Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 77 of 322
Found at i:24568342 original size:43 final size:42
Alignment explanation
Indices: 24568280--24568429 Score: 201
Period size: 43 Copynumber: 3.5 Consensus size: 42
24568270 TATCCTAGAT
* *
24568280 ATGGTCTTACATGTTATCACATACCGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACATA-CGATGCCAATGTCCCAGAC
* * *
24568323 ATGGTCTTACACGAAATCACAAACGATGCCAATGTCCGAGAC
1 ATGGTCTTACACGTAATCACATACGATGCCAATGTCCCAGAC
* *
24568365 ATGGTCTTACACGTAATCACAATACAATGCCAATTTCCCAGAC
1 ATGGTCTTACACGTAATCAC-ATACGATGCCAATGTCCCAGAC
* *
24568408 ATGATCTTACATGTAATCACAT
1 ATGGTCTTACACGTAATCACAT
24568430 CTTGGTAATC
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 39 0.41
43 55 0.59
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (42 bp):
ATGGTCTTACACGTAATCACATACGATGCCAATGTCCCAGAC
Found at i:24571919 original size:37 final size:37
Alignment explanation
Indices: 24571869--24571947 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
24571859 TTATTACGAA
* * *
24571869 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* * *
24571906 GTCTTACCTGGACAAAATCCCCACGCGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
24571943 TTCTT
1 GTCTT
24571948 TAGAGCTCGG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:24572144 original size:47 final size:47
Alignment explanation
Indices: 24572066--24573022 Score: 1752
Period size: 47 Copynumber: 20.3 Consensus size: 47
24572056 CCCTTCGGGA
* * * * * * * *
24572066 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
* ** *
24572113 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572160 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572207 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572254 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572301 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572348 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572395 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572442 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572489 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572536 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572583 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572630 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572677 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572724 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572771 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572818 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572865 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCC--ATTAGGC
* * *
24572914 CTTATCACATATATACACTTTCGCATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
24572961 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
*
24573008 CTTATCACATATATA
1 CTTACCACATATATA
24573023 TACACTTTCA
Statistics
Matches: 889, Mismatches: 19, Indels: 4
0.97 0.02 0.00
Matches are distributed among these distances:
47 845 0.95
49 44 0.05
ACGTcount: A:0.29, C:0.33, G:0.09, T:0.28
Consensus pattern (47 bp):
CTTACCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
Found at i:24575503 original size:16 final size:17
Alignment explanation
Indices: 24575482--24575515 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
24575472 ATTAAGTGAA
*
24575482 TTATATAT-TGAGCATG
1 TTATATATATAAGCATG
24575498 TTATATATATAAGCATG
1 TTATATATATAAGCATG
24575515 T
1 T
24575516 ATACTGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (17 bp):
TTATATATATAAGCATG
Found at i:24576674 original size:25 final size:25
Alignment explanation
Indices: 24576621--24576689 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
24576611 AAGTTTAAAC
* * * * *
24576621 TGAAATTACTGTAGATAGTATATTC
1 TGAAACTACTATAGATAGTAAACTA
24576646 TGAAACTACTATAGATAGTAAACTA
1 TGAAACTACTATAGATAGTAAACTA
*
24576671 TGAAAAC-ACTCTAGATAGT
1 TG-AAACTACTATAGATAGT
24576690 GTATATTGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 33 0.89
26 4 0.11
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (25 bp):
TGAAACTACTATAGATAGTAAACTA
Found at i:24579946 original size:40 final size:40
Alignment explanation
Indices: 24579868--24580128 Score: 407
Period size: 40 Copynumber: 6.5 Consensus size: 40
24579858 ACCCAAGTAT
* * * ***
24579868 CTTCGGGATTTAG-CCGGGTATAGCAACTCAAACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
* * * **
24579907 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
24579947 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
24579987 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
24580027 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
24580067 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
*
24580107 CTTCGGGACTTAGCCCAGATAT
1 CTTCGGGACTTAGCCCGGATAT
24580129 CATCCGAATA
Statistics
Matches: 205, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
39 11 0.05
40 194 0.95
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
Found at i:24587481 original size:42 final size:42
Alignment explanation
Indices: 24587422--24587503 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
24587412 CTGACCTTTG
*
24587422 TGCATTACGACTTGGATAGCTCCCTGCACAGAGCTTCAATCA
1 TGCATTACGACTTGGATAACTCCCTGCACAGAGCTTCAATCA
*
24587464 TGCATTACGATTTGGATAACTCCCTGCACAGAGCTTCAAT
1 TGCATTACGACTTGGATAACTCCCTGCACAGAGCTTCAAT
24587504 ACTGATTCCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (42 bp):
TGCATTACGACTTGGATAACTCCCTGCACAGAGCTTCAATCA
Found at i:24588409 original size:54 final size:54
Alignment explanation
Indices: 24588350--24588457 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
24588340 GACATAGATA
*
24588350 TATCGTATGATTTCACATAACCTCTCACACTGATCCGATGTCACATGATCATAG
1 TATCGTATGATTTCACATAACCTCTCACACTGATCCGATGTCACATAATCATAG
*
24588404 TATCGTATGATTTCACATCACCTCTCACACTGATCCGATGTCACATAATCATAG
1 TATCGTATGATTTCACATAACCTCTCACACTGATCCGATGTCACATAATCATAG
24588458 GAATAGTCTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (54 bp):
TATCGTATGATTTCACATAACCTCTCACACTGATCCGATGTCACATAATCATAG
Found at i:24588649 original size:37 final size:37
Alignment explanation
Indices: 24588599--24588677 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
24588589 TTATTACGAA
* * *
24588599 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
24588636 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
24588673 GTCTT
1 GTCTT
24588678 TAGAGCTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:24588873 original size:47 final size:47
Alignment explanation
Indices: 24588797--24589077 Score: 269
Period size: 47 Copynumber: 6.1 Consensus size: 47
24588787 CTTCGGGACT
* * * * *
24588797 TATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCACTCGGCCC
* * * *
24588844 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCACTCGGCCC
24588891 TATCACATATATACACTTTCACATTCATCACATCGGCCA-T------
1 TATCACATATATACACTTTCACATTCATCACATCGGCCACTCGGCCC
* * *
24588931 TA--AGC-T-TATGCACTTTCACATCCATCACATTGGCCACTCGGCCC
1 TATCA-CATATATACACTTTCACATTCATCACATCGGCCACTCGGCCC
* * * ** *
24588975 TGTCATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCACTCGGCCC
* * *
24589022 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCAC--ATATATACACTTTCACATTCATCACATCGGCCACTCGGCCC
24589071 TATCACA
1 TATCACA
24589078 ATTTAGAATT
Statistics
Matches: 195, Mismatches: 25, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
37 27 0.14
38 3 0.02
39 1 0.01
40 2 0.01
44 1 0.01
46 3 0.02
47 112 0.57
49 46 0.24
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCACTCGGCCC
Found at i:24588988 original size:84 final size:85
Alignment explanation
Indices: 24588857--24589024 Score: 266
Period size: 84 Copynumber: 2.0 Consensus size: 85
24588847 CACATATATA
* * *
24588857 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
1 CACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACACTTTCACATTCATCAC
24588922 ATCGGCCATTAAG-CTTATG
66 ATCGGCCATTAAGCCTTATG
* * * *
24588941 CACTTTCACATCCATCACATTGGCCACTCGGCCCTGTCATATATATACACTTTCACATTCATCAC
1 CACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACACTTTCACATTCATCAC
24589006 ATCGGCCATTAAGCCTTAT
66 ATCGGCCATTAAGCCTTAT
24589025 CACATATATA
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
84 71 0.93
85 5 0.07
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32
Consensus pattern (85 bp):
CACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACACTTTCACATTCATCAC
ATCGGCCATTAAGCCTTATG
Found at i:24589046 original size:49 final size:49
Alignment explanation
Indices: 24588978--24589077 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
24588968 TCGGCCCTGT
24588978 CATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCA
1 CATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCA
*
24589027 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
1 CATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCA
24589076 CA
1 CA
24589078 ATTTAGAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (49 bp):
CATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCA
Found at i:24591181 original size:16 final size:17
Alignment explanation
Indices: 24591150--24591183 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
24591140 TTTTTTTACA
*
24591150 AAAATAGTATAAAAAAT
1 AAAATACTATAAAAAAT
24591167 AAAATACTA-AAAAAAT
1 AAAATACTATAAAAAAT
24591183 A
1 A
24591184 TCTTAATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAATACTATAAAAAAT
Found at i:24591506 original size:151 final size:151
Alignment explanation
Indices: 24591250--24591769 Score: 928
Period size: 151 Copynumber: 3.5 Consensus size: 151
24591240 CGGGTTTTTT
* *
24591250 TACTAAAATAATATAAAAATAAAATATGAAAATAGTATATTTTAAAAAATAAAATCCT-AAAAT-
1 TACTAAAATAATATAAAAATAAAATA-AAAAATAAT-TATTTTAAAAAATAAAAT-CTGAAAATA
* *
24591313 AAAAAATAC-----AAACAAAGGGCCAAAATCAAGATTTTTTACTAAATTAATATAAAAAAACTA
63 AAAAAATACAAATAAAACAAAGGGCCAAAATCAGGGTTTTTTACTAAATTAATATAAAAAAACTA
24591373 AAATAATAAATTTGAAATATTATG
128 AAATAATAAATTTGAAATATTATG
24591397 TACTAAAATAATATAAAAATAAAATAAAAAATAATTATTTTAAAAAATAAAATCTGAAAATAAAA
1 TACTAAAATAATATAAAAATAAAATAAAAAATAATTATTTTAAAAAATAAAATCTGAAAATAAAA
24591462 AAATACAAATAAAACAAAGGGCCAAAATCAGGGTTTTTTACTAAATTAATATAAAAAAACTAAAA
66 AAATACAAATAAAACAAAGGGCCAAAATCAGGGTTTTTTACTAAATTAATATAAAAAAACTAAAA
24591527 TAATAAATTTGAAATATTATG
131 TAATAAATTTGAAATATTATG
24591548 TACTAAAATAATATAAAAATAAAATAAAAAATAATTATTTTAAAAAATAAAATCTGAAAATAAAA
1 TACTAAAATAATATAAAAATAAAATAAAAAATAATTATTTTAAAAAATAAAATCTGAAAATAAAA
24591613 AAATACAAATAAAACAAAGGGCCAAAATCAGGGTTTTTTACTAAATTAATATAAAAAAACTAAAA
66 AAATACAAATAAAACAAAGGGCCAAAATCAGGGTTTTTTACTAAATTAATATAAAAAAACTAAAA
24591678 TAATAAATTTGAAATATTATG
131 TAATAAATTTGAAATATTATG
24591699 TACTAAAATAATATAAAAATAAAATAAAAAATAATTATTTTAAAAAATAAAATCTGAAAATAAAA
1 TACTAAAATAATATAAAAATAAAATAAAAAATAATTATTTTAAAAAATAAAATCTGAAAATAAAA
24591764 AAATAC
66 AAATAC
24591770 CAAGAAATTT
Statistics
Matches: 362, Mismatches: 4, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
144 2 0.01
145 23 0.06
146 16 0.04
147 26 0.07
151 295 0.81
ACGTcount: A:0.61, C:0.06, G:0.05, T:0.28
Consensus pattern (151 bp):
TACTAAAATAATATAAAAATAAAATAAAAAATAATTATTTTAAAAAATAAAATCTGAAAATAAAA
AAATACAAATAAAACAAAGGGCCAAAATCAGGGTTTTTTACTAAATTAATATAAAAAAACTAAAA
TAATAAATTTGAAATATTATG
Found at i:24594005 original size:66 final size:66
Alignment explanation
Indices: 24593887--24594060 Score: 172
Period size: 66 Copynumber: 2.6 Consensus size: 66
24593877 CTTTGGGTCT
* ** * * *
24593887 TATCCACTGCAGTACAACACTTC-TCTCGGCTCGTATCCACCGTTGTACAGCACTACCCCCCGCC
1 TATCCACTACAGTACTCCACTCCTTC-CGGCTCGTATCCACCGTAGTACAGCACTACCCACCGCC
24593951 CG
65 CG
* * * ** *
24593953 TATCTACTACAGTACTCCACTCCTTCCGGCTCGTATCCACTGTAGTATAGCACTACCCATGGCCT
1 TATCCACTACAGTACTCCACTCCTTCCGGCTCGTATCCACCGTAGTACAGCACTACCCACCGCCC
24594018 G
66 G
** * *
24594019 TATCCACTGTAGTACTCCACTCC-TCCTGGGTTGTATCCACCG
1 TATCCACTACAGTACTCCACTCCTTCC-GGCTCGTATCCACCG
24594061 CAGCATGGTA
Statistics
Matches: 88, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
65 3 0.03
66 83 0.94
67 2 0.02
ACGTcount: A:0.20, C:0.38, G:0.16, T:0.27
Consensus pattern (66 bp):
TATCCACTACAGTACTCCACTCCTTCCGGCTCGTATCCACCGTAGTACAGCACTACCCACCGCCC
G
Found at i:24594054 original size:33 final size:33
Alignment explanation
Indices: 24593963--24594058 Score: 99
Period size: 33 Copynumber: 2.9 Consensus size: 33
24593953 TATCTACTAC
*
24593963 AGTACTCCACTCCTTCC-GGCTCGTATCCACTGT
1 AGTACTCCACTCC-TCCTGGCTTGTATCCACTGT
* * *
24593996 AGTA-TAGCACTACC-CATGGCCTGTATCCACTGT
1 AGTACT-CCACT-CCTCCTGGCTTGTATCCACTGT
*
24594029 AGTACTCCACTCCTCCTGGGTTGTATCCAC
1 AGTACTCCACTCCTCCTGGCTTGTATCCAC
24594059 CGCAGCATGG
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
32 4 0.08
33 43 0.86
34 3 0.06
ACGTcount: A:0.19, C:0.35, G:0.17, T:0.29
Consensus pattern (33 bp):
AGTACTCCACTCCTCCTGGCTTGTATCCACTGT
Found at i:24600870 original size:128 final size:128
Alignment explanation
Indices: 24600642--24600888 Score: 422
Period size: 128 Copynumber: 1.9 Consensus size: 128
24600632 GACAGTGTTC
**
24600642 GATGCAATAGTTGGTTCCACAAAATCAATTCCTGATGGGAAAAGATTGCTCCATGCTTCATTGAA
1 GATGCAATAGTTGGTTCCACAAAATCAATTCCCAATGGGAAAAGATTGCTCCATGCTTCATTGAA
*
24600707 GAAACATCTGTCAGGTGTTTCTTATATGAACTCATCGTTGAAACCATAGTTTGACCAGCGTTT
66 GAAACATCTGTCAGGTGTTTCTTATATGAACTCATCATTGAAACCATAGTTTGACCAGCGTTT
** * *
24600770 GATGCAATAGTTGGTTCCGTAAAATCAATTCCCAATGGGAAACGATTTCTCCATGCTTCATTGAA
1 GATGCAATAGTTGGTTCCACAAAATCAATTCCCAATGGGAAAAGATTGCTCCATGCTTCATTGAA
*
24600835 GAAACATCTGTTAGGTGTTTCTTATATGAACTCATCATTGAAACCATAGTTTGA
66 GAAACATCTGTCAGGTGTTTCTTATATGAACTCATCATTGAAACCATAGTTTGA
24600889 TCACGTGAAG
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
128 111 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (128 bp):
GATGCAATAGTTGGTTCCACAAAATCAATTCCCAATGGGAAAAGATTGCTCCATGCTTCATTGAA
GAAACATCTGTCAGGTGTTTCTTATATGAACTCATCATTGAAACCATAGTTTGACCAGCGTTT
Found at i:24607434 original size:2 final size:2
Alignment explanation
Indices: 24607427--24607451 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24607417 CCTAACTGTA
24607427 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 A
24607452 AAAGTGCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24607635 original size:44 final size:44
Alignment explanation
Indices: 24607581--24607671 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
24607571 GTTGAAGTAA
* * * * *
24607581 AATAGAAGTTGTGATAGTTATACATTTAAAAGTAATTACAATTT
1 AATAAAAGTTGTGATAATTACACATCTAAAAATAATTACAATTT
*
24607625 AATAAAAGTTGTGATAATTACACATCTAAAAATAATTATAATTT
1 AATAAAAGTTGTGATAATTACACATCTAAAAATAATTACAATTT
24607669 AAT
1 AAT
24607672 TTACAGCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.37
Consensus pattern (44 bp):
AATAAAAGTTGTGATAATTACACATCTAAAAATAATTACAATTT
Found at i:24607936 original size:21 final size:23
Alignment explanation
Indices: 24607896--24607938 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
24607886 GTTGAATATG
*
24607896 TTAAAAATGTTTTAATTATAATT
1 TTAAAAATGTTCTAATTATAATT
24607919 TTAAAAAT-TTCT-ATTATAAT
1 TTAAAAATGTTCTAATTATAAT
24607939 ATTTGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAAAAATGTTCTAATTATAATT
Found at i:24607942 original size:23 final size:25
Alignment explanation
Indices: 24607890--24607942 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
24607880 TTATATGTTG
* *
24607890 AATATGTTAAAAATGTTTTAATTAT
1 AATATTTTAAAAATGTTCTAATTAT
24607915 -A-ATTTTAAAAAT-TTCT-ATTAT
1 AATATTTTAAAAATGTTCTAATTAT
24607936 AATATTT
1 AATATTT
24607943 GAATTGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 5 0.21
22 4 0.17
23 14 0.58
24 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
AATATTTTAAAAATGTTCTAATTAT
Found at i:24609873 original size:42 final size:42
Alignment explanation
Indices: 24609800--24609881 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
24609790 GCCCAAAGGC
*
24609800 TGAACAGAAGCTCATGAAAGCTAAACAAAAACCCATAAGGAT
1 TGAACAAAAGCTCATGAAAGCTAAACAAAAACCCATAAGGAT
* * * *
24609842 TGAACAAAAGCTCGT-AAGAGCTGAACGAAAACTCATAAGG
1 TGAACAAAAGCTCATGAA-AGCTAAACAAAAACCCATAAGG
24609882 GTAAACAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.15
Consensus pattern (42 bp):
TGAACAAAAGCTCATGAAAGCTAAACAAAAACCCATAAGGAT
Found at i:24609933 original size:21 final size:21
Alignment explanation
Indices: 24609883--24609950 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
24609873 CTCATAAGGG
*
24609883 TAAACAGAAGCTTAGTAGAGT
1 TAAACAGAAGCTCAGTAGAGT
* * *
24609904 TGAATAGAATCTCA-TATGAGT
1 TAAACAGAAGCTCAGTA-GAGT
*
24609925 TAAACAGAAGCTC-GTGAGAGC
1 TAAACAGAAGCTCAGT-AGAGT
24609946 TAAAC
1 TAAAC
24609951 GGAAAGTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
20 2 0.06
21 33 0.92
22 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (21 bp):
TAAACAGAAGCTCAGTAGAGT
Found at i:24611399 original size:15 final size:17
Alignment explanation
Indices: 24611374--24611407 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
24611364 AATGTATCAC
24611374 TTTTTTAAAAT-ATTTA
1 TTTTTTAAAATAATTTA
24611390 TTTTTT-AAATAATTTA
1 TTTTTTAAAATAATTTA
24611406 TT
1 TT
24611408 ATACCCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTAAAATAATTTA
Found at i:24617386 original size:35 final size:35
Alignment explanation
Indices: 24617338--24617500 Score: 168
Period size: 35 Copynumber: 4.7 Consensus size: 35
24617328 CCATGGAAAA
* *
24617338 TTGTGAAATGTAGGTATGCTATTAACCATAATGAG
1 TTGTGAAATGTAGGTATGGTATTATCCATAATGAG
* *
24617373 TTGTGAAACGTAGGTATGGTATTATCCA-CATCGAG
1 TTGTGAAATGTAGGTATGGTATTATCCATAAT-GAG
** * *
24617408 TTAAGAAACGTAGGTATGGTATTATCCATACTGAG
1 TTGTGAAATGTAGGTATGGTATTATCCATAATGAG
** ** **
24617443 TTAAGAAATGTAGGTATGACATT-TCCCATACCGAG
1 TTGTGAAATGTAGGTATGGTATTAT-CCATAATGAG
24617478 TTGTGAAATGTAGGTATGGTATT
1 TTGTGAAATGTAGGTATGGTATT
24617501 TCAATGAGGA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
34 3 0.03
35 105 0.96
36 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (35 bp):
TTGTGAAATGTAGGTATGGTATTATCCATAATGAG
Found at i:24617431 original size:70 final size:69
Alignment explanation
Indices: 24617342--24617500 Score: 185
Period size: 70 Copynumber: 2.3 Consensus size: 69
24617332 GGAAAATTGT
* ** **
24617342 GAAATGTAGGTATGCTATTAACCATAATGAGTTGTGAAACGTAGGTATGGTATTATCCACAT-CG
1 GAAATGTAGGTATGGTATTAACCATAATGAGTTAAGAAACGTAGGTATGACATT-TCC-CATACG
24617406 AGTTAA
64 AGTTAA
* * * *
24617412 GAAACGTAGGTATGGTATTATCCATACTGAGTTAAGAAATGTAGGTATGACATTTCCCATACCGA
1 GAAATGTAGGTATGGTATTAACCATAATGAGTTAAGAAACGTAGGTATGACATTTCCCATA-CGA
**
24617477 GTTGT
65 GTTAA
24617482 GAAATGTAGGTATGGTATT
1 GAAATGTAGGTATGGTATT
24617501 TCAATGAGGA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
68 3 0.04
69 3 0.04
70 69 0.92
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (69 bp):
GAAATGTAGGTATGGTATTAACCATAATGAGTTAAGAAACGTAGGTATGACATTTCCCATACGAG
TTAA
Found at i:24618070 original size:46 final size:45
Alignment explanation
Indices: 24618004--24618100 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 45
24617994 TAGCAATAGT
*
24618004 TTGAATTTGAAAATTCATCATAAATTATGGAAATCGAATTAGAGA
1 TTGAATTTGAAAATTCATCATAAATTATGAAAATCGAATTAGAGA
24618049 TTGAACTTTGAAAATTCATCATAAATTATGAAAATCGAATTAGAGA
1 TTGAA-TTTGAAAATTCATCATAAATTATGAAAATCGAATTAGAGA
24618095 TTGAAT
1 TTGAAT
24618101 AAGATATGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 6 0.12
46 44 0.88
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.34
Consensus pattern (45 bp):
TTGAATTTGAAAATTCATCATAAATTATGAAAATCGAATTAGAGA
Found at i:24624860 original size:35 final size:35
Alignment explanation
Indices: 24624821--24624982 Score: 202
Period size: 35 Copynumber: 4.7 Consensus size: 35
24624811 CCATGGAAAA
*
24624821 TTGTGAAACGTAGGTATGGTATTAACCATACTGAG
1 TTGTGAAACGTAGGTATGGTATTATCCATACTGAG
* * *
24624856 TTGTGAAACGTAAGTATGGTATTTTCCATATTGAG
1 TTGTGAAACGTAGGTATGGTATTATCCATACTGAG
**
24624891 TTAAGAAACGTAGGTATGGTATTATCCA-ACTGAG
1 TTGTGAAACGTAGGTATGGTATTATCCATACTGAG
** * *
24624925 TTAAGAAACGTAGGTATGGCATT-TCCCATACCGAG
1 TTGTGAAACGTAGGTATGGTATTAT-CCATACTGAG
*
24624960 TTGTGAAATGTAGGTATGGTATT
1 TTGTGAAACGTAGGTATGGTATT
24624983 TCAATGAGGA
Statistics
Matches: 110, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
33 1 0.01
34 30 0.27
35 79 0.72
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TTGTGAAACGTAGGTATGGTATTATCCATACTGAG
Found at i:24624942 original size:69 final size:70
Alignment explanation
Indices: 24624825--24624982 Score: 210
Period size: 69 Copynumber: 2.3 Consensus size: 70
24624815 GGAAAATTGT
** * * **
24624825 GAAACGTAGGTATGGTATTAACCATACTGAGTTGTGAAACGTAAGTATGGTATTTTCCATATTGA
1 GAAACGTAGGTATGGTATTAACCATACTGAGTTAAGAAACGTAAGTATGGCATTTCCCATACCGA
24624890 GTTAA
66 GTTAA
* *
24624895 GAAACGTAGGTATGGTATTATCCA-ACTGAGTTAAGAAACGTAGGTATGGCATTTCCCATACCGA
1 GAAACGTAGGTATGGTATTAACCATACTGAGTTAAGAAACGTAAGTATGGCATTTCCCATACCGA
**
24624959 GTTGT
66 GTTAA
*
24624964 GAAATGTAGGTATGGTATT
1 GAAACGTAGGTATGGTATT
24624983 TCAATGAGGA
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
69 54 0.70
70 23 0.30
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (70 bp):
GAAACGTAGGTATGGTATTAACCATACTGAGTTAAGAAACGTAAGTATGGCATTTCCCATACCGA
GTTAA
Found at i:24635734 original size:266 final size:266
Alignment explanation
Indices: 24635260--24635793 Score: 987
Period size: 266 Copynumber: 2.0 Consensus size: 266
24635250 TTTTCCATGC
24635260 GTACATGCAATTGCTACATGTGCCTCAACATGTTTGGATTGCATCATCTAATAACATGTAGTTGT
1 GTACATGCAATTGCTACATGTGCCTCAACATGTTTGGATTGCATCATCTAATAACATGTAGTTGT
*
24635325 GAAGATAAAGATGATGACTCTAGCTATAAAGAAGATGAGGAGGTAGTGCACCCATCGATGCCTTG
66 GAAGATAAAGATGATGACTCTAGCTATAAAGAAGATAAGGAGGTAGTGCACCCATCGATGCCTTG
*
24635390 TGTTGAGTTGGAGTTGATGACGATTCCATCAAGGCATGTACTATCAACCTAGAATTAATGCAGGG
131 TGTTGAGTTGGAGTTGATGACGACTCCATCAAGGCATGTACTATCAACCTAGAATTAATGCAGGG
*
24635455 TTGTCTTGGCCTCCTCCTACAACGTTGCCTACTCATTTCCTTCTTCGAAAGTAGATATGACTTAT
196 TCGTCTTGGCCTCCTCCTACAACGTTGCCTACTCATTTCCTTCTTCGAAAGTAGATATGACTTAT
24635520 TGCAAT
261 TGCAAT
* * *
24635526 GTACATGCAATTGCTACATGTGCCTCGACATGTTTGGATTGCATGATCTAATAGCATGTAGTTGT
1 GTACATGCAATTGCTACATGTGCCTCAACATGTTTGGATTGCATCATCTAATAACATGTAGTTGT
*
24635591 GAAGATAAAGATGATGACTCTAGCTATGAAGAAGATAAGGAGGTAGTGCACCCATCGATGCCTTG
66 GAAGATAAAGATGATGACTCTAGCTATAAAGAAGATAAGGAGGTAGTGCACCCATCGATGCCTTG
*
24635656 TGTTGAGTTGGAGTTGATGACGACTCCATCAAGGCATGTACTATCGACCTAGAATTAATGCAGGG
131 TGTTGAGTTGGAGTTGATGACGACTCCATCAAGGCATGTACTATCAACCTAGAATTAATGCAGGG
24635721 TCGTCTTGGCCTCCTCCTACAACGTTGCCTACTCATTTCCTTCTTCGAAAGTAGATATGACTTAT
196 TCGTCTTGGCCTCCTCCTACAACGTTGCCTACTCATTTCCTTCTTCGAAAGTAGATATGACTTAT
*
24635786 TGCGAT
261 TGCAAT
24635792 GT
1 GT
24635794 CTAAATAATG
Statistics
Matches: 259, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
266 259 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (266 bp):
GTACATGCAATTGCTACATGTGCCTCAACATGTTTGGATTGCATCATCTAATAACATGTAGTTGT
GAAGATAAAGATGATGACTCTAGCTATAAAGAAGATAAGGAGGTAGTGCACCCATCGATGCCTTG
TGTTGAGTTGGAGTTGATGACGACTCCATCAAGGCATGTACTATCAACCTAGAATTAATGCAGGG
TCGTCTTGGCCTCCTCCTACAACGTTGCCTACTCATTTCCTTCTTCGAAAGTAGATATGACTTAT
TGCAAT
Found at i:24637147 original size:16 final size:17
Alignment explanation
Indices: 24637122--24637164 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
24637112 ATTCGGCTTG
24637122 ATTATATAAATATAAAAA-
1 ATTATA-AAAT-TAAAAAC
24637140 ATTATAAAATTAAAAAC
1 ATTATAAAATTAAAAAC
24637157 ATTA-AAAA
1 ATTATAAAA
24637165 CTCAATAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.42
17 8 0.33
18 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTATAAAATTAAAAAC
Found at i:24638622 original size:17 final size:17
Alignment explanation
Indices: 24638600--24638633 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
24638590 TGAGCTTCCC
*
24638600 GTTATATGGCTCGGAAG
1 GTTATATGGCTCCGAAG
24638617 GTTATATGGCTCCGAAG
1 GTTATATGGCTCCGAAG
24638634 AGCTTCCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (17 bp):
GTTATATGGCTCCGAAG
Found at i:24650161 original size:25 final size:25
Alignment explanation
Indices: 24650133--24650181 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
24650123 TACAACTCGA
**
24650133 ATGAGATTCCTGTTATATGGCTCAC
1 ATGAGATTCCCATTATATGGCTCAC
*
24650158 ATGAGCTTCCCATTATATGGCTCA
1 ATGAGATTCCCATTATATGGCTCA
24650182 AGAGAGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (25 bp):
ATGAGATTCCCATTATATGGCTCAC
Found at i:24651134 original size:42 final size:42
Alignment explanation
Indices: 24651067--24651163 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
24651057 ACGGTTAGAG
* *
24651067 ACATGGGCGTGTGTCTCAGCCGTGTGTGGCATACGGCCTCAC
1 ACATGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTCAC
* * * *
24651109 ACATGGGTGTGTGTCTCGGCTGTGTGTGACACATGGCCTCAC
1 ACATGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTCAC
*
24651151 ACATGGGCATGTG
1 ACATGGGCGTGTG
24651164 ATTTGGCCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.15, C:0.25, G:0.34, T:0.26
Consensus pattern (42 bp):
ACATGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTCAC
Found at i:24652509 original size:9 final size:9
Alignment explanation
Indices: 24652495--24652538 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
24652485 TAAAAACTTA
24652495 GAGAGAATT
1 GAGAGAATT
24652504 GAGAGAA-T
1 GAGAGAATT
24652512 -AGATGAATT
1 GAGA-GAATT
*
24652521 GAGAAAATT
1 GAGAGAATT
24652530 GAGAGAATT
1 GAGAGAATT
24652539 ACGAGAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 3 0.10
8 4 0.13
9 20 0.67
10 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.23
Consensus pattern (9 bp):
GAGAGAATT
Found at i:24655773 original size:16 final size:16
Alignment explanation
Indices: 24655752--24655783 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24655742 ACCAAGCAGA
*
24655752 AATTCATGCACGTAAG
1 AATTCATGCACATAAG
24655768 AATTCATGCACATAAG
1 AATTCATGCACATAAG
24655784 TCTTGCGGAT
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:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (16 bp):
AATTCATGCACATAAG
Found at i:24661582 original size:46 final size:46
Alignment explanation
Indices: 24661530--24661850 Score: 408
Period size: 46 Copynumber: 6.8 Consensus size: 46
24661520 GATATTTGGG
* * *
24661530 CATCCGAACTCGTTGAGTTGAGTCCAAGTTCAATTATGGATGTGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
*
24661576 CATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * * * *
24661622 CATCCGAACTCGTAGAGTTGAGTCTGAGTTCACTTAGTGAAATGTAACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-TG-GATG---CGA-A
* * *
24661674 CATCCGAACTCGTTGAGTTGAGTCCAAGTTCAATTATGGATGTGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
*
24661720 CATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* *
24661766 CATCCGAACTCGTAGAGTTGAGTCTGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** * * *
24661812 CGCCCGAGCTCGTTGAGTTGAGTTCGAGTTCGCTTATGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
24661851 GCGGGTTACA
Statistics
Matches: 237, Mismatches: 32, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
46 192 0.81
47 3 0.01
48 3 0.01
50 3 0.01
51 4 0.02
52 32 0.14
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:24661697 original size:144 final size:144
Alignment explanation
Indices: 24661528--24661801 Score: 548
Period size: 144 Copynumber: 1.9 Consensus size: 144
24661518 CGGATATTTG
24661528 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCAATTATGGATGTGAACATCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCAATTATGGATGTGAACATCCGAACTCGTTGAG
24661593 TTGAGTTCGAGTTCACTTATGGATGCGAACATCCGAACTCGTAGAGTTGAGTCTGAGTTCACTTA
66 TTGAGTTCGAGTTCACTTATGGATGCGAACATCCGAACTCGTAGAGTTGAGTCTGAGTTCACTTA
24661658 GTGAAATGTAACTA
131 GTGAAATGTAACTA
24661672 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCAATTATGGATGTGAACATCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCAATTATGGATGTGAACATCCGAACTCGTTGAG
24661737 TTGAGTTCGAGTTCACTTATGGATGCGAACATCCGAACTCGTAGAGTTGAGTCTGAGTTCACTTA
66 TTGAGTTCGAGTTCACTTATGGATGCGAACATCCGAACTCGTAGAGTTGAGTCTGAGTTCACTTA
24661802 TGGATGCGAA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 130 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (144 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCAATTATGGATGTGAACATCCGAACTCGTTGAG
TTGAGTTCGAGTTCACTTATGGATGCGAACATCCGAACTCGTAGAGTTGAGTCTGAGTTCACTTA
GTGAAATGTAACTA
Found at i:24662609 original size:21 final size:21
Alignment explanation
Indices: 24662583--24662624 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
24662573 AAGTTATGGA
24662583 ATCGAAGCTTGATGAGTCTAT
1 ATCGAAGCTTGATGAGTCTAT
*
24662604 ATCGAATCTTGATGAGTCTAT
1 ATCGAAGCTTGATGAGTCTAT
24662625 TTTCATATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (21 bp):
ATCGAAGCTTGATGAGTCTAT
Found at i:24663247 original size:16 final size:16
Alignment explanation
Indices: 24663226--24663257 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24663216 ACCATGGAGA
*
24663226 AATTCATGCACGTAAG
1 AATTCATGCACATAAG
24663242 AATTCATGCACATAAG
1 AATTCATGCACATAAG
24663258 TCTTGCGGAT
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:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (16 bp):
AATTCATGCACATAAG
Found at i:24664776 original size:28 final size:28
Alignment explanation
Indices: 24664736--24664797 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
24664726 GTCTGAATAC
* *
24664736 TGTTCTAGCTTTTGACATTTTCATTTCT
1 TGTTTTAGCTTTTGACATTTTCACTTCT
24664764 TGTTTTAGCTTTTGACATTTTCACTTCT
1 TGTTTTAGCTTTTGACATTTTCACTTCT
*
24664792 TCTTTT
1 TGTTTT
24664798 TCTTTCTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.13, C:0.18, G:0.10, T:0.60
Consensus pattern (28 bp):
TGTTTTAGCTTTTGACATTTTCACTTCT
Found at i:24664804 original size:13 final size:14
Alignment explanation
Indices: 24664788--24664820 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
24664778 ACATTTTCAC
*
24664788 TTCTTCTTTT-TCT
1 TTCTTCTTTTATAT
24664801 TTCTTCTTTTATAT
1 TTCTTCTTTTATAT
24664815 TTCTTC
1 TTCTTC
24664821 CTCACAATCG
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:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCTTCTTTTATAT
Found at i:24665461 original size:15 final size:16
Alignment explanation
Indices: 24665441--24665471 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24665431 TTAAAACTTA
24665441 ATTTAAT-TTATTTTT
1 ATTTAATATTATTTTT
24665456 ATTTAATATTATTTTT
1 ATTTAATATTATTTTT
24665472 TAACATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTAATATTATTTTT
Found at i:24668292 original size:18 final size:19
Alignment explanation
Indices: 24668259--24668298 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
24668249 AATATTAAGA
24668259 AAACTTTTATTTTTATTTT
1 AAACTTTTATTTTTATTTT
24668278 AAACTTTTA-TTTTATTTT
1 AAACTTTTATTTTTATTTT
24668296 AAA
1 AAA
24668299 AAAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
AAACTTTTATTTTTATTTT
Found at i:24672561 original size:134 final size:134
Alignment explanation
Indices: 24672321--24672567 Score: 476
Period size: 134 Copynumber: 1.8 Consensus size: 134
24672311 CGTTCGATGA
24672321 TATAAGAAAATAGAAAAGAGAGGGAGTAAGCATAAAGCCTAGTAAGAAGTATGCAAATATATAGC
1 TATAAGAAAATAGAAAAGAGAGGGAGTAAGCATAAAGCCTAGTAAGAAGTATGCAAATATATAGC
24672386 AACAACTAAACCATTCATCAACATGCTCTTAATATAAAATAGTTATAAGCATAGCTATTTAGGTG
66 AACAACTAAACCATTCATCAACATGCTCTTAATATAAAATAGTTATAAGCATAGCTATTTAGGTG
24672451 ACAC
131 ACAC
*
24672455 TATAAGAAAATAGAAAAGAGAGGGAGTAAGCATAAAGCTTAGTAAGAAGTATGCAAATATATAGC
1 TATAAGAAAATAGAAAAGAGAGGGAGTAAGCATAAAGCCTAGTAAGAAGTATGCAAATATATAGC
*
24672520 AACAACTATACCATTCATCAACATGCTCTTAATATAAAATAGTTATAA
66 AACAACTAAACCATTCATCAACATGCTCTTAATATAAAATAGTTATAA
24672568 ATATAACTTA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 111 1.00
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (134 bp):
TATAAGAAAATAGAAAAGAGAGGGAGTAAGCATAAAGCCTAGTAAGAAGTATGCAAATATATAGC
AACAACTAAACCATTCATCAACATGCTCTTAATATAAAATAGTTATAAGCATAGCTATTTAGGTG
ACAC
Found at i:24675684 original size:24 final size:24
Alignment explanation
Indices: 24675655--24675716 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
24675645 CAACCGTATT
* * *
24675655 TGCACACATAGTGCTA-ATTACAC
1 TGCACACATAGTGCCATAGTAAAC
24675678 TCGCACACATAGTGCCATAGTAAAC
1 T-GCACACATAGTGCCATAGTAAAC
24675703 TGCACACATAGTGC
1 TGCACACATAGTGC
24675717 ATTGGATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.03
24 27 0.79
25 6 0.18
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (24 bp):
TGCACACATAGTGCCATAGTAAAC
Found at i:24679200 original size:27 final size:27
Alignment explanation
Indices: 24679169--24679257 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
24679159 GATAAAATTT
24679169 TCGTATCAAAATTTTCACACGACATAC
1 TCGTATCAAAATTTTCACACGACATAC
* * * **
24679196 TCGTAATTAAACATTTAATCGATA--AAATTT
1 TCGT-ATCAAA-ATTT--TC-ACACGACATAC
24679226 TCGTATCAAAATTTTCACACGACATAC
1 TCGTATCAAAATTTTCACACGACATAC
24679253 TCGTA
1 TCGTA
24679258 ATTAAACATT
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 12 0.27
28 9 0.20
29 9 0.20
30 7 0.16
31 2 0.04
32 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (27 bp):
TCGTATCAAAATTTTCACACGACATAC
Found at i:24679210 original size:57 final size:57
Alignment explanation
Indices: 24679138--24679308 Score: 342
Period size: 57 Copynumber: 3.0 Consensus size: 57
24679128 CGATTTAGTC
24679138 CTCGTAATTAAACATTTAATCGATAAAATTTTCGTATCAAAATTTTCACACGACATA
1 CTCGTAATTAAACATTTAATCGATAAAATTTTCGTATCAAAATTTTCACACGACATA
24679195 CTCGTAATTAAACATTTAATCGATAAAATTTTCGTATCAAAATTTTCACACGACATA
1 CTCGTAATTAAACATTTAATCGATAAAATTTTCGTATCAAAATTTTCACACGACATA
24679252 CTCGTAATTAAACATTTAATCGATAAAATTTTCGTATCAAAATTTTCACACGACATA
1 CTCGTAATTAAACATTTAATCGATAAAATTTTCGTATCAAAATTTTCACACGACATA
24679309 TCTTTCATAA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 114 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (57 bp):
CTCGTAATTAAACATTTAATCGATAAAATTTTCGTATCAAAATTTTCACACGACATA
Found at i:24698450 original size:16 final size:16
Alignment explanation
Indices: 24698429--24698483 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
24698419 GTTTGGTTCA
*
24698429 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
24698445 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
24698461 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
24698477 CTGTAAT
1 CTGTAAT
24698484 AAGTAATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:24721401 original size:35 final size:35
Alignment explanation
Indices: 24721359--24721428 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
24721349 GCTACTTTTA
24721359 CTATTTTAATTTTAAATTAGTTAA-TTATATATATT
1 CTATTTTAATTTTAAATTAGTTAATTTA-ATATATT
* *
24721394 CTATTTTAGTTTTAAGTTAGTTAATTTAATATATT
1 CTATTTTAATTTTAAATTAGTTAATTTAATATATT
24721429 ATTAGCATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 29 0.91
36 3 0.09
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (35 bp):
CTATTTTAATTTTAAATTAGTTAATTTAATATATT
Found at i:24721694 original size:10 final size:9
Alignment explanation
Indices: 24721678--24721707 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
24721668 TCATTTCTTA
24721678 TTTTTATTT
1 TTTTTATTT
24721687 TATTTTATTT
1 T-TTTTATTT
24721697 TTTTTATTT
1 TTTTTATTT
24721706 TT
1 TT
24721708 AAACTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTATTT
Found at i:24732346 original size:4 final size:4
Alignment explanation
Indices: 24732337--24732375 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
24732327 CTTCGCCTAA
24732337 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
24732376 AATAAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:24733361 original size:88 final size:87
Alignment explanation
Indices: 24733212--24733941 Score: 987
Period size: 88 Copynumber: 8.3 Consensus size: 87
24733202 GAATTCGTAA
* *
24733212 GCCTTAACCCCTTAAGTAGTAGGGTAACAGGCTAAAAATTACAGATCTTGTCTCCCTAAGCAGTA
1 GCCTTAACCCC-TAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTA
*
24733277 GTGAAGCAGATCGAAGACGAAGG
65 GTGGAGCAGATCGAAGACGAAGG
* * * *
24733300 GCCTTAACCCTCTAAGCAGTAAGGTAATAGGCTGAAAATTACAAATCTCGTCTCCCTAAGCAGTA
1 GCCTTAACCC-CTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTA
*
24733365 GTGGACCTA-ATCGAAGACGAAGG
65 GTGGAGC-AGATCGAAGACGAAGG
* * *
24733388 GCCTTAACCCTCTAAGTAGTAGGGTAACAGGCTAAAAATTACAGATCTCGTCTCCCTAAGCAGTA
1 GCCTTAACCC-CTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTA
* * *
24733453 GTGGACCAGATTGAAGAAGAAGG
65 GTGGAGCAGATCGAAGACGAAGG
* * *
24733476 GCCTTAACCCCCTAAGCAGTAGGATAACAGGCTGAAAATTACAAATCTTGTCTCCCTAAGCAATA
1 GCCTTAA-CCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTA
*
24733541 GTGGAGCAGATCGAAGACTAAGG
65 GTGGAGCAGATCGAAGACGAAGG
*
24733564 GCCTTAACCCCTTAAGTAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTA
1 GCCTTAACCCC-TAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTA
* *
24733629 GTGGACCAGATCGAAGACAAAGG
65 GTGGAGCAGATCGAAGACGAAGG
* *
24733652 GCCTTAACCCCTTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTCGTTTCCCTAAGCAGTA
1 GCCTTAACCCC-TAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTA
24733717 GTGGAGCAGATCGAAGACGAAGG
65 GTGGAGCAGATCGAAGACGAAGG
* * * * *
24733740 GCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAAATTACAAATCTTGTCTCCTTAAGTAGCA
1 GCCTTAA-CCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTA
* * *
24733805 GTGGAGTAGATCGAAGACAAATG
65 GTGGAGCAGATCGAAGACGAAGG
* * * * *
24733828 GCCTTAAACCCTTAAGCAGTAGGGTAACAGGCTGAAAATTATAGATCTTATCACCATAAGCAGTA
1 GCCTT-AACCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGT-
* * * *
24733893 AG-GAAACAGATCGAAGGCGATGG
64 AGTGGAGCAGATCGAAGACGAAGG
24733916 GCCTTAACCCCCTAAGCAGTAGGGTA
1 GCCTTAA-CCCCTAAGCAGTAGGGTA
24733942 GAGCAGATTG
Statistics
Matches: 570, Mismatches: 63, Indels: 18
0.88 0.10 0.03
Matches are distributed among these distances:
87 7 0.01
88 550 0.96
89 13 0.02
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (87 bp):
GCCTTAACCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGACGAAGG
Found at i:24733932 original size:44 final size:46
Alignment explanation
Indices: 24733884--24733979 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 46
24733874 CTTATCACCA
*
24733884 TAAGCAGTAAGG-A-AACAGATCGAAGGCGATGGGCCTTAACCCCC
1 TAAGCAGTAAGGTAGAACAGATCGAAGACGATGGGCCTTAACCCCC
* * *
24733928 TAAGCAGTAGGGTAGAGCAGATTGAAGACGATGGGCCTTAACCCCC
1 TAAGCAGTAAGGTAGAACAGATCGAAGACGATGGGCCTTAACCCCC
24733974 TAAGCA
1 TAAGCA
24733980 ATAGGGTAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 11 0.24
45 1 0.02
46 34 0.74
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.16
Consensus pattern (46 bp):
TAAGCAGTAAGGTAGAACAGATCGAAGACGATGGGCCTTAACCCCC
Found at i:24733960 original size:46 final size:46
Alignment explanation
Indices: 24733899--24733987 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
24733889 AGTAAGGAAA
* *
24733899 CAGATCGAAGGCGATGGGCCTTAACCCCCTAAGCAGTAGGGTAGAG
1 CAGATCGAAGACGATGGGCCTTAACCCCCTAAGCAATAGGGTAGAG
*
24733945 CAGATTGAAGACGATGGGCCTTAACCCCCTAAGCAATAGGGTA
1 CAGATCGAAGACGATGGGCCTTAACCCCCTAAGCAATAGGGTA
24733988 ACAGGCTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.30, C:0.24, G:0.29, T:0.17
Consensus pattern (46 bp):
CAGATCGAAGACGATGGGCCTTAACCCCCTAAGCAATAGGGTAGAG
Found at i:24733978 original size:134 final size:135
Alignment explanation
Indices: 24733827--24734076 Score: 403
Period size: 134 Copynumber: 1.9 Consensus size: 135
24733817 GAAGACAAAT
* *
24733827 GGCCTTAAACCCTTAAGCAGTAGGGTAACAGGCTGAAAATTATAGATCTTATCACCATAAGCAGT
1 GGCCTTAAACCCCTAAGCAATAGGGTAACAGGCTGAAAATTATAGATCTTATCACCATAAGCAGT
* **
24733892 AAGGAAACAGATCGAAGGCGATGGGCCTTAACCCCC-TAAGCAGTAGGGTAGAGCAGATTGAAGA
66 AAGGAAACAGATCGAAGACGATAAGCCTTAACCCCCTTAAGCAGTAGGGTAGAGCAGATTGAAGA
24733956 CGATG
131 CGATG
* * *
24733961 GGCCTTAACCCCCTAAGCAATAGGGTAACAGGCTGAAAATTATAGATCTTATCACCCTAAGTAGT
1 GGCCTTAAACCCCTAAGCAATAGGGTAACAGGCTGAAAATTATAGATCTTATCACCATAAGCAGT
* *
24734026 AAGGGAATAGATCGAAGACGATAAGCCTTAACCCCCTTAAGCAGTAGGGTA
66 AAGGAAACAGATCGAAGACGATAAGCCTTAACCCCCTTAAGCAGTAGGGTA
24734077 ACAGGTTGAA
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
134 91 0.87
135 14 0.13
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (135 bp):
GGCCTTAAACCCCTAAGCAATAGGGTAACAGGCTGAAAATTATAGATCTTATCACCATAAGCAGT
AAGGAAACAGATCGAAGACGATAAGCCTTAACCCCCTTAAGCAGTAGGGTAGAGCAGATTGAAGA
CGATG
Found at i:24734230 original size:45 final size:45
Alignment explanation
Indices: 24734178--24734285 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
24734168 ATTGAGGTCA
*
24734178 CAAGTCTTATCTTCCTAAAGTTGCAGTGAAGCAGACTAAAAATAG
1 CAAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTAAAAATAG
* * * * *
24734223 CAGGTCTTATCTCCCTGAAGTTGCGGTGGAGCAGACTAAAGATAG
1 CAAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTAAAAATAG
24734268 CAAGTCTTATCTCCCTAA
1 CAAGTCTTATCTCCCTAA
24734286 GCAATAGTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (45 bp):
CAAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTAAAAATAG
Found at i:24734417 original size:86 final size:87
Alignment explanation
Indices: 24734272--24734468 Score: 297
Period size: 86 Copynumber: 2.3 Consensus size: 87
24734262 AGATAGCAAG
* * *
24734272 TCTTATCTCCCTAAGCAATAGTGGAACATATCAAAGATGATGGGCCTTAACCCCCTAAGCAATAG
1 TCTTATCTCCCTAAGCAATAGTGGAACAAATCAAAGACGATGAGCCTTAACCCCCTAAGCAATAG
*
24734337 GGTAACAGGCTG-AATTACAGA
66 GGTAACAGGCTGAAATTACAAA
* * * *
24734358 TCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACGGTGAGCCTTAACCCCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAATAGTGGAACAAATCAAAGACGATGAGCCTTAACCCCCTAAGCAATAG
24734423 GGTAACAGGCTGAAAATTACAAA
66 GGTAACAGGCTG-AAATTACAAA
*
24734446 TCTTGTCTCCCTAAGCAATAGTG
1 TCTTATCTCCCTAAGCAATAGTG
24734469 TAGTAGATTT
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 70 0.71
88 29 0.29
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (87 bp):
TCTTATCTCCCTAAGCAATAGTGGAACAAATCAAAGACGATGAGCCTTAACCCCCTAAGCAATAG
GGTAACAGGCTGAAATTACAAA
Found at i:24734655 original size:44 final size:43
Alignment explanation
Indices: 24734607--24734749 Score: 112
Period size: 44 Copynumber: 3.3 Consensus size: 43
24734597 CTAGGGAAGC
*
24734607 TCGAAGCCACAATTTGTATCTCCTTGAAGTTCCAGCAGAGTAGA
1 TCGAAGCCACAATTTGTATCTCCTTGAAGTTCCAGCGGAGT-GA
* * * * ** *
24734651 TCGAAG-CACAAATCTCT-TCTCCCTGAAATGGCA-CTGGAGCTGC
1 TCGAAGCCAC-AATTTGTATCTCCTTGAAGTTCCAGC-GGAG-TGA
* * *
24734694 TCAAAGCCACAATTCGTATCTCTTTGAAGTTCCAGCGGAGTGGA
1 TCGAAGCCACAATTTGTATCTCCTTGAAGTTCCAGCGGAGT-GA
*
24734738 TCGAAGCTACAA
1 TCGAAGCCACAA
24734750 ACCTCTTCTC
Statistics
Matches: 72, Mismatches: 20, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
42 1 0.01
43 29 0.40
44 41 0.57
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (43 bp):
TCGAAGCCACAATTTGTATCTCCTTGAAGTTCCAGCGGAGTGA
Found at i:24734703 original size:87 final size:87
Alignment explanation
Indices: 24734528--24734778 Score: 360
Period size: 87 Copynumber: 2.9 Consensus size: 87
24734518 TTGAAATCAT
* * *
24734528 CAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGATACAAATCTCTTCTCCCTAAAAT
1 CAATTCGTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAG-CACAAATCTCTTCTCCCTGAAAT
* *
24734593 GGCACTAGG-GAAGCTCGAAGCCA
65 GGCACT-GGAGCAGCTCAAAGCCA
* *
24734616 CAATTTGTATCTCCTTGAAGTTCCAGCAGAGTAGATCGAAGCACAAATCTCTTCTCCCTGAAATG
1 CAATTCGTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCACAAATCTCTTCTCCCTGAAATG
*
24734681 GCACTGGAGCTGCTCAAAGCCA
66 GCACTGGAGCAGCTCAAAGCCA
* * *
24734703 CAATTCGTATCTCTTTGAAGTTCCAGCGGAGTGGATCGAAGCTACAAACCTCTTCTCCCTGAAAT
1 CAATTCGTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGC-ACAAATCTCTTCTCCCTGAAAT
*
24734768 GGCATTGGAGC
65 GGCACTGGAGC
24734779 GATTGAAGCT
Statistics
Matches: 147, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
86 2 0.01
87 76 0.52
88 69 0.47
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (87 bp):
CAATTCGTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCACAAATCTCTTCTCCCTGAAATG
GCACTGGAGCAGCTCAAAGCCA
Found at i:24736298 original size:35 final size:35
Alignment explanation
Indices: 24736259--24736328 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
24736249 GCTACTTTTG
24736259 CTATTTTAATTTTAAGTTAGTTAA-TTATATATATT
1 CTATTTTAATTTTAAGTTAGTTAATTTA-ATATATT
*
24736294 CTATTTTATTTTTAAGTTAGTTAATTTAATATATT
1 CTATTTTAATTTTAAGTTAGTTAATTTAATATATT
24736329 GTTAGCATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 30 0.91
36 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.59
Consensus pattern (35 bp):
CTATTTTAATTTTAAGTTAGTTAATTTAATATATT
Found at i:24736656 original size:56 final size:56
Alignment explanation
Indices: 24736514--24736630 Score: 202
Period size: 56 Copynumber: 2.1 Consensus size: 56
24736504 TATTATCACT
*
24736514 TCTTCTTTTGTTTCATTTAATATA-TATTTTTTCTTTACTGTTTTTGCCTATTTCA
1 TCTTCTTTTGTTTCATTTAATATATTTTTTTTTCTTTACTGTTTTTGCCTATTTCA
*
24736569 TCTTCTTTTGTTTCATTTAATATATTTTTTTTTCTTTATTGTTTTTGCCTATTTCA
1 TCTTCTTTTGTTTCATTTAATATATTTTTTTTTCTTTACTGTTTTTGCCTATTTCA
24736625 T-TTCTT
1 TCTTCTT
24736631 ATTTTTATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
55 29 0.49
56 30 0.51
ACGTcount: A:0.15, C:0.14, G:0.05, T:0.67
Consensus pattern (56 bp):
TCTTCTTTTGTTTCATTTAATATATTTTTTTTTCTTTACTGTTTTTGCCTATTTCA
Found at i:24741357 original size:25 final size:25
Alignment explanation
Indices: 24741329--24741439 Score: 111
Period size: 25 Copynumber: 4.5 Consensus size: 25
24741319 ATACGAGCAC
*
24741329 ATAACGGGAAGCTC-TTTCGAGCCAT
1 ATAACGGGAAGCTCATGT-GAGCCAT
*
24741354 ATAATGGGAAGCTCATGTGAGCCAT
1 ATAACGGGAAGCTCATGTGAGCCAT
* *
24741379 GTAACGGGAAGCTCATGAGAGCCAT
1 ATAACGGGAAGCTCATGTGAGCCAT
* * *
24741404 A-ATCGGGAAGTTCAAGTGAGCCA-
1 ATAACGGGAAGCTCATGTGAGCCAT
* *
24741427 ATATCTGGAAGCT
1 ATAACGGGAAGCT
24741440 TCGGAGATCC
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
23 1 0.01
24 27 0.38
25 42 0.58
26 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.22
Consensus pattern (25 bp):
ATAACGGGAAGCTCATGTGAGCCAT
Found at i:24741390 original size:50 final size:49
Alignment explanation
Indices: 24741330--24741426 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 49
24741320 TACGAGCACA
* ** *
24741330 TAACGGGAAGCTCTTTCGAGCCATATAAT-GGGAAGCTCATGTGAGCCATG
1 TAACGGGAAGCTCATGAGAGCC--ATAATCGGGAAGCTCAAGTGAGCCATG
*
24741380 TAACGGGAAGCTCATGAGAGCCATAATCGGGAAGTTCAAGTGAGCCA
1 TAACGGGAAGCTCATGAGAGCCATAATCGGGAAGCTCAAGTGAGCCA
24741427 ATATCTGGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
48 5 0.12
49 17 0.41
50 19 0.46
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.21
Consensus pattern (49 bp):
TAACGGGAAGCTCATGAGAGCCATAATCGGGAAGCTCAAGTGAGCCATG
Found at i:24744647 original size:28 final size:25
Alignment explanation
Indices: 24744616--24744670 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
24744606 TATCTAATGG
24744616 AAGATTAAATTTATTAATGATATAATAA
1 AAGATT-AATTT-TTAAT-ATATAATAA
* *
24744644 AAGATTAGTTTTTCATATATAATAA
1 AAGATTAATTTTTAATATATAATAA
24744669 AA
1 AA
24744671 AAAATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.44
26 4 0.16
27 4 0.16
28 6 0.24
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (25 bp):
AAGATTAATTTTTAATATATAATAA
Found at i:24745450 original size:26 final size:26
Alignment explanation
Indices: 24745421--24745502 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
24745411 TGATACAAAT
*
24745421 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
24745447 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
24745473 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
24745499 TGAT
1 TGAT
24745503 GGGAATTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:24749921 original size:42 final size:42
Alignment explanation
Indices: 24749874--24749983 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 42
24749864 ACTGGCACAG
*
24749874 AGCCTGCTAGGTAATAAACCTGATATCATACACCGGCATCAA
1 AGCCTGCTAGGTAATAAGCCTGATATCATACACCGGCATCAA
24749916 AGCCTGCTAGGTAATAAGCCTGATATCATACACCGGCATCAA
1 AGCCTGCTAGGTAATAAGCCTGATATCATACACCGGCATCAA
* *
24749958 AGCCTGCTAGGCAATAAGCTTGATAT
1 AGCCTGCTAGGTAATAAGCCTGATAT
24749984 ATCACTGTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (42 bp):
AGCCTGCTAGGTAATAAGCCTGATATCATACACCGGCATCAA
Found at i:24750102 original size:14 final size:15
Alignment explanation
Indices: 24750085--24750135 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
24750075 TCAACCATAG
24750085 AAATTCATACA-ATT
1 AAATTCATACACATT
* *
24750099 AAATTCA-ACATATA
1 AAATTCATACACATT
*
24750113 AAAATCATACACATT
1 AAATTCATACACATT
24750128 CAAATTCA
1 -AAATTCA
24750136 AAAACGTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 3 0.10
14 15 0.52
15 5 0.17
16 6 0.21
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTCATACACATT
Found at i:24760536 original size:24 final size:24
Alignment explanation
Indices: 24760500--24760659 Score: 126
Period size: 24 Copynumber: 6.7 Consensus size: 24
24760490 GGGTCAACAT
*
24760500 TGGCACTAAGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
*
24760524 TGGCACTATGTGTGCGGAATTGAA
1 TGGCACTATGTGTGCGGATTTGAA
* *
24760548 TGGCACTATGTGTGCTGATTTGGA
1 TGGCACTATGTGTGCGGATTTGAA
* * ** * * * *
24760572 TGTCAATACATGAGTGAATCTTCAA
1 TGGCACTATGTGTGCGGAT-TTGAA
* *
24760597 -GGCACTATGTGTGCGG-TGTAGCA
1 TGGCACTATGTGTGCGGAT-TTGAA
* **
24760620 TGGCACTATGTGTGCGAATTTGTT
1 TGGCACTATGTGTGCGGATTTGAA
*
24760644 TAGCACTATGTGTGCG
1 TGGCACTATGTGTGCG
24760660 AAATCGGTTG
Statistics
Matches: 102, Mismatches: 31, Indels: 6
0.73 0.22 0.04
Matches are distributed among these distances:
23 3 0.03
24 95 0.93
25 4 0.04
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.33
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTGAA
Found at i:24762111 original size:19 final size:18
Alignment explanation
Indices: 24762087--24762123 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
24762077 TCAACAATTA
24762087 TTTATTTGTATTTATAAAT
1 TTTATTT-TATTTATAAAT
*
24762106 TTTATTTTATTTTTAAAT
1 TTTATTTTATTTATAAAT
24762124 GATAGAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTATTTTATTTATAAAT
Found at i:24766284 original size:16 final size:16
Alignment explanation
Indices: 24766263--24766331 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
24766253 TTTGGTTCGC
24766263 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
24766279 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
24766295 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
24766312 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
24766328 TGTA
1 TGTA
24766332 ATAGCAAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:24766309 original size:33 final size:32
Alignment explanation
Indices: 24766263--24766331 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
24766253 TTTGGTTCGC
24766263 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
24766295 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
24766328 TGTA
1 TGTA
24766332 ATAGCAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:24766574 original size:16 final size:16
Alignment explanation
Indices: 24766546--24766591 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
24766536 TTTAATCATA
*
24766546 ATTTTTATT-AAATAT
1 ATTTTAATTAAAATAT
24766561 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
24766577 ATAATTTAA-TAAAAT
1 AT--TTTAATTAAAAT
24766592 TCTTAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 8 0.30
16 8 0.30
17 6 0.22
18 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:24766584 original size:18 final size:17
Alignment explanation
Indices: 24766557--24766591 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
24766547 TTTTTATTAA
*
24766557 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
24766575 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
24766592 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:24766771 original size:120 final size:117
Alignment explanation
Indices: 24766532--24766801 Score: 301
Period size: 120 Copynumber: 2.2 Consensus size: 117
24766522 TCAATAATAA
* * *
24766532 ATAATTTAATCATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
1 ATAATTTAA-CATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTA
* * * * * *
24766597 ATAATTAATAGAAATTTGTTTTGGTAAATTATTATTAACAATAAATAATTTAAAAG
65 ATAATTAAT---AATTTCTTATAGTAAATTATAAATAACAATAAATAATGTAAAAG
24766653 ATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAA
1 ATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAA
* * * * * *
24766718 TAATTAAT-A-TTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAAT
66 TAATTAATAATTTCTTATAGTAAATTA-T-AAATAACAATA-A--ATAATGTAAAAG
*
24766773 ATAAATTAACATAATTATTATTAAATATA
1 ATAATTTAACATAATTATTATTAAATATA
24766802 TTNNNNNNNN
Statistics
Matches: 128, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
115 11 0.09
116 2 0.02
117 7 0.05
118 1 0.01
120 98 0.77
121 9 0.07
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (117 bp):
ATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAA
TAATTAATAATTTCTTATAGTAAATTATAAATAACAATAAATAATGTAAAAG
Found at i:24769959 original size:8 final size:8
Alignment explanation
Indices: 24769946--24769980 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
24769936 TAAAGATTCT
24769946 AAAAAAGA
1 AAAAAAGA
24769954 AAAAAAGA
1 AAAAAAGA
*
24769962 AACAAAG-
1 AAAAAAGA
24769969 AAAAAAGA
1 AAAAAAGA
24769977 AAAA
1 AAAA
24769981 GTAGAATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:24769974 original size:15 final size:16
Alignment explanation
Indices: 24769949--24769978 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24769939 AGATTCTAAA
24769949 AAAGAAAAAAAGAAAC
1 AAAGAAAAAAAGAAAC
24769965 AAAG-AAAAAAGAAA
1 AAAGAAAAAAAGAAA
24769979 AAGTAGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAGAAAC
Found at i:24773809 original size:15 final size:15
Alignment explanation
Indices: 24773789--24773820 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
24773779 GGAGGGTAAA
24773789 ACAGAGAGCAAATCG
1 ACAGAGAGCAAATCG
24773804 ACAGAGAGCAAATCG
1 ACAGAGAGCAAATCG
24773819 AC
1 AC
24773821 CGAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.22, G:0.25, T:0.06
Consensus pattern (15 bp):
ACAGAGAGCAAATCG
Found at i:24783227 original size:21 final size:22
Alignment explanation
Indices: 24783173--24783234 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
24783163 ATTACTTTAT
*
24783173 TTTTATTTAA-AATTAATTAAA
1 TTTTATTTAATAATAAATTAAA
*
24783194 TTACTTGTTTAATAATAAATTAAA
1 TT--TTATTTAATAATAAATTAAA
*
24783218 TTTT-TTTAATAGTAAAT
1 TTTTATTTAATAATAAAT
24783235 ATTATTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 14 0.40
22 2 0.06
23 7 0.20
24 12 0.34
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (22 bp):
TTTTATTTAATAATAAATTAAA
Found at i:24792015 original size:22 final size:20
Alignment explanation
Indices: 24791975--24792023 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
24791965 TAATTTAAAA
24791975 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
24791995 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
24792015 TGTAAAAAT
1 TATAAAAAT
24792024 AACTTTTCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:24792070 original size:32 final size:33
Alignment explanation
Indices: 24792034--24792118 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
24792024 AACTTTTCCG
*
24792034 GAAAATATTTTCAGGAAATCT-GCCAAACAACA
1 GAAAATATTTTCAGCAAATCTAGCCAAACAACA
* * *
24792066 GAAAATATTTTACA-CAGATTTATCCAAACAACA
1 GAAAATATTTT-CAGCAAATCTAGCCAAACAACA
*
24792099 GAAAATATTTTCAGTAAATC
1 GAAAATATTTTCAGCAAATC
24792119 ATTTTCCAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
32 17 0.40
33 26 0.60
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.27
Consensus pattern (33 bp):
GAAAATATTTTCAGCAAATCTAGCCAAACAACA
Found at i:24792136 original size:20 final size:20
Alignment explanation
Indices: 24792111--24792150 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
24792101 AAATATTTTC
24792111 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
24792131 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
24792151 TCATTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:24793916 original size:31 final size:29
Alignment explanation
Indices: 24793852--24793916 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
24793842 ACAATAACGT
** *
24793852 AAGTGACTAAAATGTAACATTTCAAACAT
1 AAGTGACTAAAATGTAACATGGCAAACAA
24793881 AAGTGACTAAAATGTAACATGAGGCAAACAA
1 AAGTGACTAAAATGTAACAT--GGCAAACAA
24793912 AAGTG
1 AAGTG
24793917 GCTATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 20 0.65
31 11 0.35
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATGGCAAACAA
Found at i:24794345 original size:21 final size:20
Alignment explanation
Indices: 24794319--24794397 Score: 51
Period size: 21 Copynumber: 4.0 Consensus size: 20
24794309 TTCAAAATTA
24794319 ATTAAATTATTTAAAAATTTT
1 ATTAAA-TATTTAAAAATTTT
* *
24794340 ATTAAAAACTCTAAAAATTTT
1 ATTAAATA-TTTAAAAATTTT
*
24794361 A--AAA-ATATAGAAAA--TT
1 ATTAAATATTTA-AAAATTTT
24794377 ATTAAAGTTATTTAAAAATTT
1 ATTAAA--TATTTAAAAATTT
24794398 CAAAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 17
0.68 0.06 0.26
Matches are distributed among these distances:
16 3 0.07
17 3 0.07
18 8 0.18
19 3 0.07
20 5 0.11
21 22 0.49
22 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTAAATATTTAAAAATTTT
Found at i:24794381 original size:19 final size:19
Alignment explanation
Indices: 24794338--24794382 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
24794328 TTTAAAAATT
*
24794338 TTATTAAAAACTCTAAAAA
1 TTATTAAAAACTATAAAAA
24794357 TT-TTAAAAA-TATAGAAAA
1 TTATTAAAAACTATA-AAAA
24794375 TTATTAAA
1 TTATTAAA
24794383 GTTATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 7 0.30
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (19 bp):
TTATTAAAAACTATAAAAA
Found at i:24796306 original size:17 final size:17
Alignment explanation
Indices: 24796263--24796308 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
24796253 AAAAATTGGT
24796263 AAAT-AATATTTCAAAA
1 AAATAAATATTTCAAAA
* *
24796279 AACAAAAATATTTCACAA
1 AA-ATAAATATTTCAAAA
24796297 AAATAAATATTT
1 AAATAAATATTT
24796309 TATGGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 10 0.40
18 13 0.52
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAAATATTTCAAAA
Found at i:24798950 original size:20 final size:20
Alignment explanation
Indices: 24798905--24798950 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
24798895 TAGGTGCAGT
*
24798905 GGTTTGCACACAGGCGTGTG
1 GGTTTTCACACAGGCGTGTG
** *
24798925 TCTTTTCACACGGGCGTGTG
1 GGTTTTCACACAGGCGTGTG
24798945 GGTTTT
1 GGTTTT
24798951 GGGGGGTTTG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.35
Consensus pattern (20 bp):
GGTTTTCACACAGGCGTGTG
Found at i:24813589 original size:17 final size:17
Alignment explanation
Indices: 24813567--24813601 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
24813557 CTCTAATGTG
*
24813567 CTTCAATAGAGAGTTAT
1 CTTCAATAGAGAGCTAT
24813584 CTTCAATAGAGAGCTAT
1 CTTCAATAGAGAGCTAT
24813601 C
1 C
24813602 AATTTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (17 bp):
CTTCAATAGAGAGCTAT
Found at i:24830668 original size:40 final size:40
Alignment explanation
Indices: 24830579--24830842 Score: 369
Period size: 40 Copynumber: 6.7 Consensus size: 40
24830569 TTGAATGATG
* *
24830579 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
24830618 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
24830658 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24830697 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24830737 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24830777 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
24830818 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
24830843 AACGAGGAGC
Statistics
Matches: 207, Mismatches: 11, Indels: 13
0.90 0.05 0.06
Matches are distributed among these distances:
39 53 0.26
40 144 0.70
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:24830860 original size:120 final size:118
Alignment explanation
Indices: 24830579--24830875 Score: 347
Period size: 120 Copynumber: 2.5 Consensus size: 118
24830569 TTGAATGATG
* *
24830579 TCCGGGCTAAGTCCCGAAGGC-TTGTG--CTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
1 TCCGGGCTAAGTCCCGAAGGCATT-TGAAC-GAGTGACTAA-ATCCGG-TTAA-ATCCCGAAGGC
*
24830639 ATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
61 ATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
* ** * *
24830697 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTT
* *
24830762 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
65 GTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
* * *
24830818 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
24830876 TACGTGATTT
Statistics
Matches: 154, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
118 23 0.15
119 64 0.42
120 65 0.42
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTG
TGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:24833651 original size:25 final size:25
Alignment explanation
Indices: 24833597--24833668 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 25
24833587 TAACTAGTGA
* * *
24833597 GAGCATACCGATCTATAGCTCTTGT
1 GAGCATACCAATCTATAGCTCGTGG
* *
24833622 AAGCATACCAATTTATAGCTCGTGG
1 GAGCATACCAATCTATAGCTCGTGG
** *
24833647 GAGCATACTGATCTACAGCTCG
1 GAGCATACCAATCTATAGCTCG
24833669 AGTGAGAATA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (25 bp):
GAGCATACCAATCTATAGCTCGTGG
Found at i:24833679 original size:25 final size:25
Alignment explanation
Indices: 24833651--24833717 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
24833641 TCGTGGGAGC
24833651 ATACTGA-TCTACAGCTCGAGTGAGA
1 ATACTGATTC-ACAGCTCGAGTGAGA
* * *
24833676 ATACCGATTCACAGCTTGAGTGAGC
1 ATACTGATTCACAGCTCGAGTGAGA
24833701 ATACTGATTCACAGCTC
1 ATACTGATTCACAGCTC
24833718 ATATAAGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
25 34 0.94
26 2 0.06
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (25 bp):
ATACTGATTCACAGCTCGAGTGAGA
Found at i:24833680 original size:50 final size:50
Alignment explanation
Indices: 24833597--24833717 Score: 118
Period size: 50 Copynumber: 2.4 Consensus size: 50
24833587 TAACTAGTGA
* * ** * * * *
24833597 GAGCATACCGATCTATAGCTCTTGTAAGCATACCAATTTATAGCTCGTGG
1 GAGCATACTGATCTACAGCTCGAGTAAGAATACCAATTCACAGCTCGAGG
* * * *
24833647 GAGCATACTGATCTACAGCTCGAGTGAGAATACCGATTCACAGCTTGAGT
1 GAGCATACTGATCTACAGCTCGAGTAAGAATACCAATTCACAGCTCGAGG
24833697 GAGCATACTGAT-TCACAGCTC
1 GAGCATACTGATCT-ACAGCTC
24833718 ATATAAGAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
49 1 0.02
50 57 0.98
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (50 bp):
GAGCATACTGATCTACAGCTCGAGTAAGAATACCAATTCACAGCTCGAGG
Found at i:24836541 original size:57 final size:57
Alignment explanation
Indices: 24836413--24836541 Score: 147
Period size: 59 Copynumber: 2.2 Consensus size: 57
24836403 ATCACTTTAA
* * *
24836413 TATTAAATTAATATAATATTTTTCAAGATAAACATTAGATTAAATTTAATCTTAAATAT
1 TATTAAATTAATAGAATATTTTTCAAGATAAACATTAAATTAAA--TAATATTAAATAT
*
24836472 TATTTAATTAATAGAATATTTATCTACAAGATAAACATTAAATT-AA-AATATTAAAT-T
1 TATTAAATTAATAGAATATTT-T-T-CAAGATAAACATTAAATTAAATAATATTAAATAT
*
24836529 TATTAAAATAATA
1 TATTAAATTAATA
24836542 TCATTTTTGG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
57 12 0.20
58 9 0.15
59 19 0.31
60 1 0.02
61 3 0.05
62 17 0.28
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (57 bp):
TATTAAATTAATAGAATATTTTTCAAGATAAACATTAAATTAAATAATATTAAATAT
Found at i:24838052 original size:19 final size:19
Alignment explanation
Indices: 24838028--24838065 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
24838018 GCCACTTATC
24838028 ATCAGTTTGAATTTAGACA
1 ATCAGTTTGAATTTAGACA
24838047 ATCAGTTTGAATTTAGACA
1 ATCAGTTTGAATTTAGACA
24838066 TCTATGTCTC
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:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
ATCAGTTTGAATTTAGACA
Found at i:24838251 original size:246 final size:246
Alignment explanation
Indices: 24837817--24838296 Score: 951
Period size: 246 Copynumber: 2.0 Consensus size: 246
24837807 TAGGTCTAGT
24837817 ACATCTATGTCTCTACCTGTGGAGTCAACTACTCCGATAGCCAAGACTAGCCATCTCCTCAGTTG
1 ACATCTATGTCTCTACCTGTGGAGTCAACTACTCCGATAGCCAAGACTAGCCATCTCCTCAGTTG
24837882 GAATTGTAGATGACATAATAATCTTTCTAAGTATTTGAATCAAATGTTCAGTTTGATTCTTTTAT
66 GAATTGTAGATGACATAATAATCTTTCTAAGTATTTGAATCAAATGTTCAGTTTGATTCTTTTAT
24837947 GGGATTACAGACTCATTTAGATTATCTATTGAAGTAAGTTATCTTTCTTGTAATGTAAACATTCT
131 GGGATTACAGACTCATTTAGATTATCTATTGAAGTAAGTTATCTTTCTTGTAATGTAAACATTCT
*
24838012 TACTAAGCCACTTATCATCAGTTTGAATTTAGACAATCAGTTTGAATTTAG
196 TACTAAGCCACTTATCATCAGTTTGAATTTAGAAAATCAGTTTGAATTTAG
24838063 ACATCTATGTCTCTACCTGTGGAGTCAACTACTCCGATAGCCAAGACTAGCCATCTCCTCAGTTG
1 ACATCTATGTCTCTACCTGTGGAGTCAACTACTCCGATAGCCAAGACTAGCCATCTCCTCAGTTG
24838128 GAATTGTAGATGACATAATAATCTTTCTAAGTATTTGAATCAAATGTTCAGTTTGATTCTTTTAT
66 GAATTGTAGATGACATAATAATCTTTCTAAGTATTTGAATCAAATGTTCAGTTTGATTCTTTTAT
24838193 GGGATTACAGACTCATTTAGATTATCTATTGAAGTAAGTTATCTTTCTTGTAATGTAAACATTCT
131 GGGATTACAGACTCATTTAGATTATCTATTGAAGTAAGTTATCTTTCTTGTAATGTAAACATTCT
24838258 TACTAAGCCACTTATCATCAGTTTGAATTTAGAAAATCA
196 TACTAAGCCACTTATCATCAGTTTGAATTTAGAAAATCA
24838297 ATGAGCTAAT
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 233 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (246 bp):
ACATCTATGTCTCTACCTGTGGAGTCAACTACTCCGATAGCCAAGACTAGCCATCTCCTCAGTTG
GAATTGTAGATGACATAATAATCTTTCTAAGTATTTGAATCAAATGTTCAGTTTGATTCTTTTAT
GGGATTACAGACTCATTTAGATTATCTATTGAAGTAAGTTATCTTTCTTGTAATGTAAACATTCT
TACTAAGCCACTTATCATCAGTTTGAATTTAGAAAATCAGTTTGAATTTAG
Found at i:24842928 original size:6 final size:6
Alignment explanation
Indices: 24842917--24842946 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
24842907 TTCTAAAATA
24842917 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
24842947 TGAATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:24842973 original size:19 final size:18
Alignment explanation
Indices: 24842951--24842995 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
24842941 ATTTTTTGAA
24842951 TTTTAAAGAGTTTTTATTT
1 TTTTAAA-AGTTTTTATTT
* *
24842970 TTTTCATAATTTTTTATTT
1 TTTT-AAAAGTTTTTATTT
24842989 TTTTAAA
1 TTTTAAA
24842996 TTATAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 2 0.09
19 18 0.82
20 2 0.09
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTAAAAGTTTTTATTT
Found at i:24843005 original size:21 final size:21
Alignment explanation
Indices: 24842975--24843022 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
24842965 TATTTTTTTC
* *
24842975 ATAATTTTTTATTTTTTTAAATT
1 ATAA-TTTTT-TTTATTTAAAAT
24842998 ATAATTTTTTTTATTTAAAAT
1 ATAATTTTTTTTATTTAAAAT
24843019 ATAA
1 ATAA
24843023 ATAATGTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 5 0.22
23 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATAATTTTTTTTATTTAAAAT
Found at i:24847204 original size:6 final size:6
Alignment explanation
Indices: 24847195--24847241 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
24847185 ACATATGTAA
* *
24847195 ATGTGC ATGTGC ATGTGC ATGTGG ATGTGC ATGTGG ATGTGC ATGTG
1 ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTG
24847242 TCTGTATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.17, C:0.11, G:0.38, T:0.34
Consensus pattern (6 bp):
ATGTGC
Found at i:24847210 original size:12 final size:12
Alignment explanation
Indices: 24847195--24847241 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
24847185 ACATATGTAA
*
24847195 ATGTGCATGTGC
1 ATGTGCATGTGG
24847207 ATGTGCATGTGG
1 ATGTGCATGTGG
24847219 ATGTGCATGTGG
1 ATGTGCATGTGG
24847231 ATGTGCATGTG
1 ATGTGCATGTG
24847242 TCTGTATATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.17, C:0.11, G:0.38, T:0.34
Consensus pattern (12 bp):
ATGTGCATGTGG
Found at i:24848174 original size:15 final size:15
Alignment explanation
Indices: 24848154--24848190 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
24848144 TGTTTGTGTT
24848154 AAATTATAGGATAAA
1 AAATTATAGGATAAA
*
24848169 AAATTATAGGTTAAA
1 AAATTATAGGATAAA
*
24848184 ATATTAT
1 AAATTAT
24848191 GTTTCTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (15 bp):
AAATTATAGGATAAA
Found at i:24851121 original size:18 final size:17
Alignment explanation
Indices: 24851089--24851122 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
24851079 AAAGTCTTTA
*
24851089 GAATCACTTTTTTTTTC
1 GAATCACTTTATTTTTC
24851106 GAATCTACTTTATTTTT
1 GAATC-ACTTTATTTTT
24851123 AAAAGTGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.59
Consensus pattern (17 bp):
GAATCACTTTATTTTTC
Found at i:24862155 original size:285 final size:285
Alignment explanation
Indices: 24861640--24862190 Score: 1021
Period size: 285 Copynumber: 1.9 Consensus size: 285
24861630 TGCGTAGCTA
*
24861640 AAGCTCGATTACCTTTTGAGGGGTTAGCAGCTTCATTCACACAGTTCGCATTCACTTTACGAGAA
1 AAGCCCGATTACCTTTTGAGGGGTTAGCAGCTTCATTCACACAGTTCGCATTCACTTTACGAGAA
24861705 GGCATTCTTGCTCAGTCTAAATGTACATGAGATACTGACTTAGTTAAGACTTCAAACACACGTAA
66 GGCATTCTTGCTCAGTCTAAATGTACATGAGATACTGACTTAGTTAAGACTTCAAACACACGTAA
*
24861770 CTGGGTATCCATAATTTAACAGATAGACTTGTGAACACAATTTGCCTAATACAACTTACACGTGA
131 CTGGGTATCCATAATTTAACAGATAGACTTGTGAACACAATTTGCCTAACACAACTTACACGTGA
24861835 ACACATTTCGCACAACTTACTTATTGGATTAAAAAGTAGTAGAGGGATGATCTGAGGCATAATCC
196 ACACATTTCGCACAACTTACTTATTGGATTAAAAAGTAGTAGAGGGATGATCTGAGGCATAATCC
24861900 TGCAAACACATGTAATCTGAGGCAT
261 TGCAAACACATGTAATCTGAGGCAT
* * *
24861925 AAGCCCGATTACCTTTTGAGGGGTTAGCAGCTTCATTCACATAGTTCGCATTCACTTTATGAGGA
1 AAGCCCGATTACCTTTTGAGGGGTTAGCAGCTTCATTCACACAGTTCGCATTCACTTTACGAGAA
* *
24861990 GGCATTCTTGCTCAGTCTTAATGTACATGAGATACTGACTTAGTTAAGACTTCAAACACATGTAA
66 GGCATTCTTGCTCAGTCTAAATGTACATGAGATACTGACTTAGTTAAGACTTCAAACACACGTAA
*
24862055 TTGGGTATCCATAATTTAACAGATAGACTTGTGAACACAATTTGCCTAACACAACTTACACGTGA
131 CTGGGTATCCATAATTTAACAGATAGACTTGTGAACACAATTTGCCTAACACAACTTACACGTGA
*
24862120 ACACCTTTCGCACAACTTACTTATTGGATTAAAAAGTAGTAGAGGGATGATCTGAGGCATAATCC
196 ACACATTTCGCACAACTTACTTATTGGATTAAAAAGTAGTAGAGGGATGATCTGAGGCATAATCC
24862185 TGCAAA
261 TGCAAA
24862191 AGATATGGTT
Statistics
Matches: 257, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
285 257 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (285 bp):
AAGCCCGATTACCTTTTGAGGGGTTAGCAGCTTCATTCACACAGTTCGCATTCACTTTACGAGAA
GGCATTCTTGCTCAGTCTAAATGTACATGAGATACTGACTTAGTTAAGACTTCAAACACACGTAA
CTGGGTATCCATAATTTAACAGATAGACTTGTGAACACAATTTGCCTAACACAACTTACACGTGA
ACACATTTCGCACAACTTACTTATTGGATTAAAAAGTAGTAGAGGGATGATCTGAGGCATAATCC
TGCAAACACATGTAATCTGAGGCAT
Found at i:24868038 original size:17 final size:18
Alignment explanation
Indices: 24868016--24868056 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
24868006 TAAATAACCA
24868016 TCTAAAGA-TTATTTCAT
1 TCTAAAGATTTATTTCAT
*
24868033 TCTAAATATTTATTTCAT
1 TCTAAAGATTTATTTCAT
*
24868051 TTTAAA
1 TCTAAA
24868057 TTGAGAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (18 bp):
TCTAAAGATTTATTTCAT
Found at i:24872142 original size:20 final size:20
Alignment explanation
Indices: 24872117--24872156 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
24872107 AATATTTTCC
*
24872117 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
24872137 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
24872157 TTATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:24872171 original size:34 final size:35
Alignment explanation
Indices: 24872105--24872171 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
24872095 CAAACACCAG
*
24872105 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
24872140 AAAACATTTTCCAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
24872172 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:24872432 original size:46 final size:44
Alignment explanation
Indices: 24872352--24872440 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 44
24872342 AATAGAAAAA
*
24872352 GAGAAATGAGAACAATTTAGGAATGATTATGGTTTTCTCAAAAATG
1 GAGAAATGAGAACAATTTAGAAATGATTATGG-TTTC-CAAAAATG
24872398 GAGAAAT-AGAATC-ATTTAGAAATGAATGTA-GGTTTCCAAAAAT
1 GAGAAATGAGAA-CAATTTAGAAATG-AT-TATGGTTTCCAAAAAT
24872441 TGAAATGGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
44 7 0.18
45 18 0.46
46 12 0.31
47 2 0.05
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (44 bp):
GAGAAATGAGAACAATTTAGAAATGATTATGGTTTCCAAAAATG
Found at i:24872632 original size:26 final size:25
Alignment explanation
Indices: 24872603--24872651 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
24872593 GAATTTTCTC
*
24872603 AAAATTTTACCGAGGGTAAAATTGTT
1 AAAATTTTACCG-GAGTAAAATTGTT
*
24872629 AAAATTTTACTGGAGTAAAATTG
1 AAAATTTTACCGGAGTAAAATTG
24872652 GGATGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (25 bp):
AAAATTTTACCGGAGTAAAATTGTT
Found at i:24873259 original size:16 final size:17
Alignment explanation
Indices: 24873234--24873267 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
24873224 TAATTATATT
*
24873234 ATTTTTAACAAAA-TTA
1 ATTTTAAACAAAACTTA
24873250 ATTTTAAACAAAACTTA
1 ATTTTAAACAAAACTTA
24873267 A
1 A
24873268 ATACAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTTAAACAAAACTTA
Found at i:24876287 original size:15 final size:15
Alignment explanation
Indices: 24876264--24876293 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24876254 GAAAAAAAAT
*
24876264 TGATGGGGGAGAAAG
1 TGATAGGGGAGAAAG
24876279 TGATAGGGGAGAAAG
1 TGATAGGGGAGAAAG
24876294 CCTAACGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.50, T:0.13
Consensus pattern (15 bp):
TGATAGGGGAGAAAG
Found at i:24885397 original size:19 final size:18
Alignment explanation
Indices: 24885356--24885399 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
24885346 TTGAGATATG
24885356 ATAAAATTACAAAAATAA
1 ATAAAATTACAAAAATAA
*
24885374 CTAAATATTA-AAAAATAAA
1 ATAAA-ATTACAAAAAT-AA
24885393 ATAAAAT
1 ATAAAAT
24885400 AAAATTGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAAAATTACAAAAATAA
Found at i:24895251 original size:12 final size:11
Alignment explanation
Indices: 24895215--24895243 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
24895205 TTTAACTTTC
24895215 TTTA-AATATT
1 TTTAGAATATT
24895225 TTTAGAATATT
1 TTTAGAATATT
24895236 TTTAGAAT
1 TTTAGAAT
24895244 TGTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (11 bp):
TTTAGAATATT
Found at i:24902186 original size:44 final size:44
Alignment explanation
Indices: 24902119--24902209 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
24902109 CGGTGATTGA
*
24902119 TGGTAGGGGCAGACGGCGATGGTCGGCGAAGGTCCTGTAGTGGT
1 TGGTAGGGGCAGACGACGATGGTCGGCGAAGGTCCTGTAGTGGT
* * *
24902163 TGGTAGGGGCAGACGATGGTGGTCGGCGAAGGTCCTGTGGTGGT
1 TGGTAGGGGCAGACGACGATGGTCGGCGAAGGTCCTGTAGTGGT
24902207 TGG
1 TGG
24902210 CGACAACTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.14, C:0.14, G:0.49, T:0.22
Consensus pattern (44 bp):
TGGTAGGGGCAGACGACGATGGTCGGCGAAGGTCCTGTAGTGGT
Found at i:24909247 original size:39 final size:40
Alignment explanation
Indices: 24909166--24909265 Score: 121
Period size: 39 Copynumber: 2.5 Consensus size: 40
24909156 CATCGAGCGG
* * *
24909166 TACCTACTGAATCTACTAAAACATATGCACTTTCGAGCCA
1 TACCTACTGAATCTACTGAAACATATGCACTCTCAAGCCA
* * * *
24909206 TACTTACTGAATCTACTGAAA-GTATGCGCTCTCAAGTCA
1 TACCTACTGAATCTACTGAAACATATGCACTCTCAAGCCA
*
24909245 TACCTACTGAATCTATTGAAA
1 TACCTACTGAATCTACTGAAA
24909266 AGAATGCTCT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
39 32 0.63
40 19 0.37
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (40 bp):
TACCTACTGAATCTACTGAAACATATGCACTCTCAAGCCA
Found at i:24913715 original size:30 final size:29
Alignment explanation
Indices: 24913667--24913840 Score: 181
Period size: 30 Copynumber: 5.8 Consensus size: 29
24913657 ACGATCCTCA
*
24913667 GCTATCAAAATAATGAAAAGGGATAGCCTTG
1 GCTATC-AAATTATGAAAAGGGATAG-CTTG
*
24913698 GCTATCAAATTATGAAAAGGGAT-G-GTG
1 GCTATCAAATTATGAAAAGGGATAGCTTG
* * *
24913725 ACGACCATCGAATAATGAAAAGGGATAGCTTCG
1 --G-CTATCAAATTATGAAAAGGGATAGCTT-G
* *
24913758 GCTATCAAATTATGAAAATGGATAGTTTTG
1 GCTATCAAATTATGAAAAGGGATAG-CTTG
*
24913788 GCTATCGAATTATGAAAAGGGATAGCTTCG
1 GCTATCAAATTATGAAAAGGGATAGCTT-G
*
24913818 GTTATCAAATTATGAAAAGGGAT
1 GCTATCAAATTATGAAAAGGGAT
24913841 GGTGACGACC
Statistics
Matches: 119, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.02
29 4 0.03
30 101 0.85
31 10 0.08
32 1 0.01
33 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (29 bp):
GCTATCAAATTATGAAAAGGGATAGCTTG
Found at i:24913768 original size:60 final size:60
Alignment explanation
Indices: 24913675--24913869 Score: 277
Period size: 60 Copynumber: 3.3 Consensus size: 60
24913665 CAGCTATCAA
24913675 AATAATGAAAAGGGATAGCCTT-GGCTATCAAATTATGAAAAGGGATGGTGACGACCATCG
1 AATAATGAAAAGGGATAG-CTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCG
* * *** * *
24913735 AATAATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAATGGATAGTTTTGGCTATCG
1 AATAATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCG
* *
24913795 AATTATGAAAAGGGATAGCTTCGGTTATCAAATTATGAAAAGGGATGGTGACGACCATC-
1 AATAATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCG
*
24913854 AACAATGAAAAGGGAT
1 AATAATGAAAAGGGAT
24913870 TATGACGACC
Statistics
Matches: 116, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
59 17 0.15
60 99 0.85
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (60 bp):
AATAATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCG
Found at i:24913855 original size:30 final size:30
Alignment explanation
Indices: 24913701--24913899 Score: 145
Period size: 30 Copynumber: 6.7 Consensus size: 30
24913691 AGCCTTGGCT
24913701 ATCAAATTATGAAAAGGGATGGTGACGACC
1 ATCAAATTATGAAAAGGGATGGTGACGACC
* * * * * *
24913731 ATCGAATAATGAAAAGGGATAGCT-TCGGCT
1 ATCAAATTATGAAAAGGGAT-GGTGACGACC
* * *** * *
24913761 ATCAAATTATGAAAATGGATAGTTTTGGCT
1 ATCAAATTATGAAAAGGGATGGTGACGACC
* * * ***
24913791 ATCGAATTATGAAAAGGGATAGCT-TCGGTT
1 ATCAAATTATGAAAAGGGAT-GGTGACGACC
24913821 ATCAAATTATGAAAAGGGATGGTGACGACC
1 ATCAAATTATGAAAAGGGATGGTGACGACC
**
24913851 ATCAACA--ATGAAAAGGGATTATGACGACC
1 ATCAA-ATTATGAAAAGGGATGGTGACGACC
*
24913880 ATCAAATAATGAAAAGGGAT
1 ATCAAATTATGAAAAGGGAT
24913900 TGAGCCATGA
Statistics
Matches: 136, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.01
29 28 0.21
30 103 0.76
31 4 0.03
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (30 bp):
ATCAAATTATGAAAAGGGATGGTGACGACC
Found at i:24913900 original size:30 final size:30
Alignment explanation
Indices: 24913821--24913900 Score: 117
Period size: 29 Copynumber: 2.7 Consensus size: 30
24913811 AGCTTCGGTT
* **
24913821 ATCAAATTATGAAAAGGGATGGTGACGACC
1 ATCAAATAATGAAAAGGGATTATGACGACC
*
24913851 ATC-AACAATGAAAAGGGATTATGACGACC
1 ATCAAATAATGAAAAGGGATTATGACGACC
24913880 ATCAAATAATGAAAAGGGATT
1 ATCAAATAATGAAAAGGGATT
24913901 GAGCCATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 25 0.57
30 19 0.43
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (30 bp):
ATCAAATAATGAAAAGGGATTATGACGACC
Found at i:24918220 original size:13 final size:14
Alignment explanation
Indices: 24918188--24918220 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24918178 AAGTGTTGCT
*
24918188 TGCGAGTTGTATAC
1 TGCGAGTAGTATAC
24918202 TGCGAGTAGTATA-
1 TGCGAGTAGTATAC
24918215 TGCGAG
1 TGCGAG
24918221 CTAAGAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.30
Consensus pattern (14 bp):
TGCGAGTAGTATAC
Done.