Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 191 of 313
Found at i:58610711 original size:41 final size:41
Alignment explanation
Indices: 58610649--58610848 Score: 319
Period size: 41 Copynumber: 4.9 Consensus size: 41
58610639 TTTAATTATT
*
58610649 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* * ** *
58610690 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
*
58610731 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
*
58610772 ATTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
*
58610813 ATTAGCAGCGCTTCTTCAAAAACGCCGCTAAAGGCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
58610849 TCAAGAACTC
Statistics
Matches: 146, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 146 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:58611009 original size:40 final size:40
Alignment explanation
Indices: 58610885--58611019 Score: 150
Period size: 40 Copynumber: 3.4 Consensus size: 40
58610875 TGGCTTAGGC
*
58610885 TTTTT-GCGGCGCTTTTTAGAAAA-CGCCACTAATGCT-TA
1 TTTTTAGCGGCG-TTTTTAGAAAAGCGCCGCTAATGCTCTA
** *
58610923 TTTTTAGCGGCGTTTTCGGAGAAGCGCCGCTAATGCTCTA
1 TTTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCTA
** * * *
58610963 CCTTTAGCAGCGTTTTTATAAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCTA
*
58611003 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
58611020 TGTCCAAGCG
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
38 13 0.17
39 18 0.23
40 47 0.60
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCTA
Found at i:58617196 original size:27 final size:27
Alignment explanation
Indices: 58617166--58617263 Score: 126
Period size: 27 Copynumber: 3.6 Consensus size: 27
58617156 ATAATTTATT
*
58617166 ACAAAAGCTTTTCTTTCATGA-TTCGCC
1 ACAAAAGCTTTTCTTTCAT-ATTTCACC
*
58617193 ACAAAGGCTTTTCTTTCATATTTCACC
1 ACAAAAGCTTTTCTTTCATATTTCACC
* *
58617220 ACAAAAGCTTTCCTTTCATATTTTACC
1 ACAAAAGCTTTTCTTTCATATTTCACC
* *
58617247 ACAAATGCTTTCCTTTC
1 ACAAAAGCTTTTCTTTC
58617264 TTGATGTGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 1 0.02
27 63 0.98
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (27 bp):
ACAAAAGCTTTTCTTTCATATTTCACC
Found at i:58618554 original size:57 final size:56
Alignment explanation
Indices: 58618443--58618554 Score: 118
Period size: 57 Copynumber: 2.0 Consensus size: 56
58618433 AAATGAAATT
* * * * * *
58618443 CGATGGATATAGGATTTTCATAATTAGTTATGGTCCTGCCTATGTTGTGGACACAG
1 CGATGGATACAGGATTTCCATAATTAGTTATGGTCCAGCATATGTTGCGAACACAG
* * *
58618499 NCGATGGATACAGGATTTCCCGT-ATTAGTTGTGGTTCAGCATATGTTGCGAACACA
1 -CGATGGATACAGGATTT-CCATAATTAGTTATGGTCCAGCATATGTTGCGAACACA
58618555 CCATAGCTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
57 43 0.96
58 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (56 bp):
CGATGGATACAGGATTTCCATAATTAGTTATGGTCCAGCATATGTTGCGAACACAG
Found at i:58622320 original size:47 final size:47
Alignment explanation
Indices: 58622242--58622490 Score: 355
Period size: 47 Copynumber: 5.4 Consensus size: 47
58622232 TTTTTTTCAC
* * * *
58622242 CAAAATTGGACAGCATAT--ATACAAAATTGGACTGCATTTATGCAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
58622287 CAAAATTTGACAACATATACATATATAATTGGACTGCATTTATACTT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* * * *
58622334 CAAAATTTAACAGCATAT--ATACAAAATTGGATTGCATTTATACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
58622379 CAAAATTTGACAGCATATACATATATAATTGGACTGCA-TTATACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
58622425 CAAAATTTGACAGCATATACATATATAATTGTACTGCATTTATACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
58622472 CAAAATTTAACAGCATATA
1 CAAAATTTGACAGCATATA
58622491 TACAAAATTG
Statistics
Matches: 181, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
45 56 0.31
46 45 0.25
47 80 0.44
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (47 bp):
CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
Found at i:58622347 original size:92 final size:91
Alignment explanation
Indices: 58622242--58622490 Score: 381
Period size: 92 Copynumber: 2.7 Consensus size: 91
58622232 TTTTTTTCAC
* * *
58622242 CAAAATTGGACAGCATATATACAAAATTGGACTGCATTTATGCATCAAAATTTGACAACATATAC
1 CAAAATTTGACAGCATATATACAAAATTGGACTGCATTTATACATCAAAATTTGACAGCATATAC
*
58622307 ATATATAATTGGACTGCATTTATACTT
66 ATATATAATTGGACTGCA-TTATACAT
* *
58622334 CAAAATTTAACAGCATATATACAAAATTGGATTGCATTTATACATCAAAATTTGACAGCATATAC
1 CAAAATTTGACAGCATATATACAAAATTGGACTGCATTTATACATCAAAATTTGACAGCATATAC
58622399 ATATATAATTGGACTGCATTATACAT
66 ATATATAATTGGACTGCATTATACAT
* * * *
58622425 CAAAATTTGACAGCATATACATATATAATTGTACTGCATTTATACATCAAAATTTAACAGCATAT
1 CAAAATTTGACAGCATAT--ATACAAAATTGGACTGCATTTATACATCAAAATTTGACAGCATAT
58622490 A
64 A
58622491 TACAAAATTG
Statistics
Matches: 143, Mismatches: 12, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
91 24 0.17
92 78 0.55
93 41 0.29
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (91 bp):
CAAAATTTGACAGCATATATACAAAATTGGACTGCATTTATACATCAAAATTTGACAGCATATAC
ATATATAATTGGACTGCATTATACAT
Found at i:58622446 original size:138 final size:137
Alignment explanation
Indices: 58622242--58622500 Score: 430
Period size: 138 Copynumber: 1.9 Consensus size: 137
58622232 TTTTTTTCAC
*
58622242 CAAAATTGGACAGCATATATACAAAATTGGACTGCATTTATGCATCAAAATTTGACAACATATAC
1 CAAAATTGGACAGCATATATACAAAATTGGACTGCATTTATACATCAAAATTTGACAACATATAC
*
58622307 ATATATAATTGGACTGCATTTATACTTCAAAATTTAACAGCATATATACAAAATTGGATTGCATT
66 ATATATAATTGGACTGCATTTATACATCAAAATTTAACAGCATATATACAAAATTGGATTGCATT
58622372 TATACAT
131 TATACAT
* * * *
58622379 CAAAATTTGACAGCATATACATATATAATTGGACTGCA-TTATACATCAAAATTTGACAGCATAT
1 CAAAATTGGACAGCATAT--ATACAAAATTGGACTGCATTTATACATCAAAATTTGACAACATAT
*
58622443 ACATATATAATTGTACTGCATTTATACATCAAAATTTAACAGCATATATACAAAATTG
64 ACATATATAATTGGACTGCATTTATACATCAAAATTTAACAGCATATATACAAAATTG
58622501 AACAGCACAT
Statistics
Matches: 113, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
137 17 0.15
138 80 0.71
139 16 0.14
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (137 bp):
CAAAATTGGACAGCATATATACAAAATTGGACTGCATTTATACATCAAAATTTGACAACATATAC
ATATATAATTGGACTGCATTTATACATCAAAATTTAACAGCATATATACAAAATTGGATTGCATT
TATACAT
Found at i:58622858 original size:14 final size:15
Alignment explanation
Indices: 58622834--58622863 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
58622824 TATATACATT
58622834 ACCATATAAATACTA
1 ACCATATAAATACTA
58622849 ACCATA-AAATACTA
1 ACCATATAAATACTA
58622863 A
1 A
58622864 TTCGTGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:58623600 original size:43 final size:43
Alignment explanation
Indices: 58623516--58623636 Score: 117
Period size: 43 Copynumber: 2.8 Consensus size: 43
58623506 TCGTACAATT
* * *
58623516 CCAACGTCACAGACGTGGTCTTACA-TATAATCACATA-TCGATG
1 CCAACATCCCAGACGTGGTCTTACACGATAA-CACA-AGTCGATG
*
58623559 TC-ACTATCCCAGACAG-GGTCTTACACG-TAAACACAAGTCGATG
1 CCAAC-ATCCCAGAC-GTGGTCTTACACGAT-AACACAAGTCGATG
*
58623602 CCAACGTCCCAGACGTGGTCTTACACGATAACACA
1 CCAACATCCCAGACGTGGTCTTACACGATAACACA
58623637 TATCTAAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
42 4 0.06
43 54 0.84
44 6 0.09
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.21
Consensus pattern (43 bp):
CCAACATCCCAGACGTGGTCTTACACGATAACACAAGTCGATG
Found at i:58632419 original size:26 final size:26
Alignment explanation
Indices: 58632389--58632446 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
58632379 CCGGAGCTCT
* *
58632389 TGATTAAAAGCTGTTTCTGAGCTTCC
1 TGATTAAAAGCTCTTTCTGAACTTCC
* *
58632415 TGATTAAAAGTTCTTTGTGAACTTCC
1 TGATTAAAAGCTCTTTCTGAACTTCC
58632441 TGATTA
1 TGATTA
58632447 TGGCTCCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (26 bp):
TGATTAAAAGCTCTTTCTGAACTTCC
Found at i:58634588 original size:25 final size:25
Alignment explanation
Indices: 58634536--58634617 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
58634526 CCCTCTTGAG
* *
58634536 AGCCATATAACCGGAAGCTCATATA
1 AGCCATATAACAGGAAGCTCATACA
* * *
58634561 AGCCATGTAACAGGAAGCTTATCCA
1 AGCCATATAACAGGAAGCTCATACA
** *
58634586 AGCTGTATAACAGAAAGCTCATA-A
1 AGCCATATAACAGGAAGCTCATACA
58634610 GAGCCATA
1 -AGCCATA
58634618 ATTGAAAAGC
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
24 1 0.02
25 42 0.98
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (25 bp):
AGCCATATAACAGGAAGCTCATACA
Found at i:58634651 original size:24 final size:24
Alignment explanation
Indices: 58634535--58634653 Score: 69
Period size: 25 Copynumber: 4.8 Consensus size: 24
58634525 GCCCTCTTGA
*
58634535 GAGCCATATAACCGGAAGCTCATAT
1 GAGCCA-ATAACAGGAAGCTCATAT
* * * **
58634560 AAGCCATGTAACAGGAAGCTTATCC
1 GAGCCA-ATAACAGGAAGCTCATAT
* ** * *
58634585 AAGCTGTATAACAGAAAGCTCATAA
1 GAGC-CAATAACAGGAAGCTCATAT
** *
58634610 GAGCC-ATAATTGAAAAGCTCATAT
1 GAGCCAATAACAG-GAAGCTCATAT
58634634 GAGCCAATAACAGGAAGCTC
1 GAGCCAATAACAGGAAGCTC
58634654 CTGATAACCA
Statistics
Matches: 70, Mismatches: 21, Indels: 7
0.71 0.21 0.07
Matches are distributed among these distances:
23 5 0.07
24 21 0.30
25 44 0.63
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (24 bp):
GAGCCAATAACAGGAAGCTCATAT
Found at i:58641866 original size:24 final size:25
Alignment explanation
Indices: 58641839--58641899 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
58641829 GGATGCTCCG
* *
58641839 AAGAGCTAT-TAGCGGAAAGCTCGC
1 AAGAGCTATATAACGGAAAGCTCGA
* *
58641863 AAGAACTATATAACGGGAAGCTCGA
1 AAGAGCTATATAACGGAAAGCTCGA
*
58641888 AAGGGCTA-ATAA
1 AAGAGCTATATAA
58641900 GGGGATGCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.16
Consensus pattern (25 bp):
AAGAGCTATATAACGGAAAGCTCGA
Found at i:58653346 original size:15 final size:17
Alignment explanation
Indices: 58653316--58653349 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
58653306 ATCATAGTTT
58653316 AATTAATTTAAAACTTA
1 AATTAATTTAAAACTTA
58653333 AATTAA-TT-AAACTTA
1 AATTAATTTAAAACTTA
58653348 AA
1 AA
58653350 ACCCTTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 2 0.12
17 6 0.35
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAATTTAAAACTTA
Found at i:58654952 original size:11 final size:11
Alignment explanation
Indices: 58654936--58654966 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
58654926 TGTGAACAAA
58654936 AGACCATGGTT
1 AGACCATGGTT
58654947 AGACCATGGTT
1 AGACCATGGTT
58654958 AGACCATGG
1 AGACCATGG
58654967 AAGTACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (11 bp):
AGACCATGGTT
Found at i:58655026 original size:37 final size:36
Alignment explanation
Indices: 58654983--58655064 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 36
58654973 ATGTGTGTAC
58654983 GTGTAAGACCATAGCTG-GGCTATGGCATCGTAATAAA
1 GTGTAAGACCATAGC-GAGGCTATGGCATCGTAAT-AA
* * *
58655020 GTGTAAGACCATAGCGAGGCTATGGCATTGTGATAT
1 GTGTAAGACCATAGCGAGGCTATGGCATCGTAATAA
58655056 GTGTAAGAC
1 GTGTAAGAC
58655065 TGTGGCAAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
36 11 0.27
37 30 0.73
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (36 bp):
GTGTAAGACCATAGCGAGGCTATGGCATCGTAATAA
Found at i:58659483 original size:262 final size:262
Alignment explanation
Indices: 58658983--58659507 Score: 953
Period size: 261 Copynumber: 2.0 Consensus size: 262
58658973 TTCATGACCC
* *
58658983 TTCCATAACACTTTTTGCGTCTTTTGATTTACGGTAATAAGGTGTTGAACAATTTCTTCTTCTGG
1 TTCCATAACACTTTTTGCATCTTTTGATTTACGGTAATAAGGTGTTGAACAATGTCTTCTTCTGG
*
58659048 TTTCATTTTGTAATCTTGCAATTCTCTCATCATCTTATCAACTTTCTCCCTTCATGTTGAAGTTG
66 TTTCATTTTGTAATCTTACAATTCTCTCATCATCTTATCAACTTTCTCCCTTCATGTTGAAGTTG
*
58659113 TTATCTCATCAGGCAATATCAGATTTATTGCTATTTCTACCAATATCTATGATAGAAAATAAATT
131 TTATCTCATCAGACAATATCAGATTTATTGCTATTTCTACCAATATCTATGATAGAAAATAAATT
*
58659178 TTTTCTCGATTTTCATTATTTATCTATTTTTCTCTGATGTCATCACAAACTAATAATTAATTTAT
196 TTTTCTCGATTTTCATTATTCATCTATTTTTCTCTGATGTCATCACAAACTAATAATTAATTTAT
58659243 AA
261 AA
*
58659245 TTCCATAACACTTTTTGCATCTTTTGATTTACGGTAATAAGGTGTTGAA-AATGTCTTCTTTTGG
1 TTCCATAACACTTTTTGCATCTTTTGATTTACGGTAATAAGGTGTTGAACAATGTCTTCTTCTGG
*
58659309 TTTCATTTTGTAATCTTACAATTCTCTCATCATCTTATTAACTTTCTCCCTTCATGTTGAAGTTG
66 TTTCATTTTGTAATCTTACAATTCTCTCATCATCTTATCAACTTTCTCCCTTCATGTTGAAGTTG
58659374 TTATCTCATCAGACAATATCAGATTTATTGCTATTTCTACCAATATCTATGATAGAAAATAAATT
131 TTATCTCATCAGACAATATCAGATTTATTGCTATTTCTACCAATATCTATGATAGAAAATAAA-T
* *
58659439 TTTTTCTCGATTTTTATTATTCATCTATTTTTCTCTGGTGTCATCACAAACTAATAATTAATTTA
195 TTTTTCTCGATTTTCATTATTCATCTATTTTTCTCTGATGTCATCACAAACTAATAATTAATTTA
58659504 TAA
260 TAA
58659507 T
1 T
58659508 AGTTACTAAC
Statistics
Matches: 253, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
261 138 0.55
262 115 0.45
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (262 bp):
TTCCATAACACTTTTTGCATCTTTTGATTTACGGTAATAAGGTGTTGAACAATGTCTTCTTCTGG
TTTCATTTTGTAATCTTACAATTCTCTCATCATCTTATCAACTTTCTCCCTTCATGTTGAAGTTG
TTATCTCATCAGACAATATCAGATTTATTGCTATTTCTACCAATATCTATGATAGAAAATAAATT
TTTTCTCGATTTTCATTATTCATCTATTTTTCTCTGATGTCATCACAAACTAATAATTAATTTAT
AA
Found at i:58659684 original size:107 final size:104
Alignment explanation
Indices: 58659510--58659753 Score: 296
Period size: 106 Copynumber: 2.3 Consensus size: 104
58659500 TTTATAATAG
* * *
58659510 TTACTAACAAAATAACGTTCAAATAAATTAAAAAAAATTAAAGATTACATTCATAACCTAACAAA
1 TTACTAACAAAATAACTTTAAAATAAATTAAAAAAAATTAAAAATTACATTCATAACCTAACAAA
* *
58659575 TCACAATAAACCCTAAAC-AAACAATTAACCTAATCAGAAAC
66 TCACAATAAACACTAAACTAAACAAATAA-CTAAT-A-AAAC
* * *
58659616 TTACTAACAAAATAACTTTAAAAGAAATTAAAAATTAA-TAAAAATTAATATTCATAACCTAACA
1 TTACTAACAAAATAACTTTAAAATAAATTAAAAA-AAATTAAAAATT-ACATTCATAACCTAACA
* * * * *
58659680 AATCACAATAAACATTAAACTAAACAAATAATTTATAATAG
64 AATCACAATAAACACTAAACTAAACAAATAACTAATAAAAC
*
58659721 TAACTAACAAAA-AACTTTAAAATAAATTAAAAA
1 TTACTAACAAAATAACTTTAAAATAAATTAAAAA
58659754 CAACATAAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
104 20 0.17
105 13 0.11
106 39 0.32
107 39 0.32
108 9 0.08
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.25
Consensus pattern (104 bp):
TTACTAACAAAATAACTTTAAAATAAATTAAAAAAAATTAAAAATTACATTCATAACCTAACAAA
TCACAATAAACACTAAACTAAACAAATAACTAATAAAAC
Found at i:58659739 original size:25 final size:25
Alignment explanation
Indices: 58659697--58659744 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
58659687 ATAAACATTA
* *
58659697 AACTAAACAAATAATTTATAATAGT
1 AACTAAACAAAAAATTTAAAATAGT
58659722 AACT-AACAAAAAACTTTAAAATA
1 AACTAAACAAAAAA-TTTAAAATA
58659745 AATTAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.27
Consensus pattern (25 bp):
AACTAAACAAAAAATTTAAAATAGT
Found at i:58663294 original size:49 final size:50
Alignment explanation
Indices: 58663228--58663461 Score: 206
Period size: 49 Copynumber: 4.6 Consensus size: 50
58663218 GTCATGTGTC
* * * *
58663228 TAGTACTAAATGCAGGCTACTATGTGTACCGGATAA-T-TGGTCGCATGTG
1 TAGTACTAAGTGCAGGCTACTATGTGTACC-GAAAACTGTGATCACATGTG
** *
58663277 TAGTACTAAGTGCAGGCTACTATGCATACCGAAAACTGTGATCACGTGTG
1 TAGTACTAAGTGCAGGCTACTATGTGTACCGAAAACTGTGATCACATGTG
* *
58663327 TAGTACTAAGTGCAGGCTACTACGTACTATGCATACCGAAAACTGTGATCACGTGTG
1 TAGTACTAAGTGCAGG---CTAC-TA-TGTG--TACCGAAAACTGTGATCACATGTG
* * ** * * *
58663384 TAGTACTAAGTGCAGGCTACTACGTGTACTAGATTA-T-TGGTCGCATATG
1 TAGTACTAAGTGCAGGCTACTATGTGTAC-CGAAAACTGTGATCACATGTG
*
58663433 TAGTACTAAGTGCAGGCTACTATGCGTAC
1 TAGTACTAAGTGCAGGCTACTATGTGTAC
58663462 TAGATAGCTT
Statistics
Matches: 154, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
48 4 0.03
49 63 0.41
50 29 0.19
51 3 0.02
52 2 0.01
53 6 0.04
54 6 0.04
55 1 0.01
57 40 0.26
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (50 bp):
TAGTACTAAGTGCAGGCTACTATGTGTACCGAAAACTGTGATCACATGTG
Found at i:58663341 original size:50 final size:50
Alignment explanation
Indices: 58663223--58663405 Score: 208
Period size: 57 Copynumber: 3.5 Consensus size: 50
58663213 GTGAGGTCAT
* * ** * * *
58663223 GTGTCTAGTACTAAATGCAGGCTACTATGTGTACCGGATAA-T-TGGTCGC
1 GTGTGTAGTACTAAGTGCAGGCTACTATGCATACC-GAAAACTGTGATCAC
*
58663272 ATGTGTAGTACTAAGTGCAGGCTACTATGCATACCGAAAACTGTGATCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTATGCATACCGAAAACTGTGATCAC
58663322 GTGTGTAGTACTAAGTGCAGGCTACTACGTACTATGCATACCGAAAACTGTGATCAC
1 GTGTGTAGTACTAAGTGCAGG------C-TACTATGCATACCGAAAACTGTGATCAC
58663379 GTGTGTAGTACTAAGTGCAGGCTACTA
1 GTGTGTAGTACTAAGTGCAGGCTACTA
58663406 CGTGTACTAG
Statistics
Matches: 116, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
48 4 0.03
49 31 0.27
50 30 0.26
51 1 0.01
56 1 0.01
57 49 0.42
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (50 bp):
GTGTGTAGTACTAAGTGCAGGCTACTATGCATACCGAAAACTGTGATCAC
Found at i:58663382 original size:57 final size:57
Alignment explanation
Indices: 58663294--58663408 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
58663284 AAGTGCAGGC
58663294 TACTATGCATACCGAAAACTGTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACG
1 TACTATGCATACCGAAAACTGTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACG
58663351 TACTATGCATACCGAAAACTGTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACG
1 TACTATGCATACCGAAAACTGTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACG
58663408 T
1 T
58663409 GTACTAGATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (57 bp):
TACTATGCATACCGAAAACTGTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACG
Found at i:58668576 original size:49 final size:49
Alignment explanation
Indices: 58668515--58668701 Score: 266
Period size: 49 Copynumber: 3.8 Consensus size: 49
58668505 TGAGGTCACG
*
58668515 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATTATTGGTCGCA
* * ** * *
58668564 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATTA-T-TGGTCGCA
*
58668615 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATTATTGGTCGCA
* *
58668664 TGTGTAGTACTAAGTGCAGGCTACAATGCGTACCAGAT
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAT
58668702 AGCTTCGGCT
Statistics
Matches: 119, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 76 0.64
50 2 0.02
51 41 0.34
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATTATTGGTCGCA
Found at i:58668693 original size:100 final size:100
Alignment explanation
Indices: 58668510--58668697 Score: 358
Period size: 100 Copynumber: 1.9 Consensus size: 100
58668500 TATTGTGAGG
*
58668510 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
*
58668575 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
66 AAGTGCAGGCTACAATGCGTACCCGAAAACTGTGA
58668610 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
58668675 AAGTGCAGGCTACAATGCGTACC
66 AAGTGCAGGCTACAATGCGTACC
58668698 AGATAGCTTC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 86 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (100 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACAATGCGTACCCGAAAACTGTGA
Found at i:58671474 original size:27 final size:27
Alignment explanation
Indices: 58671444--58671729 Score: 383
Period size: 27 Copynumber: 10.6 Consensus size: 27
58671434 TGTAAGGTAG
*
58671444 AATTATCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* * * *
58671471 AATTACTAGAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCCTGGTTTGTAA
*
58671498 AATCACCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* **
58671525 AATTACCAAAATACCCTTGGTTTACAA
1 AATTACCAAAATACCCCTGGTTTGTAA
*
58671552 AATTACCAAAATACCTCTGGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* * * *
58671579 AATTACTAAAATACCCTTTGTTTATAA
1 AATTACCAAAATACCCCTGGTTTGTAA
*
58671606 AATTACCAAAATACCACTGGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAA
58671633 AATTACCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* *
58671660 AATTATCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAA
* * *
58671687 AATTACCAAAATACCCCTGATTTTTGA
1 AATTACCAAAATACCCCTGGTTTGTAA
*
58671714 AATTACTAAAATACCC
1 AATTACCAAAATACCC
58671730 TCGACCTGAA
Statistics
Matches: 222, Mismatches: 37, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 222 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGGTTTGTAA
Found at i:58671742 original size:26 final size:27
Alignment explanation
Indices: 58671713--58671782 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
58671703 CTGATTTTTG
*
58671713 AAATTACTAAAATACCCTCGACCTG-A
1 AAATTACTAAAATACCCTCAACCTGTA
* * *
58671739 AAATTATTGAAATACCCTCAACTTGTA
1 AAATTACTAAAATACCCTCAACCTGTA
* *
58671766 AAATTACCAAAGTACCC
1 AAATTACTAAAATACCC
58671783 CTGATTTACA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
26 21 0.60
27 14 0.40
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCAACCTGTA
Found at i:58671837 original size:27 final size:27
Alignment explanation
Indices: 58671444--58671837 Score: 268
Period size: 27 Copynumber: 14.6 Consensus size: 27
58671434 TGTAAGGTAG
* *
58671444 AATTATCAAAATACCC-CTGGTTTGTAA
1 AATTACCAAAATACCCTC-GATTTGTAA
* * * * *
58671471 AATTACTAGAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCTCGATTTGTAA
* *
58671498 AATCACCAAAATACCC-CTGGTTTGTAA
1 AATTACCAAAATACCCTC-GATTTGTAA
* * **
58671525 AATTACCAAAATACCCTTGGTTTACAA
1 AATTACCAAAATACCCTCGATTTGTAA
*
58671552 AATTACCAAAATA-CCTCTGGTTTGTAA
1 AATTACCAAAATACCCTC-GATTTGTAA
* * *
58671579 AATTACTAAAATACCCTTTG-TTTATAA
1 AATTACCAAAATACCC-TCGATTTGTAA
*
58671606 AATTACCAAAATACCACT-GGTTTGTAA
1 AATTACCAAAATACC-CTCGATTTGTAA
*
58671633 AATTACCAAAATACCC-CTGGTTTGTAA
1 AATTACCAAAATACCCTC-GATTTGTAA
* *
58671660 AATTATCAAAATACCC-CTAGTTTGTAA
1 AATTACCAAAATACCCTCGA-TTTGTAA
* *
58671687 AATTACCAAAATACCC-CTGATTTTTGA
1 AATTACCAAAATACCCTC-GATTTGTAA
* **
58671714 AATTACTAAAATACCCTCGACCTG-AA
1 AATTACCAAAATACCCTCGATTTGTAA
*** * *
58671740 AATTATTGAAATACCCTCAACTTGTAA
1 AATTACCAAAATACCCTCGATTTGTAA
* ** *
58671767 AATTACCAAAGTACCC-CTGATTTACAG
1 AATTACCAAAATACCCTC-GATTTGTAA
*** **
58671794 AATTACCATTTTACCCTCGATTTACAA
1 AATTACCAAAATACCCTCGATTTGTAA
*
58671821 AATTACCGAAATACCCT
1 AATTACCAAAATACCCT
58671838 TGTAGGGTAG
Statistics
Matches: 296, Mismatches: 55, Indels: 32
0.77 0.14 0.08
Matches are distributed among these distances:
26 27 0.09
27 261 0.88
28 7 0.02
29 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTCGATTTGTAA
Found at i:58671854 original size:27 final size:27
Alignment explanation
Indices: 58671824--58671998 Score: 206
Period size: 27 Copynumber: 6.5 Consensus size: 27
58671814 TTTACAAAAT
*
58671824 TACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
*
58671851 TACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
** * * *
58671878 TACTTAAATACCCCTATAGAGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
** *
58671905 TACTAAAATACCCATGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAA
*
58671932 TACCGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
** * *
58671959 TACTAAAATACCCCTGTAGGGTGGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAA
*
58671986 TACCGAGATACCC
1 TACCGAAATACCC
58671999 TTACGGGGTA
Statistics
Matches: 127, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 127 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (27 bp):
TACCGAAATACCCCTGTAGGGTAGAAA
Found at i:58671887 original size:54 final size:54
Alignment explanation
Indices: 58671824--58671998 Score: 233
Period size: 54 Copynumber: 3.2 Consensus size: 54
58671814 TTTACAAAAT
* * ** *
58671824 TACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCATGTAGGGTAGAAA
** * *
58671878 TACTTAAATACCCCTATAGAGTAGAATTACTAAAATACCCATGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCATGTAGGGTAGAAA
* * *
58671932 TACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTGGAAT
1 TACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCATGTAGGGTAGAAA
*
58671986 TACCGAGATACCC
1 TACCGAAATACCC
58671999 TTACGGGGTA
Statistics
Matches: 104, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (54 bp):
TACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCATGTAGGGTAGAAA
Found at i:58671997 original size:81 final size:81
Alignment explanation
Indices: 58671821--58671998 Score: 266
Period size: 81 Copynumber: 2.2 Consensus size: 81
58671811 CGATTTACAA
* * *
58671821 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAAATACTTAAA
1 AATTACCGAAATACCCATGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAAATACTAAAA
58671886 TACCCCTATAGAGTAG
66 TACCCCTATAGAGTAG
** *
58671902 AATTACTAAAATACCCATGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACTAAAA
1 AATTACCGAAATACCCATGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAAATACTAAAA
* * *
58671967 TACCCCTGTAGGGTGG
66 TACCCCTATAGAGTAG
*
58671983 AATTACCGAGATACCC
1 AATTACCGAAATACCC
58671999 TTACGGGGTA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24
Consensus pattern (81 bp):
AATTACCGAAATACCCATGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAAATACTAAAA
TACCCCTATAGAGTAG
Found at i:58672449 original size:6 final size:6
Alignment explanation
Indices: 58672418--58672505 Score: 83
Period size: 6 Copynumber: 14.3 Consensus size: 6
58672408 TTGCATTCAC
* *
58672418 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
*
58672467 -TCACGTG ATTCTG ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 AT-TC-TG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
58672506 AATGTTTCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
5 4 0.06
6 55 0.81
7 7 0.10
8 2 0.03
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:58672456 original size:31 final size:31
Alignment explanation
Indices: 58672418--58672496 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
58672408 TTGCATTCAC
* *
58672418 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
* *
58672449 ATTCTGATTCTGATTCTGTCACGTGATTCTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
58672480 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
58672497 AGTTCTGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTG
Found at i:58680589 original size:79 final size:81
Alignment explanation
Indices: 58680487--58680670 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 81
58680477 GCTCCTCGTT
* * *
58680487 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATACCTTC-GGATCTTAACC
*
58680549 CGGAT-TTAGTAAC-TCGCA
63 CGGATATT-GTAACTTAGCA
**
58680567 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATACCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATACCTTCGGATCTTAACCCGG
*
58680631 ATATTGTCACTTAGCA
66 ATATTGTAACTTAGCA
58680647 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
58680671 CATCATTCAA
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 14 0.15
79 55 0.60
80 22 0.24
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATACCTTCGGATCTTAACCCGG
ATATTGTAACTTAGCA
Found at i:58680604 original size:39 final size:41
Alignment explanation
Indices: 58680487--58680670 Score: 190
Period size: 40 Copynumber: 4.6 Consensus size: 41
58680477 GCTCCTCGTT
* *
58680487 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCA
* *
58680527 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAA-CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
58680567 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * * *
58680606 CAAATACCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
58680647 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
58680671 CATCATTCAA
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
38 3 0.02
39 46 0.37
40 66 0.52
41 11 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:58697079 original size:20 final size:20
Alignment explanation
Indices: 58697042--58697079 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58697032 CACATATATG
*
58697042 TAATATTAATTATATTTTTA
1 TAATATTAATGATATTTTTA
58697062 TAATATTTAATGAT-TTTT
1 TAATA-TTAATGATATTTT
58697080 CAAAATCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TAATATTAATGATATTTTTA
Found at i:58700304 original size:22 final size:22
Alignment explanation
Indices: 58700276--58700347 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
58700266 ACAAATCTTA
58700276 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
58700298 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
*
58700320 TCTCAATTTCATTCCAAAAAT-C
1 TCTCAATTTCCTTCC-AAAATCC
58700342 TCTCAA
1 TCTCAA
58700348 ATCCATATTA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 43 0.90
23 5 0.10
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:58700417 original size:30 final size:30
Alignment explanation
Indices: 58700381--58700445 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
58700371 CCTCAATTTC
58700381 ATTTTTTT-AAATAATTTCAAATTTTTTTAT
1 ATTTTTTTAAAATAATTTCAAA-TTTTTTAT
*
58700411 ATTTTTTTAAAATAATTTTAAATTTTTTAT
1 ATTTTTTTAAAATAATTTCAAATTTTTTAT
58700441 ATTTT
1 ATTTT
58700446 CATCAATGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 21 0.64
31 12 0.36
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (30 bp):
ATTTTTTTAAAATAATTTCAAATTTTTTAT
Found at i:58702805 original size:29 final size:29
Alignment explanation
Indices: 58702770--58703941 Score: 1964
Period size: 29 Copynumber: 41.3 Consensus size: 29
58702760 TTTATTTCAT
58702770 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58702799 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58702828 ACCCTAACCCTAACCTAACTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* * *
58702857 CCCCTAACCTTAACCTAACTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
58702886 CCCCTAACCTTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58702914 ACCCTAACCCTACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
58702943 ACCCTAACCTTAACCTAATTTATTTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58702972 ACCCTAACCCTAACCTAATTTATTTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703001 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703030 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703059 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703088 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703117 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703146 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703175 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703204 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703233 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703262 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703291 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703320 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703349 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703378 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703407 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703436 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703465 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703494 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703523 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703552 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703581 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58703610 ACCCTAACCCTAACCTAACTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
58703639 CCCCTAACCTTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58703667 ACCCTAACCCTACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
58703696 ACCCTAACCTTAACCTAATTT-ATT-TAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703723 A----AACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58703748 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58703777 ACCCTAACCCTACCCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58703805 A---T--CCCTACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703829 A-CC---C--TAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58703852 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58703881 ACCCTAACCCTACCCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
58703909 A---T--CCCTACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
58703933 ACCCTAACC
1 ACCCTAACC
58703942 TAATTTATTT
Statistics
Matches: 1090, Mismatches: 30, Indels: 46
0.93 0.03 0.04
Matches are distributed among these distances:
23 70 0.06
24 13 0.01
25 6 0.01
27 5 0.00
28 61 0.06
29 935 0.86
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (29 bp):
ACCCTAACCCTAACCTAATTTAATTAAAA
Found at i:58703832 original size:18 final size:18
Alignment explanation
Indices: 58703788--58703858 Score: 52
Period size: 23 Copynumber: 3.4 Consensus size: 18
58703778 CCCTAACCCT
58703788 ACCCTAATTTAATTAAAA
1 ACCCTAATTTAATTAAAA
58703806 TCCCTACCCTAATTTAATTAAAA
1 -----ACCCTAATTTAATTAAAA
58703829 ACCCTAACCTAATTTAATTAAAA
1 A--C---CCTAATTTAATTAAAA
58703852 ACCCTAA
1 ACCCTAA
58703859 CCTTAACCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
18 6 0.14
20 1 0.02
21 1 0.02
23 35 0.81
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (18 bp):
ACCCTAATTTAATTAAAA
Found at i:58703936 original size:18 final size:19
Alignment explanation
Indices: 58703892--58703939 Score: 53
Period size: 23 Copynumber: 2.4 Consensus size: 19
58703882 CCCTAACCCT
58703892 ACCCTAATTTAATTAAAATCCC
1 ACCCTAATTTAATTAAAA---C
58703914 TACCCTAATTTAATTAAAA-
1 -ACCCTAATTTAATTAAAAC
58703933 ACCCTAA
1 ACCCTAA
58703940 CCTAATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.28
23 18 0.72
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (19 bp):
ACCCTAATTTAATTAAAAC
Found at i:58704024 original size:56 final size:56
Alignment explanation
Indices: 58703964--58704088 Score: 180
Period size: 56 Copynumber: 2.2 Consensus size: 56
58703954 AAACCATAAC
* * ** *
58703964 ATAATTTTACCTAATTTGAT-AATCTTACTAACCATTAACACACTTTTTTGGGCTTA
1 ATAATTTTACATAATTTGATAAAT-TTACTAACCATTAACAAAAGTTATTGGGCTTA
*
58704020 ATAATTTTACATTATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTA
1 ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTA
58704076 ATAATTTTACATA
1 ATAATTTTACATA
58704089 GTTTTACATA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 58 0.95
57 3 0.05
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (56 bp):
ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTA
Found at i:58707463 original size:8 final size:8
Alignment explanation
Indices: 58707450--58707474 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
58707440 TCCACGAGGG
58707450 CACAATTT
1 CACAATTT
58707458 CACAATTT
1 CACAATTT
58707466 CACAATTT
1 CACAATTT
58707474 C
1 C
58707475 TTCTCAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (8 bp):
CACAATTT
Found at i:58707529 original size:131 final size:125
Alignment explanation
Indices: 58707232--58707530 Score: 453
Period size: 131 Copynumber: 2.4 Consensus size: 125
58707222 CAAAATCACG
58707232 TCCACGAGGGCGCGATTTTATACTATTTG-CTCAGAAACGTCAAAAAAATTTTATTTCTTACATG
1 TCCACGAGGGCGCGATTTTATACTATTTGACTCAGAAACGTCAAAAAAA-TTTATTTCTTACATG
* *
58707296 ACCAATTGTAGCGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAATTAGCA
65 ACCAACTGTAGCGAAATCGCGTCCACGAGGGCACAATTTCACAATTTCTTCTCAATTAGCA
58707357 TCCACGAGGGCGCGATTTTATACTATTT-ACTCAGAAACGTCAAAAAAA-TTATTTCTTACATGA
1 TCCACGAGGGCGCGATTTTATACTATTTGACTCAGAAACGTCAAAAAAATTTATTTCTTACATGA
58707420 CCAACTGTAGCGAAATCGCGTCCACGAGGGCACAATTTCACAATTTCACAATTTCTTCTCAATTA
66 CCAACTGTAGCGAAATCGCGTCCACGAGGG--------CACAATTTCACAATTTCTTCTCAATTA
58707485 GCA
123 GCA
* *
58707488 TCCTCGATGGCGCGATTTTATACTATTTGAC-CAGAAACGTCAA
1 TCCACGAGGGCGCGATTTTATACTATTTGACTCAGAAACGTCAA
58707531 CTCGAAATAA
Statistics
Matches: 160, Mismatches: 4, Indels: 14
0.90 0.02 0.08
Matches are distributed among these distances:
123 44 0.28
125 47 0.29
131 67 0.42
132 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (125 bp):
TCCACGAGGGCGCGATTTTATACTATTTGACTCAGAAACGTCAAAAAAATTTATTTCTTACATGA
CCAACTGTAGCGAAATCGCGTCCACGAGGGCACAATTTCACAATTTCTTCTCAATTAGCA
Found at i:58714716 original size:3 final size:3
Alignment explanation
Indices: 58714708--58714751 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
58714698 AATAACTAGG
58714708 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
58714752 GAGGGGAGGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:58722222 original size:38 final size:38
Alignment explanation
Indices: 58722180--58722253 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
58722170 ACGTTCAACT
58722180 GAGTCGACTTGATTCTCTAAAGTTCACGAGTTTTAGTA
1 GAGTCGACTTGATTCTCTAAAGTTCACGAGTTTTAGTA
58722218 GAGTCGACTTGATTCTCTAAAGTTCACGAGTTTTAG
1 GAGTCGACTTGATTCTCTAAAGTTCACGAGTTTTAG
58722254 CAGTCACCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (38 bp):
GAGTCGACTTGATTCTCTAAAGTTCACGAGTTTTAGTA
Found at i:58723019 original size:11 final size:11
Alignment explanation
Indices: 58723003--58723071 Score: 79
Period size: 11 Copynumber: 6.3 Consensus size: 11
58722993 AGAGTGAACT
58723003 GAGAGAATTGA
1 GAGAGAATTGA
* *
58723014 GTGAGAATTAA
1 GAGAGAATTGA
58723025 GAGAGAATTGA
1 GAGAGAATTGA
58723036 GAGA-AGATTGA
1 GAGAGA-ATTGA
58723047 GA-ATGAATTGA
1 GAGA-GAATTGA
*
58723058 GAGAGAGTTGA
1 GAGAGAATTGA
58723069 GAG
1 GAG
58723072 TAAATTGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
10 2 0.04
11 45 0.92
12 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.20
Consensus pattern (11 bp):
GAGAGAATTGA
Found at i:58723046 original size:33 final size:32
Alignment explanation
Indices: 58722993--58723079 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
58722983 AAAAAAAATG
* * *
58722993 AGAGTGAACTGAGAG-AATTGAGTGA-GAATTA
1 AGAGAGAATTGAGAGAAATTGAG-AATGAATTA
*
58723024 AGAGAGAATTGAGAGAAGATTGAGAATGAATTG
1 AGAGAGAATTGAGAGAA-ATTGAGAATGAATTA
*
58723057 AGAGAGAGTTGAGAGTAAATTGA
1 AGAGAGAATTGAGAG-AAATTGA
58723080 AAAGGTAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
31 13 0.28
32 2 0.04
33 30 0.64
34 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.33, T:0.22
Consensus pattern (32 bp):
AGAGAGAATTGAGAGAAATTGAGAATGAATTA
Found at i:58723054 original size:22 final size:22
Alignment explanation
Indices: 58723007--58723079 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
58722997 TGAACTGAGA
* * *
58723007 GAATTGAGTGAGAATTAAGAGA-
1 GAATTGAGAGAGAGTTGAGA-AT
58723029 GAATTGAGAGA-AGATTGAGAAT
1 GAATTGAGAGAGAG-TTGAGAAT
*
58723051 GAATTGAGAGAGAGTTGAGAGT
1 GAATTGAGAGAGAGTTGAGAAT
*
58723073 AAATTGA
1 GAATTGA
58723080 AAAGGTAAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 2 0.05
22 39 0.91
23 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (22 bp):
GAATTGAGAGAGAGTTGAGAAT
Found at i:58723079 original size:11 final size:10
Alignment explanation
Indices: 58723002--58723079 Score: 52
Period size: 11 Copynumber: 7.3 Consensus size: 10
58722992 GAGAGTGAAC
58723002 TGAGAG-AAT
1 TGAGAGAAAT
*
58723011 TGAGTGAGAAT
1 TGAGAGA-AAT
*
58723022 TAAGAGAGAAT
1 TGAGAGA-AAT
58723033 TGAGAGAAGAT
1 TGAGAGAA-AT
58723044 TGAGA-ATGAAT
1 TGAGAGA--AAT
*
58723055 TGAGAGAGAGT
1 TGAGAGA-AAT
58723066 TGAGAGTAAAT
1 TGAGAG-AAAT
58723077 TGA
1 TGA
58723080 AAAGGTAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
9 5 0.09
10 2 0.04
11 46 0.82
12 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (10 bp):
TGAGAGAAAT
Found at i:58726253 original size:24 final size:24
Alignment explanation
Indices: 58726223--58726274 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
58726213 AATCAAAGTC
*
58726223 AAATATATTATGCTAATAAATGCA
1 AAATATATTATACTAATAAATGCA
* *
58726247 AAATATATTATACTCATAAATGCT
1 AAATATATTATACTAATAAATGCA
58726271 AAAT
1 AAAT
58726275 CTTCTAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCA
Found at i:58730455 original size:24 final size:24
Alignment explanation
Indices: 58730440--58730491 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
58730430 AATTAAAGTC
58730440 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
58730464 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
58730488 AAAT
1 AAAT
58730492 CTTCTAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:58734880 original size:22 final size:22
Alignment explanation
Indices: 58734852--58734950 Score: 101
Period size: 22 Copynumber: 4.5 Consensus size: 22
58734842 GCTACACCAC
* *
58734852 ATCAGTAGGCACCAAAGTGCGA
1 ATCAGTAGGCACCATAGTGCAA
* *
58734874 ATCAGTAGGCACCGTAGTGTAA
1 ATCAGTAGGCACCATAGTGCAA
* * * *
58734896 ATTAGTAGGCACCGTACTGTAGA
1 ATCAGTAGGCACCATAGTGCA-A
58734919 A-CAGTAGGCACCATAGTGCAA
1 ATCAGTAGGCACCATAGTGCAA
*
58734940 AACAGTAGGCA
1 ATCAGTAGGCA
58734951 TCGAAATGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
21 2 0.03
22 61 0.94
23 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.18
Consensus pattern (22 bp):
ATCAGTAGGCACCATAGTGCAA
Found at i:58734924 original size:44 final size:44
Alignment explanation
Indices: 58734854--58734968 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 44
58734844 TACACCACAT
* * * *
58734854 CAGTAGGCACC-AAA-GTGCGAATCAGTAGGCACCGTAGTGTAAAT
1 CAGTAGGCACCGAAATGT-AGAA-CAGTAGGCACCATAGTGCAAAA
* * *
58734898 TAGTAGGCACCGTACTGTAGAACAGTAGGCACCATAGTGCAAAA
1 CAGTAGGCACCGAAATGTAGAACAGTAGGCACCATAGTGCAAAA
*
58734942 CAGTAGGCATCGAAATGTAGAACAGTA
1 CAGTAGGCACCGAAATGTAGAACAGTA
58734969 ACCACCAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
44 52 0.90
45 4 0.07
46 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (44 bp):
CAGTAGGCACCGAAATGTAGAACAGTAGGCACCATAGTGCAAAA
Found at i:58734965 original size:22 final size:21
Alignment explanation
Indices: 58734899--58734968 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
58734889 AGTGTAAATT
* *
58734899 AGTAGGCACCGTACTGTAGAAC
1 AGTAGGCA-CGAAATGTAGAAC
* * * *
58734921 AGTAGGCACCATAGTGCAAAAC
1 AGTAGGCACGA-AATGTAGAAC
58734943 AGTAGGCATCGAAATGTAGAAC
1 AGTAGGCA-CGAAATGTAGAAC
58734965 AGTA
1 AGTA
58734969 ACCACCAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
21 1 0.03
22 34 0.92
23 2 0.05
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.17
Consensus pattern (21 bp):
AGTAGGCACGAAATGTAGAAC
Found at i:58737216 original size:20 final size:20
Alignment explanation
Indices: 58737180--58737217 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58737170 TTTATAAATT
* *
58737180 TTATAAAAATTATTAAAAAC
1 TTATAAAAATAAATAAAAAC
58737200 TTATAAAAATAAATAAAA
1 TTATAAAAATAAATAAAA
58737218 TTTATTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TTATAAAAATAAATAAAAAC
Found at i:58739249 original size:18 final size:18
Alignment explanation
Indices: 58739203--58739260 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
58739193 TTTATAAAAC
* *
58739203 AATTTTTAAAAATTATTAG
1 AATTTTTTAAAA-TATTAT
* *
58739222 AAATTATTAAAATATTAT
1 AATTTTTTAAAATATTAT
58739240 AATTTTTTAAAATAATTAT
1 AATTTTTTAAAAT-ATTAT
58739259 AA
1 AA
58739261 ATTAGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
AATTTTTTAAAATATTAT
Found at i:58739432 original size:21 final size:21
Alignment explanation
Indices: 58739387--58739432 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
58739377 TTATTTATTT
*
58739387 ATTTATAAATTTTAATAATTT
1 ATTTATAAATTTTAATAATTC
58739408 ATTTAT-AATTTCT-ATAAATTC
1 ATTTATAAATTT-TAAT-AATTC
58739429 ATTT
1 ATTT
58739433 TTATACCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTATAAATTTTAATAATTC
Found at i:58750569 original size:18 final size:16
Alignment explanation
Indices: 58750538--58750573 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
58750528 CTACATTTTA
58750538 CAAAATTAAAAAAAAT
1 CAAAATTAAAAAAAAT
58750554 CAAATATTACAAAAAAAT
1 CAAA-ATTA-AAAAAAAT
58750572 CA
1 CA
58750574 TTAGTTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 4 0.22
18 10 0.56
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.19
Consensus pattern (16 bp):
CAAAATTAAAAAAAAT
Found at i:58759530 original size:18 final size:18
Alignment explanation
Indices: 58759479--58759530 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
58759469 TATAGAATTT
*
58759479 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
58759498 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
58759516 TTGTATTAAAA-AATT
1 TTGTA-TAAAATAATT
58759531 GAACATGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:58759566 original size:22 final size:20
Alignment explanation
Indices: 58759541--58759588 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
58759531 GAACATGTTA
*
58759541 ATTTTTAGTCAATTTTACAATT
1 ATTTTTAGTCAAATTT--AATT
*
58759563 ATTTTTAGTGAAATTTAATT
1 ATTTTTAGTCAAATTTAATT
58759583 ATTTTT
1 ATTTTT
58759589 GACAGATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
22 14 0.58
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTTAGTCAAATTTAATT
Found at i:58761804 original size:91 final size:91
Alignment explanation
Indices: 58761692--58761962 Score: 490
Period size: 91 Copynumber: 3.0 Consensus size: 91
58761682 GAGTACAAGC
58761692 AATGCTTTACAACTTAGTCAATTGATTAGTGGTAGTAGTTGTGTTTGGTAGAAAAGATTGTCTAT
1 AATGCTTTACAACTTAGTCAATTGATTAGTGGTAGTAGTTGTGTTTGGTAGAAAAGATTGTCTAT
58761757 AAAAGTCATCGTAATGGGTCGGAAGA
66 AAAAGTCATCGTAATGGGTCGGAAGA
58761783 AATGCTTTACAACTTAGTCAATTGATTAGTGGTAGTAGTTGTGTTTGGTAGAAAAGATTGTCTAT
1 AATGCTTTACAACTTAGTCAATTGATTAGTGGTAGTAGTTGTGTTTGGTAGAAAAGATTGTCTAT
*
58761848 AAAAGTCATCATAATGGGTCGGAAGA
66 AAAAGTCATCGTAATGGGTCGGAAGA
*
58761874 AATGCTTTACAACTTAGTCAATTGATTAGTGGTAGTAGTTTTGTTTGGTAGAAAAGATTGTCTAT
1 AATGCTTTACAACTTAGTCAATTGATTAGTGGTAGTAGTTGTGTTTGGTAGAAAAGATTGTCTAT
* *
58761939 AAAAGTTAT-GATAATGGGTAGGAA
66 AAAAGTCATCG-TAATGGGTCGGAA
58761963 AATAGTTTTC
Statistics
Matches: 174, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
91 174 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (91 bp):
AATGCTTTACAACTTAGTCAATTGATTAGTGGTAGTAGTTGTGTTTGGTAGAAAAGATTGTCTAT
AAAAGTCATCGTAATGGGTCGGAAGA
Found at i:58763983 original size:49 final size:49
Alignment explanation
Indices: 58763809--58764131 Score: 502
Period size: 49 Copynumber: 6.8 Consensus size: 49
58763799 CCCTTCGGGA
* * * * *
58763809 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
58763855 CTCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CT-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58763903 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58763950 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58763999 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58764048 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
58764097 CTTATTAC--ATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATATACACTTTCACATTCATCACAT
58764132 AGAATCCTAA
Statistics
Matches: 261, Mismatches: 10, Indels: 11
0.93 0.04 0.04
Matches are distributed among these distances:
46 3 0.01
47 112 0.43
48 2 0.01
49 144 0.55
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:58772856 original size:44 final size:44
Alignment explanation
Indices: 58772807--58773210 Score: 269
Period size: 44 Copynumber: 8.9 Consensus size: 44
58772797 GGGAATTGTC
*
58772807 GCTTCAACCTGCTCCACTGCAACTTCGAGGAGATAAGATTTG-T-
1 GCTTCAATCTGCTCCACTGCAACTTC-AGGAGATAAGATTTGCTA
* *
58772850 GACTTCAAGCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTAACTTGTA
1 G-CTTCAATCTGCTCCACTGCAACTTCA-GGAGATAAGATTTG---C---TA
* * * * * * *
58772902 GCTTTAATCTGTTACACTGCAACTTCAAGGAAAAAAGGTTCGCTA
1 GCTTCAATCTGCTCCACTGCAACTTC-AGGAGATAAGATTTGCTA
** * * * *
58772947 TATTCAATCTGCTCTACTGGAACTTCAGGGAGATAAGACTT-ATA
1 GCTTCAATCTGCTCCACTGCAACTTCA-GGAGATAAGATTTGCTA
* * * ** *
58772991 GCTTTAATATACTTTACTGCAACTTCAAAGAGATAAGATTTGCTA
1 GCTTCAATCTGCTCCACTGCAACTTC-AGGAGATAAGATTTGCTA
* * * *
58773036 TCTTCAATCCTGCTCCACTACATCTTCAGGGAGATAAGGTTTG-TA
1 GCTTCAAT-CTGCTCCACTGCAACTTCA-GGAGATAAGATTTGCTA
* * * * * *
58773081 GCTTTAACCTACTCTACTGAAACTTCAGAGAGAGAAGATTTGCTA
1 GCTTCAATCTGCTCCACTGCAACTTCAG-GAGATAAGATTTGCTA
* * *
58773126 TCTTCAATCTGCTCCATTGCAACTTCAGGGAGATAAGGTTTG-TA
1 GCTTCAATCTGCTCCACTGCAACTTCA-GGAGATAAGATTTGCTA
* * * *
58773170 GCTTTAATCTACTCTACTGTAACTTCAGAGAGATAAGATTT
1 GCTTCAATCTGCTCCACTGCAACTTCAG-GAGATAAGATTT
58773211 TCCACGATGA
Statistics
Matches: 271, Mismatches: 70, Indels: 39
0.71 0.18 0.10
Matches are distributed among these distances:
43 4 0.01
44 129 0.48
45 79 0.29
46 25 0.09
48 1 0.00
51 31 0.11
52 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (44 bp):
GCTTCAATCTGCTCCACTGCAACTTCAGGAGATAAGATTTGCTA
Found at i:58773016 original size:89 final size:89
Alignment explanation
Indices: 58772822--58773210 Score: 392
Period size: 89 Copynumber: 4.3 Consensus size: 89
58772812 AACCTGCTCC
* * * *
58772822 ACTGCAACTTCGAGGAGATAAGATTTG-TGA-CTTCAAGCTGCTCCACTACAACTTCAGGGAGAT
1 ACTGCAACTTCAAGGAGAAAAGATTTGCT-ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGAT
**
58772885 AAGATTTGTAACTTGTAGCTTTAATCTGTTAC-
65 AAG----GT---TTGTAGCTTTAATCTACT-CT
* * * * * *
58772917 ACTGCAACTTCAAGGAAAAAAGGTTCGCTATATTCAATCTGCTCTACTGGAACTTCAGGGAGATA
1 ACTGCAACTTCAAGGAGAAAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
** * * *
58772982 AGACTTATAGCTTTAATATACTTT
66 AGGTTTGTAGCTTTAATCTACTCT
* * * *
58773006 ACTGCAACTTCAAAGAGATAAGATTTGCTATCTTCAATCCTGCTCCACTACATCTTCAGGGAGAT
1 ACTGCAACTTCAAGGAGAAAAGATTTGCTATCTTCAAT-CTGCTCCACTGCAACTTCAGGGAGAT
*
58773071 AAGGTTTGTAGCTTTAACCTACTCT
65 AAGGTTTGTAGCTTTAATCTACTCT
* * *
58773096 ACTGAAACTTC-AGAGAGAGAAGATTTGCTATCTTCAATCTGCTCCATTGCAACTTCAGGGAGAT
1 ACTGCAACTTCAAG-GAGAAAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGAT
58773160 AAGGTTTGTAGCTTTAATCTACTCT
65 AAGGTTTGTAGCTTTAATCTACTCT
* *
58773185 ACTGTAACTTC-AGAGAGATAAGATTT
1 ACTGCAACTTCAAG-GAGAAAAGATTT
58773211 TCCACGATGA
Statistics
Matches: 247, Mismatches: 42, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
89 118 0.48
90 74 0.30
95 23 0.09
96 32 0.13
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (89 bp):
ACTGCAACTTCAAGGAGAAAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
AGGTTTGTAGCTTTAATCTACTCT
Found at i:58773152 original size:179 final size:179
Alignment explanation
Indices: 58772822--58773210 Score: 446
Period size: 179 Copynumber: 2.1 Consensus size: 179
58772812 AACCTGCTCC
* * *
58772822 ACTGCAACTTCGAGGAGATAAGATTTGTGACTTCAAGCTGCTCCACTACAACTTCAGGGAGATAA
1 ACTGCAACTTCAAAGAGATAAGATTTGTGACTTCAACCTGCTCCACTACAACTTCAGGGAGATAA
* ** * *
58772887 GATTTGTAACTTGTAGCTTTAATCTGTTACACTGCAACTTCAAGGAAAAAAGGTTCGCTATATTC
66 G---TGT-A-TTGTAGCTTTAACCTACTACACTGAAACTTCAAGGAAAAAAGATTCGCTATATTC
* * *
58772952 AATCTGCTCTACTGGAACTTCAGGGAGATAAGACTTATAGCTTTAATATACTTT
126 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAATATACTCT
*
58773006 ACTGCAACTTCAAAGAGATAAGATTTGCT-ATCTTCAATCCTGCTCCACTACATCTTCAGGGAGA
1 ACTGCAACTTCAAAGAGATAAGATTTG-TGA-CTTCAA-CCTGCTCCACTACAACTTCAGGGAGA
* * * *
58773070 TAAG-GT-TTGTAGCTTTAACCTACT-CTACTGAAACTTC-AGAGAGAGAAGATTTGCTATCTTC
63 TAAGTGTATTGTAGCTTTAACCTACTAC-ACTGAAACTTCAAG-GAAAAAAGATTCGCTATATTC
* ** * *
58773131 AATCTGCTCCATTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTACTCT
126 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAATATACTCT
* *
58773185 ACTGTAACTTCAGAGAGATAAGATTT
1 ACTGCAACTTCAAAGAGATAAGATTT
58773211 TCCACGATGA
Statistics
Matches: 177, Mismatches: 23, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
178 3 0.02
179 111 0.63
182 2 0.01
184 26 0.15
185 7 0.04
186 28 0.16
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (179 bp):
ACTGCAACTTCAAAGAGATAAGATTTGTGACTTCAACCTGCTCCACTACAACTTCAGGGAGATAA
GTGTATTGTAGCTTTAACCTACTACACTGAAACTTCAAGGAAAAAAGATTCGCTATATTCAATCT
GCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAATATACTCT
Found at i:58786611 original size:16 final size:16
Alignment explanation
Indices: 58786590--58786621 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
58786580 AATATATGGG
58786590 TTACACGAGTTTAAAA
1 TTACACGAGTTTAAAA
58786606 TTACACGAGTTTAAAA
1 TTACACGAGTTTAAAA
58786622 AGAATGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
TTACACGAGTTTAAAA
Found at i:58786980 original size:3 final size:3
Alignment explanation
Indices: 58786974--58787015 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
58786964 CGGTTGTCTT
58786974 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
58787016 ACAGCAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58789697 original size:26 final size:26
Alignment explanation
Indices: 58789631--58789703 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
58789621 TACTAATACA
* *
58789631 ACACCAGCACAAAGCCTACTAAATAT
1 ACACCAACACAAAGCCTGCTAAATAT
* ** *
58789657 ACATCAATTCGAAGCCTGCTAAATAT
1 ACACCAACACAAAGCCTGCTAAATAT
*
58789683 ACACCAACACCAAGCCTGCTA
1 ACACCAACACAAAGCCTGCTA
58789704 CACCCTAATG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.41, C:0.32, G:0.10, T:0.18
Consensus pattern (26 bp):
ACACCAACACAAAGCCTGCTAAATAT
Found at i:58794348 original size:19 final size:16
Alignment explanation
Indices: 58794323--58794369 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 16
58794313 ATCAGTCCAA
58794323 CAAAAGGAGCATTCTT
1 CAAAAGGAGCATTCTT
58794339 ACGTAAAAGGAGC-TT-TT
1 -C--AAAAGGAGCATTCTT
58794356 CAAAAGGAGCATTC
1 CAAAAGGAGCATTC
58794370 AAAGCTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 1 0.04
17 3 0.12
18 2 0.08
19 9 0.35
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (16 bp):
CAAAAGGAGCATTCTT
Found at i:58798344 original size:15 final size:15
Alignment explanation
Indices: 58798324--58798357 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
58798314 ACCAATACAT
58798324 GCCATTATAACCTTA
1 GCCATTATAACCTTA
58798339 GCCATTATAACCTTA
1 GCCATTATAACCTTA
58798354 GCCA
1 GCCA
58798358 AAAATGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.29
Consensus pattern (15 bp):
GCCATTATAACCTTA
Found at i:58799187 original size:20 final size:20
Alignment explanation
Indices: 58799154--58799225 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
58799144 TGCATAATAG
* *
58799154 GGGCACCAAAGTGAAATCAA
1 GGGCACGAATGTGAAATCAA
* * *
58799174 GAGCACGAATGTGAGATCAG
1 GGGCACGAATGTGAAATCAA
*
58799194 GGGCACCGAA-GTGCAATCAA
1 GGGCA-CGAATGTGAAATCAA
*
58799214 GGGCACAAATGT
1 GGGCACGAATGT
58799226 TTCTCCTTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 3 0.08
20 33 0.82
21 4 0.10
ACGTcount: A:0.38, C:0.19, G:0.31, T:0.12
Consensus pattern (20 bp):
GGGCACGAATGTGAAATCAA
Found at i:58799648 original size:40 final size:40
Alignment explanation
Indices: 58799594--58799782 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
58799584 AATTATACTC
* * * *
58799594 ATGTGCGA-TCAGGGGCACTGAAGTGCAATTAGGGGCACAA
1 ATGTGC-ATTCAGGGGTACTGAAGTACAAATAGGGGCACAG
* * *
58799634 ATGTGCATTTAGGGGTACCGAAGTACAAACAGGGGCACAG
1 ATGTGCATTCAGGGGTACTGAAGTACAAATAGGGGCACAG
58799674 ATGTGCATTCAGGGGTACTGAAGTACAAATAGGGGCACAG
1 ATGTGCATTCAGGGGTACTGAAGTACAAATAGGGGCACAG
* ** ** **
58799714 ATGTGCATTCAGGGGTGCCAAAGTACAAGCAATGGCACAG
1 ATGTGCATTCAGGGGTACTGAAGTACAAATAGGGGCACAG
*
58799754 ATGTGCATTCAGGGGTACCGAAGTACAAA
1 ATGTGCATTCAGGGGTACTGAAGTACAAA
58799783 CAATGACACT
Statistics
Matches: 128, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
39 1 0.01
40 127 0.99
ACGTcount: A:0.32, C:0.17, G:0.32, T:0.19
Consensus pattern (40 bp):
ATGTGCATTCAGGGGTACTGAAGTACAAATAGGGGCACAG
Found at i:58799727 original size:20 final size:20
Alignment explanation
Indices: 58799602--58799728 Score: 89
Period size: 20 Copynumber: 6.3 Consensus size: 20
58799592 TCATGTGCGA
*
58799602 TCAGGGGCACTGAAGTGCAAT
1 TCAGGGGCACAGAAGTGC-AT
58799623 T-AGGGGCACA-AATGTGCAT
1 TCAGGGGCACAGAA-GTGCAT
* * * * *
58799642 TTAGGGGTACCGAAGTACAA
1 TCAGGGGCACAGAAGTGCAT
* *
58799662 ACAGGGGCACAGATGTGCAT
1 TCAGGGGCACAGAAGTGCAT
* * * *
58799682 TCAGGGGTACTGAAGTACAAA
1 TCAGGGGCACAGAAGTGC-AT
*
58799703 T-AGGGGCACAGATGTGCAT
1 TCAGGGGCACAGAAGTGCAT
58799722 TCAGGGG
1 TCAGGGG
58799729 TGCCAAAGTA
Statistics
Matches: 78, Mismatches: 23, Indels: 11
0.70 0.21 0.10
Matches are distributed among these distances:
19 7 0.09
20 66 0.85
21 5 0.06
ACGTcount: A:0.31, C:0.17, G:0.34, T:0.19
Consensus pattern (20 bp):
TCAGGGGCACAGAAGTGCAT
Found at i:58799728 original size:80 final size:80
Alignment explanation
Indices: 58799594--58799782 Score: 263
Period size: 80 Copynumber: 2.4 Consensus size: 80
58799584 AATTATACTC
* * * * *
58799594 ATGTGCGA-TCAGGGGCACTGAAGTGCAATTAGGGGCACAAATGTGCATTTAGGGGTACCGAAGT
1 ATGTGC-ATTCAGGGGTACTGAAGTACAAATAGGGGCACAAATGTGCATTCAGGGGTACCAAAGT
*
58799658 ACAAACAGGGGCACAG
65 ACAAACAAGGGCACAG
* *
58799674 ATGTGCATTCAGGGGTACTGAAGTACAAATAGGGGCACAGATGTGCATTCAGGGGTGCCAAAGTA
1 ATGTGCATTCAGGGGTACTGAAGTACAAATAGGGGCACAAATGTGCATTCAGGGGTACCAAAGTA
* *
58799739 CAAGCAATGGCACAG
66 CAAACAAGGGCACAG
*
58799754 ATGTGCATTCAGGGGTACCGAAGTACAAA
1 ATGTGCATTCAGGGGTACTGAAGTACAAA
58799783 CAATGACACT
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 1 0.01
80 96 0.99
ACGTcount: A:0.32, C:0.17, G:0.32, T:0.19
Consensus pattern (80 bp):
ATGTGCATTCAGGGGTACTGAAGTACAAATAGGGGCACAAATGTGCATTCAGGGGTACCAAAGTA
CAAACAAGGGCACAG
Found at i:58799787 original size:40 final size:40
Alignment explanation
Indices: 58799626--58799785 Score: 230
Period size: 40 Copynumber: 4.0 Consensus size: 40
58799616 GTGCAATTAG
* * *
58799626 GGGCACAAATGTGCATTTAGGGGTACCGAAGTACAAACAG
1 GGGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAA
* * *
58799666 GGGCACAGATGTGCATTCAGGGGTACTGAAGTACAAATAG
1 GGGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAA
* * *
58799706 GGGCACAGATGTGCATTCAGGGGTGCCAAAGTACAAGCAA
1 GGGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAA
*
58799746 TGGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAA
1 GGGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAA
58799786 TGACACTTCT
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 106 1.00
ACGTcount: A:0.34, C:0.18, G:0.31, T:0.17
Consensus pattern (40 bp):
GGGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAA
Found at i:58810865 original size:4 final size:4
Alignment explanation
Indices: 58810856--58810894 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
58810846 GTGATATTGG
58810856 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
58810895 AATTTATGAT
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:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:58810902 original size:12 final size:12
Alignment explanation
Indices: 58810860--58810906 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
58810850 TATTGGATGT
*
58810860 ATGTATGTATGT
1 ATGTATGTATGA
*
58810872 ATGTATGTATGT
1 ATGTATGTATGA
58810884 ATGTATGTATGA
1 ATGTATGTATGA
*
58810896 ATTTATG-ATGA
1 ATGTATGTATGA
58810907 GATGAATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
11 4 0.12
12 29 0.88
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (12 bp):
ATGTATGTATGA
Found at i:58813801 original size:18 final size:16
Alignment explanation
Indices: 58813768--58813798 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58813758 TATGTTAGAG
58813768 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
58813784 CATATATATTTGAAA
1 CATATAAATTTGAAA
58813799 AATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:58813958 original size:20 final size:20
Alignment explanation
Indices: 58813901--58813969 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
58813891 TTTTAGAAAA
* *
58813901 TTTTAAAATT-TTAAAATTC
1 TTTTAAAATTATTATAATTT
* *
58813920 CTTTATATATTATTTATAATTT
1 TTTTA-AAATTA-TTATAATTT
58813942 TTTTAAAATTATTATAATTT
1 TTTTAAAATTATTATAATTT
58813962 TTTTAAAA
1 TTTTAAAA
58813970 AATATAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
19 4 0.10
20 21 0.51
21 5 0.12
22 11 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAAAATTATTATAATTT
Found at i:58813980 original size:20 final size:20
Alignment explanation
Indices: 58813937--58813982 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
58813927 TATTATTTAT
* *
58813937 AATTTTTTTAAAATTATTAT
1 AATTTTTTTAAAAATATTAA
58813957 AATTTTTTTAAAAA-ATATAA
1 AATTTTTTTAAAAATAT-TAA
58813977 AATTTT
1 AATTTT
58813983 GAATTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTTTTTTAAAAATATTAA
Found at i:58813993 original size:18 final size:19
Alignment explanation
Indices: 58813972--58814007 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
58813962 TTTTAAAAAA
58813972 TATAAA-ATTTTGAATTTT
1 TATAAATATTTTGAATTTT
58813990 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
58814008 GAAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:58814047 original size:19 final size:19
Alignment explanation
Indices: 58813978--58814047 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
58813968 AAAATATAAA
*
58813978 ATTTTGAATTTTTATAAA-T
1 ATTTTGAATTTTGA-AAATT
58813997 ATTTTGAA-TTTGAAATATT
1 ATTTTGAATTTTGAAA-ATT
*
58814016 ATTTTAAAATTTTGAAAATT
1 ATTTT-GAATTTTGAAAATT
*
58814036 AATTTGAATTTT
1 ATTTTGAATTTT
58814048 TTATAATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 2 0.05
18 5 0.12
19 20 0.47
20 9 0.21
21 7 0.16
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (19 bp):
ATTTTGAATTTTGAAAATT
Found at i:58817290 original size:4 final size:5
Alignment explanation
Indices: 58817252--58817289 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
58817242 GTCTATTTAC
58817252 AAAAT AAAAT AAAA- ATAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAA
58817290 TCCAAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 1 0.03
5 29 0.94
6 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:58818319 original size:41 final size:43
Alignment explanation
Indices: 58818256--58818364 Score: 116
Period size: 44 Copynumber: 2.6 Consensus size: 43
58818246 CATTAGTTTG
*
58818256 CTCCGCTGCAACTAT-AGGGAGATAAGACCTG-A-TGCAATCCA
1 CTCCACTGCAACT-TCAGGGAGATAAGACCTGCACTGCAATCCA
** * * **
58818297 CTTTACTGCAACTTCAGTGAGATAAGATCTGCTACTTTAATCCA
1 CTCCACTGCAACTTCAGGGAGATAAGACCTGC-ACTGCAATCCA
58818341 CTCCACTGCAACTTCAGGGAGATA
1 CTCCACTGCAACTTCAGGGAGATA
58818365 GGATTAGTGG
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
40 1 0.02
41 24 0.44
43 1 0.02
44 28 0.52
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAGATAAGACCTGCACTGCAATCCA
Found at i:58832113 original size:27 final size:26
Alignment explanation
Indices: 58832072--58832122 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
58832062 ACTGTGGACC
58832072 TTTAATTTTTAATTTGGTTTTATTTTA
1 TTTAATTTTTAATTTGG-TTTATTTTA
* *
58832099 TTTATTTTTTTATTTGGTTTATTT
1 TTTAATTTTTAATTTGGTTTATTT
58832123 CACTAATGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.75
Consensus pattern (26 bp):
TTTAATTTTTAATTTGGTTTATTTTA
Found at i:58832119 original size:17 final size:17
Alignment explanation
Indices: 58832089--58832122 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58832079 TTTAATTTGG
*
58832089 TTTTATTTTATTTATTT
1 TTTTATTTGATTTATTT
*
58832106 TTTTATTTGGTTTATTT
1 TTTTATTTGATTTATTT
58832123 CACTAATGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTATTTGATTTATTT
Found at i:58834027 original size:8 final size:8
Alignment explanation
Indices: 58834011--58834111 Score: 53
Period size: 9 Copynumber: 11.5 Consensus size: 8
58834001 AAATAATAGA
58834011 AAAATATTT
1 AAAA-ATTT
58834020 AAAAATTT
1 AAAAATTT
58834028 -AAAATTT
1 AAAAATTT
58834035 -AAAATTT
1 AAAAATTT
58834042 AAAATAATTAT
1 -AAA-AATT-T
58834053 AAAAATATT
1 AAAAAT-TT
**
58834062 AAACCGTATT
1 AAA-AAT-TT
58834072 AAAAATAATAT
1 AAAAAT--T-T
*
58834083 AAAAATTA
1 AAAAATTT
*
58834091 AAAAAATT
1 AAAAATTT
58834099 AAAGAATTT
1 AAA-AATTT
58834108 AAAA
1 AAAA
58834112 TTATGTAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 19
0.74 0.08 0.19
Matches are distributed among these distances:
7 14 0.19
8 14 0.19
9 22 0.29
10 17 0.23
11 8 0.11
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (8 bp):
AAAAATTT
Found at i:58834033 original size:7 final size:7
Alignment explanation
Indices: 58834016--58834046 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
58834006 ATAGAAAAAT
58834016 ATTTAAAA
1 ATTT-AAA
58834024 ATTTAAA
1 ATTTAAA
58834031 ATTTAAA
1 ATTTAAA
58834038 ATTTAAA
1 ATTTAAA
58834045 AT
1 AT
58834047 AATTATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTTAAA
Found at i:58834106 original size:17 final size:18
Alignment explanation
Indices: 58834069--58834122 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
58834059 ATTAAACCGT
58834069 ATTAAAAATAATATAAAA
1 ATTAAAAATAATATAAAA
58834087 ATTAAAAA-AAT-TAAAGA
1 ATTAAAAATAATATAAA-A
* * *
58834104 ATTTAAAATTATGTAAAA
1 ATTAAAAATAATATAAAA
58834122 A
1 A
58834123 GAGTTTGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 4 0.13
17 11 0.35
18 12 0.39
19 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
ATTAAAAATAATATAAAA
Found at i:58834426 original size:16 final size:17
Alignment explanation
Indices: 58834405--58834436 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
58834395 AATCAAGTGC
58834405 AATTTTTTT-AATTTTT
1 AATTTTTTTCAATTTTT
58834421 AATTTTTTTCAATTTT
1 AATTTTTTTCAATTTT
58834437 AAATAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
AATTTTTTTCAATTTTT
Found at i:58837868 original size:23 final size:23
Alignment explanation
Indices: 58837836--58837879 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
58837826 ACTACCATTT
58837836 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
58837859 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
58837880 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:58837872 original size:13 final size:11
Alignment explanation
Indices: 58837840--58837882 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
58837830 CCATTTTCTA
*
58837840 AATAAAATAAT
1 AATAAAATATT
58837851 AAT-AAATATCT
1 AATAAAATAT-T
58837862 AAGTAAAATATT
1 AA-TAAAATATT
58837874 AATAAAATA
1 AATAAAATA
58837883 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:58839162 original size:38 final size:38
Alignment explanation
Indices: 58839120--58839254 Score: 101
Period size: 38 Copynumber: 3.4 Consensus size: 38
58839110 TAGAGGAATG
* * *
58839120 AAATTGAAGATAATATTTTATTATTTTGTATAGTAATT
1 AAATTGAAGATAATATTTTATTATTTTGAACAGAAATT
* * *
58839158 AAATTGCAA-ATAAAATTTATTGGGGATTATTTTGGACAGGAATT
1 AAATTG-AAGATAATA-TT-TT----ATTATTTTGAACAGAAATT
* * * * *
58839202 GAATTGAAGATTATATTTGATTATTTTAAAGAGAAATT
1 AAATTGAAGATAATATTTTATTATTTTGAACAGAAATT
58839240 AAATTGAAGATAATA
1 AAATTGAAGATAATA
58839255 CATGTTGGAA
Statistics
Matches: 75, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
38 39 0.52
39 4 0.05
40 2 0.03
42 1 0.01
43 4 0.05
44 25 0.33
ACGTcount: A:0.42, C:0.01, G:0.16, T:0.41
Consensus pattern (38 bp):
AAATTGAAGATAATATTTTATTATTTTGAACAGAAATT
Found at i:58839982 original size:343 final size:343
Alignment explanation
Indices: 58839414--58840071 Score: 1262
Period size: 343 Copynumber: 1.9 Consensus size: 343
58839404 TTGTTATTTT
*
58839414 CATTTTATAGGAGAGTGATATTTATCTTTGCTTGAAATGGTAGTTTTAAGGGAGAGTGAATGTAA
1 CATTTTATAGGAGAGTGATATTTATCTTTGCTTGAAATAGTAGTTTTAAGGGAGAGTGAATGTAA
58839479 ACAAATTGTGCAACTTTGAGGCAACAAATATCCTTGGCGTGTTTGGATAGATTAGGTTGGTTATG
66 ACAAATTGTGCAACTTTGAGGCAACAAATATCCTTGGCGTGTTTGGATAGATTAGGTTGGTTATG
58839544 AAAGGTTGTACTATGAAAATTATATAGGGGATTCATTCTCTGAATAAGATTCTACAGAAATAGGT
131 AAAGGTTGTACTATGAAAATTATATAGGGGATTCATTCTCTGAATAAGATTCTACAGAAATAGGT
*
58839609 TGTTGAAGTGAACTACATAATCAATTCATTGTCTCCTCTGCTTCTTATTCTTTACTATTTCTTAT
196 TGTTGAAGTGAACTACATAATCAATTCATTGTCTCATCTGCTTCTTATTCTTTACTATTTCTTAT
*
58839674 TATTTCATTAGCATTGCAACCAAACTTGTGCACTTTCAAACTCACTATAAGTTGGTAGTTTCAAA
261 TATTTCATTAACATTGCAACCAAACTTGTGCACTTTCAAACTCACTATAAGTTGGTAGTTTCAAA
58839739 CTCACTTTCAAACTTGTG
326 CTCACTTTCAAACTTGTG
*
58839757 CATTTTATAGGAGAGTGATATTTATCTTTGCTTGAAATAGTAGTTTTAAGGGTGAGTGAATGTAA
1 CATTTTATAGGAGAGTGATATTTATCTTTGCTTGAAATAGTAGTTTTAAGGGAGAGTGAATGTAA
58839822 ACAAATTGTGCAACTTTGAGGCAACAAATATCCTTGGCGTGTTTGGATAGATTAGGTTGGTTATG
66 ACAAATTGTGCAACTTTGAGGCAACAAATATCCTTGGCGTGTTTGGATAGATTAGGTTGGTTATG
*
58839887 AAAGGTTGTACTATGAAAATTATATAGTGGATTCATTCTCTGAATAAGATTCTACAGAAATAGGT
131 AAAGGTTGTACTATGAAAATTATATAGGGGATTCATTCTCTGAATAAGATTCTACAGAAATAGGT
58839952 TGTTGAAGTGAACTACATAATCAATTCATTGTCTCATCTGCTTCTTATTCTTTACTATTTCTTAT
196 TGTTGAAGTGAACTACATAATCAATTCATTGTCTCATCTGCTTCTTATTCTTTACTATTTCTTAT
*
58840017 TATTTCATTAACATTGCAACCAAACTTGTGCATTTTCAAACTCACTATAAGTTGG
261 TATTTCATTAACATTGCAACCAAACTTGTGCACTTTCAAACTCACTATAAGTTGG
58840072 ATGACTAATA
Statistics
Matches: 309, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
343 309 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (343 bp):
CATTTTATAGGAGAGTGATATTTATCTTTGCTTGAAATAGTAGTTTTAAGGGAGAGTGAATGTAA
ACAAATTGTGCAACTTTGAGGCAACAAATATCCTTGGCGTGTTTGGATAGATTAGGTTGGTTATG
AAAGGTTGTACTATGAAAATTATATAGGGGATTCATTCTCTGAATAAGATTCTACAGAAATAGGT
TGTTGAAGTGAACTACATAATCAATTCATTGTCTCATCTGCTTCTTATTCTTTACTATTTCTTAT
TATTTCATTAACATTGCAACCAAACTTGTGCACTTTCAAACTCACTATAAGTTGGTAGTTTCAAA
CTCACTTTCAAACTTGTG
Found at i:58858163 original size:17 final size:18
Alignment explanation
Indices: 58858128--58858165 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
58858118 ATAATCTTTT
* *
58858128 AAATAATAATATACGATA
1 AAATAATAATAAACAATA
58858146 AAATAAT-ATAAACAATA
1 AAATAATAATAAACAATA
58858163 AAA
1 AAA
58858166 ATCAGCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATAATAATAAACAATA
Found at i:58862157 original size:79 final size:82
Alignment explanation
Indices: 58862046--58862230 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
58862036 GCTACTCGTT
* *
58862046 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
58862109 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
58862126 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
58862189 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
58862206 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
58862231 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:58862230 original size:40 final size:40
Alignment explanation
Indices: 58862027--58862230 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
58862017 CGGAATTTAA
** *
58862027 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
58862067 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
58862107 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
58862146 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
58862186 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
58862226 CCGGA
1 CCGGA
58862231 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:58877700 original size:26 final size:26
Alignment explanation
Indices: 58877664--58877724 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
58877654 ACATATTTTC
58877664 TCAAAATTTTA-CCAGGGGAAAAATCA
1 TCAAAATTTTACCCA-GGGAAAAATCA
* *
58877690 TCAAAATTTTACCCAGGGTAAAATCT
1 TCAAAATTTTACCCAGGGAAAAATCA
58877716 TC-AAATTTT
1 TCAAAATTTT
58877725 GCTGGGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 7 0.22
26 22 0.69
27 3 0.09
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (26 bp):
TCAAAATTTTACCCAGGGAAAAATCA
Found at i:58888398 original size:34 final size:34
Alignment explanation
Indices: 58888355--58888422 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
58888345 TCACTAAGTC
58888355 TGCGAAACAGGAAGATAATGACCCACTCACATAT
1 TGCGAAACAGGAAGATAATGACCCACTCACATAT
58888389 TGCGAAACAGGAAGATAATGACCCACTCACATAT
1 TGCGAAACAGGAAGATAATGACCCACTCACATAT
58888423 GACGAAGCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (34 bp):
TGCGAAACAGGAAGATAATGACCCACTCACATAT
Found at i:58895252 original size:11 final size:11
Alignment explanation
Indices: 58895211--58895252 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 11
58895201 ATCGAAAATG
58895211 ATCAAAA-TTA
1 ATCAAAATTTA
58895221 ATCAAAATTTA
1 ATCAAAATTTA
58895232 TTAT-AAAATTTA
1 --ATCAAAATTTA
58895244 ATCAAAATT
1 ATCAAAATT
58895253 CAACATGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 9 0.32
11 9 0.32
12 8 0.29
13 2 0.07
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (11 bp):
ATCAAAATTTA
Found at i:58895960 original size:8 final size:8
Alignment explanation
Indices: 58895945--58895999 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
58895935 ACATATGCTC
58895945 TCTTTTTT
1 TCTTTTTT
*
58895953 T-ATTTTT
1 TCTTTTTT
58895960 TCTTTGTTTT
1 TC-TT-TTTT
*
58895970 TCTTTCTT
1 TCTTTTTT
*
58895978 TCTTTCTT
1 TCTTTTTT
58895986 TCTTTTTT
1 TCTTTTTT
58895994 T-TTTTT
1 TCTTTTT
58896000 GAAGAGATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
7 11 0.28
8 20 0.50
9 3 0.08
10 6 0.15
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.84
Consensus pattern (8 bp):
TCTTTTTT
Found at i:58895979 original size:18 final size:17
Alignment explanation
Indices: 58895949--58896000 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
58895939 ATGCTCTCTT
58895949 TTTTTATTTTTTCTTTG
1 TTTTTATTTTTTCTTTG
* *
58895966 TTTTTCTTTCTTTCTTTC
1 TTTTTATTT-TTTCTTTG
*
58895984 TTTCTT-TTTTTTTTTTG
1 TTT-TTATTTTTTCTTTG
58896001 AAGAGATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 14 0.48
18 13 0.45
19 2 0.07
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.83
Consensus pattern (17 bp):
TTTTTATTTTTTCTTTG
Found at i:58899966 original size:25 final size:26
Alignment explanation
Indices: 58899938--58899996 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
58899928 TAAGCACCTC
* *
58899938 CGAGCTGAATAACC-GTAAGCTCATG
1 CGAGCTGAAGAACCGGTAAGCTCATA
*
58899963 CGAGCTG-AGAACCGGTAATCTCATA
1 CGAGCTGAAGAACCGGTAAGCTCATA
*
58899988 CGAGTTGAA
1 CGAGCTGAA
58899997 ATCGATAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 5 0.18
25 22 0.79
26 1 0.04
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (26 bp):
CGAGCTGAAGAACCGGTAAGCTCATA
Found at i:58905393 original size:3 final size:3
Alignment explanation
Indices: 58905365--58905431 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
58905355 AAAATCCATC
* * *
58905365 ATA ATA GTA ATA AGA CTA AGTA ATA ATA AT- ATA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
58905409 ATA ATA A-A ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
58905432 CTAACTAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 6 0.11
3 45 0.83
4 3 0.06
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:58905417 original size:17 final size:17
Alignment explanation
Indices: 58905385--58905431 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
58905375 TAAGACTAAG
58905385 TAATAATAAT-ATAAAA
1 TAATAATAATAATAAAA
58905401 TAATAATAATAATAAAA
1 TAATAATAATAATAAAA
58905418 TAATAATAATAATA
1 TAATAATAATAATA
58905432 CTAACTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAATAATAATAATAAAA
Found at i:58905547 original size:3 final size:3
Alignment explanation
Indices: 58905541--58905596 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
58905531 AAAACAAATC
*
58905541 ATA ATA A-A TATA ATA ACA A-A ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
58905585 ATA ATA ATA ATA
1 ATA ATA ATA ATA
58905597 GACAGTGGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
2 3 0.06
3 45 0.92
4 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:58906719 original size:8 final size:8
Alignment explanation
Indices: 58906702--58906735 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
58906692 TTTTTTTAAA
58906702 ATTTAATT
1 ATTTAATT
*
58906710 ATTTAGTT
1 ATTTAATT
58906718 ATTTAATT
1 ATTTAATT
58906726 AATTTAATT
1 -ATTTAATT
58906735 A
1 A
58906736 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (8 bp):
ATTTAATT
Found at i:58919285 original size:12 final size:12
Alignment explanation
Indices: 58919268--58919293 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58919258 AACATCACCA
58919268 AAATAAATGTCC
1 AAATAAATGTCC
58919280 AAATAAATGTCC
1 AAATAAATGTCC
58919292 AA
1 AA
58919294 TGTCCATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (12 bp):
AAATAAATGTCC
Found at i:58922187 original size:26 final size:27
Alignment explanation
Indices: 58922158--58922216 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
58922148 GAAAGAAACT
* * **
58922158 AAAAGAATAAAATCTACTTTAAAAA-G
1 AAAAGAAGAAAACCTAAATTAAAAATG
58922184 AAAAG-AGAAAACCTAAATTAAAAATG
1 AAAAGAAGAAAACCTAAATTAAAAATG
58922210 AAAAGAA
1 AAAAGAA
58922217 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 15 0.56
26 11 0.41
27 1 0.04
ACGTcount: A:0.66, C:0.07, G:0.10, T:0.17
Consensus pattern (27 bp):
AAAAGAAGAAAACCTAAATTAAAAATG
Found at i:58923086 original size:6 final size:6
Alignment explanation
Indices: 58923075--58923237 Score: 326
Period size: 6 Copynumber: 27.2 Consensus size: 6
58923065 GTTATAAAAT
58923075 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
58923123 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
58923171 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
58923219 TATATG TATATG TATATG T
1 TATATG TATATG TATATG T
58923238 TTAGGACAAA
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 157 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:58933392 original size:19 final size:19
Alignment explanation
Indices: 58933368--58933442 Score: 96
Period size: 19 Copynumber: 3.8 Consensus size: 19
58933358 AATCATCTAT
58933368 TCCAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
58933387 TCCAAGATTGCATATATCATA
1 TCCAAGATTGC--ATATCATA
*
58933408 TCTAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
* * *
58933427 GCTAAGAGTGCATATC
1 TCCAAGATTGCATATC
58933443 GTTGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:58933405 original size:21 final size:21
Alignment explanation
Indices: 58933368--58933422 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
58933358 AATCATCTAT
58933368 TCCAAGATTGC--ATATCATA
1 TCCAAGATTGCATATATCATA
58933387 TCCAAGATTGCATATATCATA
1 TCCAAGATTGCATATATCATA
*
58933408 TCTAAGATTGCATAT
1 TCCAAGATTGCATAT
58933423 CATAGCTAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 11 0.33
21 22 0.67
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (21 bp):
TCCAAGATTGCATATATCATA
Found at i:58933864 original size:44 final size:44
Alignment explanation
Indices: 58933815--58934155 Score: 391
Period size: 44 Copynumber: 7.8 Consensus size: 44
58933805 ACCAGTATGG
* * * * *
58933815 GAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * *
58933859 GAAGACAATATTTGCTTTCTTCGATCTACTT--CGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * * ***
58933901 GAAGACAAGATCTACTTTCTTCGAACTACTTCGCCACCAATATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
58933946 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * * * ***
58933990 GAAGACAAGATCTGCTTTCTTTGATCTCCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
58934035 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
58934079 GAAGACAAAATCTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
58934123 GAAGACAAGATCTGCT-TCCTTCGATCTACTTCA
1 GAAGACAAGATCTGCTAT-CTTCGATCTACTTCA
58934156 TGACAACCCA
Statistics
Matches: 246, Mismatches: 46, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
42 36 0.15
43 1 0.00
44 138 0.56
45 71 0.29
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
Found at i:58934008 original size:89 final size:89
Alignment explanation
Indices: 58933859--58934155 Score: 422
Period size: 89 Copynumber: 3.4 Consensus size: 89
58933849 GCCGATACAT
* * * *
58933859 GAAGACAATATTTGCTTTCTTCGATCTACTT--CGCCAATACATGAAGACAAGATCTACTTTCTT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
* *
58933922 CGAACTACTTCGCCACCAATATGG
66 TGATCTACTTCGCCACCAATATGG
58933946 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
* *
58934011 TGATCTCCTTCGCCACCAGTATGG
66 TGATCTACTTCGCCACCAATATGG
* *
58934035 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAAATCTGCTATCTT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
* * ***
58934100 TGATCTACTTC-ACGCCAATACAT
66 TGATCTACTTCGCCACCAATATGG
58934123 GAAGACAAGATCTGCT-TCCTTCGATCTACTTCA
1 GAAGACAAGATCTGCTAT-CTTCGATCTACTTCA
58934156 TGACAACCCA
Statistics
Matches: 190, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
87 29 0.15
88 37 0.19
89 124 0.65
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (89 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
TGATCTACTTCGCCACCAATATGG
Found at i:58934022 original size:131 final size:133
Alignment explanation
Indices: 58933785--58934154 Score: 503
Period size: 131 Copynumber: 2.8 Consensus size: 133
58933775 ATAAGACTTG
* * * *
58933785 TATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTACCTTTGATCTATTTCATG
1 TATCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACG
* * * *
58933850 CCGATACATGAAGACAATATTTGCTTTCTTCGATCTACTTCGCCA-A-TACATGAAGACAAGATC
66 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACAGTACAGGAAGACAAGATC
58933913 TAC
131 TAC
* * *
58933916 TTTCTTCGAACTACTTCGCCACCAATATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
1 TATCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACG
* * **
58933981 CCAATACATGAAGACAAGATCTGCTTTCTTTGATCTCCTTCGCCACCAGTATGGGAAGACAAGAT
66 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA-CAGTACAGGAAGACAAGAT
*
58934046 CTGC
130 CTAC
* * *** *
58934050 TATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAAATCTGCTATCTTTGATCTACTTCACG
1 TATCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACG
*
58934114 CCAATACATGAAGACAAGATCTGCTTCCTTCGATCTACTTC
66 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC
58934155 ATGACAACCC
Statistics
Matches: 208, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
131 98 0.47
133 79 0.38
134 31 0.15
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (133 bp):
TATCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACG
CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACAGTACAGGAAGACAAGATC
TAC
Found at i:58934220 original size:88 final size:88
Alignment explanation
Indices: 58934158--58935234 Score: 1557
Period size: 88 Copynumber: 12.2 Consensus size: 88
58934148 CTACTTCATG
* * * *
58934158 ACAACCCAAGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATC
58934223 TGCTATCTTCAACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* *
58934246 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGT-CTAGGAAGGCAAGAT
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATAC-AGGAAGGCAAGAT
58934310 CTGCTATCTTCAACCTGCTCCACT
65 CTGCTATCTTCAACCTGCTCCACT
* * * * *
58934334 ACGACCCAGGGAGGCAAGGCTGGTATCTTCGATCCGCTTCACTGTTGGTACAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATC
*
58934399 TGCTATCTTCAACTTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* * * *
58934422 ACAACCCAGGGAGGCAAGGCTGGTATCTTCAATCTGCTTCGCTGTCGATGCACGAAGGCAAGATA
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATC
58934487 TGCTATCTTCAACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* * *
58934510 ACAACCCAAGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATC
*
58934575 TACTATCTTCAACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
** *
58934598 ATGACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTC-AGTACAGGAAGGCAAGAT
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGA-TACAGGAAGGCAAGAT
*
58934662 CTGTTATCTTCAACCTGCTCCACT
65 CTGCTATCTTCAACCTGCTCCACT
** * * *
58934686 ATGACCCAGGGAGGCAAGGCTGGTATCTTCGAGCTACTTCGCTGTCGATTCAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATC
*
58934751 TGCTATCTTCAACCTACTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* * * *
58934774 ACAACCTAGGGAGGCAAGGCTGGTATCTTCGAGCTACTTCGCTGTCGATTCAGGAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATC
* *
58934839 TGCTATCTTCAACCTGCTTCATT
66 TGCTATCTTCAACCTGCTCCACT
* * ** *
58934862 ACAACCCAGGGAGGCAAGGCCGGTATCTTCGATCTGCCTCGCTGTCGATGTAGGAAGGCAATATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATC
58934927 TGCTATCTTCAACCTGCTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* * *
58934950 ACAACCTAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGAAAGGCAAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATC
*
58935015 TGCTATCTTCAACCTGCTCTACT
66 TGCTATCTTCAACCTGCTCCACT
** * *
58935038 ACAACTTAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCGAGATC
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATC
* *
58935103 TTCTATCTTCAACCTACTCCACT
66 TGCTATCTTCAACCTGCTCCACT
* * *
58935126 ACATCCCAGTGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCCGTC-AGTACAGGAAGGCAAGAT
1 ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGA-TACAGGAAGGCAAGAT
* * * *
58935190 TTGTTATTTTCAACCTGCTCCGCT
65 CTGCTATCTTCAACCTGCTCCACT
* * *
58935214 GCAAACCAGGAAGGCAAGGCT
1 ACAACCCAGGGAGGCAAGGCT
58935235 TTGTGATTTC
Statistics
Matches: 901, Mismatches: 83, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
87 2 0.00
88 897 1.00
89 2 0.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (88 bp):
ACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATC
TGCTATCTTCAACCTGCTCCACT
Found at i:58934222 original size:176 final size:176
Alignment explanation
Indices: 58934034--58935234 Score: 953
Period size: 176 Copynumber: 6.8 Consensus size: 176
58934024 CACCAGTATG
* * * * * *
58934034 GGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAAATCTGCTATCT
1 GGAAGGCAAGATCTGCTATCTTCGATCTACTCCACGACAACACAGGAAGAC-AAAGCTGCTATCT
* * * * *
58934099 TTGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCT-TCCTTCGATCTACTTCA-TGACA
65 TCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTAT-CTTCAACCTACTCCACT-ACA
*
58934161 ACCCAAGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTACA
128 ACCCAAGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACA
* * * * * * * * *
58934210 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTT
1 GGAAGGCAAGATCTGCTATCTTCGATCTACTCCACGACAACACAGGAAGACAAAGCTGCTATCTT
* * ** * * *
58934275 CGATCTGCTTCACTGTCGGT-CTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGAC
66 CGATCTACTTCACTGCCAATAC-AGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTACAAC
* * *
58934339 CCAGGGAGGCAAGGCTGGTATCTTCGATCCGCTTCACTGTTGGTACA
130 CCAAGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACA
* * * * * * * *
58934386 GGAAGGCAAGATCTGCTATCTTC-AACTTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCT
1 GGAAGGCAAGATCTGCTATCTTCGATC-TACTCCACGACAACACAGGAAGACAAAGCTGCTATCT
* * * * * * * * * *
58934450 TCAATCTGCTTCGCTGTCGATGCACGAAGGCAAGATATGCTATCTTCAACCTGCTCCACTACAAC
65 TCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTACAAC
58934515 CCAAGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACA
130 CCAAGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACA
* * * * * ** * * * * *
58934562 GGAAGGCAAGATCTACTATCTTCAACCTGCTCCACTATGACCCAGGGAGGCAAGGCTGGTATCTT
1 GGAAGGCAAGATCTGCTATCTTCGATCTACTCCACGACAACACAGGAAGACAAAGCTGCTATCTT
* * * * * * **
58934627 CGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAACCTGCTCCACTATGACC
66 CGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTACAACC
* * * * * *
58934692 CAGGGAGGCAAGGCTGGTATCTTCGAGCTACTTCGCTGTCGATTCA
131 CAAGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACA
* * * * * * *
58934738 GGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAAC-CTAGGGAGGCAAGGCTGGTATCT
1 GGAAGGCAAGATCTGCTATCTTCGATCTACTCCACGACAACAC-AGGAAGACAAAGCTGCTATCT
* * * * * * * * *
58934802 TCGAGCTACTTCGCTGTCGATTCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTTCATTACAAC
65 TCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTACAAC
* * * * * **
58934867 CCAGGGAGGCAAGGCCGGTATCTTCGATCTGCCTCGCTGTCGATGTA
130 CCAAGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACA
* * * * * * * * *
58934914 GGAAGGCAATATCTGCTATCTTCAACCTGCTCCACTACAAC-CTAGGGAGGCAAGGCTGGTATCT
1 GGAAGGCAAGATCTGCTATCTTCGATCTACTCCACGACAACAC-AGGAAGACAAAGCTGCTATCT
* * * * * * * * *
58934978 TCGATCTGCTTCGCTGTCGATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAC
65 TCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTACAAC
** * * * *
58935043 TTAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATGCA
130 CCAAGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACA
* * * * * * * * * *
58935090 GGAAGGCGAGATCTTCTATCTTCAACCTACTCCACTACATCCCAGTG-AGGCAAGGCTGGTATCT
1 GGAAGGCAAGATCTGCTATCTTCGATCTACTCCACGACAACACAG-GAAGACAAAGCTGCTATCT
* * * * * * * * * * * * *
58935154 TCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATTTGTTATTTTCAACCTGCTCCGCTGCAAA
65 TCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTACAAC
58935219 CC-AGGAAGGCAAGGCT
130 CCAAGG-AGGCAAGGCT
58935235 TTGTGATTTC
Statistics
Matches: 898, Mismatches: 116, Indels: 22
0.87 0.11 0.02
Matches are distributed among these distances:
175 28 0.03
176 863 0.96
177 7 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (176 bp):
GGAAGGCAAGATCTGCTATCTTCGATCTACTCCACGACAACACAGGAAGACAAAGCTGCTATCTT
CGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTACAACC
CAAGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGGTACA
Found at i:58936845 original size:10 final size:10
Alignment explanation
Indices: 58936830--58936854 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
58936820 CTTGGAAGAG
58936830 TTTTTTCTTT
1 TTTTTTCTTT
58936840 TTTTTTCTTT
1 TTTTTTCTTT
58936850 TTTTT
1 TTTTT
58936855 GCACCATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:58942160 original size:19 final size:19
Alignment explanation
Indices: 58942136--58942187 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
58942126 TCATATCTTT
58942136 CAAGATTGCATATCATATC
1 CAAGATTGCATATCATATC
58942155 CAAGATTGCATATCATATC
1 CAAGATTGCATATCATATC
58942174 CAAGATTGCATATC
1 CAAGATTGCATATC
58942188 CTTAAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.31
Consensus pattern (19 bp):
CAAGATTGCATATCATATC
Found at i:58943343 original size:18 final size:18
Alignment explanation
Indices: 58943309--58943343 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58943299 AAGAAGTGAT
* *
58943309 AAAAAAAGATACAAAAAC
1 AAAAAAAAATAAAAAAAC
58943327 AAAAAAAAATAAAAAAA
1 AAAAAAAAATAAAAAAA
58943344 ATTATGTGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.86, C:0.06, G:0.03, T:0.06
Consensus pattern (18 bp):
AAAAAAAAATAAAAAAAC
Done.