-TT
1 TTTTTATAACTT
3754423 TTT
1 TTT
3754426 ATGATTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTTATAACTT
Found at i:3756122 original size:44 final size:44
Alignment explanation
Indices: 3756063--3756147 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
3756053 CCTCATAGAT
*
3756063 ACGGCACAGGATTCTGCTCAAACAGACTGCGCATGGTGTCATAC
1 ACGGCACAGGATTCTGCTCAAACAGACTGCGCATAGTGTCATAC
* * * *
3756107 ACGGCACA-GATTTCTGTTCAAAGAGGCTGCGGATAGTGTCA
1 ACGGCACAGGA-TTCTGCTCAAACAGACTGCGCATAGTGTCA
3756148 GCTATCGGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.06
44 33 0.94
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (44 bp):
ACGGCACAGGATTCTGCTCAAACAGACTGCGCATAGTGTCATAC
Found at i:3756664 original size:20 final size:20
Alignment explanation
Indices: 3756639--3756678 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3756629 CTTTATATAT
3756639 TTTTTATAATTTTTGTAAAA
1 TTTTTATAATTTTTGTAAAA
* *
3756659 TTTTTATAGTTTTTTTAAAA
1 TTTTTATAATTTTTGTAAAA
3756679 ATATAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTTATAATTTTTGTAAAA
Found at i:3756727 original size:19 final size:19
Alignment explanation
Indices: 3756683--3756729 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3756673 TTAAAAATAT
*
3756683 AAATTTTGAAATTTTTATA
1 AAATTTTGAAATTTTTAAA
* **
3756702 AATTTTTGATTTTTTTAAA
1 AAATTTTGAAATTTTTAAA
3756721 AAATTTTGA
1 AAATTTTGA
3756730 GAGAGAGTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
AAATTTTGAAATTTTTAAA
Found at i:3768853 original size:37 final size:38
Alignment explanation
Indices: 3768785--3768864 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 38
3768775 AAATAGTCCC
* * *
3768785 TAAAATTTTAATTTTATAGTTTTTACGATTTAA-TCTT
1 TAAAATTTTAATTTTATAGTTCTTACAATTTAATTCCT
3768822 TAAAATTTTAATTTTTACTA-TTCTT-CAATTTAATTCCT
1 TAAAATTTTAA-TTTTA-TAGTTCTTACAATTTAATTCCT
3768860 TAAAA
1 TAAAA
3768865 ACAGATTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
37 18 0.49
38 17 0.46
39 2 0.05
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.54
Consensus pattern (38 bp):
TAAAATTTTAATTTTATAGTTCTTACAATTTAATTCCT
Found at i:3769836 original size:21 final size:20
Alignment explanation
Indices: 3769810--3769863 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
3769800 TCTAGTAAAA
3769810 TAAAAAAATAATTCATGAAGT
1 TAAAAAAATAATTC-TGAAGT
* *
3769831 TAAAAAAATTAATTCTTAATT
1 TAAAAAAA-TAATTCTGAAGT
3769852 TAAAGAAAATAA
1 TAAA-AAAATAA
3769864 ATGTAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (20 bp):
TAAAAAAATAATTCTGAAGT
Found at i:3790149 original size:27 final size:26
Alignment explanation
Indices: 3790117--3790214 Score: 115
Period size: 27 Copynumber: 3.7 Consensus size: 26
3790107 AAAAAGTATT
3790117 TTAAAAATATTTTAAAATTTAAAAAAA
1 TTAAAAATATTTTAAAA-TTAAAAAAA
3790144 TTAAAAATATTTTAAAATTAAAAATAA
1 TTAAAAATATTTTAAAATTAAAAA-AA
* * **
3790171 TAAAAAAGTATTTTAAAAATATTAAAA
1 TTAAAAA-TATTTTAAAATTAAAAAAA
* *
3790198 TTAAAAAAAATTTAAAA
1 TTAAAAATATTTTAAAA
3790215 AATAAATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
26 15 0.24
27 33 0.53
28 14 0.23
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAAAAATATTTTAAAATTAAAAAAA
Found at i:3790839 original size:11 final size:11
Alignment explanation
Indices: 3790823--3790861 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3790813 TCAATTATTT
3790823 TCTCAATTTCC
1 TCTCAATTTCC
3790834 TCTCAATTTCC
1 TCTCAATTTCC
*
3790845 TCTGAAATTT-C
1 TCT-CAATTTCC
3790856 TCTCAA
1 TCTCAA
3790862 ATCCCTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 2 0.08
11 18 0.72
12 5 0.20
ACGTcount: A:0.23, C:0.31, G:0.03, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:3793253 original size:21 final size:21
Alignment explanation
Indices: 3793206--3793279 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
3793196 AAACCCTAAC
3793206 AAAAACCCTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
*
3793227 -AAAACCCTATCCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
*
3793247 AAAAACCCTAACCTTTAACTT
1 AAAAACCCTAACCCTTAACTT
3793268 AAAAACCCTAAC
1 AAAAACCCTAAC
3793280 TGTAACTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 19 0.39
21 30 0.61
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAACCCTAACCCTTAACTT
Found at i:3793255 original size:15 final size:15
Alignment explanation
Indices: 3793256--3793315 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
3793246 TAAAAACCCT
*
3793256 AACCTTTAACTTAAA
1 AACCCTTAACTTAAA
3793271 AACCC-TAACTGT---
1 AACCCTTAACT-TAAA
*
3793283 AACTCTTAACTTAAA
1 AACCCTTAACTTAAA
3793298 AACCCTTAACTTAAA
1 AACCCTTAACTTAAA
3793313 AAC
1 AAC
3793316 ACCAAAACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 5 0.14
13 5 0.14
14 5 0.14
15 22 0.59
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.28
Consensus pattern (15 bp):
AACCCTTAACTTAAA
Found at i:3793259 original size:27 final size:26
Alignment explanation
Indices: 3793229--3793303 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 26
3793219 CTTAACTTAA
3793229 AACCCTATCCCTTAACTTAAAAACCCT
1 AACCCTAT-CCTTAACTTAAAAACCCT
3793256 AA-CC--T--TTAACTTAAAAACCCT
1 AACCCTATCCTTAACTTAAAAACCCT
** *
3793277 AACTGTAACTCTTAACTTAAAAACCCT
1 AACCCTATC-CTTAACTTAAAAACCCT
3793304 TAACTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
21 18 0.46
24 1 0.03
26 2 0.05
27 18 0.46
ACGTcount: A:0.40, C:0.31, G:0.01, T:0.28
Consensus pattern (26 bp):
AACCCTATCCTTAACTTAAAAACCCT
Found at i:3793286 original size:41 final size:40
Alignment explanation
Indices: 3793206--3793286 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
3793196 AAACCCTAAC
*
3793206 AAAAACCCTAACCCTTAACTTAAAACCCTATCCCTTAACTT
1 AAAAACCCTAACCCTTAACTTAAAACCCTA-CACTTAACTT
*
3793247 AAAAACCCTAACCTTTAACTTAAAAACCCTA-ACTGTAACT
1 AAAAACCCTAACCCTTAACTT-AAAACCCTACACT-TAACT
3793287 CTTAACTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
40 2 0.06
41 25 0.69
42 9 0.25
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.26
Consensus pattern (40 bp):
AAAAACCCTAACCCTTAACTTAAAACCCTACACTTAACTT
Found at i:3793503 original size:104 final size:103
Alignment explanation
Indices: 3793369--3793591 Score: 299
Period size: 104 Copynumber: 2.2 Consensus size: 103
3793359 CCCTAATATG
3793369 ATATAATTTGATA-AA-TTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAACAAA-
1 ATATAATTTGATACAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAACAAAT
** * *
3793431 ATGTTAGATTGTACAAAATGTTTTGACTGGTACTAACAA
66 A-GCCAGATTGTACAAAATGTTTTGACTGGTACAAAAAA
* * * **
3793470 TTAATAATTTGATACAATTTTACTAACAATTAATACAATTAATAATTAATAATTTTACTAACATT
1 AT-ATAATTTGATACAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAACAAA
* *
3793535 TAGCCATATTTTACAAAATGTTTTGACTGGTACAAAAAA
65 TAGCCAGATTGTACAAAATGTTTTGACTGGTACAAAAAA
3793574 ATATAATTTGATTACAAT
1 ATATAATTTGA-TACAAT
3793592 GACATTCAAC
Statistics
Matches: 105, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
101 1 0.01
102 11 0.10
103 11 0.10
104 81 0.77
105 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (103 bp):
ATATAATTTGATACAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAACAAAT
AGCCAGATTGTACAAAATGTTTTGACTGGTACAAAAAA
Found at i:3796760 original size:125 final size:125
Alignment explanation
Indices: 3796538--3796854 Score: 517
Period size: 125 Copynumber: 2.5 Consensus size: 125
3796528 CCCAAACATG
* * * * *
3796538 CTACTGTAGCAAAAACGCGTCTACGAGGGCGCGATTTCATAAATTCATCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* *
3796603 TTGAAGCGTTTTTTATATTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * *
3796663 CTACTGTAGCAAAAGCACGTCCACGTTGGCGCGATTTCAAAAATTCTTTTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* *
3796728 TTGAAGCATTTTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTTTTCAGTAC
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
*
3796788 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
3796853 TT
66 TT
3796855 TGATTTTATC
Statistics
Matches: 176, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 176 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:3797537 original size:55 final size:55
Alignment explanation
Indices: 3797457--3797570 Score: 221
Period size: 55 Copynumber: 2.1 Consensus size: 55
3797447 GAAAAGAACA
3797457 ACTTTAATGAATGCTCGAATCCTATTATTATGCATAAATTATGAATTTAGTCTTT
1 ACTTTAATGAATGCTCGAATCCTATTATTATGCATAAATTATGAATTTAGTCTTT
3797512 ACTTTAATGAATGCTCGAATCCTATTATTATGCATAAATTATGAATTTAGTCTTT
1 ACTTTAATGAATGCTCGAATCCTATTATTATGCATAAATTATGAATTTAGTCTTT
3797567 -CTTT
1 ACTTT
3797571 GTAATTTTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 4 0.07
55 55 0.93
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (55 bp):
ACTTTAATGAATGCTCGAATCCTATTATTATGCATAAATTATGAATTTAGTCTTT
Found at i:3799501 original size:3 final size:3
Alignment explanation
Indices: 3799467--3799531 Score: 53
Period size: 3 Copynumber: 21.3 Consensus size: 3
3799457 ATTAAATTGC
* * *
3799467 ATT ATT GTT ATT -GT ATT ATT -GT ATT ATCT ATT ATTT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT A-TT ATT AT-T ATT
*
3799513 ATT ATT ATT AGT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
3799532 CTTCCATACG
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
2 2 0.04
3 38 0.78
4 9 0.18
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3799505 original size:14 final size:14
Alignment explanation
Indices: 3799480--3799530 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
3799470 ATTGTTATTG
*
3799480 TATTATTGTATTATC
1 TATTATT-TATTATA
3799495 TATTATTTATTATA
1 TATTATTTATTATA
3799509 TATTA-TTATTATTA
1 TATTATTTATTA-TA
3799523 GTATTATT
1 -TATTATT
3799531 ACTTCCATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 6 0.19
14 13 0.41
15 12 0.38
16 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (14 bp):
TATTATTTATTATA
Found at i:3806851 original size:95 final size:95
Alignment explanation
Indices: 3806690--3806880 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
3806680 TTGAATAAAA
3806690 TTTTAGATCCATTTTTTGAACCCGAACCTAACAAATGGGCCTAAATTTTTTTTTCCAATCAAAAT
1 TTTTAGATCCATTTTTTGAACCCGAACCTAACAAATGGGCCTAAATTTTTTTTTCCAATCAAAAT
3806755 ATTGAAATATATATATATAACTTGGTATAT
66 ATTGAAATATATATATATAACTTGGTATAT
3806785 TTTTAGATCCATTTTTTGAACCCGAACCTAACAAATGGGCCTAAATTTTTTTTTCCAATCAAAAT
1 TTTTAGATCCATTTTTTGAACCCGAACCTAACAAATGGGCCTAAATTTTTTTTTCCAATCAAAAT
3806850 ATTGAAATATATATATATAACTTGGTATAT
66 ATTGAAATATATATATATAACTTGGTATAT
3806880 T
1 T
3806881 GTAGCAGTTG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (95 bp):
TTTTAGATCCATTTTTTGAACCCGAACCTAACAAATGGGCCTAAATTTTTTTTTCCAATCAAAAT
ATTGAAATATATATATATAACTTGGTATAT
Found at i:3809830 original size:41 final size:41
Alignment explanation
Indices: 3809771--3810010 Score: 270
Period size: 41 Copynumber: 5.9 Consensus size: 41
3809761 GATTTTTTAA
* *
3809771 ACCTTTAGCGTCGTTTTTATCTAAGCGCCACTAATGCTCGG
1 ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGG
* * *
3809812 ATCTTTAGCGGCGTTTTTATCTAAGCCCCGCTAATGCACGG
1 ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGG
* * * *
3809853 ATCTTTAGCGGTGTTTTTATCTAAGCGCCGCTAATTCTC-T
1 ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGG
* * *
3809893 AGCCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCTGG
1 A-CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTC-GG
* * **
3809936 -CCTTTAGCGGCGTTTGTAGCTAAGCGCCGCTAATGCAT-TT
1 ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGC-TCGG
* *
3809976 ACCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAAT
1 ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAT
3810011 AGTAACAAAA
Statistics
Matches: 169, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.01
41 167 0.99
42 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (41 bp):
ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGG
Found at i:3809992 original size:123 final size:123
Alignment explanation
Indices: 3809772--3810010 Score: 336
Period size: 123 Copynumber: 1.9 Consensus size: 123
3809762 ATTTTTTAAA
* * * *
3809772 CCTTTAGCGTCGTTTTTATCTAAGCGCCACTAATGCTCGGATCTTTAGCGGCGTTTTTATCTAAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTCGGACCTTTAGCGGCGTTTGTAGCTAAG
* * * *
3809837 CCCCGCTAATGCACGGATCTTTAGCGGTGTTTTTATCTAAGCGCCGCTAATTCTCTAG
66 CCCCGCTAATGCACGGACCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAATTCTCTAG
* *
3809895 CCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCTGG-CCTTTAGCGGCGTTTGTAGCTAA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTC-GGACCTTTAGCGGCGTTTGTAGCTAA
* ***
3809959 GCGCCGCTAATGCATTTACCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAAT
65 GCCCCGCTAATGCACGGACCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAAT
3810011 AGTAACAAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 99 0.98
124 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (123 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTCGGACCTTTAGCGGCGTTTGTAGCTAAG
CCCCGCTAATGCACGGACCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAATTCTCTAG
Found at i:3815797 original size:13 final size:14
Alignment explanation
Indices: 3815779--3815811 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3815769 TTGTTTTTAA
*
3815779 TTATTTTTAGT-GT
1 TTATTTTTAATGGT
3815792 TTATTTTTAATGGT
1 TTATTTTTAATGGT
3815806 TTATTT
1 TTATTT
3815812 CATCTATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (14 bp):
TTATTTTTAATGGT
Found at i:3816275 original size:21 final size:21
Alignment explanation
Indices: 3816250--3816298 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3816240 CTGCAGCTTA
*
3816250 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
* *
3816271 AAGCAGAGGCTGCAGCAAGGG
1 AAGCAGAGGCGGCAGCAAGAG
3816292 AAGCAGA
1 AAGCAGA
3816299 CCAGCATAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.18, G:0.43, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:3816426 original size:19 final size:19
Alignment explanation
Indices: 3816402--3816439 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3816392 GTAAATATTT
3816402 TTATCATTTTAACTTTTAA
1 TTATCATTTTAACTTTTAA
3816421 TTATCATTTTAACTTTTAA
1 TTATCATTTTAACTTTTAA
3816440 CATTTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATCATTTTAACTTTTAA
Found at i:3816669 original size:43 final size:43
Alignment explanation
Indices: 3816616--3816842 Score: 276
Period size: 43 Copynumber: 5.3 Consensus size: 43
3816606 ACTGCCAAAA
* * * * ** *
3816616 TTAGTGGCGTTTTTTAAAAAAGCGCCGTTAAAGGTTAGGGTCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGACAAGGTCT
* *
3816659 TTAGCGGCGTTTGTGAAAAAAGTGCCGCTAAATGACAAGGTCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGACAAGGTCT
** * * *
3816702 TTAGCGGCGTTTGTGGGAAAAGCACTGCTAAAGGTCAAGGTCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGACAAGGTCT
3816745 TTAGCGGCGTTTGTAGAAAAAA-CGCCGCTAAAGGACAAGGTCT
1 TTAGCGGCGTTTGT-GAAAAAAGCGCCGCTAAAGGACAAGGTCT
** * *
3816788 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGACATGATCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGACAAGGTCT
3816831 TTAGCGGCGTTT
1 TTAGCGGCGTTT
3816843 TTAGCGGCGC
Statistics
Matches: 157, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
42 5 0.03
43 147 0.94
44 5 0.03
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGACAAGGTCT
Found at i:3816744 original size:86 final size:86
Alignment explanation
Indices: 3816633--3816842 Score: 305
Period size: 86 Copynumber: 2.4 Consensus size: 86
3816623 CGTTTTTTAA
* * * * * *
3816633 AAAAGCGCCGTTAAAGGTTAGGGTCTTTAGCGGCGTTTGT-GAAAAAAGTGCCGCTAAATGACAA
1 AAAAGCACCGCTAAAGGTCAAGGTCTTTAGCGGCGTTTGTAGAAAAAA-CGCCGCTAAAGGACAA
3816697 GGTCTTTAGCGGCGTTTGTGGG
65 GGTCTTTAGCGGCGTTTGTGGG
*
3816719 AAAAGCACTGCTAAAGGTCAAGGTCTTTAGCGGCGTTTGTAGAAAAAACGCCGCTAAAGGACAAG
1 AAAAGCACCGCTAAAGGTCAAGGTCTTTAGCGGCGTTTGTAGAAAAAACGCCGCTAAAGGACAAG
3816784 GTCTTTAGCGGCGTTTGTGGG
66 GTCTTTAGCGGCGTTTGTGGG
* * * *
3816805 AAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTT
1 AAAAGCACCGCTAAAGGTCAAGGTCTTTAGCGGCGTTT
3816843 TTAGCGGCGC
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
86 104 0.94
87 7 0.06
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (86 bp):
AAAAGCACCGCTAAAGGTCAAGGTCTTTAGCGGCGTTTGTAGAAAAAACGCCGCTAAAGGACAAG
GTCTTTAGCGGCGTTTGTGGG
Found at i:3819909 original size:2 final size:2
Alignment explanation
Indices: 3819896--3819931 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3819886 CTCACAACCA
*
3819896 AT AT AA AT 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 AT AT AT AT
3819932 CAATAACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3830814 original size:88 final size:88
Alignment explanation
Indices: 3830658--3830833 Score: 316
Period size: 88 Copynumber: 2.0 Consensus size: 88
3830648 TTGAAACATC
*
3830658 CCATGCATGTTCATATCAAAAGTAGAGAGCAATGATCAGCAATTATTGCTCAACGCCAATGACGA
1 CCATGCATGTTCATATCAAAAGTAGAGAGCAATGATCAGCAATTATTGCTCAACGCCAATGACAA
3830723 CAGAAAATCCGGAAGAAAGCCAT
66 CAGAAAATCCGGAAGAAAGCCAT
* **
3830746 CCATGCATGTTCATATCAAAAGTAGAGAGTAATGATCAGCAATTATTGCTCAACGCCAATGGTAA
1 CCATGCATGTTCATATCAAAAGTAGAGAGCAATGATCAGCAATTATTGCTCAACGCCAATGACAA
3830811 CAGAAAATCCGGAAGAAAGCCAT
66 CAGAAAATCCGGAAGAAAGCCAT
3830834 TACAACCCAA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (88 bp):
CCATGCATGTTCATATCAAAAGTAGAGAGCAATGATCAGCAATTATTGCTCAACGCCAATGACAA
CAGAAAATCCGGAAGAAAGCCAT
Found at i:3833288 original size:13 final size:13
Alignment explanation
Indices: 3833270--3833299 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3833260 TTTCCTTCTC
3833270 TTTTTTTCTTTGT
1 TTTTTTTCTTTGT
*
3833283 TTTTTTTTTTTGT
1 TTTTTTTCTTTGT
3833296 TTTT
1 TTTT
3833300 GTTTTCCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (13 bp):
TTTTTTTCTTTGT
Done.