Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold482
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: 210603
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 22842 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:129793 original size:23 final size:24
Alignment explanation
Indices: 129758--129807 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 24
129748 AATTTTGAAA
129758 TCTGAAAAGTAAAAA-GACTAAAAT
1 TCTGAAAAGTAAAAAGGACT-AAAT
129782 TCTGAAAA-TAAAAAGGACTAAAT
1 TCTGAAAAGTAAAAAGGACTAAAT
129805 TCT
1 TCT
129808 AAATCTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
TCTGAAAAGTAAAAAGGACTAAAT
Found at i:133019 original size:16 final size:16
Alignment explanation
Indices: 132995--133025 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
132985 TAGGGTTTAA
132995 AAAAATTATTAAATTC
1 AAAAATTATTAAATTC
*
133011 AAAACTTATTAAATT
1 AAAAATTATTAAATT
133026 TACATATTTA
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:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAAATTATTAAATTC
Found at i:133666 original size:48 final size:48
Alignment explanation
Indices: 133607--133703 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
133597 GGAAAATTCT
*
133607 AATCTTACAGTAAATTTATAAATCGTATCATTTCAGGGAAAATAAGAA
1 AATCTTACAGTAAATTTATAAATCATATCATTTCAGGGAAAATAAGAA
133655 AATCTTACAGTAAATTTATAAATCATATCATTTCAGGGAAAATAAGAA
1 AATCTTACAGTAAATTTATAAATCATATCATTTCAGGGAAAATAAGAA
133703 A
1 A
133704 CAATCATAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.31
Consensus pattern (48 bp):
AATCTTACAGTAAATTTATAAATCATATCATTTCAGGGAAAATAAGAA
Found at i:134654 original size:28 final size:28
Alignment explanation
Indices: 134623--134676 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
134613 ATAAATTTTG
134623 AATTT-TTTATAAATATTTTAAAATTTAA
1 AATTTATTT-TAAATATTTTAAAATTTAA
*
134651 AATTTATTTTAAATTTTTTAAAATTT
1 AATTTATTTTAAATATTTTAAAATTT
134677 TTTGATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
AATTTATTTTAAATATTTTAAAATTTAA
Found at i:134672 original size:21 final size:21
Alignment explanation
Indices: 134617--134676 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
134607 AAAAATATAA
*
134617 ATTTTGAATTTTTTATAAA--T
1 ATTTTAAATTTTTTA-AAATTT
*
134637 ATTTTAAA--ATTTAAAATTT
1 ATTTTAAATTTTTTAAAATTT
134656 ATTTTAAATTTTTTAAAATTT
1 ATTTTAAATTTTTTAAAATTT
134677 TTTGATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 3 0.09
18 4 0.12
19 9 0.27
20 7 0.21
21 10 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTAAATTTTTTAAAATTT
Found at i:134688 original size:28 final size:27
Alignment explanation
Indices: 134618--134688 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
134608 AAAATATAAA
134618 TTTTGAATTTTTTATAAATATTTTAAAAT
1 TTTTG-ATTTTTT-TAAATATTTTAAAAT
*** *
134647 TTAAAATTTATTTTAAATTTTTTAAAATT
1 TTTTGATTT-TTTTAAATATTTTAAAA-T
134676 TTTTGATTTTTTT
1 TTTTGATTTTTTT
134689 TGTAATTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
28 21 0.64
29 12 0.36
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (27 bp):
TTTTGATTTTTTTAAATATTTTAAAAT
Found at i:136216 original size:19 final size:17
Alignment explanation
Indices: 136184--136218 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
136174 TGTTTAAAAT
136184 TCTATTTAAATAATAAC
1 TCTATTTAAATAATAAC
136201 TCTACTTTACAATAATAA
1 TCTA-TTTA-AATAATAA
136219 AATTAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (17 bp):
TCTATTTAAATAATAAC
Found at i:136726 original size:122 final size:122
Alignment explanation
Indices: 136309--136689 Score: 762
Period size: 122 Copynumber: 3.1 Consensus size: 122
136299 ATTTAAATTT
136309 TAATTATTTTTAAATATATAATTCTCACCATTTTTATTACATTATAATTTTTCAATGTTTTAATT
1 TAATTATTTTTAAATATATAATTCTCACCATTTTTATTACATTATAATTTTTCAATGTTTTAATT
136374 ATCATAACTTATATTTCATTTAAGCTTATTTAACTAATAATTTTAAATTAAATATCA
66 ATCATAACTTATATTTCATTTAAGCTTATTTAACTAATAATTTTAAATTAAATATCA
136431 TAATTATTTTTAAATATATAATTCTCACCATTTTTATTACATTATAATTTTTCAATGTTTTAATT
1 TAATTATTTTTAAATATATAATTCTCACCATTTTTATTACATTATAATTTTTCAATGTTTTAATT
136496 ATCATAACTTATATTTCATTTAAGCTTATTTAACTAATAATTTTAAATTAAATATCA
66 ATCATAACTTATATTTCATTTAAGCTTATTTAACTAATAATTTTAAATTAAATATCA
136553 TAATTATTTTTAAATATATAATTCTCACCATTTTTATTACATTATAATTTTTCAATGTTTTAATT
1 TAATTATTTTTAAATATATAATTCTCACCATTTTTATTACATTATAATTTTTCAATGTTTTAATT
136618 ATCATAACTTATATTTCATTTAAGCTTATTTAACTAATAATTTTAAATTAAATATCA
66 ATCATAACTTATATTTCATTTAAGCTTATTTAACTAATAATTTTAAATTAAATATCA
136675 TAATTATTTTTAAAT
1 TAATTATTTTTAAAT
136690 GTAAATTTAA
Statistics
Matches: 259, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 259 1.00
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (122 bp):
TAATTATTTTTAAATATATAATTCTCACCATTTTTATTACATTATAATTTTTCAATGTTTTAATT
ATCATAACTTATATTTCATTTAAGCTTATTTAACTAATAATTTTAAATTAAATATCA
Found at i:156913 original size:84 final size:85
Alignment explanation
Indices: 156798--156977 Score: 332
Period size: 84 Copynumber: 2.2 Consensus size: 85
156788 TTATAAATTT
156798 ATAA-TAAATTA--GTTTAGGGTTTAGTGTTTTAGAGTTTTTAAGTAAAAACTCAAATGAATTAG
1 ATAATTAAATTATTGTTTAGGGTTTAGTGTTTTAGAGTTTTTAAGTAAAAACTCAAATGAATTAG
156860 GATTTGGGGTTTACGATTAC
66 GATTTGGGGTTTACGATTAC
156880 ATAATTAAATTATTGTTTAGGG-TTAGTGTTTTAGAGTTTTTAAGTAAAAACTCAAATGAATTAG
1 ATAATTAAATTATTGTTTAGGGTTTAGTGTTTTAGAGTTTTTAAGTAAAAACTCAAATGAATTAG
156944 GATTTGGGGTTTACGATTAC
66 GATTTGGGGTTTACGATTAC
156964 ATAATTAAATTATT
1 ATAATTAAATTATT
156978 AATTTAAAGA
Statistics
Matches: 95, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
82 4 0.04
83 7 0.07
84 76 0.80
85 8 0.08
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (85 bp):
ATAATTAAATTATTGTTTAGGGTTTAGTGTTTTAGAGTTTTTAAGTAAAAACTCAAATGAATTAG
GATTTGGGGTTTACGATTAC
Found at i:157219 original size:126 final size:126
Alignment explanation
Indices: 156987--157270 Score: 397
Period size: 126 Copynumber: 2.3 Consensus size: 126
156977 TAATTTAAAG
* * * * * * *
156987 AAGCTCCCATGTGGACGCTCTTTTACTACAGTGGCTCCTGAGAAAATAATTTCGAGTAGACGTTT
1 AAGCTCACACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGACGTTT
* *
157052 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAAGATACTTTGTCAGCAGAAGTATTGAAAA
66 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAAGATACTTTGTCAACAGAAGTACTGAAAA
* * * *
157113 AAGCTTACACGTGGACGCGCTTTTGCTACAGTAGCTCTTAAAAAAATAATTTTGAGTAGATGTTT
1 AAGCTCACACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGACGTTT
* * * * *
157178 CTGAGCGAACAGTGTCAAAAATGCTTTAAGTAGGATGCTTTGTCAACAGAAGTACTGAAAG
66 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAAGATACTTTGTCAACAGAAGTACTGAAAA
*
157239 AAGCTCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCTCACACGTGGACGCGCTTTTGCTACAGT
157271 GGCGCATGGC
Statistics
Matches: 138, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
126 138 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (126 bp):
AAGCTCACACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGACGTTT
CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAAGATACTTTGTCAACAGAAGTACTGAAAA
Found at i:160617 original size:21 final size:21
Alignment explanation
Indices: 160591--160635 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
160581 TCGTCTAGCT
*
160591 TCCGGCAGGGG-TTGTGGTTGC
1 TCCGGC-GGGGATTGTGGTTCC
*
160612 TCCGGCGGGGATTTTGGTTCC
1 TCCGGCGGGGATTGTGGTTCC
160633 TCC
1 TCC
160636 AGTAGGGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.04, C:0.24, G:0.40, T:0.31
Consensus pattern (21 bp):
TCCGGCGGGGATTGTGGTTCC
Found at i:162789 original size:11 final size:12
Alignment explanation
Indices: 162773--162825 Score: 67
Period size: 11 Copynumber: 4.7 Consensus size: 12
162763 TTAAATAGGG
162773 ATTTGAGA-GAA
1 ATTTGAGAGGAA
162784 ATTTGAGAGGAA
1 ATTTGAGAGGAA
*
162796 A-TTGAGAGCAA
1 ATTTGAGAGGAA
162807 A-TTGAGAGGAA
1 ATTTGAGAGGAA
*
162818 ATTAGAGA
1 ATTTGAGA
162826 AAGGATTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.45, C:0.02, G:0.30, T:0.23
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:162803 original size:22 final size:21
Alignment explanation
Indices: 162775--162827 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
162765 AAATAGGGAT
162775 TTGAGAGAAATTTGAGAGGAAA
1 TTGAGAGAAA-TTGAGAGGAAA
162797 TTGAGAGCAAATTGAGAGGAAA
1 TTGAGAG-AAATTGAGAGGAAA
162819 TT-AGAGAAA
1 TTGAGAGAAA
162828 GGATTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.10
21 4 0.13
22 20 0.67
23 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.30, T:0.21
Consensus pattern (21 bp):
TTGAGAGAAATTGAGAGGAAA
Found at i:164380 original size:25 final size:25
Alignment explanation
Indices: 164334--164382 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
164324 ATTATATATT
* * * *
164334 AAATATTTATTTTTTATTTTTAATC
1 AAATATATATTATATATATTTAATC
164359 AAATATATATTATATATATTTAAT
1 AAATATATATTATATATATTTAAT
164383 ATGGGCCGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATATATATTATATATATTTAATC
Found at i:166499 original size:11 final size:11
Alignment explanation
Indices: 166485--166523 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
166475 GTTTTCTCCA
166485 TATTTTACTAT
1 TATTTTACTAT
166496 TATTTTACTAT
1 TATTTTACTAT
* * *
166507 TATGTTGCTAC
1 TATTTTACTAT
166518 TATTTT
1 TATTTT
166524 GTTGTTATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (11 bp):
TATTTTACTAT
Found at i:166595 original size:30 final size:30
Alignment explanation
Indices: 166561--166623 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
166551 ACTTATTTTA
166561 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* *
166591 TTGTTGATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
166621 TTG
1 TTG
166624 CTTATTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:166728 original size:10 final size:11
Alignment explanation
Indices: 166711--166735 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
166701 TTTTATTTTG
166711 ATTTTTTTAGT
1 ATTTTTTTAGT
166722 ATTTTTTTAGT
1 ATTTTTTTAGT
166733 ATT
1 ATT
166736 ATATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (11 bp):
ATTTTTTTAGT
Found at i:171285 original size:23 final size:21
Alignment explanation
Indices: 171243--171285 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
171233 GAATAATAGT
*
171243 AATACAAATAACAAATACAAC
1 AATACAAATAACAAAGACAAC
*
171264 AATACGAATATAACAACGACAA
1 AATAC-AA-ATAACAAAGACAA
171286 TGCATATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 2 0.11
23 11 0.61
ACGTcount: A:0.63, C:0.19, G:0.05, T:0.14
Consensus pattern (21 bp):
AATACAAATAACAAAGACAAC
Found at i:172813 original size:44 final size:43
Alignment explanation
Indices: 172654--175309 Score: 578
Period size: 44 Copynumber: 59.7 Consensus size: 43
172644 ACAAATCTCT
* * *
172654 TCTCTCTGAAGTTGCAGTAGAGCAGA-T-CATAT-CAAACTTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACAATC-TTA
* * * * *
172695 TCTCTCTGAAGTTGCAGTAGAGCAGGTTGATATAGAAAACCTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGA-AGATACAATCTTA
* *
172739 TC-CCCATGAAGTTGCAGTGGAGCA-AGTTGAAGATACAAGTCTTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAGA-TTGAAGATACAA-TCTTA
* * *
172783 TCTCTCTGAAGTTGCAGTAAAGCAGATTGAAGTTACTAATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAC-AATCTTA
* * * * * *
172827 CCTCCCTGAAGTTGCAGTGGAGCAAATT-AAAATA-ATGGATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACA---ATCTTA
* * * *
172871 TCTAC-CTGAATTTGCAAT-GAAGCAGATTAAAGATAGCAAATCGTA
1 TCT-CTCTGAAGTTGCAGTAG-AGCAGATTGAAGATA-C-AATCTTA
* * * * * * * * **
172916 TTTCCCTAAAGTTGCAGTGGAACAAATTAAATCTACCATAACAGATCTCG
1 TCTCTCTGAAGTTGCAGTAGAGCAGATT-GA---A-GAT-ACA-ATCTTA
* * * * *
172966 TCTCTCTGATGTTGCAGTAGAGTAGA-T-CATAT-CAAACTTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACAATC-TTA
* * * *
173007 TCTCTTTGAAGTTGCAGCAGAGCAGGTTGAA-ATAGCAAACCTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-C-AATCTTA
* *
173051 TCTC-CATGAAGTTGCAGTAGGGCA-AGTTGAAGACACAAGTCTTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAGA-TTGAAGATACAA-TCTTA
* * * * * * *
173095 TCTCCCTAAAATTGCAGTGGAGCATATTGAAGTTACTAATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAC-AATCTTA
* * * * ** *
173139 CCTCCCTGAAGTTGCAGTGGAGC-GAATT-AAAATGATGGATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAG-ATTGAAGAT-A-CAATCTTA
* * * *
173183 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGAAAAT-TGTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGAT--ACAATCT-TA
* * * * * **
173228 T-TTTCTTGAAGTTGCAGTGGAACAGATTAAATCTACCATAACAAATCTCG
1 TCTCTC-TGAAGTTGCAGTAGAGCAGATT-GA---A-GAT-AC-AATCTTA
* * *
173278 TCTCTCTGAAGTTGCAGTAGAGCAGA-T-CATAT-CAAACTTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACAATC-TTA
* *
173319 TCTCTCTGAAGTTGCAGTAGAGCAGGTTGAA-ATAGCAAACATTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-CAATC-TTA
* * * *
173363 TC-CCCATGAAGTTGCAATGGGGCA-AGTTGAAGATACAAGTCTTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAGA-TTGAAGATACAA-TCTTA
* * * * *
173407 TTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAC-AATCTTA
* * * * * **
173451 CCAC-CTTAAAGTTGCAGTGGAGC-GAATT-AACATGATGGATCTTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAG-ATTGAAGAT-A-CAATCTTA
* * * *
173495 TCTC-CTTGAAGTTGCAGTTGAGCAAATTAAAGATAGCAAGTCGTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAGATTGAAGATA-CAA-TCTTA
* * * * ** * * **
173540 TTTCCCTGAAGTTGTAGTGGAATAGATTAAATCTACCATAACAGATCTCG
1 TCTCTCTGAAGTTGCAGTAGAGCAGATT-GA---A-GAT-ACA-ATCTTA
* * *
173590 TCTCTCTGAAGTTGCAGTAGAGCAGA-T-CATAT-CAAACTTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACAATC-TTA
* * * *
173631 TCTCTCTAAAGTTACAGTAGAGCAGGTTGAA-ATAGCAAACCTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-C-AATCTTA
* * * * * * *
173675 TCCCTATAAAATTGTAGTGGGGCA-AGTTGAAGATACAAGTCTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGA-TTGAAGATACAA-TCTTA
* * * * *
173719 TCTCCCTGAAATTGCAGTGGAGCAGATTGAAGTTACTAATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAC-AATCTTA
* * * * * * ** *
173763 CCTCCCTGAAGTTACAGTGGAGCAAATT-AAAATGATGGATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGAT-A-CAATCTTA
* * * * * *
173807 TCTCCCTGAATTTGCAATGGAGCAGATTAAAGATAGCAAATCGTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-C-AATCTTA
* * * * * * * ** * *
173852 TTTCCCTAAAGTTGTAGTGGAACAGATTAAATCTACCATAATAGATCTG
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-C--AAT--CT-TA
* * * * *
173901 TCTCTCTGATGTTGCAGTAGAGTAGA-T-CATAT-CAAACTTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACAATC-TTA
* * *
173942 TCTCTCTAAAGTTGCAGTAGAGCAGGTTGAA-ATAGCAAACCTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-C-AATCTTA
* * *
173986 TCTC-CATGAAGTTGCAGTAGGGCA-AGTTGAAGACAGAAGTCTTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAGA-TTGAAGATACAA-TCTTA
* * * * * *
174030 TCTCCCTAAAGTTGCAGTGGAGCATATTGAAGTTACTAATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAC-AATCTTA
* * * ** ** *
174074 TCTCTCTAAAGTTGCAGTGGAGCGAAATAAAATGAT-GGATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGC-AGATTGAA-GATACAATCTTA
* * * * *
174118 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGAAAATTTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGAT--ACAATCTTA
* * * * * * **
174163 T-TTTCCTGAAGTTGCAGTGGAACAGATTAAATCTACCATAACAGATATCG
1 TCTCT-CTGAAGTTGCAGTAGAGCAGATT-GA---A-GAT-ACA-ATCTTA
* * * * *
174213 TCTCTCTGAAGTTGCAGTAGATCAG-GT-CATAT-CAAACTTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACAATC-TTA
* * *
174254 TCTCTCTGAAGTTGTAGTAGAGCAGGTTGAA-ATAGCAAACCTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-C-AATCTTA
* * *
174298 TC-CCCATGAAGTTGCAGTGGGGCA-AGTTGAAGATACAAGTCTTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAGA-TTGAAGATACAA-TCTTA
* * * * *
174342 TTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAC-AATCTTA
* * * * ** *
174386 CCTCCCTGAAGTTGCAGTGGAGC-GAATT-AACATGATGGATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAG-ATTGAAGAT-A-CAATCTTA
* * * * *
174430 TCTC-CTTGAAGTTGCAGTGGAACAAATTAAAGATAGCAAATCGTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAGATTGAAGATA-C-AATCTTA
* * * ** * * **
174475 TTTCCCTGAAGTTGTAGTAGAATAGATTAAATCTACCATAACAGATCTCG
1 TCTCTCTGAAGTTGCAGTAGAGCAGATT-GA---A-GAT-ACA-ATCTTA
* * *
174525 TCTCTCTGAAGTTGCAGTAGAGCAGA-T-CATAT-CAAACTTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACAATC-TTA
* * *
174566 TCTCTCTGAAGTTACAGTAGAGCAGGTTGAA-ATAGCAAACCTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-C-AATCTTA
* * *
174610 TC-CCCATGAAGTTGCAGTGGGGCA-AGTTGAAGATACAAGTCTTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAGA-TTGAAGATACAA-TCTTA
* * * * * *
174654 TCTCCCTGAAATTACAGTGGAGCAGATTGAAGTTACTAATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAC-AATCTTA
* * * * * ** *
174698 CCTCCCTGAAGTTGTAGTGGAACAGATT-AAGATGATGGATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGAT-A-CAATCTTA
* * *
174742 TCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGATAGCAAATCGTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-C-AATCTTA
* * * * ** **
174787 TTTCCCTGAAGTTGCAGTAGAACAGAGTAAATCTACCATAACAGATCTCG
1 TCTCTCTGAAGTTGCAGTAGAGCAGA-T---T-GAAGAT-ACA-ATCTTA
* * * *
174837 TCTCTCTGAAGTTGCAGTAGAGTAGA-T-CATAT-CAAACTTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACAATC-TTA
* * * *
174878 TCTCTCTGAAATTACAGTAGAGCAGGTTGAA-ATAGCAAACCTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-C-AATCTTA
* * * *
174922 TC-CCCATGAAGTTGTAGTGGGGCA-AGTTGAAGATACAAGTCTTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAGA-TTGAAGATACAA-TCTTA
* * * * *
174966 TCTCCCTGAAATTGCAGTGGAGCAGATTGAAGTTACTAATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAC-AATCTTA
* * * * * ** *
175010 CCTCTCTGAAGTTGTAGTGGAACGGATT-AAGATGATGGATCCTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGAT-A-CAATCTTA
* * * * * *
175054 TCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGATAGTAAATCGTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA--CAATCTTA
* * * * * * *
175099 TTTCCCTGAAGTTGCAATAGAACAGATTAAATCTACCATAACAGATCTCA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATT-GA---A-GAT-ACA-ATCTTA
* * * *
175149 TCTCTCTGAAGTTACAGTAGAGCAGA-T-CATAT-CAAACTTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACAATC-TTA
* * *
175190 TCTCTCTGAAGTTACAGTAGAGCAGGTTGAA-ATAGCAACCCTTA
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATA-CAA-TCTTA
* * * *
175234 TC-CCCATAAAGTTGCAGTGGGGCA-AGTTGAAGATACAAGTCTTA
1 TCTCTC-TGAAGTTGCAGTAGAGCAGA-TTGAAGATACAA-TCTTA
* * * *
175278 TCTCCCTGAAATTGCAGTGGAGCATATTGAAG
1 TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAG
175310 TTATTAATCC
Statistics
Matches: 1960, Mismatches: 439, Indels: 429
0.69 0.16 0.15
Matches are distributed among these distances:
40 14 0.01
41 233 0.12
42 29 0.01
43 89 0.05
44 989 0.50
45 346 0.18
46 23 0.01
47 3 0.00
48 2 0.00
49 39 0.02
50 181 0.09
51 12 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
TCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATACAATCTTA
Found at i:173185 original size:312 final size:312
Alignment explanation
Indices: 172620--175529 Score: 4488
Period size: 312 Copynumber: 9.3 Consensus size: 312
172610 GCTATTACAG
* *
172620 GTGGAACAGATTAAATCTACCATAACAAATCTCTTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
1 GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
* *
172685 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGATATAGAAAACCTTATCCCCATGAAG
66 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
* * * **
172750 TTGCAGTGGAGCAAGTTGAAGATACAAGTCTTATCTCTCTGAAGTTGCAGTAAAGCAGATTGAAG
131 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
* * *
172815 TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATAATGGATCCTATCTACCTGA
196 TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATGATGGATCCTATCTCCCTGA
* * *
172880 ATTTGCAATGAAGCAGATTAAAGATAGCAAATCGTATTTCCCTAAAGTTGCA
261 AGTTGCAGTGAAGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
* * *
172932 GTGGAACAAATTAAATCTACCATAACAGATCTCGTCTCTCTGATGTTGCAGTAGAGTAGATCATA
1 GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
* * *
172997 TCAAACTTTATCTCTTTGAAGTTGCAGCAGAGCAGGTTGAAATAGCAAACCTTATCTCCATGAAG
66 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
* * * *
173062 TTGCAGTAGGGCAAGTTGAAGACACAAGTCTTATCTCCCTAAAATTGCAGTGGAGCATATTGAAG
131 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
173127 TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATGATGGATCCTATCTCCCTGA
196 TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATGATGGATCCTATCTCCCTGA
* * * * *
173192 AGTTGCAGTGGAGCAGATTAAAGATAGAAAATTGTATTTTCTTGAAGTTGCA
261 AGTTGCAGTGAAGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
*
173244 GTGGAACAGATTAAATCTACCATAACAAATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
1 GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
*
173309 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACATTATCCCCATGAAG
66 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
* * *
173374 TTGCAATGGGGCAAGTTGAAGATACAAGTCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
131 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
* * * * * *
173439 TTACTAATCCTACCACCTTAAAGTTGCAGTGGAGCGAATTAACATGATGGATCTTATCTCCTTGA
196 TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATGATGGATCCTATCTCCCTGA
* * *
173504 AGTTGCAGTTG-AGCAAATTAAAGATAGCAAGTCGTATTTCCCTGAAGTTGTA
261 AGTTGCAG-TGAAGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
*
173556 GTGGAATAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
1 GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
* * * * *
173621 TCAAACTTTATCTCTCTAAAGTTACAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCTATAAAA
66 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
*
173686 TTGTAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
131 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
* *
173751 TTACTAATCCTACCTCCCTGAAGTTACAGTGGAGCAAATTAAAATGATGGATCCTATCTCCCTGA
196 TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATGATGGATCCTATCTCCCTGA
* * * * *
173816 ATTTGCAATGGAGCAGATTAAAGATAGCAAATCGTATTTCCCTAAAGTTGTA
261 AGTTGCAGTGAAGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
* * *
173868 GTGGAACAGATTAAATCTACCATAATAGATCT-GTCTCTCTGATGTTGCAGTAGAGTAGATCATA
1 GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
* *
173932 TCAAACTTTATCTCTCTAAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCTCCATGAAG
66 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
* * * *
173997 TTGCAGTAGGGCAAGTTGAAGACAGAAGTCTTATCTCCCT-AAAGTTGCAGTGGAGCATATTGAA
131 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAA-TTGCAGTGGAGCAGATTGAA
* * * *
174061 GTTACTAATCCTATCTCTCTAAAGTTGCAGTGGAGCGAAATAAAATGATGGATCCTATCTCCCTG
195 GTTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATGATGGATCCTATCTCCCTG
* * ** *
174126 AAGTTGCAGTGGAGCAGATTAAAGATAGAAAATTTTATTTTCCTGAAGTTGCA
260 AAGTTGCAGTGAAGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
* * *
174179 GTGGAACAGATTAAATCTACCATAACAGATATCGTCTCTCTGAAGTTGCAGTAGATCAGGTCATA
1 GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
*
174244 TCAAACTTTATCTCTCTGAAGTTGTAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
66 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
* *
174309 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
131 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
* *
174374 TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGAATTAACATGATGGATCCTATCTCCTTGA
196 TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATGATGGATCCTATCTCCCTGA
* *
174439 AGTTGCAGTGGAA-CAAATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGTA
261 AGTTGCAGT-GAAGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
* *
174491 GTAGAATAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
1 GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
*
174556 TCAAACTTTATCTCTCTGAAGTTACAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
66 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
*
174621 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAG
131 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
* * *
174686 TTACTAATCCTACCTCCCTGAAGTTGTAGTGGAAC-AGATTAAGATGATGGATCCTATCTCCCTG
196 TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGA-ATTAAAATGATGGATCCTATCTCCCTG
174750 AAGTTGCAGT-AGAGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
260 AAGTTGCAGTGA-AGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
* * *
174803 GTAGAACAGAGTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGTAGATCATA
1 GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
* *
174868 TCAAACTTTATCTCTCTGAAATTACAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
66 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
*
174933 TTGTAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
131 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
* * * * *
174998 TTACTAATCCTACCTCTCTGAAGTTGTAGTGGAACGGATTAAGATGATGGATCCTATCTCCCTGA
196 TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATGATGGATCCTATCTCCCTGA
* * *
175063 AGTTGTAGTGGAGCAGATTAAAGATAGTAAATCGTATTTCCCTGAAGTTGCA
261 AGTTGCAGTGAAGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
* * * *
175115 ATAGAACAGATTAAATCTACCATAACAGATCTCATCTCTCTGAAGTTACAGTAGAGCAGATCATA
1 GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
* * *
175180 TCAAACTTTATCTCTCTGAAGTTACAGTAGAGCAGGTTGAAATAGCAACCCTTATCCCCATAAAG
66 TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
*
175245 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCATATTGAAG
131 TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
* * * * * *
175310 TTATTAATCCTACCTTCCTGGAA-TTGCAGTGGAACGGATTAAGATGATGGATCCTATCTCCTTG
196 TTACTAATCCTACCTCCCT-GAAGTTGCAGTGGAGCGAATTAAAATGATGGATCCTATCTCCCTG
** * *
175374 AAGTTTTAGTGGAA-CAGATTAAAGATAGCGAATCGTATTTCCCTGAAGTTTCA
260 AAGTTGCAGT-GAAGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
* * *
175427 GTGGAACATATTAAATCTATCATAACAGATCTCATCT-TCCTGAAGTTGCAGTAGAGCAGATCAT
1 GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCT-CTGAAGTTGCAGTAGAGCAGATCAT
* * * * *
175491 ATCAAACCTTATCTCCCTGAAGTTTCAGTGGAGAAGGTT
65 ATCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTT
175530 AAACCAATCT
Statistics
Matches: 2388, Mismatches: 196, Indels: 28
0.91 0.08 0.01
Matches are distributed among these distances:
310 4 0.00
311 284 0.12
312 2089 0.87
313 11 0.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (312 bp):
GTGGAACAGATTAAATCTACCATAACAGATCTCGTCTCTCTGAAGTTGCAGTAGAGCAGATCATA
TCAAACTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAGCAAACCTTATCCCCATGAAG
TTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAG
TTACTAATCCTACCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATGATGGATCCTATCTCCCTGA
AGTTGCAGTGAAGCAGATTAAAGATAGCAAATCGTATTTCCCTGAAGTTGCA
Found at i:176269 original size:14 final size:11
Alignment explanation
Indices: 176236--176262 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
176226 GACACCACCT
176236 ACAAGAAGCCA
1 ACAAGAAGCCA
176247 ACAAGAAGCCA
1 ACAAGAAGCCA
176258 ACAAG
1 ACAAG
176263 CAGAAGCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.26, G:0.19, T:0.00
Consensus pattern (11 bp):
ACAAGAAGCCA
Found at i:176648 original size:7 final size:6
Alignment explanation
Indices: 176629--176659 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
176619 CGAAAGACCA
176629 TTCTTT TTCTTT TTCTTT TTCTTT TTACTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TT-CTTT
176660 CATTTCACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:179892 original size:114 final size:107
Alignment explanation
Indices: 179757--180028 Score: 305
Period size: 107 Copynumber: 2.5 Consensus size: 107
179747 CCTTTTTTTC
**
179757 CCAAATTTTTTTTTTACTTTTTTCGTATACTGGTGCTTGCCATTGAAACGA-AAAAAGTGAAAAA
1 CCAAATTTTTTTTTTACTTTTTTCGTATACTGGTGCCAGCCATTGAAA-GACAAAAAGT-AAAAA
* * *** *
179821 AAAACTTTTTTTTTACCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCA
64 AAAA---ATCTGGGA---A-AAAGGTGGTGCCGGCCATTAGCAGGCCACCA
* * * **
179872 CC-AATTTTTTTTTTACTTTTTTCTTATACTGGTGCCAGCAATTGACAGACCGAAAGTAAAAAAA
1 CCAAATTTTTTTTTTACTTTTTTCGTATACTGGTGCCAGCCATTGAAAGACAAAAAGTAAAAAAA
*
179936 AAATCTGGGAAAATGGTGGTGCCGGCCATTAGCAGGCCACCA
66 AAATCTGGGAAAAAGGTGGTGCCGGCCATTAGCAGGCCACCA
* *
179978 CCAAATTTTTTTTTTACTTTTTTCGTATTCTGGTGCCAGCCATTGACAGAC
1 CCAAATTTTTTTTTTACTTTTTTCGTATACTGGTGCCAGCCATTGAAAGAC
180029 CAATACCCGA
Statistics
Matches: 138, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
106 31 0.22
107 46 0.33
110 3 0.02
113 11 0.08
114 45 0.33
115 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (107 bp):
CCAAATTTTTTTTTTACTTTTTTCGTATACTGGTGCCAGCCATTGAAAGACAAAAAGTAAAAAAA
AAATCTGGGAAAAAGGTGGTGCCGGCCATTAGCAGGCCACCA
Found at i:181928 original size:42 final size:42
Alignment explanation
Indices: 181860--181953 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
181850 ACGAAAAGGA
* *
181860 AAGAAGGGAGCAACACAAGGTCCTTAGAAATGCTTGCAAGTG
1 AAGAAGGGAGCAACACAAGGTCCTTAGAAATACTTACAAGTG
* * * * *
181902 AAGAAGGGAGCAGCACAGGGTTCTTAGAGATACTTACAGGTG
1 AAGAAGGGAGCAACACAAGGTCCTTAGAAATACTTACAAGTG
181944 AAGAAGGGAG
1 AAGAAGGGAG
181954 GGCTATTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.14, G:0.33, T:0.16
Consensus pattern (42 bp):
AAGAAGGGAGCAACACAAGGTCCTTAGAAATACTTACAAGTG
Found at i:182689 original size:108 final size:108
Alignment explanation
Indices: 182552--182818 Score: 304
Period size: 108 Copynumber: 2.4 Consensus size: 108
182542 CTTTTTTCCC
* *
182552 CAAAAAATATTTTTTTTACTTTTTTCGTATTCTAGTGCCTGCCATTGACACAAAAAAAGTGAAAA
1 CAAAAAATATTTTTTTTACTTTTTTCGTATTCTGGTGCC-GCCATTGACACAAAAAAAGTAAAAA
*
182617 AAAATTTACCCATAAAGCTGGTGCCAGCCATTGGCAGGCCACCA
65 AAAATTTACCCAAAAAGCTGGTGCCAGCCATTGGCAGGCCACCA
* ** * * * * **
182661 C-CAATTTTTTTTTTTTACTTTTTTCGTATACTGGTGCCGACATTTGACAGACCAAAAGTAAAAA
1 CAAAAAATATTTTTTTTACTTTTTTCGTATTCTGGTGCCGCCA-TTGACACAAAAAAAGTAAAAA
**** * * *
182725 AAAATTTGGGGAAAAAGGTGGTGCCGGCCATTGGTAGGCCACCA
65 AAAATTTACCCAAAAAGCTGGTGCCAGCCATTGGCAGGCCACCA
182769 CAAAAAAATATTTTTTTT-CTTTTTTTCGTATTCTGGTGCCAGCCATTGAC
1 C-AAAAAATATTTTTTTTAC-TTTTTTCGTATTCTGGTGCC-GCCATTGAC
182819 TGAACAATAC
Statistics
Matches: 128, Mismatches: 25, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
107 3 0.02
108 85 0.66
109 2 0.02
110 35 0.27
111 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (108 bp):
CAAAAAATATTTTTTTTACTTTTTTCGTATTCTGGTGCCGCCATTGACACAAAAAAAGTAAAAAA
AAATTTACCCAAAAAGCTGGTGCCAGCCATTGGCAGGCCACCA
Found at i:183295 original size:23 final size:23
Alignment explanation
Indices: 183268--183322 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
183258 ATAATTTCTT
183268 TAATAAATATATTTATTT-TTAAA-
1 TAATAAATA-A-TTATTTATTAAAG
183291 TAATATAATAATTATTTATTAAAG
1 TAATA-AATAATTATTTATTAAAG
*
183315 TACTAAAT
1 TAATAAAT
183323 TTTAACATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 6 0.21
23 14 0.50
24 8 0.29
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATAAATAATTATTTATTAAAG
Found at i:184045 original size:158 final size:158
Alignment explanation
Indices: 183870--184179 Score: 620
Period size: 158 Copynumber: 2.0 Consensus size: 158
183860 TTTGAAGGGA
183870 AGAAGAAATAATAAATAAATAAATAAATAAAATAAAATAAAAAATTTGTGGAAAGGTTGAAATAA
1 AGAAGAAATAATAAATAAATAAATAAATAAAATAAAATAAAAAATTTGTGGAAAGGTTGAAATAA
183935 AATAGATTAATTGAACTTAAAAGTAGAAATTTAAATAGTAAAACTATAAAATATAAAAATGCAAA
66 AATAGATTAATTGAACTTAAAAGTAGAAATTTAAATAGTAAAACTATAAAATATAAAAATGCAAA
184000 AGTGTTTAAAAAAAATAAAAATTTGAAG
131 AGTGTTTAAAAAAAATAAAAATTTGAAG
184028 AGAAGAAATAATAAATAAATAAATAAATAAAATAAAATAAAAAATTTGTGGAAAGGTTGAAATAA
1 AGAAGAAATAATAAATAAATAAATAAATAAAATAAAATAAAAAATTTGTGGAAAGGTTGAAATAA
184093 AATAGATTAATTGAACTTAAAAGTAGAAATTTAAATAGTAAAACTATAAAATATAAAAATGCAAA
66 AATAGATTAATTGAACTTAAAAGTAGAAATTTAAATAGTAAAACTATAAAATATAAAAATGCAAA
184158 AGTGTTTAAAAAAAATAAAAAT
131 AGTGTTTAAAAAAAATAAAAAT
184180 AAAATAAGGA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 152 1.00
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (158 bp):
AGAAGAAATAATAAATAAATAAATAAATAAAATAAAATAAAAAATTTGTGGAAAGGTTGAAATAA
AATAGATTAATTGAACTTAAAAGTAGAAATTTAAATAGTAAAACTATAAAATATAAAAATGCAAA
AGTGTTTAAAAAAAATAAAAATTTGAAG
Found at i:184142 original size:79 final size:80
Alignment explanation
Indices: 183901--184152 Score: 270
Period size: 80 Copynumber: 3.2 Consensus size: 80
183891 AATAAATAAA
183901 ATAAAATA-AAAAATTTGTGGAAAGGTTGAAATAAAATAGATTAATTGAACTTAAAAGTAGAAAT
1 ATAAAATATAAAAATTTGTGGAAAGGTTGAAATAAAATAGATTAATTGAACTTAAAAGTAGAAAT
183965 TTAAATAGTAAAACT
66 TTAAATAGTAAAACT
** * * * *** *
183980 ATAAAATATAAAAA--TG-CAAAAGTGTTTAAAAAAAATA-A-AAATTTGAAGAGAAGAAATA-A
1 ATAAAATATAAAAATTTGTGGAAAG-GTTGAAATAAAATAGATTAA-TTGAACTTAA-AAGTAGA
* * **
184039 TAA-ATAAATAAATAAATAAA
63 -AATTTAAAT-AGTAAA-ACT
184059 ATAAAATA-AAAAATTTGTGGAAAGGTTGAAATAAAATAGATTAATTGAACTTAAAAGTAGAAAT
1 ATAAAATATAAAAATTTGTGGAAAGGTTGAAATAAAATAGATTAATTGAACTTAAAAGTAGAAAT
184123 TTAAATAGTAAAACT
66 TTAAATAGTAAAACT
184138 ATAAAATATAAAAAT
1 ATAAAATATAAAAAT
184153 GCAAAAGTGT
Statistics
Matches: 132, Mismatches: 26, Indels: 29
0.71 0.14 0.16
Matches are distributed among these distances:
76 2 0.02
77 18 0.14
78 30 0.23
79 26 0.20
80 36 0.27
81 18 0.14
82 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.27
Consensus pattern (80 bp):
ATAAAATATAAAAATTTGTGGAAAGGTTGAAATAAAATAGATTAATTGAACTTAAAAGTAGAAAT
TTAAATAGTAAAACT
Found at i:184958 original size:42 final size:42
Alignment explanation
Indices: 184896--184988 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
184886 ACGAAAAGGA
* * *
184896 AAGAAGGGAGCAACACAGGGTCCTTAGAGATGCTTGCAAGTG
1 AAGAAGGGAGCAACACAGGGTCATTAGAGATACTTACAAGTG
** * * *
184938 AAGAAGGGAGCCGCATAGGGTTATTAGAGATACTTACAGGTG
1 AAGAAGGGAGCAACACAGGGTCATTAGAGATACTTACAAGTG
184980 AAG-AGGGAG
1 AAGAAGGGAG
184989 GGCTATTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 6 0.14
42 37 0.86
ACGTcount: A:0.34, C:0.13, G:0.35, T:0.17
Consensus pattern (42 bp):
AAGAAGGGAGCAACACAGGGTCATTAGAGATACTTACAAGTG
Found at i:185916 original size:104 final size:106
Alignment explanation
Indices: 185800--185991 Score: 248
Period size: 104 Copynumber: 1.8 Consensus size: 106
185790 GCCTGCTATT
* * *
185800 ACGAAAAAAGTGAAAAAAAAATTTACCCATAAAGGT-GATGCCT-GCGATTGGC-GGCCACCACC
1 ACGAAAAAAGTGAAAAAAAAATTTACCCATAAAGGTAG-TG-CTAACCATTGGCAGGCCAACACC
185862 AATTTTTTTTT-CTTTTTTCGTATATTGATACTAGTCATTGAC
64 AATTTTTTTTTACTTTTTTCGTATATTGATACTAGTCATTGAC
****** *
185904 ACGAAAAAAGTGAAATTTTTTTTTACCCATCAAGGTAGTGCTAACCATTGGCAGGCCAACACCAA
1 ACGAAAAAAGTGAAAAAAAAATTTACCCATAAAGGTAGTGCTAACCATTGGCAGGCCAACACCAA
185969 TTTTTTTTTACTTTTTTCGTATA
66 TTTTTTTTTACTTTTTTCGTATA
185992 CTGGTGCCAG
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
103 2 0.03
104 38 0.51
105 21 0.28
106 13 0.18
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (106 bp):
ACGAAAAAAGTGAAAAAAAAATTTACCCATAAAGGTAGTGCTAACCATTGGCAGGCCAACACCAA
TTTTTTTTTACTTTTTTCGTATATTGATACTAGTCATTGAC
Found at i:186069 original size:23 final size:22
Alignment explanation
Indices: 186017--186069 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
186007 CATTTATGGG
186017 TAAATATATTTATTATTAAATAA
1 TAAAT-TATTTATTATTAAATAA
*
186040 TATAATTA-TTATGTATTAAATTAC
1 TA-AATTATTTAT-TATTAAA-TAA
186064 TAAATT
1 TAAATT
186070 TTGACATGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.15
23 15 0.58
24 7 0.27
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAATTATTTATTATTAAATAA
Found at i:187355 original size:42 final size:42
Alignment explanation
Indices: 187293--187374 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
187283 TAGCCCTCCC
* *
187293 TTCTTCACCTGTAAGTATCTCTAAAAACCCTATGTTGCTCTT
1 TTCTTCACCTGCAAGCATCTCTAAAAACCCTATGTTGCTCTT
** *
187335 TTCTTCACCTGCAAGCATCTCTAAGGACCCTGTGTTGCTC
1 TTCTTCACCTGCAAGCATCTCTAAAAACCCTATGTTGCTC
187375 CCTTATTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (42 bp):
TTCTTCACCTGCAAGCATCTCTAAAAACCCTATGTTGCTCTT
Found at i:187879 original size:23 final size:23
Alignment explanation
Indices: 187834--187888 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
187824 GCATGTCAAA
*
187834 ATTTAGTACTTTAATAAATAATA-
1 ATTTATTA-TTTAATAAATAATAT
187857 ATTATATTATTTAA-AAATAAATAT
1 ATT-TATTATTTAATAAAT-AATAT
187881 ATTTATTA
1 ATTTATTA
187889 AAGAAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 4 0.14
23 17 0.61
24 7 0.25
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTATTATTTAATAAATAATAT
Found at i:187889 original size:19 final size:20
Alignment explanation
Indices: 187843--187890 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
187833 AATTTAGTAC
* *
187843 TTTAATAAATAATAATTATA
1 TTTATTAAATAATAAATATA
187863 -TTATTTAAA-AATAAATATA
1 TTTA-TTAAATAATAAATATA
187882 TTTATTAAA
1 TTTATTAAA
187891 GAAATTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTATTAAATAATAAATATA
Found at i:188092 original size:107 final size:108
Alignment explanation
Indices: 187940--188159 Score: 370
Period size: 107 Copynumber: 2.0 Consensus size: 108
187930 AATTTTGTGG
*
187940 ATTTTTATTGAGTTTAGATAAAAAAATAAGAATATAATTAAAATAATGTAAATATAATTTATTTT
1 ATTTTTATTGAGTTTAGATAAAAAAATAAGAACATAATTAAAATAATGTAAATATAATTTATTTT
188005 GTGATTTTAAAAGATATGATATCACACAATTTCATTTTCGGCT
66 GTGATTTTAAAAGATATGATATCACACAATTTCATTTTCGGCT
* *
188048 ATTTTTATTGAGTTTATA-AAAAAAATAAGAACATATTTAAAATAATGTAAATATAATTTATTTT
1 ATTTTTATTGAGTTTAGATAAAAAAATAAGAACATAATTAAAATAATGTAAATATAATTTATTTT
* * * *
188112 GTGATTTTCAAAGATATGATATCACATAATTTCTTTTTTGGCT
66 GTGATTTTAAAAGATATGATATCACACAATTTCATTTTCGGCT
188155 ATTTT
1 ATTTT
188160 ACCAAAATAG
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
107 88 0.84
108 17 0.16
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (108 bp):
ATTTTTATTGAGTTTAGATAAAAAAATAAGAACATAATTAAAATAATGTAAATATAATTTATTTT
GTGATTTTAAAAGATATGATATCACACAATTTCATTTTCGGCT
Found at i:188558 original size:20 final size:21
Alignment explanation
Indices: 188523--188569 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
188513 CCAGCACCAC
188523 CTTTTTCCCAATTTTTTTTTA
1 CTTTTTCCCAATTTTTTTTTA
*
188544 CTTTTTCTCAATTTTTTTTTA
1 CTTTTTCCCAATTTTTTTTTA
188565 CTTTT
1 CTTTT
188570 GGTATATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (21 bp):
CTTTTTCCCAATTTTTTTTTA
Found at i:191111 original size:101 final size:102
Alignment explanation
Indices: 190977--191181 Score: 403
Period size: 101 Copynumber: 2.0 Consensus size: 102
190967 AATTGTGTGA
190977 TATCATATCTTTTAAAATCACAAAATAAATTATATTTACATTATTTTAATTATATTCTTATTTTT
1 TATCATATCTTTTAAAATCACAAAATAAATTATATTTACATTATTTTAATTATATTCTTATTTTT
191042 TTATCTAAACTCAATAAAAATCCACAAAATTAAAATT
66 TTATCTAAACTCAATAAAAATCCACAAAATTAAAATT
191079 TATCATATC-TTTAAAATCACAAAATAAATTATATTTACATTATTTTAATTATATTCTTATTTTT
1 TATCATATCTTTTAAAATCACAAAATAAATTATATTTACATTATTTTAATTATATTCTTATTTTT
191143 TTATCTAAACTCAATAAAAATCCACAAAATTAAAATT
66 TTATCTAAACTCAATAAAAATCCACAAAATTAAAATT
191180 TA
1 TA
191182 AACCTTTAAC
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 94 0.91
102 9 0.09
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (102 bp):
TATCATATCTTTTAAAATCACAAAATAAATTATATTTACATTATTTTAATTATATTCTTATTTTT
TTATCTAAACTCAATAAAAATCCACAAAATTAAAATT
Found at i:191242 original size:23 final size:23
Alignment explanation
Indices: 191215--191270 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
191205 ATAATTTCTT
191215 TAATAAATATATTTATTT-TTAAA-
1 TAATAAAT-TA-TTATTTATTAAAG
191238 TAATATAATTATTATTTATTAAAG
1 TAATA-AATTATTATTTATTAAAG
*
191262 TACTAAATT
1 TAATAAATT
191271 TTGACATGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 6 0.21
23 16 0.55
24 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TAATAAATTATTATTTATTAAAG
Found at i:193644 original size:23 final size:23
Alignment explanation
Indices: 193617--193672 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
193607 ATAATTTCTT
193617 TAATAAATATATTTATTT-TTAAA-
1 TAATAAAT-TA-TTATTTATTAAAG
193640 TAATATAATTATTATTTATTAAAG
1 TAATA-AATTATTATTTATTAAAG
*
193664 TACTAAATT
1 TAATAAATT
193673 TTGACATGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 6 0.21
23 16 0.55
24 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TAATAAATTATTATTTATTAAAG
Found at i:195071 original size:3 final size:3
Alignment explanation
Indices: 195046--195105 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
195036 TTAGTTTAGT
* * * *
195046 TTA TT- TTA TTA ATA TTG TTA TTA TTA TTT TTA TTA -TA TTA TACA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
195090 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
195106 ACCTACATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 4 0.09
3 40 0.87
4 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:195079 original size:24 final size:25
Alignment explanation
Indices: 195049--195104 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
195039 GTTTAGTTTA
* *
195049 TTTTATTAATATTGT-TATTATTAT
1 TTTTATTAATATTATACATTATTAT
195073 TTTTATT-ATATTATACATTATTAT
1 TTTTATTAATATTATACATTATTAT
*
195097 TATTATTA
1 TTTTATTA
195105 TACCTACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTATTAATATTATACATTATTAT
Found at i:198732 original size:104 final size:104
Alignment explanation
Indices: 198589--198901 Score: 317
Period size: 111 Copynumber: 2.9 Consensus size: 104
198579 CGAAAAAAGT
*
198589 AAAAAAAA-TTGTATAAAGGGGGTGCCGGCCATTGCCAGGCCACCCCAATTTTTTTTTTACTTTT
1 AAAAAAAATTTGTATAAAAGGGGTGCCGGCCATTGCCAGGCCACCCCAATTTTTTTTTTACTTTT
*** * *
198653 TTCGTATACAGGTGTTGGCTATTGACAGACCAAAAGTAA
66 TTCGTATACAGGTGCCAGCCATTGACACACCAAAAGTAA
* *
198692 AAAAAAAATTTGTATAAAAGGGTTGCCAGCCATTGCCAGGCCACCCCAAAAAGTTTTTTTTTTTT
1 AAAAAAAATTTGTATAAAAGGGGTGCCGGCCATTGCCAGGCCACCCC---AA----TTTTTTTTT
* *
198757 TACTTTTTTCATATACTGGTGCCAGCCATTGACACACCAAAAGTAA
59 TACTTTTTTCGTATACAGGTGCCAGCCATTGACACACCAAAAGTAA
* * * * ** *
198803 AAAAAAAATTATTGTA-GAAAGGAGGTGCCGGCCATTGCTAGG-CAACCAAATTTTTTTTAAATT
1 AAAAAAAA-T-TTGTATAAAAGG-GGTGCCGGCCATTGCCAGGCCACCCCAATTTTTTTTTTACT
*** * *
198866 TTTTTCGTATTTTGGTGCCGGCCATTGACAGACCAA
63 TTTTTCGTATACAGGTGCCAGCCATTGACACACCAA
198902 CACCCGAAAT
Statistics
Matches: 175, Mismatches: 24, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
103 8 0.05
104 35 0.20
105 41 0.23
107 2 0.01
109 2 0.01
111 56 0.32
112 10 0.06
113 21 0.12
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (104 bp):
AAAAAAAATTTGTATAAAAGGGGTGCCGGCCATTGCCAGGCCACCCCAATTTTTTTTTTACTTTT
TTCGTATACAGGTGCCAGCCATTGACACACCAAAAGTAA
Found at i:199152 original size:102 final size:104
Alignment explanation
Indices: 199034--199307 Score: 315
Period size: 102 Copynumber: 2.6 Consensus size: 104
199024 GAAAAAAAAG
* * **** *
199034 TTTTTTTTTACTTTTTTCGAGTCAATGTCAGGCACCAGTATACGAAAAAAGTAAAGTTTTTTTTG
1 TTTTTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAGTATACGAAAAAAGTAAAAAAATTTTGG
*
199099 TGGT-GACCTGCCAATGGCCAGCACCA-CTTTTAT-GAAA-
66 TGGTAG-CCTGCCAATGGCCAGCACCACCTTTT-TCCAAAT
* * *
199136 TTTTTTTTTACTTTTTTCGTCTCAATGGCAGGCACTACTATACGAAAAAAGTTAAAAAAAATTTT
1 TTTTTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAGTATACGAAAAAAG-T-AAAAAAATTTT
199201 GGTGGTAGCCTGCCAATGGCCAGCACCACCTTTTTCCAAATTGT
64 GGTGGTAGCCTGCCAATGGCCAGCACCACCTTTTTCCAAA---T
* * *
199245 TTTTTTTTTACTTTTGGTC-TGTCAATGGCCGGCACCAGTATACGAAAAAAGTAAAAAACTTTT
1 TTTTTTTTTACTTTT-TTCGTGTCAATGGCAGGCACCAGTATACGAAAAAAGTAAAAAAATTTT
199308 TTCGTATACT
Statistics
Matches: 145, Mismatches: 17, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
102 46 0.32
103 1 0.01
104 33 0.23
105 9 0.06
107 10 0.07
108 1 0.01
109 43 0.30
110 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (104 bp):
TTTTTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAGTATACGAAAAAAGTAAAAAAATTTTGG
TGGTAGCCTGCCAATGGCCAGCACCACCTTTTTCCAAAT
Found at i:200272 original size:104 final size:105
Alignment explanation
Indices: 200083--200333 Score: 355
Period size: 104 Copynumber: 2.4 Consensus size: 105
200073 TCAGTATATG
* *
200083 AATTTTTTTTACTTTTTTTCTTATACTGGTGCCTTCCATTGACACAAAAAAAGTAAAAAAAAATT
1 AATTTTTTTTAC-TTTTTTCGTATACTGGTGCCTGCCATTGACACAAAAAAAGTAAAAAAAAATT
**
200148 CTCACATAAAGGTGGTGCCGGTC-ATTGGCAGGTCACCACCA
65 CTCACATAAAGGTGGTGCCGG-CAATTGGCAGACCACCACCA
* * *
200189 ATTTTTTTTTACTTTTTTCGTATACTGGTGTCTGCCATTGACACGAAAAAAGTAAAAAAAAATT-
1 AATTTTTTTTACTTTTTTCGTATACTGGTGCCTGCCATTGACACAAAAAAAGTAAAAAAAAATTC
200253 TCTA-ATAAAGGTGGTGCCGGCAATTGGCAGACCACCACCA
66 TC-ACATAAAGGTGGTGCCGGCAATTGGCAGACCACCACCA
* * * *
200293 AATTTTTTTTACTTTTTTCGTATTCTGATGCCGGCTATTGA
1 AATTTTTTTTACTTTTTTCGTATACTGGTGCCTGCCATTGA
200334 TAGACCAATA
Statistics
Matches: 130, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
103 1 0.01
104 69 0.53
105 49 0.38
106 11 0.08
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (105 bp):
AATTTTTTTTACTTTTTTCGTATACTGGTGCCTGCCATTGACACAAAAAAAGTAAAAAAAAATTC
TCACATAAAGGTGGTGCCGGCAATTGGCAGACCACCACCA
Found at i:204390 original size:21 final size:21
Alignment explanation
Indices: 204366--204411 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
204356 TTATTATTTC
* *
204366 AAATGCATTAAAATTGCACAA
1 AAATGCACTAAAATTGCAAAA
**
204387 AAATTTACTAAAATTGCAAAA
1 AAATGCACTAAAATTGCAAAA
204408 AAAT
1 AAAT
204412 TACACAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.26
Consensus pattern (21 bp):
AAATGCACTAAAATTGCAAAA
Found at i:206427 original size:43 final size:42
Alignment explanation
Indices: 206380--206481 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 42
206370 TGTGTGATAT
*
206380 CGTGTAAGACCATGTCTGGGACATT-GACATCGAT-TAGAGATTA
1 CGTGTAAGACCATGTCTAGGACATTGGA-ATC-ATATA-AGATTA
* *
206423 CGTGTAAGACCATGTCTAGGACATTGGAATCATATATGATTT
1 CGTGTAAGACCATGTCTAGGACATTGGAATCATATAAGATTA
*
206465 CGTGTAAGACCTTGTCT
1 CGTGTAAGACCATGTCT
206482 TGGATAGTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
42 22 0.42
43 29 0.55
44 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTAGGACATTGGAATCATATAAGATTA
Found at i:207839 original size:53 final size:54
Alignment explanation
Indices: 207716--207841 Score: 155
Period size: 54 Copynumber: 2.4 Consensus size: 54
207706 GCATGTGGCA
* * * * *
207716 GGCCATGTGGCCAAGACAGTGAGTTGCACGGGCTGGACACACAGACGTGTGACT
1 GGCCGTGTGGCCAAGTCAGAGAGTTACACGGGCTGGACACACAGACGTGTAACT
** * *
207770 GGCCGTGTGGTTAAGTCAGAGAGTTACACGGGCTGGA-ACACGGGCGTGTAACT
1 GGCCGTGTGGCCAAGTCAGAGAGTTACACGGGCTGGACACACAGACGTGTAACT
*
207823 GGCCGTGTGACCAAGTCAG
1 GGCCGTGTGGCCAAGTCAG
207842 TAATCTAGCT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
53 29 0.48
54 31 0.52
ACGTcount: A:0.23, C:0.22, G:0.37, T:0.18
Consensus pattern (54 bp):
GGCCGTGTGGCCAAGTCAGAGAGTTACACGGGCTGGACACACAGACGTGTAACT
Done.