Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: Chr09 85040211 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: 85040211 ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33 Warning! 160 characters in sequence are not A, C, G, or T File 135 of 292 Found at i:40023565 original size:78 final size:79 Alignment explanation
Indices: 40023400--40023551 Score: 200 Period size: 78 Copynumber: 1.9 Consensus size: 79 40023390 TCGAATGATG * * * 40023400 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC 1 TCCGGGCTAA-TCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC * * 40023465 GTGCGAGTTAATAAA 65 GTGCAAGTCAATAAA * ** 40023480 TCCGGGCTAATCCCGAAGGCTTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATTC 1 TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATTC 40023543 GTGCAAGTC 65 GTGCAAGTC 40023552 GCTATAACCG Statistics Matches: 63, Mismatches: 8, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 77 1 0.02 78 35 0.56 79 17 0.27 80 10 0.16 ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24 Consensus pattern (79 bp): TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTCG TGCAAGTCAATAAA Found at i:40025403 original size:43 final size:48 Alignment explanation
Indices: 40025356--40025481 Score: 127 Period size: 51 Copynumber: 2.7 Consensus size: 48 40025346 GCATCAGAGT 40025356 TCGTTGAGAGGTCCGAGTTCATTATGGATGTGA-GCA-T-C-C-GAAC 1 TCGTTGAGAGGTCCGAGTTCATTATGGATGTGATGCAGTACGCTGAAC * * * * * * 40025399 TCGTTGAGACGTCCAAGTTCATAATAGATGTGATTCATGTAACGTCTGAGC 1 TCGTTGAGAGGTCCGAGTTCATTATGGATGTGATGCA-GT-ACG-CTGAAC * 40025450 TCATTGAGAGGTCCGAGTTCATTATGGATGTG 1 TCGTTGAGAGGTCCGAGTTCATTATGGATGTG 40025482 TTACATGTTA Statistics Matches: 64, Mismatches: 11, Indels: 8 0.77 0.13 0.10 Matches are distributed among these distances: 43 29 0.45 44 2 0.03 46 1 0.02 48 1 0.02 50 1 0.02 51 30 0.47 ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31 Consensus pattern (48 bp): TCGTTGAGAGGTCCGAGTTCATTATGGATGTGATGCAGTACGCTGAAC Found at i:40028780 original size:55 final size:53 Alignment explanation
Indices: 40028625--40028831 Score: 198 Period size: 53 Copynumber: 3.8 Consensus size: 53 40028615 TTCCTTTTTA * * * 40028625 AACTTATCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTACCTTATG 1 AACTTATCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATC * * * * * * 40028678 AACTCACCATTTCCATGTCTTGGCATGGTCTTACATGGGATCTTTGCCTTATC 1 AACTTATCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATC * * * * * * 40028731 ATAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA 1 A-A-CTTATCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-C * * * * * * 40028787 AACTTACCAATGCCATGCCTTGGCTTGGTCTTACTTGGTATCCTT 1 AACTTATCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTT 40028832 AAATCCTAAT Statistics Matches: 122, Mismatches: 29, Indels: 5 0.78 0.19 0.03 Matches are distributed among these distances: 53 45 0.37 54 36 0.30 55 40 0.33 56 1 0.01 ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39 Consensus pattern (53 bp): AACTTATCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATC Found at i:40032777 original size:29 final size:29 Alignment explanation
Indices: 40032742--40032905 Score: 283 Period size: 29 Copynumber: 5.7 Consensus size: 29 40032732 ATAAACGATC ** * 40032742 TCGCACACTTAGTGCCATGCAATTTAAGC 1 TCGCACACTTAGTGCCATATAATTTAAGT * 40032771 TCGCACACATAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT * 40032800 TTGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT 40032829 TCGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT 40032858 TCGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT 40032887 TCGCACACTTAGTGCCATA 1 TCGCACACTTAGTGCCATA 40032906 CCTTCCAAGC Statistics Matches: 128, Mismatches: 7, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 29 128 1.00 ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32 Consensus pattern (29 bp): TCGCACACTTAGTGCCATATAATTTAAGT Found at i:40032921 original size:87 final size:87 Alignment explanation
Indices: 40032743--40032932 Score: 274 Period size: 87 Copynumber: 2.2 Consensus size: 87 40032733 TAAACGATCT * * 40032743 CGCACACTTAGTGCCATGCAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTTGCACAC 1 CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC * ** 40032808 TTAGTGCCATATAATTTAAGTT 66 TTAGTGCCATATAATTCAAGCC * * * 40032830 CGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATTTAAGTTCGCACAC 1 CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC ** 40032895 TTAGTGCCATA-CCTTCCAAGCC 66 TTAGTGCCATATAATT-CAAGCC 40032917 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 40032933 ATCTTGTCAC Statistics Matches: 92, Mismatches: 10, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 86 2 0.02 87 90 0.98 ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30 Consensus pattern (87 bp): CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC TTAGTGCCATATAATTCAAGCC Found at i:40040823 original size:29 final size:29 Alignment explanation
Indices: 40040788--40040951 Score: 283 Period size: 29 Copynumber: 5.7 Consensus size: 29 40040778 ATAAACGATC ** * 40040788 TCGCACACTTAGTGCCATGCAATTTAAGC 1 TCGCACACTTAGTGCCATATAATTTAAGT * 40040817 TCGCACACATAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT * 40040846 TTGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT 40040875 TCGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT 40040904 TCGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT 40040933 TCGCACACTTAGTGCCATA 1 TCGCACACTTAGTGCCATA 40040952 CCTTCCAAGC Statistics Matches: 128, Mismatches: 7, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 29 128 1.00 ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32 Consensus pattern (29 bp): TCGCACACTTAGTGCCATATAATTTAAGT Found at i:40040967 original size:87 final size:87 Alignment explanation
Indices: 40040789--40040978 Score: 274 Period size: 87 Copynumber: 2.2 Consensus size: 87 40040779 TAAACGATCT * * 40040789 CGCACACTTAGTGCCATGCAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTTGCACAC 1 CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC * ** 40040854 TTAGTGCCATATAATTTAAGTT 66 TTAGTGCCATATAATTCAAGCC * * * 40040876 CGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATTTAAGTTCGCACAC 1 CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC ** 40040941 TTAGTGCCATA-CCTTCCAAGCC 66 TTAGTGCCATATAATT-CAAGCC 40040963 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 40040979 ATCTTGTCAC Statistics Matches: 92, Mismatches: 10, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 86 2 0.02 87 90 0.98 ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30 Consensus pattern (87 bp): CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC TTAGTGCCATATAATTCAAGCC Found at i:40048862 original size:29 final size:29 Alignment explanation
Indices: 40048827--40048990 Score: 283 Period size: 29 Copynumber: 5.7 Consensus size: 29 40048817 ATAAACGATC ** * 40048827 TCGCACACTTAGTGCCATGCAATTTAAGC 1 TCGCACACTTAGTGCCATATAATTTAAGT * 40048856 TCGCACACATAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT * 40048885 TTGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT 40048914 TCGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT 40048943 TCGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT 40048972 TCGCACACTTAGTGCCATA 1 TCGCACACTTAGTGCCATA 40048991 CCTTCCAAGC Statistics Matches: 128, Mismatches: 7, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 29 128 1.00 ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32 Consensus pattern (29 bp): TCGCACACTTAGTGCCATATAATTTAAGT Found at i:40049006 original size:87 final size:87 Alignment explanation
Indices: 40048828--40049017 Score: 274 Period size: 87 Copynumber: 2.2 Consensus size: 87 40048818 TAAACGATCT * * 40048828 CGCACACTTAGTGCCATGCAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTTGCACAC 1 CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC * ** 40048893 TTAGTGCCATATAATTTAAGTT 66 TTAGTGCCATATAATTCAAGCC * * * 40048915 CGCACACTTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATTTAAGTTCGCACAC 1 CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC ** 40048980 TTAGTGCCATA-CCTTCCAAGCC 66 TTAGTGCCATATAATT-CAAGCC 40049002 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 40049018 ATCTTGTCAC Statistics Matches: 92, Mismatches: 10, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 86 2 0.02 87 90 0.98 ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30 Consensus pattern (87 bp): CGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTCGCACAC TTAGTGCCATATAATTCAAGCC Found at i:40056908 original size:29 final size:29 Alignment explanation
Indices: 40056872--40057033 Score: 211 Period size: 29 Copynumber: 5.6 Consensus size: 29 40056862 AATAAACGAT ** 40056872 CTCGCACACTTAGTGCCATGCAATTTAAG 1 CTCGCACACTTAGTGCCATATAATTTAAG * 40056901 CTCGCACACATAGTGCCATATAATTTAAG 1 CTCGCACACTTAGTGCCATATAATTTAAG * * 40056930 TTTGCACACTTAGTGCCATATAATTTAAG 1 CTCGCACACTTAGTGCCATATAATTTAAG * 40056959 TTCGCACACTTAGTGCCATATAATTTAAG 1 CTCGCACACTTAGTGCCATATAATTTAAG * ** * 40056988 TTCGCACACTTAGTGCCATA-CCTTCCAAG 1 CTCGCACACTTAGTGCCATATAATT-TAAG 40057017 C-CGCACACTTAGTGCCA 1 CTCGCACACTTAGTGCCA 40057034 ATCTTGTCAC Statistics Matches: 121, Mismatches: 11, Indels: 3 0.90 0.08 0.02 Matches are distributed among these distances: 28 18 0.15 29 103 0.85 ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30 Consensus pattern (29 bp): CTCGCACACTTAGTGCCATATAATTTAAG Found at i:40061748 original size:44 final size:45 Alignment explanation
Indices: 40061676--40061765 Score: 137 Period size: 44 Copynumber: 2.0 Consensus size: 45 40061666 ACTAAAGAAA * 40061676 AAGTGAAAGTAATTCGTGATAGTCTAAAAGCAGCTTCAGATCGAC 1 AAGTGAAAGTAATTCGTGATAGTCTAAAAGCAGCTTCAAATCGAC * * * 40061721 AAGTGAAAGT-ATTTGTGATAGTTTAAAAGTAGCTTCAAATCGAC 1 AAGTGAAAGTAATTCGTGATAGTCTAAAAGCAGCTTCAAATCGAC 40061765 A 1 A 40061766 GAAATCGTAT Statistics Matches: 41, Mismatches: 4, Indels: 1 0.89 0.09 0.02 Matches are distributed among these distances: 44 31 0.76 45 10 0.24 ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28 Consensus pattern (45 bp): AAGTGAAAGTAATTCGTGATAGTCTAAAAGCAGCTTCAAATCGAC Found at i:40063464 original size:49 final size:50 Alignment explanation
Indices: 40063400--40063528 Score: 163 Period size: 49 Copynumber: 2.6 Consensus size: 50 40063390 ACAAGTCGAT 40063400 GCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATC-GAG-GCCGAC 1 GCCATGTCCCAGACATGGTCTTACACTGACTATC-AAATCTGAGTGCCGAC * * * * ** * 40063449 GCCATGTCCTAGACATGGTCTTACACTGGCTCTCACATCTTCGTGCCGAT 1 GCCATGTCCCAGACATGGTCTTACACTGACTATCAAATCTGAGTGCCGAC * 40063499 GCTATGTCCCAGACATGGTCTTACACTGAC 1 GCCATGTCCCAGACATGGTCTTACACTGAC 40063529 ACATTTCGTA Statistics Matches: 68, Mismatches: 10, Indels: 3 0.84 0.12 0.04 Matches are distributed among these distances: 48 4 0.06 49 32 0.47 50 32 0.47 ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26 Consensus pattern (50 bp): GCCATGTCCCAGACATGGTCTTACACTGACTATCAAATCTGAGTGCCGAC Found at i:40063600 original size:46 final size:45 Alignment explanation
Indices: 40063396--40063709 Score: 149 Period size: 46 Copynumber: 6.7 Consensus size: 45 40063386 TCTGACAAGT * ** 40063396 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATCG-AGGC 1 CGATG-CATGTCCCAGACATCGTCTTACACTGAC-A-C-ATCTCGTA-GC * * * * 40063445 CGACGCCATGTCCTAGACATGGTCTTACACTGGCTCTCACATCTTCGT-GC 1 CGATG-CATGTCCCAGACATCGTCTTACACT-G---ACACATC-TCGTAGC * * 40063495 CGATGCTATGTCCCAGACATGGTCTTACACTGACACATTTCGTAGC 1 CGATGC-ATGTCCCAGACATCGTCTTACACTGACACATCTCGTAGC * * 40063541 CAATGCATGTCCCAGACA-CGTCTTACATTGACTTACATCTCG-AGAC 1 CGATGCATGTCCCAGACATCGTCTTACACTGAC--ACATCTCGTAG-C * * * * * * * 40063587 TGATGCATGTCCCAAACAT-ATCTTACACTAGCTCTCATCTC-AATGT 1 CGATGCATGTCCCAGACATCGTCTTACACT-G-ACACATCTCGTA-GC * * * * * * 40063633 CGATGCCATGTCCCAGAAATGGTCTTACACTGGCTC-TCATAATGTGGC 1 CGATG-CATGTCCCAGACATCGTCTTACACTGACACATC-T--CGTAGC * 40063681 CGATGCATGTCCTAGACAT-GTCTTACACT 1 CGATGCATGTCCCAGACATCGTCTTACACT 40063710 AGCGCACAAA Statistics Matches: 211, Mismatches: 32, Indels: 47 0.73 0.11 0.16 Matches are distributed among these distances: 44 12 0.06 45 20 0.09 46 68 0.32 47 27 0.13 48 16 0.08 49 31 0.15 50 31 0.15 51 4 0.02 52 1 0.00 53 1 0.00 ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28 Consensus pattern (45 bp): CGATGCATGTCCCAGACATCGTCTTACACTGACACATCTCGTAGC Found at i:40064847 original size:55 final size:54 Alignment explanation
Indices: 40064780--40064891 Score: 206 Period size: 55 Copynumber: 2.1 Consensus size: 54 40064770 GCTAAAATTA * 40064780 ATTCACCAAAATTTTCATGCATCTTTATAAACATGCCATCACACATAAAATAAAT 1 ATTCACCAAAATTTTCATGCATCTTTATAAA-ATACCATCACACATAAAATAAAT 40064835 ATTCACCAAAATTTTCATGCATCTTTATAAAATACCATCACACATAAAATAAAT 1 ATTCACCAAAATTTTCATGCATCTTTATAAAATACCATCACACATAAAATAAAT 40064889 ATT 1 ATT 40064892 AAAAATAATT Statistics Matches: 56, Mismatches: 1, Indels: 1 0.97 0.02 0.02 Matches are distributed among these distances: 54 25 0.45 55 31 0.55 ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32 Consensus pattern (54 bp): ATTCACCAAAATTTTCATGCATCTTTATAAAATACCATCACACATAAAATAAAT Found at i:40064902 original size:54 final size:55 Alignment explanation
Indices: 40064787--40064902 Score: 182 Period size: 54 Copynumber: 2.1 Consensus size: 55 40064777 TTAATTCACC * ** 40064787 AAAATTTTCATGCATCTTTATAAACATGCCATCACACATAAAATAAATATTCACC 1 AAAATTTTCATGCATCTTTATAAACATACCATCACACATAAAATAAATATTCAAA 40064842 AAAATTTTCATGCATCTTTATAAA-ATACCATCACACATAAAATAAATATT-AAA 1 AAAATTTTCATGCATCTTTATAAACATACCATCACACATAAAATAAATATTCAAA 40064895 AATAATTT 1 AA-AATTT 40064903 CTCTGACCTC Statistics Matches: 57, Mismatches: 3, Indels: 3 0.90 0.05 0.05 Matches are distributed among these distances: 53 3 0.05 54 30 0.53 55 24 0.42 ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33 Consensus pattern (55 bp): AAAATTTTCATGCATCTTTATAAACATACCATCACACATAAAATAAATATTCAAA Found at i:40070495 original size:40 final size:38 Alignment explanation
Indices: 40070365--40070512 Score: 111 Period size: 40 Copynumber: 3.8 Consensus size: 38 40070355 TGAGAAATTG * * * 40070365 AATG-ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGA 1 AATGTATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCA * * * * 40070405 AAT-TATAACCGGGTTAAGACCCGAAGGCAATTGTGCT 1 AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA * * 40070442 AGTGGCTACATCCGGGCTAAGACCCGAAGGCATTTGTGCA 1 AAT-G-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA * * * 40070482 AATCGTGATATCCGGGTTAAGTCCCGTAGGC 1 AAT-GT-ATATCCGGGCTAAGACCCGAAGGC 40070513 CTTGGTGCGG Statistics Matches: 84, Mismatches: 19, Indels: 10 0.74 0.17 0.09 Matches are distributed among these distances: 37 4 0.05 38 2 0.02 39 3 0.04 40 75 0.89 ACGTcount: A:0.28, C:0.22, G:0.27, T:0.22 Consensus pattern (38 bp): AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA Found at i:40077248 original size:40 final size:39 Alignment explanation
Indices: 40077121--40077250 Score: 172 Period size: 40 Copynumber: 3.3 Consensus size: 39 40077111 ATGCTGGAAA * 40077121 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG * * * 40077161 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG * 40077201 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG 40077241 TTATATCCGG 1 TTATATCCGG 40077251 TTGTATTCCG Statistics Matches: 78, Mismatches: 10, Indels: 4 0.85 0.11 0.04 Matches are distributed among these distances: 39 4 0.05 40 74 0.95 ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24 Consensus pattern (39 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG Found at i:40085322 original size:38 final size:37 Alignment explanation
Indices: 40085231--40085338 Score: 146 Period size: 38 Copynumber: 2.8 Consensus size: 37 40085221 CTGGAAATTA * 40085231 TATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGC 1 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCTAGTGC * * 40085268 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCGTCGTTC 1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGC-TAGTGC 40085308 TATCCGGGCTAAGACCCGAAGGCATTCGTGC 1 TATCCGGGCTAAGACCCGAAGGCATTCGTGC 40085339 ACGTGGTTAT Statistics Matches: 64, Mismatches: 3, Indels: 7 0.86 0.04 0.09 Matches are distributed among these distances: 37 1 0.02 38 33 0.52 39 25 0.39 40 5 0.08 ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22 Consensus pattern (37 bp): TATCCGGGCTAAGACCCGAAGGCATTCGTGCTAGTGC Found at i:40086840 original size:39 final size:40 Alignment explanation
Indices: 40086738--40086920 Score: 167 Period size: 40 Copynumber: 4.6 Consensus size: 40 40086728 ACAAATGATG * * * 40086738 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA 1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA * * * * * 40086778 TCCGGACTAGGAT-CCGAAAGCATTCGTGCGAGTTAATAAA 1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA * 40086818 TCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA * * * * 40086857 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA 1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA ** * 40086898 -CCGGGCTTCGTCCCAAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATT 40086921 TGAGCGAGTC Statistics Matches: 115, Mismatches: 23, Indels: 10 0.78 0.16 0.07 Matches are distributed among these distances: 39 32 0.28 40 74 0.64 41 9 0.08 ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA Found at i:40086902 original size:79 final size:81 Alignment explanation
Indices: 40086738--40086922 Score: 209 Period size: 79 Copynumber: 2.3 Consensus size: 81 40086728 ACAAATGATG * * * 40086738 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAAGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAAGCATT * 40086802 CGTGCGAGTTAATAAA 66 CGTGCGAGTCAATAAA * ** * 40086818 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAAGCAT * 40086880 TCGTGCGAGTCACTATAA 65 TCGTGCGAGTCAATA-AA ** * 40086898 -CCGGGCTTCGTCCCAAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 40086923 AGCGAGTCGT Statistics Matches: 89, Mismatches: 12, Indels: 8 0.82 0.11 0.07 Matches are distributed among these distances: 78 1 0.01 79 55 0.62 80 33 0.37 ACGTcount: A:0.25, C:0.24, G:0.26, T:0.24 Consensus pattern (81 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAAGCATT CGTGCGAGTCAATAAA Found at i:40115863 original size:190 final size:190 Alignment explanation
Indices: 40115640--40116208 Score: 1066 Period size: 190 Copynumber: 3.0 Consensus size: 190 40115630 TTAAGTTTTG 40115640 GTATGGTTTGAATGAGTTGTTGAATGATGATGAAATAGTTGTAATGAAGCATGTTTTGAGCATGA 1 GTATGGTTTGAATGAGTTGTTGAATGATGATGAAATAGTTGTAATGAAGCATGTTTTGAGCATGA 40115705 ATTGGCTGAATATTTTATATGAATGCTGCTTAATTTGGCATGTAGGAATGACCCATAAAGGGGTG 66 ATTGGCTGAATATTTTATATGAATGCTGCTTAATTTGGCATGTAGGAATGACCCATAAAGGGGTG * 40115770 GCAAATTAGCTTAAACTAAGCCTGCACTGTGCCACACGGCCATAGCACACGGGCGTGTTT 131 GCAAATTAGCTTAAACTAAGCCTGCATTGTGCCACACGGCCATAGCACACGGGCGTGTTT 40115830 GTATGGTTTGAATGAGTTGTTGAATGATGATGAAATAGTTGTAATGAAGCATGTTTTGAGCATGA 1 GTATGGTTTGAATGAGTTGTTGAATGATGATGAAATAGTTGTAATGAAGCATGTTTTGAGCATGA * 40115895 ATTGGCTGAAAATTTTATATGAATGCTGCTTAATTTGGCATGTAGGAATGACCCATAAAGGGGTG 66 ATTGGCTGAATATTTTATATGAATGCTGCTTAATTTGGCATGTAGGAATGACCCATAAAGGGGTG * 40115960 GCAAATTAGCTTAAACTAAGCCTGCATTGTGCCACACGGCCATAGCACATGGGCGTGTTT 131 GCAAATTAGCTTAAACTAAGCCTGCATTGTGCCACACGGCCATAGCACACGGGCGTGTTT 40116020 GTATGGTTTGAATGAGTTGTTGAATGATGATGAAATAGTTGTAATGAAGCATGTTTTGAGCATGA 1 GTATGGTTTGAATGAGTTGTTGAATGATGATGAAATAGTTGTAATGAAGCATGTTTTGAGCATGA * * * 40116085 ATTAGCTGAATATTTTATATGAATGCTGCTTAATTTGGCTTGTAAGAATGACCCATAAAGGGGTG 66 ATTGGCTGAATATTTTATATGAATGCTGCTTAATTTGGCATGTAGGAATGACCCATAAAGGGGTG * * 40116150 GAAAATTAGCTTAAACTAAGCCTGCATTGTGCCATACGGCCATAGCACACGGGCGTGTT 131 GCAAATTAGCTTAAACTAAGCCTGCATTGTGCCACACGGCCATAGCACACGGGCGTGTT 40116209 AGTTGGCCGC Statistics Matches: 369, Mismatches: 10, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 190 369 1.00 ACGTcount: A:0.30, C:0.13, G:0.26, T:0.32 Consensus pattern (190 bp): GTATGGTTTGAATGAGTTGTTGAATGATGATGAAATAGTTGTAATGAAGCATGTTTTGAGCATGA ATTGGCTGAATATTTTATATGAATGCTGCTTAATTTGGCATGTAGGAATGACCCATAAAGGGGTG GCAAATTAGCTTAAACTAAGCCTGCATTGTGCCACACGGCCATAGCACACGGGCGTGTTT Found at i:40116934 original size:43 final size:43 Alignment explanation
Indices: 40116887--40117002 Score: 135 Period size: 43 Copynumber: 2.7 Consensus size: 43 40116877 TAACACATAT * * * * * 40116887 CGATGCCACTATCCTAGACAGGGTCTTACACGAAATC-GATTAA 1 CGATGCCAATGTCCTAGACATGGTCTTACACGAAATCTCAAT-A * * * 40116930 CGATGCCAATGTCCCAGACATGTTCTTACACGTAATCTCAATA 1 CGATGCCAATGTCCTAGACATGGTCTTACACGAAATCTCAATA * 40116973 CAATGCCAATGTCCTAGACATGGTCTTACA 1 CGATGCCAATGTCCTAGACATGGTCTTACA 40117003 TGTAATCACA Statistics Matches: 61, Mismatches: 11, Indels: 2 0.82 0.15 0.03 Matches are distributed among these distances: 43 59 0.97 44 2 0.03 ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26 Consensus pattern (43 bp): CGATGCCAATGTCCTAGACATGGTCTTACACGAAATCTCAATA Found at i:40135981 original size:40 final size:39 Alignment explanation
Indices: 40135816--40135999 Score: 138 Period size: 40 Copynumber: 4.6 Consensus size: 39 40135806 AAATTGAATG * * * 40135816 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T 1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT * * * * * * 40135856 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T * * * * * 40135896 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT * 40135936 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT * * * 40135975 GATATCCGGGTTAAGTCCCGTAGGC 1 -ATATCCGGGCTAAGACCCGAAGGC 40136000 CTTGGTGCGG Statistics Matches: 113, Mismatches: 26, Indels: 10 0.76 0.17 0.07 Matches are distributed among these distances: 37 4 0.04 38 2 0.02 39 3 0.03 40 104 0.92 ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT Found at i:40136024 original size:80 final size:81 Alignment explanation
Indices: 40135856--40136044 Score: 186 Period size: 80 Copynumber: 2.4 Consensus size: 81 40135846 GCTGGAAATT * * * * 40135856 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA * 40135921 TTCGTGCGAGTCATTC 66 TTCGTGCGAGTCATCC * * * * * * 40135937 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC * * * * 40136000 CTTGGTGCGGGTTA-CC 65 ATTCGTGCGAGTCATCC * * * 40136016 ATAACCGGGCTATGTCCCGAAGGCGATTG 1 ATAACCGGGCTAAGACCCGAAGGCAATTG 40136045 ATCGAGTAGC Statistics Matches: 86, Mismatches: 20, Indels: 5 0.77 0.18 0.05 Matches are distributed among these distances: 79 2 0.02 80 84 0.98 ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23 Consensus pattern (81 bp): ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA TTCGTGCGAGTCATCC Found at i:40144098 original size:40 final size:39 Alignment explanation
Indices: 40143933--40144116 Score: 138 Period size: 40 Copynumber: 4.6 Consensus size: 39 40143923 AAATTGAATG * * * 40143933 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T 1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT * * * * * * 40143973 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T * * * * * 40144013 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT * 40144053 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT * * * 40144092 GATATCCGGGTTAAGTCCCGTAGGC 1 -ATATCCGGGCTAAGACCCGAAGGC 40144117 CTTGGTGCGG Statistics Matches: 113, Mismatches: 26, Indels: 10 0.76 0.17 0.07 Matches are distributed among these distances: 37 4 0.04 38 2 0.02 39 3 0.03 40 104 0.92 ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT Found at i:40144141 original size:80 final size:81 Alignment explanation
Indices: 40143973--40144161 Score: 186 Period size: 80 Copynumber: 2.4 Consensus size: 81 40143963 GCTGGAAATT * * * * 40143973 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA * 40144038 TTCGTGCGAGTCATTC 66 TTCGTGCGAGTCATCC * * * * * * 40144054 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC * * * * 40144117 CTTGGTGCGGGTTA-CC 65 ATTCGTGCGAGTCATCC * * * 40144133 ATAACCGGGCTATGTCCCGAAGGCGATTG 1 ATAACCGGGCTAAGACCCGAAGGCAATTG 40144162 ATCGAGTAGC Statistics Matches: 86, Mismatches: 20, Indels: 5 0.77 0.18 0.05 Matches are distributed among these distances: 79 2 0.02 80 84 0.98 ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23 Consensus pattern (81 bp): ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA TTCGTGCGAGTCATCC Found at i:40145947 original size:40 final size:40 Alignment explanation
Indices: 40145873--40146020 Score: 133 Period size: 40 Copynumber: 3.7 Consensus size: 40 40145863 CACATTCAAA * * 40145873 TGCCTTCGGGA-CATAGCCCGG-TTACAGTAACTCGCACGAT 1 TGCCTTC-GGATCTTAGCCCGGATT-TAGTAACTCGCACGAT * * * * 40145913 TGCCTTCGGGA-CTTAACCCGGATTTAGTAGCTCGCTCGAA 1 TGCCTTC-GGATCTTAGCCCGGATTTAGTAACTCGCACGAT * * * 40145953 AGCCTTCGGATCTTAGTCTGGATTTAGTAACTCGCACG-T 1 TGCCTTCGGATCTTAGCCCGGATTTAGTAACTCGCACGAT * * 40145992 ATGCCATCGGATCTTAGTCCGGATTTAGT 1 -TGCCTTCGGATCTTAGCCCGGATTTAGT 40146021 CACTTAGCAC Statistics Matches: 89, Mismatches: 16, Indels: 6 0.80 0.14 0.05 Matches are distributed among these distances: 39 3 0.03 40 84 0.94 41 2 0.02 ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29 Consensus pattern (40 bp): TGCCTTCGGATCTTAGCCCGGATTTAGTAACTCGCACGAT Found at i:40146048 original size:40 final size:39 Alignment explanation
Indices: 40145902--40146041 Score: 131 Period size: 40 Copynumber: 3.5 Consensus size: 39 40145892 GGTTACAGTA ** ** 40145902 ACTCGCACGATTGCCTTCGGGA-CTTAACCCGGATTTAGT 1 ACTCGCACGAAAGCCTTC-GGATCTTAGTCCGGATTTAGT * * 40145941 AGCTCGCTCGAAAGCCTTCGGATCTTAGTCTGGATTTAGT 1 A-CTCGCACGAAAGCCTTCGGATCTTAGTCCGGATTTAGT * * * 40145981 AACTCGCACGTATGCCATCGGATCTTAGTCCGGATTTAGT 1 -ACTCGCACGAAAGCCTTCGGATCTTAGTCCGGATTTAGT * 40146021 CACTTAGCAC-AAAGCCTTCGG 1 -AC-TCGCACGAAAGCCTTCGG 40146042 GACTTAGCCC Statistics Matches: 81, Mismatches: 16, Indels: 7 0.78 0.15 0.07 Matches are distributed among these distances: 39 4 0.05 40 71 0.88 41 6 0.07 ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29 Consensus pattern (39 bp): ACTCGCACGAAAGCCTTCGGATCTTAGTCCGGATTTAGT Found at i:40153055 original size:47 final size:47 Alignment explanation
Indices: 40152838--40153062 Score: 183 Period size: 47 Copynumber: 4.7 Consensus size: 47 40152828 TCGGAATGCA * * 40152838 AGCCAGTGTAAGA-CATGCCTGGGACAT-GCATCGGCT-ATGAGATGT 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTGATG-GATGT * * * ** * 40152883 -GCCAATATAAGACCATGTCTGGGACATGGCATCAGCACGGATATATGAG 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTGATGGATG-T * ** * ** * 40152932 AGCTAGTGTAAGACCATGTCTGGGACATGGTGTCAGCCTCGATTTCA-AT 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GACT-GA-TGGATGT * * 40152981 AGTCAGTGTAAGACCATGTCTGAGACATGGCATCGACTTGATGGAT-T 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TGATGGATGT 40153028 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCG 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCG 40153063 GCATTATACC Statistics Matches: 140, Mismatches: 29, Indels: 20 0.74 0.15 0.11 Matches are distributed among these distances: 44 10 0.07 45 13 0.09 46 5 0.04 47 37 0.26 48 8 0.06 49 33 0.24 50 32 0.23 51 2 0.01 ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24 Consensus pattern (47 bp): AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTGATGGATGT Found at i:40156638 original size:39 final size:39 Alignment explanation
Indices: 40156584--40156813 Score: 388 Period size: 39 Copynumber: 5.9 Consensus size: 39 40156574 AATGTTCGAG * 40156584 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA 1 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA 40156623 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA 1 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA 40156662 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA 1 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA * 40156701 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA 1 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA * * 40156740 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG 1 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA * * * 40156779 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG 1 TGATACCCGGGCTAAG-CCCGAAGGCAATTGTGCG 40156814 GGTTACCATA Statistics Matches: 182, Mismatches: 8, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 39 165 0.91 40 17 0.09 ACGTcount: A:0.24, C:0.23, G:0.31, T:0.21 Consensus pattern (39 bp): TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA Found at i:40156871 original size:79 final size:78 Alignment explanation
Indices: 40156590--40156882 Score: 297 Period size: 78 Copynumber: 3.7 Consensus size: 78 40156580 CGAGTGATAT ** * * 40156590 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA-TGATACCCGGGCTAAGCCCGAAGGCAATTGT 1 CCGGGCTAAGCCCGAAGGCAATTGAACGAG-TAGTGATATCCGGGTTAAGCCCGAAGGCAATTGT ** * 40156654 GCGAGCTATGATAC 65 GCGAGCTACCATAA ** * 40156668 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA-TGATATCCGGGCTAAGCCCGAAGGCAATTGT 1 CCGGGCTAAGCCCGAAGGCAATTGAACGAG-TAGTGATATCCGGGTTAAGCCCGAAGGCAATTGT ** * 40156732 GCGAGCTATGATAC 65 GCGAGCTACCATAA ** * * 40156746 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGT 1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGGTTAAG-CCCGAAGGCAATTGT * * 40156811 GCGGGTTACCATAA 65 GCGAGCTACCATAA * ** * 40156825 CCGGGCTATGTCCCGAAGGCGTTTGAACGAGTAGCT-ATATCC-GGTTAAACTCCGAAGG 1 CCGGGCTAAG-CCCGAAGGCAATTGAACGAGTAG-TGATATCCGGGTTAAGC-CCGAAGG 40156883 TATGTGATTT Statistics Matches: 194, Mismatches: 16, Indels: 9 0.89 0.07 0.04 Matches are distributed among these distances: 77 1 0.01 78 123 0.63 79 45 0.23 80 24 0.12 81 1 0.01 ACGTcount: A:0.25, C:0.24, G:0.31, T:0.21 Consensus pattern (78 bp): CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGGTTAAGCCCGAAGGCAATTGTG CGAGCTACCATAA Found at i:40171275 original size:14 final size:13 Alignment explanation
Indices: 40171255--40171286 Score: 55 Period size: 14 Copynumber: 2.4 Consensus size: 13 40171245 AATATTTAAC 40171255 TTGTTCTTAATTA 1 TTGTTCTTAATTA 40171268 TGTGTTCTTAATTA 1 T-TGTTCTTAATTA 40171282 TTGTT 1 TTGTT 40171287 TTGATATCCC Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 13 5 0.28 14 13 0.72 ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62 Consensus pattern (13 bp): TTGTTCTTAATTA Found at i:40180067 original size:40 final size:40 Alignment explanation
Indices: 40180022--40180151 Score: 165 Period size: 40 Copynumber: 3.2 Consensus size: 40 40180012 CGGAATACAA 40180022 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC * ** * 40180062 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC * * * 40180102 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC 40180142 CCGGATATAA 1 CCGGATATAA 40180152 TTTCCAGCAT Statistics Matches: 76, Mismatches: 12, Indels: 4 0.83 0.13 0.04 Matches are distributed among these distances: 39 3 0.04 40 73 0.96 ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23 Consensus pattern (40 bp): CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC Found at i:40180166 original size:40 final size:40 Alignment explanation
Indices: 40180022--40180185 Score: 145 Period size: 40 Copynumber: 4.1 Consensus size: 40 40180012 CGGAATACAA * ** 40180022 CCGGATATAACCACGTGCACGAA-TGCCTTCGGGTCTTAGC 1 CCGGATATAATCACCAGCAC-AATTGCCTTCGGGTCTTAGC * * 40180062 CCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC * ** * * 40180102 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC ** * * * 40180142 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC 1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC 40180182 CCGG 1 CCGG 40180186 GTATCATTCA Statistics Matches: 100, Mismatches: 21, Indels: 6 0.79 0.17 0.05 Matches are distributed among these distances: 39 2 0.02 40 98 0.98 ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25 Consensus pattern (40 bp): CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC Found at i:40187059 original size:40 final size:40 Alignment explanation
Indices: 40187003--40187153 Score: 139 Period size: 40 Copynumber: 3.8 Consensus size: 40 40186993 CGGAATTTAA * * * 40187003 CCGGATATAATGACTCGCTCAAATGCCTTCGGGAC-GAAGC 1 CCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTGAA-C * * 40187043 CCGGTTATAGTGACTCGCACGAATGCCTTCGGGACTTAAC 1 CCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTGAAC * * * * 40187083 CCGGGTT-TAGTAACTTGCACAAATGCCTTCGGG-CTTAGC 1 CC-GGTTATAGTGACTCGCACAAATGCCTTCGGGACTGAAC * * * 40187122 CCGGATT-TATTAACTCGCACGAATGCCTTCGG 1 CCGG-TTATAGTGACTCGCACAAATGCCTTCGG 40187154 ATCCTAGTCC Statistics Matches: 96, Mismatches: 12, Indels: 7 0.83 0.10 0.06 Matches are distributed among these distances: 38 2 0.02 39 31 0.32 40 57 0.59 41 6 0.06 ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25 Consensus pattern (40 bp): CCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTGAAC Found at i:40187123 original size:79 final size:81 Alignment explanation
Indices: 40187022--40187204 Score: 223 Period size: 79 Copynumber: 2.3 Consensus size: 81 40187012 ATGACTCGCT ** * * 40187022 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC 1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC * * 40187085 GGGTTTAGTAACTT-GCA 64 GGATATAGTAACTTAGCA * ** 40187102 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG * 40187166 ATATAGTCACTTAGCA 66 ATATAGTAACTTAGCA 40187182 CAAA-GCCTTCGGGACTTAGCCCG 1 CAAATGCCTTCGGGACTTAGCCCG 40187205 ACATCATTCG Statistics Matches: 89, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 3 0.03 79 54 0.61 80 32 0.36 ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25 Consensus pattern (81 bp): CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG ATATAGTAACTTAGCA Found at i:40192043 original size:42 final size:42 Alignment explanation
Indices: 40191986--40192065 Score: 133 Period size: 42 Copynumber: 1.9 Consensus size: 42 40191976 GTCCTGGCCA * * * 40191986 CCAGTATAACTCACGAAGGTCTTGGTACATCTTGTTCCCAGG 1 CCAGCATAACTCACGAAGGTCTCGGTACACCTTGTTCCCAGG 40192028 CCAGCATAACTCACGAAGGTCTCGGTACACCTTGTTCC 1 CCAGCATAACTCACGAAGGTCTCGGTACACCTTGTTCC 40192066 TACTGGGATG Statistics Matches: 35, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 42 35 1.00 ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26 Consensus pattern (42 bp): CCAGCATAACTCACGAAGGTCTCGGTACACCTTGTTCCCAGG Found at i:40200754 original size:194 final size:195 Alignment explanation
Indices: 40200410--40200770 Score: 444 Period size: 194 Copynumber: 1.9 Consensus size: 195 40200400 ACTTTACGCG * * * * * 40200410 ATTTAGTCCTTTTTATTAAATTGACTAATCAAACGATAAAATTTCTTAACGAAATTTTCACACCA 1 ATTTAGTCCTTCTAATCAAATTGACTAATCAAACAATAAAATTTCTTAACAAAATTTTCACACCA * * * 40200475 ATAAAATATCATACTGTAAACCTTAAAATAATAATAAAATAAATATTTTAATATCATATTTTTGG 66 ATAAAATATCATACTGTAAACCGTAAAAAAATAATAAAATAAATATTTTAATATCATATTTGTGG * * 40200540 CCCTAAAACCATTGTTTTGATTTGA-CTAAAAATGGGTTGTTACACAAATTTTGCACTTATTGCA 131 CCCTAAAACCACTATTTTGATTTGACCTAAAAATGGGTTGTTACACAAATTTTGCACTTATTGCA * * 40200604 ATTTAGTCCTTCTAATCAAATTGAGC-ACTCAATCAATAAAATTTCTTAACAAAATTTTCACA-C 1 ATTTAGTCCTTCTAATCAAATTGA-CTAATCAAACAATAAAATTTCTTAACAAAATTTTCACACC *** * * * * * 40200667 AATTATTCTATCATGCTGTAGACCGTAAAAAAATAATAAAATAAATATTTTTACTTTGA-ATTTG 65 AA-TAAAATATCATACTGTAAACCGTAAAAAAATAATAAAATAAATA-TTTTAATATCATATTTG ** * 40200731 TGG-TTTCGAAACCACTATTTTGATTTGACCTAAAAATGGG 128 TGGCCCT-AAAACCACTATTTTGATTTGACCTAAAAATGGG 40200771 ATTTTCGTCC Statistics Matches: 139, Mismatches: 23, Indels: 9 0.81 0.13 0.05 Matches are distributed among these distances: 193 4 0.03 194 115 0.83 195 20 0.14 ACGTcount: A:0.39, C:0.14, G:0.09, T:0.37 Consensus pattern (195 bp): ATTTAGTCCTTCTAATCAAATTGACTAATCAAACAATAAAATTTCTTAACAAAATTTTCACACCA ATAAAATATCATACTGTAAACCGTAAAAAAATAATAAAATAAATATTTTAATATCATATTTGTGG CCCTAAAACCACTATTTTGATTTGACCTAAAAATGGGTTGTTACACAAATTTTGCACTTATTGCA Found at i:40206731 original size:100 final size:100 Alignment explanation
Indices: 40206558--40206745 Score: 297 Period size: 100 Copynumber: 1.9 Consensus size: 100 40206548 TATGGTGAGG * * 40206558 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACAGGATAATTGGTCGCATGTGTAGTACT 1 TCACGTGTGTAGTACTAAATGCAGGCTACTACGTGTACAGGATAATTGGTCGCATGTGTAGTACT * 40206623 AAGTGCAGGCTAGTATGCGTACCCGAAAACTGTGA 66 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA * * * * 40206658 TCACGTTTGTAGTACTAAATGCGGGCTACTACGTGTACCA-GATTATTGGTTGCATGTGTAGTAC 1 TCACGTGTGTAGTACTAAATGCAGGCTACTACGTGTA-CAGGATAATTGGTCGCATGTGTAGTAC 40206722 TAAGTGCAGGCTACTATGCGTACC 65 TAAGTGCAGGCTACTATGCGTACC 40206746 AGATAGCTTC Statistics Matches: 80, Mismatches: 7, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 100 78 0.98 101 2 0.03 ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30 Consensus pattern (100 bp): TCACGTGTGTAGTACTAAATGCAGGCTACTACGTGTACAGGATAATTGGTCGCATGTGTAGTACT AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA Found at i:40206734 original size:49 final size:49 Alignment explanation
Indices: 40206563--40206750 Score: 209 Period size: 49 Copynumber: 3.8 Consensus size: 49 40206553 TGAGGTCACG * * 40206563 TGTGTAGTACTAAGTGCAGGCTACTATGTGTA-CAGGATAATTGGTCGCA 1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCA-GATAATTGGTTGCA * * * * * 40206612 TGTGTAGTACTAAGTGCAGGCTAGTATGCGTACCCGAAAACTGTGAT-CA 1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTG-GTTGCA * * * * * * 40206661 CGTTTGTAGTACTAAATGCGGGCTACTACGTGTACCAGATTATTGGTTGCA 1 --TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTTGCA 40206712 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA 1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA 40206751 GCTTCGGCTA Statistics Matches: 110, Mismatches: 24, Indels: 10 0.76 0.17 0.07 Matches are distributed among these distances: 49 71 0.65 50 4 0.04 51 35 0.32 ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30 Consensus pattern (49 bp): TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTTGCA Found at i:40217564 original size:40 final size:39 Alignment explanation
Indices: 40217519--40217726 Score: 202 Period size: 40 Copynumber: 5.2 Consensus size: 39 40217509 CGGAATACAA * 40217519 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 40217559 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 40217599 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * *** * 40217639 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC ** * * * 40217679 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC 40217719 CCGGATAT 1 CCGGATAT 40217727 CATTCAATTG Statistics Matches: 141, Mismatches: 24, Indels: 6 0.82 0.14 0.04 Matches are distributed among these distances: 39 4 0.03 40 134 0.95 41 3 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (39 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC Found at i:40217659 original size:80 final size:80 Alignment explanation
Indices: 40217519--40217725 Score: 238 Period size: 80 Copynumber: 2.6 Consensus size: 80 40217509 CGGAATACAA * * * 40217519 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT- 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG * 40217583 GCCTTCGGGTATTAGC 65 GCCTTCGGGTATTAAC * * ** 40217599 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG * 40217663 GCCTTCGGGTCTTAAC 65 GCCTTCGGGTATTAAC ** * ** * * 40217679 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA 40217726 TCATTCAATT Statistics Matches: 107, Mismatches: 18, Indels: 5 0.82 0.14 0.04 Matches are distributed among these distances: 79 3 0.03 80 102 0.95 81 2 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (80 bp): CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG CCTTCGGGTATTAAC Found at i:40225615 original size:40 final size:39 Alignment explanation
Indices: 40225570--40225777 Score: 202 Period size: 40 Copynumber: 5.2 Consensus size: 39 40225560 CGGAATACAA * 40225570 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 40225610 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 40225650 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * *** * 40225690 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC ** * * * 40225730 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC 40225770 CCGGATAT 1 CCGGATAT 40225778 CATTCAATTG Statistics Matches: 141, Mismatches: 24, Indels: 6 0.82 0.14 0.04 Matches are distributed among these distances: 39 4 0.03 40 134 0.95 41 3 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (39 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC Found at i:40225710 original size:80 final size:80 Alignment explanation
Indices: 40225570--40225776 Score: 238 Period size: 80 Copynumber: 2.6 Consensus size: 80 40225560 CGGAATACAA * * * 40225570 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT- 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG * 40225634 GCCTTCGGGTATTAGC 65 GCCTTCGGGTATTAAC * * ** 40225650 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG * 40225714 GCCTTCGGGTCTTAAC 65 GCCTTCGGGTATTAAC ** * ** * * 40225730 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA 40225777 TCATTCAATT Statistics Matches: 107, Mismatches: 18, Indels: 5 0.82 0.14 0.04 Matches are distributed among these distances: 79 3 0.03 80 102 0.95 81 2 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (80 bp): CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG CCTTCGGGTATTAAC Found at i:40228426 original size:122 final size:120 Alignment explanation
Indices: 40228210--40228427 Score: 287 Period size: 122 Copynumber: 1.8 Consensus size: 120 40228200 AATTATGTGG * * * * 40228210 AATGAAATATGGATGTATTGATTATTGATTTATGTGTGTATGAGTATTCGAATATACCCGGGCTA 1 AATGAAATATGGATGTAATGATTATTGATGTATGTGTGCATGAGAATTCGAATATACCCGGGCTA * * ** 40228275 AGTCCCGAAGGCGATTATGCTAGTGATTATAATTGTGTTTGAGCCTTAGTAACGA 66 AGTCCCGAAGACAATTATGCTAGAAATTATAATTGTGTTTGAGCCTTAGTAACGA * * 40228330 AATGAAATATGTATGTCCAATGATTATTGATGTATGTGTGCATGAGAAATT-GAATGATATCCGG 1 AATGAAATATGGATGT--AATGATTATTGATGTATGTGTGCATGAG-AATTCGAAT-ATACCCGG * 40228394 GCTAAG-CCCGAAGACAATTATGCTGGAAATTATA 62 GCTAAGTCCCGAAGACAATTATGCTAGAAATTATA 40228428 TCCGGGTTAA Statistics Matches: 83, Mismatches: 11, Indels: 6 0.83 0.11 0.06 Matches are distributed among these distances: 120 15 0.18 122 52 0.63 123 16 0.19 ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33 Consensus pattern (120 bp): AATGAAATATGGATGTAATGATTATTGATGTATGTGTGCATGAGAATTCGAATATACCCGGGCTA AGTCCCGAAGACAATTATGCTAGAAATTATAATTGTGTTTGAGCCTTAGTAACGA Found at i:40228452 original size:40 final size:40 Alignment explanation
Indices: 40228386--40228536 Score: 155 Period size: 40 Copynumber: 3.8 Consensus size: 40 40228376 AAATTGAATG * * 40228386 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT * * **** 40228425 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT * * 40228465 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GAAATT * * 40228505 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC 40228537 ACGTGGTTAT Statistics Matches: 90, Mismatches: 18, Indels: 7 0.78 0.16 0.06 Matches are distributed among these distances: 39 16 0.18 40 72 0.80 41 2 0.02 ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT Found at i:40228550 original size:40 final size:40 Alignment explanation
Indices: 40228423--40228552 Score: 154 Period size: 40 Copynumber: 3.2 Consensus size: 40 40228413 ATGCTGGAAA * * * 40228423 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG * * * *** 40228463 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG * 40228503 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG 40228543 TTATATCCGG 1 TTATATCCGG 40228553 TTATATTCCG Statistics Matches: 72, Mismatches: 17, Indels: 2 0.79 0.19 0.02 Matches are distributed among these distances: 39 1 0.01 40 71 0.99 ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG Found at i:40228551 original size:80 final size:79 Alignment explanation
Indices: 40228386--40228552 Score: 205 Period size: 80 Copynumber: 2.1 Consensus size: 79 40228376 AAATTGAATG * 40228386 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA 1 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA 40228451 TTGTGCTAGTGGCT 66 TTGTGCTAGTGGCT * * * * * 40228465 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG 1 ATATCCGGGCTAAG-CCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG * * 40228528 CATTTGTGC-ACGTGGTT 63 CAATTGTGCTA-GTGGCT 40228545 ATATCCGG 1 ATATCCGG 40228553 TTATATTCCG Statistics Matches: 75, Mismatches: 9, Indels: 7 0.82 0.10 0.08 Matches are distributed among these distances: 79 18 0.24 80 57 0.76 ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23 Consensus pattern (79 bp): ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA TTGTGCTAGTGGCT Found at i:40236747 original size:29 final size:28 Alignment explanation
Indices: 40236677--40236751 Score: 87 Period size: 28 Copynumber: 2.6 Consensus size: 28 40236667 ATACTCGATT * * 40236677 TCGCACACTTAGTGCCATGCGATTTAGC 1 TCGCACACTTAGTGCCATGCCATTGAGC * ** * 40236705 CCGCACACACAGTGCCATGCCCTTCGAGC 1 TCGCACACTTAGTGCCATGCCATT-GAGC 40236734 TCGCACACTTAGTGCCAT 1 TCGCACACTTAGTGCCAT 40236752 ATATTTCCAG Statistics Matches: 37, Mismatches: 9, Indels: 1 0.79 0.19 0.02 Matches are distributed among these distances: 28 19 0.51 29 18 0.49 ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23 Consensus pattern (28 bp): TCGCACACTTAGTGCCATGCCATTGAGC Found at i:40236768 original size:29 final size:29 Alignment explanation
Indices: 40236735--40236808 Score: 139 Period size: 29 Copynumber: 2.6 Consensus size: 29 40236725 CCTTCGAGCT 40236735 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA * 40236764 TGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 40236793 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 40236809 ATCTCGTCAC Statistics Matches: 43, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 29 43 1.00 ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:40239798 original size:22 final size:23 Alignment explanation
Indices: 40239768--40239813 Score: 58 Period size: 23 Copynumber: 2.0 Consensus size: 23 40239758 TTTCATGTTT * * * 40239768 CGATGCTTCG-ACGTTATAGATC 1 CGATCCTTCGCACGTAATAAATC 40239790 CGATCCTTCGCACGTAATAAATC 1 CGATCCTTCGCACGTAATAAATC 40239813 C 1 C 40239814 CTCCGAGGTC Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 22 9 0.45 23 11 0.55 ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28 Consensus pattern (23 bp): CGATCCTTCGCACGTAATAAATC Found at i:40241687 original size:40 final size:40 Alignment explanation
Indices: 40241639--40241844 Score: 317 Period size: 40 Copynumber: 5.2 Consensus size: 40 40241629 GAACTAAGAT * 40241639 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC 1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC * 40241679 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC 1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC * 40241719 CCGAAGGCATTTGTGCTAGTGACTATATCTGGGCTAAGTC 1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC * 40241759 CCGAAGGCATTTGTGCTAGTGACTATGTCCGGGCTAAGTC 1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC * * * * 40241799 CCGAAGGCATTCGTGCGAGTTG-CTATATCC-GGCTAAATT 1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC 40241838 CCGAAGG 1 CCGAAGG 40241845 TACTTGGGTT Statistics Matches: 156, Mismatches: 9, Indels: 3 0.93 0.05 0.02 Matches are distributed among these distances: 39 14 0.09 40 140 0.90 41 2 0.01 ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28 Consensus pattern (40 bp): CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC Found at i:40243219 original size:20 final size:20 Alignment explanation
Indices: 40243194--40243241 Score: 87 Period size: 20 Copynumber: 2.4 Consensus size: 20 40243184 GGGTGTTACA 40243194 CACATGATATGTACGATATG 1 CACATGATATGTACGATATG * 40243214 CACATGATATGTATGATATG 1 CACATGATATGTACGATATG 40243234 CACATGAT 1 CACATGAT 40243242 GTATTCATAA Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 20 27 1.00 ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31 Consensus pattern (20 bp): CACATGATATGTACGATATG Found at i:40243224 original size:11 final size:11 Alignment explanation
Indices: 40243194--40243241 Score: 50 Period size: 9 Copynumber: 4.7 Consensus size: 11 40243184 GGGTGTTACA 40243194 CACATGATATG 1 CACATGATATG * 40243205 TAC--GATATG 1 CACATGATATG 40243214 CACATGATATG 1 CACATGATATG * 40243225 --TATGATATG 1 CACATGATATG 40243234 CACATGAT 1 CACATGAT 40243242 GTATTCATAA Statistics Matches: 29, Mismatches: 4, Indels: 8 0.71 0.10 0.20 Matches are distributed among these distances: 9 16 0.55 11 13 0.45 ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31 Consensus pattern (11 bp): CACATGATATG Found at i:40246294 original size:51 final size:51 Alignment explanation
Indices: 40246220--40246327 Score: 146 Period size: 51 Copynumber: 2.1 Consensus size: 51 40246210 AGATATGGTG * * 40246220 AAATGGAGAAATAGGAAACATTTGAAAATGATTATGGTTTTCTCCAAAATGA 1 AAATGGAGAAATA-GAAACATTTGAAAATGACTATGGTTTTCTCAAAAATGA * * * 40246272 AAATGGGGAAAT-GAAATCATTTGGAAATGACTGTGGTTTTCTCAAAAATGA 1 AAATGGAGAAATAGAAA-CATTTGAAAATGACTATGGTTTTCTCAAAAATGA 40246323 AAATG 1 AAATG 40246328 ACATGAAAAA Statistics Matches: 50, Mismatches: 5, Indels: 3 0.86 0.09 0.05 Matches are distributed among these distances: 50 4 0.08 51 35 0.70 52 11 0.22 ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29 Consensus pattern (51 bp): AAATGGAGAAATAGAAACATTTGAAAATGACTATGGTTTTCTCAAAAATGA Found at i:40259619 original size:103 final size:104 Alignment explanation
Indices: 40259424--40259638 Score: 414 Period size: 104 Copynumber: 2.1 Consensus size: 104 40259414 CATACATACA 40259424 TATTAGTAGTAATTTTTTGTTTTTGAGCTTAATTATTTAATTCTATATTCCATAAAGAAAAAGCT 1 TATTAGTAGTAATTTTTTGTTTTTGAGCTTAATTATTTAATTCTATATTCCATAAAGAAAAAGCT 40259489 CAATTCTAGGATCTTCTAATTAGGAATGTAATTTGTCAG 66 CAATTCTAGGATCTTCTAATTAGGAATGTAATTTGTCAG 40259528 TATTAGTAGTAATTTTTTGTTTTTGAGCTTAATTATTTAATTCTATATTCCATAAAG-AAAAGCT 1 TATTAGTAGTAATTTTTTGTTTTTGAGCTTAATTATTTAATTCTATATTCCATAAAGAAAAAGCT 40259592 CAATTCTAGGATCTTCTAATTAGGAATGTAATTTGTCAG 66 CAATTCTAGGATCTTCTAATTAGGAATGTAATTTGTCAG * 40259631 TTTTAGTA 1 TATTAGTA 40259639 CTTTTCTAGT Statistics Matches: 110, Mismatches: 1, Indels: 1 0.98 0.01 0.01 Matches are distributed among these distances: 103 53 0.48 104 57 0.52 ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45 Consensus pattern (104 bp): TATTAGTAGTAATTTTTTGTTTTTGAGCTTAATTATTTAATTCTATATTCCATAAAGAAAAAGCT CAATTCTAGGATCTTCTAATTAGGAATGTAATTTGTCAG Found at i:40260414 original size:13 final size:13 Alignment explanation
Indices: 40260396--40260423 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 40260386 CTAAGCCACC 40260396 TCACACGGGCGTG 1 TCACACGGGCGTG 40260409 TCACACGGGCGTG 1 TCACACGGGCGTG 40260422 TC 1 TC 40260424 CCTGTCGAGC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 15 1.00 ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18 Consensus pattern (13 bp): TCACACGGGCGTG Found at i:40264055 original size:15 final size:17 Alignment explanation
Indices: 40264021--40264055 Score: 56 Period size: 16 Copynumber: 2.2 Consensus size: 17 40264011 TATCACATTT 40264021 ATAACCATTTCAAGATC 1 ATAACCATTTCAAGATC 40264038 ATAA-CATTTCAA-ATC 1 ATAACCATTTCAAGATC 40264053 ATA 1 ATA 40264056 TCAATATCCC Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 15 6 0.33 16 8 0.44 17 4 0.22 ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31 Consensus pattern (17 bp): ATAACCATTTCAAGATC Found at i:40278230 original size:27 final size:26 Alignment explanation
Indices: 40278190--40278305 Score: 99 Period size: 27 Copynumber: 4.3 Consensus size: 26 40278180 AGCATGGCTG * 40278190 CCAGAACAGATATTGTCACAGAGTCA 1 CCAGAACAGATATTGTCACAGAGCCA ** 40278216 CCAGATACAGATATTGTGGCAGAGCCA 1 CCAGA-ACAGATATTGTCACAGAGCCA ** 40278243 CCAGAACAGATATTTGTGGC-GTAGCCA 1 CCAGAACAGATA-TTGTCACAG-AGCCA * ** * 40278270 CCAGAAACACATATTTGTGGCATAGCCA 1 CCAG-AACAGATA-TTGTCACAGAGCCA 40278298 CCAGAACA 1 CCAGAACA 40278306 CTTCCTCCAT Statistics Matches: 80, Mismatches: 5, Indels: 9 0.85 0.05 0.10 Matches are distributed among these distances: 26 13 0.16 27 43 0.54 28 24 0.30 ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19 Consensus pattern (26 bp): CCAGAACAGATATTGTCACAGAGCCA Found at i:40278287 original size:28 final size:28 Alignment explanation
Indices: 40278214--40278303 Score: 123 Period size: 28 Copynumber: 3.3 Consensus size: 28 40278204 GTCACAGAGT * 40278214 CACCAGATACAGATA-TTGTGGCAG-AGC 1 CACCAGAAACAGATATTTGTGGC-GTAGC 40278241 CACCAG-AACAGATATTTGTGGCGTAGC 1 CACCAGAAACAGATATTTGTGGCGTAGC * * 40278268 CACCAGAAACACATATTTGTGGCATAGC 1 CACCAGAAACAGATATTTGTGGCGTAGC 40278296 CACCAGAA 1 CACCAGAA 40278304 CACTTCCTCC Statistics Matches: 57, Mismatches: 3, Indels: 5 0.88 0.05 0.08 Matches are distributed among these distances: 26 8 0.14 27 22 0.39 28 27 0.47 ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19 Consensus pattern (28 bp): CACCAGAAACAGATATTTGTGGCGTAGC Found at i:40284434 original size:20 final size:21 Alignment explanation
Indices: 40284386--40284438 Score: 63 Period size: 20 Copynumber: 2.5 Consensus size: 21 40284376 TTTCCAGGTG 40284386 GTATCGATACCACTTAAAGGAA 1 GTATCGATACCAC-TAAAGGAA * * * 40284408 ATATCGATACCA-TAGAGGCA 1 GTATCGATACCACTAAAGGAA 40284428 GTATCGATACC 1 GTATCGATACC 40284439 TACATAACAT Statistics Matches: 27, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 20 16 0.59 22 11 0.41 ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23 Consensus pattern (21 bp): GTATCGATACCACTAAAGGAA Found at i:40285886 original size:32 final size:32 Alignment explanation
Indices: 40285844--40285939 Score: 93 Period size: 32 Copynumber: 3.0 Consensus size: 32 40285834 ATGCGGCTCT * * 40285844 AAGCCTTCAGTAGCGGTATTATAATTGGCACA 1 AAGCCATCAGTAACGGTATTATAATTGGCACA * ** 40285876 AAGCCATCAGTAACTGTATTATGTTTGGCACA 1 AAGCCATCAGTAACGGTATTATAATTGGCACA * * ** * * 40285908 TAGCCATTAGCGACGGTAATATAATCGGCACA 1 AAGCCATCAGTAACGGTATTATAATTGGCACA 40285940 CAACCGTGGG Statistics Matches: 50, Mismatches: 14, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 32 50 1.00 ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27 Consensus pattern (32 bp): AAGCCATCAGTAACGGTATTATAATTGGCACA Found at i:40286500 original size:54 final size:54 Alignment explanation
Indices: 40286442--40286623 Score: 233 Period size: 54 Copynumber: 3.4 Consensus size: 54 40286432 GCCCTACATA * * * * * 40286442 GGTATTTCGGTAATTTTACACTACAAGGGTATTTGGGTAATTTTACACTA-TAAG 1 GGTATTTCGATAATTTTACACTACAAGGGTATTTCGATAATTTTACA-AACTGAG * * * 40286496 GGTATTTCGATAATTTTACACTATAAGGGTATTTTGATAATTTTACAAACTGGG 1 GGTATTTCGATAATTTTACACTACAAGGGTATTTCGATAATTTTACAAACTGAG * * * 40286550 GGTATTTCAATAATTTTACA-AACCGAGGGTATTTCGATAATTTTACAAACTGAG 1 GGTATTTCGATAATTTTACACTA-CAAGGGTATTTCGATAATTTTACAAACTGAG 40286604 GGTATTTCGATAATTTTACA 1 GGTATTTCGATAATTTTACA 40286624 AACAGGGCTT Statistics Matches: 112, Mismatches: 14, Indels: 4 0.86 0.11 0.03 Matches are distributed among these distances: 53 2 0.02 54 110 0.98 ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39 Consensus pattern (54 bp): GGTATTTCGATAATTTTACACTACAAGGGTATTTCGATAATTTTACAAACTGAG Found at i:40286624 original size:27 final size:27 Alignment explanation
Indices: 40286442--40286626 Score: 205 Period size: 27 Copynumber: 6.9 Consensus size: 27 40286432 GCCCTACATA * * 40286442 GGTATTTCGGTAATTTTACACTAC-AAG 1 GGTATTTCGATAATTTTACA-AACTAAG * * * 40286469 GGTATTTGGGTAATTTTACACTA-TAAG 1 GGTATTTCGATAATTTTACA-AACTAAG * 40286496 GGTATTTCGATAATTTTACACTA-TAAG 1 GGTATTTCGATAATTTTACA-AACTAAG * ** 40286523 GGTATTTTGATAATTTTACAAACTGGG 1 GGTATTTCGATAATTTTACAAACTAAG * ** 40286550 GGTATTTCAATAATTTTACAAACCGAG 1 GGTATTTCGATAATTTTACAAACTAAG * 40286577 GGTATTTCGATAATTTTACAAACTGAG 1 GGTATTTCGATAATTTTACAAACTAAG 40286604 GGTATTTCGATAATTTTACAAAC 1 GGTATTTCGATAATTTTACAAAC 40286627 AGGGCTTTCC Statistics Matches: 143, Mismatches: 13, Indels: 4 0.89 0.08 0.03 Matches are distributed among these distances: 26 1 0.01 27 142 0.99 ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38 Consensus pattern (27 bp): GGTATTTCGATAATTTTACAAACTAAG Found at i:40289465 original size:28 final size:29 Alignment explanation
Indices: 40289392--40289479 Score: 94 Period size: 28 Copynumber: 3.1 Consensus size: 29 40289382 AGCATGGCTG * * * * 40289392 CCAGATACAGA-AA-ATGTGACAGAGTCA 1 CCAGATACAGATAATTTGTGGCATAGCCA * 40289419 CCAGATACAGATATTTTGTGGCAGT-GCCA 1 CCAGATACAGATAATTTGTGGCA-TAGCCA 40289448 CCAGA-ACAGATAATTTGTGGCATAGCCA 1 CCAGATACAGATAATTTGTGGCATAGCCA 40289476 CCAG 1 CCAG 40289480 GACGCTTCCT Statistics Matches: 51, Mismatches: 6, Indels: 7 0.80 0.09 0.11 Matches are distributed among these distances: 27 12 0.24 28 25 0.49 29 14 0.27 ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20 Consensus pattern (29 bp): CCAGATACAGATAATTTGTGGCATAGCCA Found at i:40289625 original size:28 final size:28 Alignment explanation
Indices: 40289593--40289697 Score: 210 Period size: 28 Copynumber: 3.8 Consensus size: 28 40289583 CCTAGGGGTC 40289593 ATTTTGCATACATAGGGGTATAATGGTA 1 ATTTTGCATACATAGGGGTATAATGGTA 40289621 ATTTTGCATACATAGGGGTATAATGGTA 1 ATTTTGCATACATAGGGGTATAATGGTA 40289649 ATTTTGCATACATAGGGGTATAATGGTA 1 ATTTTGCATACATAGGGGTATAATGGTA 40289677 ATTTTGCATACATAGGGGTAT 1 ATTTTGCATACATAGGGGTAT 40289698 TCTAGTACAT Statistics Matches: 77, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 77 1.00 ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36 Consensus pattern (28 bp): ATTTTGCATACATAGGGGTATAATGGTA Found at i:40297295 original size:27 final size:27 Alignment explanation
Indices: 40297257--40297345 Score: 117 Period size: 27 Copynumber: 3.2 Consensus size: 27 40297247 GTGACAGAGT * 40297257 CACCAGATACAGATATTTTTGGCAGTGC 1 CACCAGA-ACAGATATTTGTGGCAGTGC * * 40297285 CACCAGAACAGATATATGTGGCAGGGC 1 CACCAGAACAGATATTTGTGGCAGTGC 40297312 CACCAGAACAGATAATTTGTGGCA-TAGC 1 CACCAGAACAGAT-ATTTGTGGCAGT-GC 40297340 CACCAG 1 CACCAG 40297346 GACGCTTCCT Statistics Matches: 54, Mismatches: 5, Indels: 4 0.86 0.08 0.06 Matches are distributed among these distances: 27 30 0.56 28 24 0.44 ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20 Consensus pattern (27 bp): CACCAGAACAGATATTTGTGGCAGTGC Found at i:40297304 original size:55 final size:55 Alignment explanation
Indices: 40297232--40297345 Score: 135 Period size: 55 Copynumber: 2.1 Consensus size: 55 40297222 AGCATGGCTG * * 40297232 CCAGATACAGAAAATGTGACAGAGTCACCAGATACAGAT-ATTTTTGGCAGT-GCCA 1 CCAGATACAGAAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA * * * 40297287 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA 1 CCAGATACAGA-AAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA 40297342 CCAG 1 CCAG 40297346 GACGCTTCCT Statistics Matches: 51, Mismatches: 5, Indels: 6 0.82 0.08 0.10 Matches are distributed among these distances: 54 12 0.24 55 39 0.76 ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19 Consensus pattern (55 bp): CCAGATACAGAAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA Found at i:40297528 original size:28 final size:28 Alignment explanation
Indices: 40297451--40297570 Score: 206 Period size: 28 Copynumber: 4.3 Consensus size: 28 40297441 AAATTAACCC * ** 40297451 TAGGGGTATAAAGGCCATTTTGCATACA 1 TAGGGGTATAATGGTAATTTTGCATACA 40297479 TAGGGGTAT-ATGGTAATTTTGCATACA 1 TAGGGGTATAATGGTAATTTTGCATACA 40297506 TAGGGGTATAATGGTAATTTTGCATACA 1 TAGGGGTATAATGGTAATTTTGCATACA 40297534 TAGGGGTATAATGGTAATTTTGCATACA 1 TAGGGGTATAATGGTAATTTTGCATACA 40297562 TAGGGGTAT 1 TAGGGGTAT 40297571 TCTAGTACAT Statistics Matches: 88, Mismatches: 3, Indels: 2 0.95 0.03 0.02 Matches are distributed among these distances: 27 24 0.27 28 64 0.73 ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34 Consensus pattern (28 bp): TAGGGGTATAATGGTAATTTTGCATACA Found at i:40297535 original size:55 final size:56 Alignment explanation
Indices: 40297451--40297570 Score: 206 Period size: 55 Copynumber: 2.2 Consensus size: 56 40297441 AAATTAACCC * 40297451 TAGGGGTATAAAGGCCATTTTGCATACATAGGGGTAT-ATGGTAATTTTGCATACA 1 TAGGGGTATAAAGGCAATTTTGCATACATAGGGGTATAATGGTAATTTTGCATACA * * 40297506 TAGGGGTATAATGGTAATTTTGCATACATAGGGGTATAATGGTAATTTTGCATACA 1 TAGGGGTATAAAGGCAATTTTGCATACATAGGGGTATAATGGTAATTTTGCATACA 40297562 TAGGGGTAT 1 TAGGGGTAT 40297571 TCTAGTACAT Statistics Matches: 61, Mismatches: 3, Indels: 1 0.94 0.05 0.02 Matches are distributed among these distances: 55 34 0.56 56 27 0.44 ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34 Consensus pattern (56 bp): TAGGGGTATAAAGGCAATTTTGCATACATAGGGGTATAATGGTAATTTTGCATACA Found at i:40303234 original size:17 final size:17 Alignment explanation
Indices: 40303213--40303260 Score: 53 Period size: 17 Copynumber: 2.8 Consensus size: 17 40303203 TGGTTTACTG 40303213 ATTTTAGTTGTTTA-TT 1 ATTTTAGTTGTTTATTT ** 40303229 ATTTTTTCTTGTTTATTT 1 A-TTTTAGTTGTTTATTT * 40303247 ATTTTAGTTATTTA 1 ATTTTAGTTGTTTA 40303261 AATTCTCTTA Statistics Matches: 25, Mismatches: 5, Indels: 3 0.76 0.15 0.09 Matches are distributed among these distances: 16 1 0.04 17 21 0.84 18 3 0.12 ACGTcount: A:0.19, C:0.02, G:0.08, T:0.71 Consensus pattern (17 bp): ATTTTAGTTGTTTATTT Found at i:40306040 original size:40 final size:40 Alignment explanation
Indices: 40306008--40306240 Score: 403 Period size: 40 Copynumber: 5.8 Consensus size: 40 40305998 CCAGCATGAT * * * 40306008 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA 1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA 40306048 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA 1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA * * 40306088 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA 1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA * 40306128 TGCTCTTCGGGACTTGGCCCGGATATATCACTTAGCACGAA 1 TGCTCTTCGGGACTTAGCCCGGATATATCAC-TAGCACGAA 40306169 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA 1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA 40306209 TGCTCTTCGGGACTTAGCCCGGATATATCACT 1 TGCTCTTCGGGACTTAGCCCGGATATATCACT 40306241 CTCAATTCTC Statistics Matches: 183, Mismatches: 9, Indels: 2 0.94 0.05 0.01 Matches are distributed among these distances: 40 144 0.79 41 39 0.21 ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25 Consensus pattern (40 bp): TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA Found at i:40306200 original size:81 final size:81 Alignment explanation
Indices: 40306008--40306240 Score: 405 Period size: 81 Copynumber: 2.9 Consensus size: 81 40305998 CCAGCATGAT * * * 40306008 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATA 1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA 40306073 TATCAC-TAGCACGAA 66 TATCACTTAGCACGAA * * * 40306088 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTGGCCCGGATA 1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA 40306153 TATCACTTAGCACGAA 66 TATCACTTAGCACGAA 40306169 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA 1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA 40306234 TATCACT 66 TATCACT 40306241 CTCAATTCTC Statistics Matches: 143, Mismatches: 9, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 80 65 0.45 81 78 0.55 ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25 Consensus pattern (81 bp): TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA TATCACTTAGCACGAA Found at i:40306221 original size:121 final size:120 Alignment explanation
Indices: 40306008--40306240 Score: 403 Period size: 121 Copynumber: 1.9 Consensus size: 120 40305998 CCAGCATGAT 40306008 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATA 1 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATA * 40306073 TATCACTAGCACGAATGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA 66 TATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA * * * * 40306128 TGCTCTTCGGGACTTGGCCCGGATATATCACTTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT 1 TGCTCTTCGGGACCTAGCCCGGATATAACAC-CAGCACGAATGCTCTTCGGGACTTAGCCCGGAT * 40306193 ATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT 65 ATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACT 40306241 CTCAATTCTC Statistics Matches: 106, Mismatches: 6, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 120 28 0.26 121 78 0.74 ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25 Consensus pattern (120 bp): TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATA TATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA Found at i:40307569 original size:37 final size:37 Alignment explanation
Indices: 40307510--40307618 Score: 173 Period size: 37 Copynumber: 2.9 Consensus size: 37 40307500 AGCTCAGACG * * * * 40307510 AAATCTCTATACGAAGTTATCGGGTCTTACCCGGACA 1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA 40307547 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA 1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA * 40307584 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA 1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA 40307619 ATATATTTCC Statistics Matches: 67, Mismatches: 5, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 37 67 1.00 ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25 Consensus pattern (37 bp): AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA Found at i:40307822 original size:50 final size:50 Alignment explanation
Indices: 40307767--40307864 Score: 162 Period size: 50 Copynumber: 2.0 Consensus size: 50 40307757 CATCGCCTAC 40307767 ATATTTCACACTAG-CCATTCGGCTTTACCACATATACATATCTCATATAT 1 ATATTTCACA-TAGACCATTCGGCTTTACCACATATACATATCTCATATAT * * 40307817 ATATTTCACATTGACCATTCGGCTTTACCACATATGCATATCTCATAT 1 ATATTTCACATAGACCATTCGGCTTTACCACATATACATATCTCATAT 40307865 TCACCACATT Statistics Matches: 45, Mismatches: 2, Indels: 2 0.92 0.04 0.04 Matches are distributed among these distances: 49 2 0.04 50 43 0.96 ACGTcount: A:0.31, C:0.26, G:0.07, T:0.37 Consensus pattern (50 bp): ATATTTCACATAGACCATTCGGCTTTACCACATATACATATCTCATATAT Found at i:40307921 original size:47 final size:47 Alignment explanation
Indices: 40307822--40308014 Score: 246 Period size: 47 Copynumber: 4.1 Consensus size: 47 40307812 TATATATATT * * * * 40307822 TCACATTGACCATTCGGCTTTA-C-CACATATGCATATCTCATATTCA 1 TCACATTGGCCATTCGGCCTTATCACACATATGCAT-GCTCACATTCA * 40307868 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA 1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA * * 40307915 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA 1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA * * * *** 40307962 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA 1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA 40308009 TCACAT 1 TCACAT 40308015 AAAATCCTAA Statistics Matches: 133, Mismatches: 12, Indels: 3 0.90 0.08 0.02 Matches are distributed among these distances: 46 19 0.14 47 103 0.77 48 11 0.08 ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33 Consensus pattern (47 bp): TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA Found at i:40307941 original size:22 final size:22 Alignment explanation
Indices: 40307914--40307985 Score: 58 Period size: 22 Copynumber: 3.1 Consensus size: 22 40307904 GCTCACATTC 40307914 ATCACATTGGCCATTCGGCCTT 1 ATCACATTGGCCATTCGGCCTT * * * 40307936 ATCACATATATG-CATGTTC-ACATT 1 ATCACAT-T-GGCCA--TTCGGCCTT 40307960 CATCACATTGGCCATTCGGCCTT 1 -ATCACATTGGCCATTCGGCCTT 40307983 ATC 1 ATC 40307986 TCATATATAC Statistics Matches: 37, Mismatches: 6, Indels: 14 0.65 0.11 0.25 Matches are distributed among these distances: 22 13 0.35 23 7 0.19 24 7 0.19 25 10 0.27 ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33 Consensus pattern (22 bp): ATCACATTGGCCATTCGGCCTT Found at i:40316003 original size:29 final size:29 Alignment explanation
Indices: 40315911--40315992 Score: 146 Period size: 29 Copynumber: 2.8 Consensus size: 29 40315901 TGACGAGATC 40315911 GGCACTAAGTGTGCGTGCTGGAAATATAT 1 GGCACTAAGTGTGCGTGCTGGAAATATAT 40315940 GGCACTAAGTGTGCGTGCTGGAAATATAT 1 GGCACTAAGTGTGCGTGCTGGAAATATAT ** 40315969 GGCACTAAGTGTGCAAGCTGGAAA 1 GGCACTAAGTGTGCGTGCTGGAAA 40315993 AATACAGCAC Statistics Matches: 51, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 29 51 1.00 ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24 Consensus pattern (29 bp): GGCACTAAGTGTGCGTGCTGGAAATATAT Found at i:40323939 original size:30 final size:30 Alignment explanation
Indices: 40323903--40324004 Score: 127 Period size: 30 Copynumber: 3.5 Consensus size: 30 40323893 GACAAGATTG * * * 40323903 GCACTAAGTGTGCGGGTTTAAAATTGTACA 1 GCACTAAGTGTGCGAGTTTAAAATTATATA * 40323933 GCACTAAGTGTGCGAGTTT--GATTATATA 1 GCACTAAGTGTGCGAGTTTAAAATTATATA * * * 40323961 GCACTAAGTGTGCGAGCTGAAAAATATATA 1 GCACTAAGTGTGCGAGTTTAAAATTATATA 40323991 GCACTAAGTGTGCG 1 GCACTAAGTGTGCG 40324005 GATTCACTAT Statistics Matches: 62, Mismatches: 8, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 28 23 0.37 30 39 0.63 ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28 Consensus pattern (30 bp): GCACTAAGTGTGCGAGTTTAAAATTATATA Found at i:40327515 original size:27 final size:28 Alignment explanation
Indices: 40327475--40327542 Score: 81 Period size: 27 Copynumber: 2.5 Consensus size: 28 40327465 AGCATGGCTG * * 40327475 CCAGA-ACAGATAAT-GT-GACAGAGTCA 1 CCAGATACAGATAATCATGGAC-GAGCCA 40327501 CCAGATACAGATAATCATGGACGAGCCA 1 CCAGATACAGATAATCATGGACGAGCCA 40327529 CCAGAT-CAGATAAT 1 CCAGATACAGATAAT 40327543 TGTTGCATAG Statistics Matches: 37, Mismatches: 2, Indels: 5 0.84 0.05 0.11 Matches are distributed among these distances: 26 5 0.14 27 17 0.46 28 12 0.32 29 3 0.08 ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16 Consensus pattern (28 bp): CCAGATACAGATAATCATGGACGAGCCA Found at i:40331488 original size:14 final size:14 Alignment explanation
Indices: 40331469--40331497 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 40331459 CATGTGTAGG 40331469 ATTTGTGAGTTTTT 1 ATTTGTGAGTTTTT 40331483 ATTTGTGAGTTTTT 1 ATTTGTGAGTTTTT 40331497 A 1 A 40331498 GTTAAGGGGT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.17, C:0.00, G:0.21, T:0.62 Consensus pattern (14 bp): ATTTGTGAGTTTTT Found at i:40334473 original size:29 final size:29 Alignment explanation
Indices: 40334440--40334541 Score: 150 Period size: 29 Copynumber: 3.5 Consensus size: 29 40334430 TGACGAGATC 40334440 GGCACTAAGTGTGCGTGCTGGAAATATAT 1 GGCACTAAGTGTGCGTGCTGGAAATATAT 40334469 GGCACTAAGTGTGCGTGCTGGAAATATAT 1 GGCACTAAGTGTGCGTGCTGGAAATATAT ** * * 40334498 GGCACTAAGTGTGCAAGCTGGAAAAATAC 1 GGCACTAAGTGTGCGTGCTGGAAATATAT ** 40334527 GGCACTGGGTGTGCG 1 GGCACTAAGTGTGCG 40334542 AGCTCGGAGG Statistics Matches: 66, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 29 66 1.00 ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24 Consensus pattern (29 bp): GGCACTAAGTGTGCGTGCTGGAAATATAT Found at i:40340431 original size:42 final size:42 Alignment explanation
Indices: 40340378--40340491 Score: 117 Period size: 43 Copynumber: 2.7 Consensus size: 42 40340368 TTAGAATTTA * 40340378 CGTGTAAGACCATATCTGGGATATGGCATCAG-TATGAGAAT-T 1 CGTGTAAGACCATATCTGGGATATGGCAT-AGATATGAG-ATCC * * * * 40340420 CGTGTAAGACCATAGT-GGGGCTATTGGAATTGATATGAGATCC 1 CGTGTAAGACCATA-TCTGGGATA-TGGCATAGATATGAGATCC * 40340463 CATGTAAGACCATATCTGGGATATGGCAT 1 CGTGTAAGACCATATCTGGGATATGGCAT 40340492 TGGTATATTA Statistics Matches: 58, Mismatches: 9, Indels: 10 0.75 0.12 0.13 Matches are distributed among these distances: 42 28 0.48 43 30 0.52 ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28 Consensus pattern (42 bp): CGTGTAAGACCATATCTGGGATATGGCATAGATATGAGATCC Found at i:40345526 original size:39 final size:39 Alignment explanation
Indices: 40345471--40345651 Score: 274 Period size: 39 Copynumber: 4.6 Consensus size: 39 40345461 CAGCGATGTT ** 40345471 TATCCGGACTTTGGGTCCGCAGGCTATGTGCTGGAATTA 1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA * 40345510 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA 1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA 40345549 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA 1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA * * * 40345588 TAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATA 1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA * * 40345627 TATCCGGGC-TAAAGTCCCGCAGGCT 1 TATCCGGACTTAAGGT-CCGCAGGCT 40345652 TCGAGCTAGT Statistics Matches: 133, Mismatches: 8, Indels: 2 0.93 0.06 0.01 Matches are distributed among these distances: 38 5 0.04 39 128 0.96 ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26 Consensus pattern (39 bp): TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA Found at i:40353583 original size:40 final size:40 Alignment explanation
Indices: 40353498--40353600 Score: 129 Period size: 40 Copynumber: 2.6 Consensus size: 40 40353488 CCCTGCACAC * * 40353498 CAACTCCATCCAACCCGACACACC--ATGTGAGGATAAAAT 1 CAAC-CCATCCAACCCTACACACCAAATATGAGGATAAAAT ** * * 40353537 TGACCCATCCATCTCTACACACCAAATATGAGGATAAAAT 1 CAACCCATCCAACCCTACACACCAAATATGAGGATAAAAT 40353577 CAACCCATCCAACCCTACACACCA 1 CAACCCATCCAACCCTACACACCA 40353601 TAAAGTATCG Statistics Matches: 52, Mismatches: 10, Indels: 3 0.80 0.15 0.05 Matches are distributed among these distances: 38 16 0.31 39 2 0.04 40 34 0.65 ACGTcount: A:0.39, C:0.36, G:0.09, T:0.17 Consensus pattern (40 bp): CAACCCATCCAACCCTACACACCAAATATGAGGATAAAAT Found at i:40357102 original size:16 final size:16 Alignment explanation
Indices: 40357050--40357109 Score: 59 Period size: 16 Copynumber: 3.7 Consensus size: 16 40357040 CTGTTTTGAT * 40357050 TATTTTTA-TTTTGAA 1 TATTTTTATTTTTAAA * * 40357065 TTTTTTTAGTTAATTAAA 1 TATTTTTA-TT-TTTAAA * 40357083 TATTTTTATTTTTTAA 1 TATTTTTATTTTTAAA 40357099 TATTTTTATTT 1 TATTTTTATTT 40357110 ACCTTGTTGA Statistics Matches: 36, Mismatches: 6, Indels: 5 0.77 0.13 0.11 Matches are distributed among these distances: 15 7 0.19 16 15 0.42 17 3 0.08 18 11 0.31 ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70 Consensus pattern (16 bp): TATTTTTATTTTTAAA Found at i:40359754 original size:22 final size:22 Alignment explanation
Indices: 40359715--40359773 Score: 70 Period size: 21 Copynumber: 2.8 Consensus size: 22 40359705 GTTTTAAGAA * 40359715 TTGTTTTAGTA-TTATTTTTAT 1 TTGTTTTAATATTTATTTTTAT 40359736 TTGTTTTAATATTTATTTTTAT 1 TTGTTTTAATATTTATTTTTAT * * 40359758 AT-TTTTAA-ATATATTT 1 TTGTTTTAATATTTATTT 40359774 GATTTATTAT Statistics Matches: 34, Mismatches: 3, Indels: 3 0.85 0.08 0.08 Matches are distributed among these distances: 20 7 0.21 21 16 0.47 22 11 0.32 ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69 Consensus pattern (22 bp): TTGTTTTAATATTTATTTTTAT Found at i:40359771 original size:24 final size:25 Alignment explanation
Indices: 40359744--40359803 Score: 88 Period size: 26 Copynumber: 2.4 Consensus size: 25 40359734 ATTTGTTTTA 40359744 ATATTTATTT-TTATATTTTTAAAT 1 ATATTTATTTATTATATTTTTAAAT 40359768 ATATTTGATTTATTATATTTTTAAAT 1 ATATTT-ATTTATTATATTTTTAAAT * 40359794 -TTTTTATTTA 1 ATATTTATTTA 40359804 ATAAAATAAG Statistics Matches: 33, Mismatches: 1, Indels: 4 0.87 0.03 0.11 Matches are distributed among these distances: 24 11 0.33 25 8 0.24 26 14 0.42 ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67 Consensus pattern (25 bp): ATATTTATTTATTATATTTTTAAAT Found at i:40364209 original size:16 final size:16 Alignment explanation
Indices: 40364188--40364220 Score: 57 Period size: 16 Copynumber: 2.1 Consensus size: 16 40364178 CCATATTCAA * 40364188 TCAGAATTTGTTTAAG 1 TCAGAATCTGTTTAAG 40364204 TCAGAATCTGTTTAAG 1 TCAGAATCTGTTTAAG 40364220 T 1 T 40364221 GACCTAGCTC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42 Consensus pattern (16 bp): TCAGAATCTGTTTAAG Found at i:40367138 original size:16 final size:16 Alignment explanation
Indices: 40367117--40367150 Score: 68 Period size: 16 Copynumber: 2.1 Consensus size: 16 40367107 CCATACTATG 40367117 AAAGAATTGAAACATA 1 AAAGAATTGAAACATA 40367133 AAAGAATTGAAACATA 1 AAAGAATTGAAACATA 40367149 AA 1 AA 40367151 TCTTTTTTCC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18 Consensus pattern (16 bp): AAAGAATTGAAACATA Found at i:40368328 original size:54 final size:54 Alignment explanation
Indices: 40368194--40368328 Score: 234 Period size: 54 Copynumber: 2.5 Consensus size: 54 40368184 GTTGTTAAAA ** 40368194 GGGATTTAGCCTGGACTGGTAATCCTAACATTGCTCTATGAGTTTTTACTACGG 1 GGGATTTAGCCTGGACTGGTAATCCCGACATTGCTCTATGAGTTTTTACTACGG * * 40368248 GGGATTTAGCTTGGACTGGTAATCCCGGCATTGCTCTATGAGTTTTTACTACGG 1 GGGATTTAGCCTGGACTGGTAATCCCGACATTGCTCTATGAGTTTTTACTACGG 40368302 GGGATTTAGCCTGGACTGGTAATCCCG 1 GGGATTTAGCCTGGACTGGTAATCCCG 40368329 CCGTAAGATG Statistics Matches: 76, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 54 76 1.00 ACGTcount: A:0.20, C:0.19, G:0.27, T:0.33 Consensus pattern (54 bp): GGGATTTAGCCTGGACTGGTAATCCCGACATTGCTCTATGAGTTTTTACTACGG Found at i:40370246 original size:27 final size:28 Alignment explanation
Indices: 40370193--40370246 Score: 65 Period size: 27 Copynumber: 2.0 Consensus size: 28 40370183 TAAAATTTAA * 40370193 AAAAAAATAAAATATTATAAAGGTCATG 1 AAAAAAATAAAATATTATAAAAGTCATG * * * 40370221 AAAAATATAAAA-ATTTTAAAATTCAT 1 AAAAAAATAAAATATTATAAAAGTCAT 40370247 TATCAAAATA Statistics Matches: 22, Mismatches: 4, Indels: 1 0.81 0.15 0.04 Matches are distributed among these distances: 27 11 0.50 28 11 0.50 ACGTcount: A:0.61, C:0.04, G:0.06, T:0.30 Consensus pattern (28 bp): AAAAAAATAAAATATTATAAAAGTCATG Found at i:40374007 original size:146 final size:149 Alignment explanation
Indices: 40373720--40374019 Score: 473 Period size: 146 Copynumber: 2.0 Consensus size: 149 40373710 GAATCATCCC * 40373720 CATTTTGCAGAATATAAGATAAAATAAAAACTATACAACACAGAATGCTATCAAAGGTATCAATG 1 CATTCTGCAGAATATAAGATAAAATAAAAACTATACAACACAGAATGCTATCAAAGGTATCAATG 40373785 TCTGCTACCATATAAAATGACAGTTGATGAAGGAAGCAAACTTTTTCTTTGAAGAACGTAAAATT 66 TCTG---CCATAT--AATGACAGTTGATGAAGGAAGCAAACTTTTTCTTTGAAGAACGTAAAATT 40373850 CAAGCATAAAATCAGTGAAATCAA 126 CAAGCATAAAATCAGTGAAATCAA * * * 40373874 CATTCTGCAGAATATAGGATAAAATAAAAACTATACACCATAGAATGCTA-CAAAAGGTATCAAT 1 CATTCTGCAGAATATAAGATAAAATAAAAACTATACAACACAGAATGCTATC-AAAGGTATCAAT 40373938 GTCTG-C-TAT-ATGACAGTTGATGAAGGAAGCAAACTTTTTCTTTGAAGAACGTAAAATTCAAG 65 GTCTGCCATATAATGACAGTTGATGAAGGAAGCAAACTTTTTCTTTGAAGAACGTAAAATTCAAG * 40374000 CCTAAAATCAGTGAAATCAA 130 CATAAAATCAGTGAAATCAA 40374020 TCTATCTTAC Statistics Matches: 140, Mismatches: 5, Indels: 10 0.90 0.03 0.06 Matches are distributed among these distances: 146 72 0.51 149 3 0.02 150 1 0.01 153 1 0.01 154 63 0.45 ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26 Consensus pattern (149 bp): CATTCTGCAGAATATAAGATAAAATAAAAACTATACAACACAGAATGCTATCAAAGGTATCAATG TCTGCCATATAATGACAGTTGATGAAGGAAGCAAACTTTTTCTTTGAAGAACGTAAAATTCAAGC ATAAAATCAGTGAAATCAA Found at i:40374950 original size:25 final size:26 Alignment explanation
Indices: 40374907--40374959 Score: 74 Period size: 24 Copynumber: 2.1 Consensus size: 26 40374897 TATTGTTTAA * 40374907 TTTTAATTTTTTTCATTTCTAACATTT 1 TTTTAATTTTTTTCATTTC-AAAATTT 40374934 TTTTAA-TTTTTTC-TTTCAAAATTT 1 TTTTAATTTTTTTCATTTCAAAATTT 40374958 TT 1 TT 40374960 GTGCTGAGTT Statistics Matches: 25, Mismatches: 1, Indels: 3 0.86 0.03 0.10 Matches are distributed among these distances: 24 8 0.32 25 4 0.16 26 7 0.28 27 6 0.24 ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68 Consensus pattern (26 bp): TTTTAATTTTTTTCATTTCAAAATTT Found at i:40375062 original size:8 final size:8 Alignment explanation
Indices: 40375045--40375117 Score: 76 Period size: 8 Copynumber: 8.9 Consensus size: 8 40375035 ATATTAAATA * 40375045 TTAAAATT 1 TTAAATTT * 40375053 TTAAGTTT 1 TTAAATTT 40375061 TT-AATTT 1 TTAAATTT * 40375068 TTTAATTT 1 TTAAATTT 40375076 TTAAATTT 1 TTAAATTT * 40375084 TTAATTTT 1 TTAAATTT 40375092 TTGAAGATTT 1 TT-AA-ATTT 40375102 TTATAATTT 1 TTA-AATTT 40375111 TTAAATT 1 TTAAATT 40375118 AACATATAAA Statistics Matches: 55, Mismatches: 6, Indels: 8 0.80 0.09 0.12 Matches are distributed among these distances: 7 6 0.11 8 33 0.60 9 10 0.18 10 6 0.11 ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63 Consensus pattern (8 bp): TTAAATTT Found at i:40375386 original size:21 final size:21 Alignment explanation
Indices: 40375357--40375397 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 21 40375347 TTAGGGCTTG * * 40375357 GGGTTTAAGGATTGGGGTTTA 1 GGGTCTAAGGATTGGAGTTTA * 40375378 GGGTCTAAGGGTTGGAGTTT 1 GGGTCTAAGGATTGGAGTTT 40375398 TAAGGGTTTA Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.17, C:0.02, G:0.44, T:0.37 Consensus pattern (21 bp): GGGTCTAAGGATTGGAGTTTA Found at i:40375486 original size:22 final size:22 Alignment explanation
Indices: 40375396--40375490 Score: 83 Period size: 21 Copynumber: 4.4 Consensus size: 22 40375386 GGGTTGGAGT 40375396 TTTAAGGGTTTATGATTTGAGA 1 TTTAAGGGTTTATGATTTGAGA * * * 40375418 TTT-AGGGTTTAGGGTGTTGGGA 1 TTTAAGGGTTTATGAT-TTGAGA * * 40375440 -TTAA-GGTTTATCG-TTTATAGT 1 TTTAAGGGTTTAT-GATTT-GAGA 40375461 TTTAAGGGTTTATGATTTGAGA 1 TTTAAGGGTTTATGATTTGAGA 40375483 TTT-AGGGT 1 TTTAAGGGT 40375491 CTGGTGTTTA Statistics Matches: 57, Mismatches: 9, Indels: 15 0.70 0.11 0.19 Matches are distributed among these distances: 20 2 0.04 21 25 0.44 22 20 0.35 23 10 0.18 ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46 Consensus pattern (22 bp): TTTAAGGGTTTATGATTTGAGA Found at i:40375551 original size:66 final size:66 Alignment explanation
Indices: 40375452--40375576 Score: 214 Period size: 66 Copynumber: 1.9 Consensus size: 66 40375442 AAGGTTTATC * * * 40375452 GTTTATAGTTTTAAGGGTTTATGATTTGAGATTTAGGGTCTGGTGTTTAAAGAGTTATTAATTAG 1 GTTTATAGTTTTAAGGGTTTATGATTAGAGATTTAGGGTCTGGGGGTTAAAGAGTTATTAATTAG 40375517 T 66 T * 40375518 GTTTATAGTTTTAAGGGTTTATGATTAGAGATTTAGGGTCTGGGGGTTAAAGGGTTATT 1 GTTTATAGTTTTAAGGGTTTATGATTAGAGATTTAGGGTCTGGGGGTTAAAGAGTTATT 40375577 GATTTAAGAG Statistics Matches: 55, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 66 55 1.00 ACGTcount: A:0.25, C:0.02, G:0.29, T:0.45 Consensus pattern (66 bp): GTTTATAGTTTTAAGGGTTTATGATTAGAGATTTAGGGTCTGGGGGTTAAAGAGTTATTAATTAG T Found at i:40375604 original size:66 final size:66 Alignment explanation
Indices: 40375462--40375590 Score: 159 Period size: 66 Copynumber: 1.9 Consensus size: 66 40375452 GTTTATAGTT * * * * * * 40375462 TTAAGGGTTTATGATTTGAGATTTAGGGTCTGGTGTTTAAAGAGTTATTAATTAGTGTTTATAGT 1 TTAAGGGTTTATGATTAGAGATTTAGGGTCTGGGGGTTAAAGAGTTATTAATTAGAGGTTATAGG * 40375527 T 66 G * * 40375528 TTAAGGGTTTATGATTAGAGATTTAGGGTCTGGGGGTTAAAGGGTTATTGATTTAAGAGGTTA 1 TTAAGGGTTTATGATTAGAGATTTAGGGTCTGGGGGTTAAAGAGTTATT-AATT-AGAGGTTA 40375591 GGGGTTAGTG Statistics Matches: 54, Mismatches: 7, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 66 45 0.83 67 3 0.06 68 6 0.11 ACGTcount: A:0.26, C:0.02, G:0.29, T:0.43 Consensus pattern (66 bp): TTAAGGGTTTATGATTAGAGATTTAGGGTCTGGGGGTTAAAGAGTTATTAATTAGAGGTTATAGG G Found at i:40376335 original size:41 final size:40 Alignment explanation
Indices: 40376262--40376533 Score: 355 Period size: 41 Copynumber: 6.7 Consensus size: 40 40376252 TTAAAAAAGT * ** 40376262 GCCGCTAATGCTCGACCTTTAGCGATGCTTTCTTAAAAAC 1 GCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAAC * * * * 40376302 GCCGCTAATGCTCAGATCTTTTGCGGTGATTTCTTAAAAAT 1 GCCGCTAATGCTC-GATCTTTAGCGGCGCTTTCTTAAAAAC 40376343 GCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAAC 1 GCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAAC * 40376383 GCCGCTAATGCTCAGATCTTTAGCGGCGCTTTCTTAAAAAAGT 1 GCCGCTAATGCTC-GATCTTTAGCGGCGCTTTCTT-AAAAA-C * * * 40376426 GCCGCTAGTGCTCGATCTTTAGTGGCACTTTCTTAAAAAC 1 GCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAAC * * * * 40376466 CCCGCTAATGCTCACATCATTAGCGGCGCTTTTTTAAAAAC 1 GCCGCTAATGCTC-GATCTTTAGCGGCGCTTTCTTAAAAAC * 40376507 GCCGCTAATACTCGATCTTTAGCGGCG 1 GCCGCTAATGCTCGATCTTTAGCGGCG 40376534 TTTTAAAAAA Statistics Matches: 202, Mismatches: 25, Indels: 10 0.85 0.11 0.04 Matches are distributed among these distances: 40 72 0.36 41 94 0.47 42 24 0.12 43 12 0.06 ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31 Consensus pattern (40 bp): GCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAAC Found at i:40376363 original size:81 final size:82 Alignment explanation
Indices: 40376255--40376564 Score: 401 Period size: 81 Copynumber: 3.8 Consensus size: 82 40376245 GGTGTTTTTA * ** 40376255 AAAAAGTGCCGCTAATGCTCGACCTTTAGCGATGCTTTCTTAAAAACGCCGCTAATGCTCAGATC 1 AAAAAGTGCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAATGCTCAGATC * * * 40376320 TTTTGCGGTGATTTCTT 66 TTTAGCGGCGCTTTCTT 40376337 AAAAA-TGCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAATGCTCAGATC 1 AAAAAGTGCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAATGCTCAGATC 40376401 TTTAGCGGCGCTTTCTT 66 TTTAGCGGCGCTTTCTT * * * * * 40376418 AAAAAAGTGCCGCTAGTGCTCGATCTTTAGTGGCACTTTCTTAAAAACCCCGCTAATGCTCACAT 1 -AAAAAGTGCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAATGCTCAGAT * * 40376483 CATTAGCGGCGCTTTTTT 65 CTTTAGCGGCGCTTTCTT * * * *** * * 40376501 AAAAA-CGCCGCTAATACTCGATCTTTAGCGGCGTTTTAAAAAAAAGGCCGCTAATACTCA-ATC 1 AAAAAGTGCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAATGCTCAGATC 40376564 T 66 T 40376565 ATTCGATTTT Statistics Matches: 200, Mismatches: 26, Indels: 6 0.86 0.11 0.03 Matches are distributed among these distances: 80 3 0.01 81 113 0.56 82 15 0.08 83 69 0.34 ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30 Consensus pattern (82 bp): AAAAAGTGCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAACGCCGCTAATGCTCAGATC TTTAGCGGCGCTTTCTT Found at i:40376523 original size:164 final size:163 Alignment explanation
Indices: 40376252--40376564 Score: 428 Period size: 164 Copynumber: 1.9 Consensus size: 163 40376242 AGTGGTGTTT ** * * 40376252 TTAAAAAAGTGCCGCTAATGCTCGACCTTTAGCGATGCTTTCTTAAAAACGCCGCTAATGCTCAG 1 TTAAAAAAGTGCCGCTAATGCTCGACCTTTAGCGACACTTTCTTAAAAACCCCGCTAATGCTCAC * * * * * *** 40376317 ATCTTTTGCGGTGATTTCTTAAAAATGCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAA 66 ATCATTAGCGGCGATTTCTTAAAAACGCCGCTAATACTCGATCTTTAGCGGCGCTTTAAAAAAAA * 40376382 CGCCGCTAATGCTCAGATCTTTAGCGGCGCTTTC 131 CGCCGCTAATACTCA-ATCTTTAGCGGCGCTTTC * * * * 40376416 TTAAAAAAGTGCCGCTAGTGCTCGATCTTTAGTGGCACTTTCTTAAAAACCCCGCTAATGCTCAC 1 TTAAAAAAGTGCCGCTAATGCTCGACCTTTAGCGACACTTTCTTAAAAACCCCGCTAATGCTCAC * * * 40376481 ATCATTAGCGGCGCTTTTTTAAAAACGCCGCTAATACTCGATCTTTAGCGGCGTTTTAAAAAAAA 66 ATCATTAGCGGCGATTTCTTAAAAACGCCGCTAATACTCGATCTTTAGCGGCGCTTTAAAAAAAA * 40376546 GGCCGCTAATACTCAATCT 131 CGCCGCTAATACTCAATCT 40376565 ATTCGATTTT Statistics Matches: 128, Mismatches: 21, Indels: 1 0.85 0.14 0.01 Matches are distributed among these distances: 163 4 0.03 164 124 0.97 ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31 Consensus pattern (163 bp): TTAAAAAAGTGCCGCTAATGCTCGACCTTTAGCGACACTTTCTTAAAAACCCCGCTAATGCTCAC ATCATTAGCGGCGATTTCTTAAAAACGCCGCTAATACTCGATCTTTAGCGGCGCTTTAAAAAAAA CGCCGCTAATACTCAATCTTTAGCGGCGCTTTC Found at i:40376545 original size:40 final size:40 Alignment explanation
Indices: 40376262--40376564 Score: 320 Period size: 40 Copynumber: 7.5 Consensus size: 40 40376252 TTAAAAAAGT * ** * 40376262 GCCGCTAATGCTCGACCTTTAGCGATGCTTTCTTAAAAAC 1 GCCGCTAATGCTCGATCTTTAGCGGCGTTTTCTTAAAAAC * * * * 40376302 GCCGCTAATGCTCAGATCTTTTGCGGTGATTTCTTAAAAAT 1 GCCGCTAATGCTC-GATCTTTAGCGGCGTTTTCTTAAAAAC * 40376343 GCCGCTAATGCTCGATCTTTAGCGGCGCTTTCTTAAAAAC 1 GCCGCTAATGCTCGATCTTTAGCGGCGTTTTCTTAAAAAC * * 40376383 GCCGCTAATGCTCAGATCTTTAGCGGCGCTTTCTTAAAAAAGT 1 GCCGCTAATGCTC-GATCTTTAGCGGCGTTTTCTT-AAAAA-C * * ** 40376426 GCCGCTAGTGCTCGATCTTTAGTGGCACTTTCTTAAAAAC 1 GCCGCTAATGCTCGATCTTTAGCGGCGTTTTCTTAAAAAC * * * 40376466 CCCGCTAATGCTCACATCATTAGCGGCGCTTTT-TTAAAAAC 1 GCCGCTAATGCTC-GATCTTTAGCGGCG-TTTTCTTAAAAAC * *** * 40376507 GCCGCTAATACTCGATCTTTAGCGGCGTTTTAAAAAAAAG 1 GCCGCTAATGCTCGATCTTTAGCGGCGTTTTCTTAAAAAC * * 40376547 GCCGCTAATACTCAATCT 1 GCCGCTAATGCTCGATCT 40376565 ATTCGATTTT Statistics Matches: 227, Mismatches: 29, Indels: 14 0.84 0.11 0.05 Matches are distributed among these distances: 39 4 0.02 40 94 0.41 41 90 0.40 42 27 0.12 43 12 0.05 ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31 Consensus pattern (40 bp): GCCGCTAATGCTCGATCTTTAGCGGCGTTTTCTTAAAAAC Found at i:40386441 original size:25 final size:25 Alignment explanation
Indices: 40386407--40386456 Score: 100 Period size: 25 Copynumber: 2.0 Consensus size: 25 40386397 TCGGGATCGG 40386407 GAGGCATCACACTATCACAGGTAGT 1 GAGGCATCACACTATCACAGGTAGT 40386432 GAGGCATCACACTATCACAGGTAGT 1 GAGGCATCACACTATCACAGGTAGT 40386457 AATATAGCAT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 25 1.00 ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20 Consensus pattern (25 bp): GAGGCATCACACTATCACAGGTAGT Found at i:40389543 original size:93 final size:93 Alignment explanation
Indices: 40389414--40389585 Score: 299 Period size: 93 Copynumber: 1.8 Consensus size: 93 40389404 CGCCCATAAG * * 40389414 CGAACTCGGACTCAACTCAAAGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 CGAACTCGGACTCAACTCAAAGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 40389479 ACAAGTTCGGATGCCTAGTTACATTTCA 66 ACAAGTTCGGATGCCTAGTTACATTTCA * * 40389507 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 CGAACTCGGACTCAACTCAAAGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA * 40389572 ACGAGTTCGGATGC 66 ACAAGTTCGGATGC 40389586 TCAACCATCC Statistics Matches: 74, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 93 74 1.00 ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22 Consensus pattern (93 bp): CGAACTCGGACTCAACTCAAAGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA ACAAGTTCGGATGCCTAGTTACATTTCA Found at i:40389582 original size:46 final size:46 Alignment explanation
Indices: 40389407--40389582 Score: 189 Period size: 46 Copynumber: 3.8 Consensus size: 46 40389397 TGTAACCCGC * * * * 40389407 CCATAAGCGAACTCGGACTCAACTCAAAGAGCTCGGGCGTTCGCAT 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT * * * 40389453 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGATGCCTAGTT-ACAT 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT * * 40389503 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT * 40389546 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA 40389583 TGCTCAACCA Statistics Matches: 106, Mismatches: 15, Indels: 18 0.76 0.11 0.13 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 44 1 0.01 45 2 0.02 46 61 0.58 47 28 0.26 48 2 0.02 49 1 0.01 50 3 0.03 51 2 0.02 ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21 Consensus pattern (46 bp): CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT Found at i:40389601 original size:46 final size:46 Alignment explanation
Indices: 40389456--40389594 Score: 126 Period size: 47 Copynumber: 3.0 Consensus size: 46 40389446 TTCGCATCCA * * 40389456 TAAGTGAACTCGGACTCAACTCAACAAGTTCGGATGC-CTAGTTA-CATT 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC * * * * * 40389504 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA-- 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC 40389549 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC 40389595 CTAGTGACAT Statistics Matches: 74, Mismatches: 10, Indels: 16 0.74 0.10 0.16 Matches are distributed among these distances: 44 8 0.11 45 2 0.03 46 28 0.38 47 29 0.39 48 2 0.03 49 4 0.05 50 1 0.01 ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23 Consensus pattern (46 bp): TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC Found at i:40390039 original size:30 final size:30 Alignment explanation
Indices: 40390004--40390060 Score: 87 Period size: 30 Copynumber: 1.9 Consensus size: 30 40389994 TAACTCAAAT 40390004 TTTTGCAAAATTACAATTTTGCCCCTAAAC 1 TTTTGCAAAATTACAATTTTGCCCCTAAAC * * * 40390034 TTTTGCATATTTACATTTTTGCCCCTA 1 TTTTGCAAAATTACAATTTTGCCCCTA 40390061 GGCTCGGGAT Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 30 24 1.00 ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44 Consensus pattern (30 bp): TTTTGCAAAATTACAATTTTGCCCCTAAAC Found at i:40391948 original size:28 final size:28 Alignment explanation
Indices: 40391903--40391971 Score: 122 Period size: 28 Copynumber: 2.5 Consensus size: 28 40391893 CTTAAAACCC * 40391903 TAGGGGT-ATATCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 40391930 TAGGGGTAATTTCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 40391958 TAGGGGTAATTTCG 1 TAGGGGTAATTTCG 40391972 TCATCTACGC Statistics Matches: 40, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 27 7 0.17 28 33 0.82 ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43 Consensus pattern (28 bp): TAGGGGTAATTTCGGTAATTTTGCTCTT Found at i:40393821 original size:19 final size:18 Alignment explanation
Indices: 40393784--40393827 Score: 54 Period size: 19 Copynumber: 2.4 Consensus size: 18 40393774 ATACATACAG 40393784 TAAT-ATTTTTCTAATAA 1 TAATAATTTTTCTAATAA * 40393801 TAATAATTTTATCTCATAA 1 TAATAATTTT-TCTAATAA * 40393820 TACTAATT 1 TAATAATT 40393828 AAAATTTCAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 17 4 0.17 18 5 0.22 19 14 0.61 ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50 Consensus pattern (18 bp): TAATAATTTTTCTAATAA Found at i:40396251 original size:27 final size:28 Alignment explanation
Indices: 40396207--40396274 Score: 113 Period size: 27 Copynumber: 2.5 Consensus size: 28 40396197 CTTAAAACCC * 40396207 TAGGGGT-ATATCGGTAATTTTGCT-TT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 40396233 TAGGGGTAATTTCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 40396261 TAGGGGTAATTTCG 1 TAGGGGTAATTTCG 40396275 TGATCTACGC Statistics Matches: 39, Mismatches: 1, Indels: 2 0.93 0.02 0.05 Matches are distributed among these distances: 26 7 0.18 27 16 0.41 28 16 0.41 ACGTcount: A:0.19, C:0.09, G:0.28, T:0.44 Consensus pattern (28 bp): TAGGGGTAATTTCGGTAATTTTGCTCTT Found at i:40398118 original size:19 final size:18 Alignment explanation
Indices: 40398081--40398124 Score: 54 Period size: 19 Copynumber: 2.4 Consensus size: 18 40398071 ATACATACAG 40398081 TAAT-ATTTTTCTAATAA 1 TAATAATTTTTCTAATAA * 40398098 TAATAATTTTATCTCATAA 1 TAATAATTTT-TCTAATAA * 40398117 TACTAATT 1 TAATAATT 40398125 AAAATTTCAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 17 4 0.17 18 5 0.22 19 14 0.61 ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50 Consensus pattern (18 bp): TAATAATTTTTCTAATAA Found at i:40398534 original size:68 final size:64 Alignment explanation
Indices: 40398420--40398573 Score: 168 Period size: 68 Copynumber: 2.3 Consensus size: 64 40398410 ACATGGAACT * * * * * 40398420 ATACATGCGACCTAGCTACATATATCCTGTAGCTCTCTTGTCTACATGGTGTACACAT-AGTATC 1 ATACATGTGACCTAGCTACATATATCCTGTAGCTCTCTTGTATACATGATGTACAC-TCAGCACC * * * 40398484 ACT-CATGTGACCTAGCTACATCATAATGTCTCGTATCTCTCTTGTATACATGATGTGCACTCAG 1 A-TACATGTGACCTAGCTACAT-AT-AT-CCT-GTAGCTCTCTTGTATACATGATGTACACTCAG 40398548 CACC 61 CACC 40398552 ATACATGTGACCTAGCTACATA 1 ATACATGTGACCTAGCTACATA 40398574 CCATCTGTAT Statistics Matches: 75, Mismatches: 8, Indels: 11 0.80 0.09 0.12 Matches are distributed among these distances: 64 18 0.24 65 3 0.04 66 2 0.03 67 5 0.07 68 47 0.63 ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32 Consensus pattern (64 bp): ATACATGTGACCTAGCTACATATATCCTGTAGCTCTCTTGTATACATGATGTACACTCAGCACC Found at i:40399076 original size:30 final size:30 Alignment explanation
Indices: 40399042--40399098 Score: 87 Period size: 30 Copynumber: 1.9 Consensus size: 30 40399032 TAACTCAAAA 40399042 TTTTGCAAAATTACAATTTTGCCCCTAAAC 1 TTTTGCAAAATTACAATTTTGCCCCTAAAC * * * 40399072 TTTTGCATATTTACACTTTTGCCCCTA 1 TTTTGCAAAATTACAATTTTGCCCCTA 40399099 GGCTCGAGAA Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 30 24 1.00 ACGTcount: A:0.26, C:0.25, G:0.07, T:0.42 Consensus pattern (30 bp): TTTTGCAAAATTACAATTTTGCCCCTAAAC Found at i:40409800 original size:28 final size:29 Alignment explanation
Indices: 40409733--40409804 Score: 112 Period size: 29 Copynumber: 2.5 Consensus size: 29 40409723 ATACTGAATC * 40409733 CGCACACTTAGTGCTATATATATTCAGCT 1 CGCACACTTAGTGCTATATATATTCAACT 40409762 CGCACACTTAGTGCTATATA-A-TCAAACT 1 CGCACACTTAGTGCTATATATATTC-AACT 40409790 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 40409805 GTACAATTTT Statistics Matches: 41, Mismatches: 1, Indels: 3 0.91 0.02 0.07 Matches are distributed among these distances: 27 2 0.05 28 19 0.46 29 20 0.49 ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31 Consensus pattern (29 bp): CGCACACTTAGTGCTATATATATTCAACT Found at i:40409826 original size:30 final size:28 Alignment explanation
Indices: 40409732--40409833 Score: 89 Period size: 28 Copynumber: 3.5 Consensus size: 28 40409722 TATACTGAAT * * 40409732 CCGCACACTTAGTGCTATATATATTC-AGC 1 CCGCACACTTAGTGCTATACA-A-TCAAAC * * 40409761 TCGCACACTTAGTGCTATATAATCAAAC 1 CCGCACACTTAGTGCTATACAATCAAAC * * * 40409789 TCGCACACTTAGTGCTGTACAATTTTAAAC 1 CCGCACACTTAGTGCTATACAA--TCAAAC * 40409819 CCGCACACTCAGTGC 1 CCGCACACTTAGTGC 40409834 CAATCTTGTC Statistics Matches: 63, Mismatches: 7, Indels: 5 0.84 0.09 0.07 Matches are distributed among these distances: 27 2 0.03 28 23 0.37 29 20 0.32 30 18 0.29 ACGTcount: A:0.29, C:0.28, G:0.14, T:0.28 Consensus pattern (28 bp): CCGCACACTTAGTGCTATACAATCAAAC Found at i:40411145 original size:18 final size:17 Alignment explanation
Indices: 40411122--40411165 Score: 52 Period size: 17 Copynumber: 2.5 Consensus size: 17 40411112 TCCACACTCT 40411122 TTTTTTTTCATCATTTTC 1 TTTTTTTTCATCA-TTTC ** 40411140 TTTTTTTTTTTCATTTC 1 TTTTTTTTCATCATTTC * 40411157 TTTATTTTC 1 TTTTTTTTC 40411166 CTTCCATAAT Statistics Matches: 22, Mismatches: 4, Indels: 1 0.81 0.15 0.04 Matches are distributed among these distances: 17 11 0.50 18 11 0.50 ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77 Consensus pattern (17 bp): TTTTTTTTCATCATTTC Found at i:40413164 original size:43 final size:43 Alignment explanation
Indices: 40413082--40413165 Score: 134 Period size: 43 Copynumber: 2.0 Consensus size: 43 40413072 TGAGGTATGT * 40413082 AGCATCCGAGCTCGTTGAGAGGTTCGAGTTCATTATGGATGCA 1 AGCATCCGAGCTCGTTGAGAGGTTCGAGTTCATGATGGATGCA * 40413125 AGCATCCGAGCTCGTTGAGAGG-TCTGAGTTCATGGTGGATG 1 AGCATCCGAGCTCGTTGAGAGGTTC-GAGTTCATGATGGATG 40413166 TGATTCATGT Statistics Matches: 38, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 42 2 0.05 43 36 0.95 ACGTcount: A:0.21, C:0.18, G:0.33, T:0.27 Consensus pattern (43 bp): AGCATCCGAGCTCGTTGAGAGGTTCGAGTTCATGATGGATGCA Found at i:40413208 original size:51 final size:51 Alignment explanation
Indices: 40413127--40413226 Score: 130 Period size: 51 Copynumber: 2.0 Consensus size: 51 40413117 TGGATGCAAG * * * * 40413127 CATCCGAGCTCGTTGAGAGGTCTGAGTTCATGGTGGATGTGATT-CATGTAA 1 CATCCAAGCTCATTGAAAGGTCTGAGTTCATGATGGATGTG-TTACATGTAA * * 40413178 CATCCAAGCTCATTGAAAGGTCTGATTTCATTATGGATGTGTTACATGT 1 CATCCAAGCTCATTGAAAGGTCTGAGTTCATGATGGATGTGTTACATGT 40413227 TATGTGGTAG Statistics Matches: 42, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 50 2 0.05 51 40 0.95 ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34 Consensus pattern (51 bp): CATCCAAGCTCATTGAAAGGTCTGAGTTCATGATGGATGTGTTACATGTAA Done.