Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: Scaffold160 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: 5021213 ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32 Warning! 92036 characters in sequence are not A, C, G, or T File 18 of 30 Found at i:2845063 original size:59 final size:58 Alignment explanation
Indices: 2844957--2845068 Score: 154 Period size: 59 Copynumber: 1.9 Consensus size: 58 2844947 ACCCTGTCAA * 2844957 AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTTCG 1 AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTTTTTCG * * * * 2845015 AAGCCCATAAGTCAGTGGCATCTTTTCCAAAGCCCACAAG-CTAGTGGCAACCTT 1 AAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTC-AGTGGCAACCTT 2845069 CAAAAGTCCA Statistics Matches: 47, Mismatches: 5, Indels: 3 0.85 0.09 0.05 Matches are distributed among these distances: 58 21 0.45 59 26 0.55 ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21 Consensus pattern (58 bp): AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTTTTTCG Found at i:2845237 original size:29 final size:29 Alignment explanation
Indices: 2845204--2845354 Score: 81 Period size: 34 Copynumber: 4.9 Consensus size: 29 2845194 ACTCTTTTTC * 2845204 CTTTTTAAAGCCCACAACTCTGTGGCACT 1 CTTTTTAAAGCCCACAACTCAGTGGCACT * * * 2845233 CTTTTTCCTTTTAAGCCTACAACTCCGTGGCACT 1 C---TT--TTTAAAGCCCACAACTCAGTGGCACT * * * 2845267 CTTTTTCCTTTTAAGTCCACAACTCTGTGGCAC- 1 C---TT--TTTAAAGCCCACAACTCAGTGGCACT * * * 2845300 CCTTTT-AAGCCCACAAGTCAGTGGCACC 1 CTTTTTAAAGCCCACAACTCAGTGGCACT * * * 2845328 CCTTTCAAAGCCCACAAGTCAGTGGCA 1 CTTTTTAAAGCCCACAACTCAGTGGCA 2845355 ACCTTCAAAA Statistics Matches: 104, Mismatches: 11, Indels: 14 0.81 0.09 0.11 Matches are distributed among these distances: 27 18 0.17 28 8 0.08 29 21 0.20 30 1 0.01 32 2 0.02 33 1 0.01 34 53 0.51 ACGTcount: A:0.23, C:0.32, G:0.15, T:0.30 Consensus pattern (29 bp): CTTTTTAAAGCCCACAACTCAGTGGCACT Found at i:2845255 original size:34 final size:35 Alignment explanation
Indices: 2845071--2845305 Score: 293 Period size: 34 Copynumber: 6.8 Consensus size: 35 2845061 GCAACCTTCA * * * 2845071 AAAGTCCACAACTCCGTGGCACAT-TTTTTCTTTTT 1 AAAGCCCACAACTCTGTGGCAC-TCTTTTTCCTTTT * * 2845106 AAAGCCCACAACTCTATGGCACTC-TTTTCCTTCT 1 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT * * * 2845140 -AAGTCCACAACTCCGTGGCAC-CTTTCTTCTTTTT 1 AAAGCCCACAACTCTGTGGCACTCTTT-TTCCTTTT 2845174 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTT 1 AAAGCCCACAACTCTGTGGCACTCTTTTTCC-TTTT 2845210 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT 1 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT * * 2845245 -AAGCCTACAACTCCGTGGCACTCTTTTTCCTTTT 1 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT * * 2845279 -AAGTCCACAACTCTGTGGCACCCTTTT 1 AAAGCCCACAACTCTGTGGCACTCTTTT 2845306 AAGCCCACAA Statistics Matches: 175, Mismatches: 19, Indels: 13 0.85 0.09 0.06 Matches are distributed among these distances: 32 1 0.01 33 20 0.11 34 70 0.40 35 45 0.26 36 39 0.22 ACGTcount: A:0.20, C:0.31, G:0.11, T:0.37 Consensus pattern (35 bp): AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT Found at i:2845287 original size:104 final size:103 Alignment explanation
Indices: 2845071--2845305 Score: 343 Period size: 104 Copynumber: 2.3 Consensus size: 103 2845061 GCAACCTTCA * 2845071 AAAGTCCACAACTCCGTGGCACAT-TTTTTCTTTTTAAAGCCCACAACTCTATGGCACTCTTTTC 1 AAAGTCCACAACTCTGTGGCAC-TCTTTTTCTTTTTAAAGCCCACAACTCTATGGCACTCTTTTC * 2845135 CTTCTAAGTCCACAACTCCGTGGCACCTTTCTTCTTTTT 65 CTTCTAAGTCCACAACTCCGTGGCACCTTTCTTCCTTTT * * 2845174 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT 1 AAAGTCCACAACTCTGTGGCACTCTTTTT-CTTTTTAAAGCCCACAACTCTATGGCACTC-TTTT * 2845239 CCTTTTAAG-CCTACAACTCCGTGGCACTCTTT-TTCCTTTT 64 CCTTCTAAGTCC-ACAACTCCGTGGCAC-CTTTCTTCCTTTT * 2845279 -AAGTCCACAACTCTGTGGCACCCTTTT 1 AAAGTCCACAACTCTGTGGCACTCTTTT 2845306 AAGCCCACAA Statistics Matches: 120, Mismatches: 7, Indels: 9 0.88 0.05 0.07 Matches are distributed among these distances: 102 1 0.01 103 25 0.21 104 56 0.47 105 34 0.28 106 4 0.03 ACGTcount: A:0.20, C:0.31, G:0.11, T:0.37 Consensus pattern (103 bp): AAAGTCCACAACTCTGTGGCACTCTTTTTCTTTTTAAAGCCCACAACTCTATGGCACTCTTTTCC TTCTAAGTCCACAACTCCGTGGCACCTTTCTTCCTTTT Found at i:2845304 original size:27 final size:27 Alignment explanation
Indices: 2845273--2845359 Score: 102 Period size: 27 Copynumber: 3.1 Consensus size: 27 2845263 CACTCTTTTT * * 2845273 CCTTTTAAGTCCACAACTCTGTGGCAC 1 CCTTTTAAGCCCACAACTCAGTGGCAC * 2845300 CCTTTTAAGCCCACAAGTCAGTGGCACC 1 CCTTTTAAGCCCACAACTCAGTGGCA-C * * * 2845328 CCTTTCAAAGCCCACAAGTCAGTGGCAA 1 CCTTT-TAAGCCCACAACTCAGTGGCAC 2845356 CCTT 1 CCTT 2845360 CAAAAGCACA Statistics Matches: 53, Mismatches: 5, Indels: 3 0.87 0.08 0.05 Matches are distributed among these distances: 27 23 0.43 28 10 0.19 29 20 0.38 ACGTcount: A:0.25, C:0.34, G:0.16, T:0.24 Consensus pattern (27 bp): CCTTTTAAGCCCACAACTCAGTGGCAC Found at i:2845382 original size:27 final size:30 Alignment explanation
Indices: 2845327--2845410 Score: 90 Period size: 28 Copynumber: 2.9 Consensus size: 30 2845317 TCAGTGGCAC * 2845327 CCCTTTC-AAAGCC-CACAAG-TCAGTGGCAA 1 CCCTTTCAAAAGCCACACAAGTTGA-T-GCAA 2845356 -CC-TTCAAAAG-CACACAAGTTGATGCAA 1 CCCTTTCAAAAGCCACACAAGTTGATGCAA 2845383 CCCTTTCAAAAGCCCACACAAGTTGATG 1 CCCTTTCAAAAG-CCACACAAGTTGATG 2845411 GCGTCTTCTT Statistics Matches: 47, Mismatches: 1, Indels: 12 0.78 0.02 0.20 Matches are distributed among these distances: 27 8 0.17 28 15 0.32 29 10 0.21 31 14 0.30 ACGTcount: A:0.35, C:0.31, G:0.15, T:0.19 Consensus pattern (30 bp): CCCTTTCAAAAGCCACACAAGTTGATGCAA Found at i:2845541 original size:21 final size:21 Alignment explanation
Indices: 2845477--2845541 Score: 55 Period size: 21 Copynumber: 3.0 Consensus size: 21 2845467 TCTTTAAAAC 2845477 CCAATATCGCTGGCCTTGAAT 1 CCAATATCGCTGGCCTTGAAT * * 2845498 -CAGCATATTGAC--ACCTTGAAAT 1 CCA--ATATCG-CTGGCCTTG-AAT 2845520 CCAATATCGCTGGCCTTGAAT 1 CCAATATCGCTGGCCTTGAAT 2845541 C 1 C 2845542 AGTATACTGA Statistics Matches: 33, Mismatches: 4, Indels: 14 0.65 0.08 0.27 Matches are distributed among these distances: 20 3 0.09 21 14 0.42 22 13 0.39 23 3 0.09 ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28 Consensus pattern (21 bp): CCAATATCGCTGGCCTTGAAT Found at i:2845592 original size:91 final size:93 Alignment explanation
Indices: 2845429--2845696 Score: 237 Period size: 91 Copynumber: 2.9 Consensus size: 93 2845419 TTCTAAGTCT * * * * 2845429 AATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACCCAATATCGCTGGCCTT 1 AATATCGCTGGCCTTGAACCAGCATACTGACACCTTTATCTCTAAAACCCAATATCGCTAGCCTT * 2845494 GAATCAGCATATTGACACCTTGAAATCC 66 GAATCAGCACATTGACACCTTGAAATCC * * * * * * 2845522 AATATCGCTGGCCTTGAATCAGTATACTGACA-CTTTGTCTCTAAGA-CCAATGTTGCTAGCCTT 1 AATATCGCTGGCCTTGAACCAGCATACTGACACCTTTATCTCTAAAACCCAATATCGCTAGCCTT * 2845585 GAATCAGCACATTGGCA-C---AAGA-CC 66 GAATCAGCACATTGACACCTTGAA-ATCC * * * * * * * * * * 2845609 AATGTCGCTGGCCATGAATCAGCATATTGGCACCTTAACCATCTTTAAGA-CCAATGTCGCTGGC 1 AATATCGCTGGCCTTGAACCAGCATACTGACACCTT---TATCTCTAAAACCCAATATCGCTAGC * 2845673 CTTGAATCAGCACATTGGCACCTT 63 CTTGAATCAGCACATTGACACCTT 2845697 TATCTTTTAG Statistics Matches: 145, Mismatches: 22, Indels: 15 0.80 0.12 0.08 Matches are distributed among these distances: 87 31 0.21 88 4 0.03 90 1 0.01 91 69 0.48 92 12 0.08 93 28 0.19 ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28 Consensus pattern (93 bp): AATATCGCTGGCCTTGAACCAGCATACTGACACCTTTATCTCTAAAACCCAATATCGCTAGCCTT GAATCAGCACATTGACACCTTGAAATCC Found at i:2845627 original size:39 final size:39 Alignment explanation
Indices: 2845564--2845641 Score: 120 Period size: 39 Copynumber: 2.0 Consensus size: 39 2845554 CTTTGTCTCT * * 2845564 AAGACCAATGTTGCTAGCCTTGAATCAGCACATTGGCAC 1 AAGACCAATGTCGCTAGCCATGAATCAGCACATTGGCAC * * 2845603 AAGACCAATGTCGCTGGCCATGAATCAGCATATTGGCAC 1 AAGACCAATGTCGCTAGCCATGAATCAGCACATTGGCAC 2845642 CTTAACCATC Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 39 35 1.00 ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22 Consensus pattern (39 bp): AAGACCAATGTCGCTAGCCATGAATCAGCACATTGGCAC Found at i:2845722 original size:49 final size:49 Alignment explanation
Indices: 2845603--2845837 Score: 170 Period size: 52 Copynumber: 4.7 Consensus size: 49 2845593 ACATTGGCAC * * * 2845603 AAGACCAATGTCGCTGGCCATGAATCAGCATATTGGCACCTTAACCATCTTT 1 AAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT---TATCTTT * * 2845655 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTT 1 AAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTT * * * * * * * 2845704 TAGTCCAATATTGTTGGCCTTGAATCAGTATATTGGCATCTTTAACATTTCT 1 AAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC--TT-T * * * * * * 2845756 AAGCCCAATGTCGCTGGCCTT-ATCTCAGCACATTGGCA--TTTTTCTTC 1 AAGACCAATATCGCTGGCCTTGA-ATCAGCATATTGGCACCTTTATCTTT * * * * * * 2845803 AAGTCTAATGTCACTGGTCATGAATCAGCATATTG 1 AAGACCAATATCGCTGGCCTTGAATCAGCATATTG 2845838 TCATTCTTCG Statistics Matches: 148, Mismatches: 30, Indels: 15 0.77 0.16 0.08 Matches are distributed among these distances: 47 26 0.18 48 3 0.02 49 43 0.29 50 4 0.03 51 3 0.02 52 69 0.47 ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33 Consensus pattern (49 bp): AAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTT Found at i:2845794 original size:52 final size:51 Alignment explanation
Indices: 2845603--2845794 Score: 203 Period size: 52 Copynumber: 3.8 Consensus size: 51 2845593 ACATTGGCAC * * * 2845603 AAGACCAATGTCGCTGGCCATGAATCAGCATATTGGCA-CCTTAACCATCTTT 1 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTAA-CAT-TTT * * 2845655 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC-TTTT 1 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTAACATTTT * * * * * * 2845705 -AGTCCAATATTGTTGGCCTTGAATCAGTATATTGGCATCTTTAACATTTCT 1 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTAACATTT-T * * 2845756 AAGCCCAATGTCGCTGGCCTT-ATCTCAGCACATTGGCAT 1 AAGACCAATGTCGCTGGCCTTGA-ATCAGCACATTGGCAT 2845795 TTTTCTTCAA Statistics Matches: 116, Mismatches: 19, Indels: 10 0.80 0.13 0.07 Matches are distributed among these distances: 49 37 0.32 50 6 0.05 51 3 0.03 52 66 0.57 53 4 0.03 ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32 Consensus pattern (51 bp): AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTAACATTTT Found at i:2846580 original size:13 final size:13 Alignment explanation
Indices: 2846562--2846650 Score: 70 Period size: 13 Copynumber: 5.9 Consensus size: 13 2846552 TTCAACAATT 2846562 TGTATCGATACAA 1 TGTATCGATACAA 2846575 TGTATCGATACATAA 1 TGTATCGATAC--AA 2846590 GTGTTGTATCGATACAA 1 ----TGTATCGATACAA 2846607 TGTATCGATACATAA 1 TGTATCGATAC--AA 2846622 GTGTTGTATCGATACAA 1 ----TGTATCGATACAA 2846639 TGTATCGATACA 1 TGTATCGATACA 2846651 TAAGTTTTTT Statistics Matches: 64, Mismatches: 0, Indels: 24 0.73 0.00 0.27 Matches are distributed among these distances: 13 34 0.53 15 4 0.06 17 4 0.06 19 22 0.34 ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34 Consensus pattern (13 bp): TGTATCGATACAA Found at i:2846599 original size:19 final size:18 Alignment explanation
Indices: 2846575--2846669 Score: 84 Period size: 19 Copynumber: 5.7 Consensus size: 18 2846565 ATCGATACAA 2846575 TGTATCGATACATAAGTGT 1 TGTATCGATACATAAGT-T 2846594 TGTATCGATAC--AA--- 1 TGTATCGATACATAAGTT 2846607 TGTATCGATACATAAGTGT 1 TGTATCGATACATAAGT-T 2846626 TGTATCGATAC--AA--- 1 TGTATCGATACATAAGTT 2846639 TGTATCGATACATAAGTTT 1 TGTATCGATACATAAG-TT * 2846658 TTTATCGATACA 1 TGTATCGATACA 2846670 ATGTATCGCT Statistics Matches: 63, Mismatches: 1, Indels: 24 0.72 0.01 0.27 Matches are distributed among these distances: 13 22 0.35 15 4 0.06 17 4 0.06 19 33 0.52 ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37 Consensus pattern (18 bp): TGTATCGATACATAAGTT Found at i:2846602 original size:32 final size:32 Alignment explanation
Indices: 2846561--2846682 Score: 217 Period size: 32 Copynumber: 3.8 Consensus size: 32 2846551 TTTCAACAAT 2846561 TTGTATCGATACAATGTATCGATACATAAGTG 1 TTGTATCGATACAATGTATCGATACATAAGTG 2846593 TTGTATCGATACAATGTATCGATACATAAGTG 1 TTGTATCGATACAATGTATCGATACATAAGTG * 2846625 TTGTATCGATACAATGTATCGATACATAAGTT 1 TTGTATCGATACAATGTATCGATACATAAGTG * * 2846657 TTTTATCGATACAATGTATCGCTACA 1 TTGTATCGATACAATGTATCGATACA 2846683 AAGCTACTGC Statistics Matches: 87, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 87 1.00 ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36 Consensus pattern (32 bp): TTGTATCGATACAATGTATCGATACATAAGTG Found at i:2852141 original size:3 final size:3 Alignment explanation
Indices: 2852133--2852163 Score: 53 Period size: 3 Copynumber: 10.3 Consensus size: 3 2852123 CAATTATCTC * 2852133 ATG ATG ATG ATG ATG ATG ATG ATT ATG ATG A 1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A 2852164 AATAATGCAT Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 3 26 1.00 ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35 Consensus pattern (3 bp): ATG Found at i:2854558 original size:89 final size:89 Alignment explanation
Indices: 2854447--2854616 Score: 234 Period size: 89 Copynumber: 1.9 Consensus size: 89 2854437 ATGAGGTTGA * * * * * 2854447 AGTATCCCCTCGAAGTAGTGGGGATGAAG-TTTCTCCAAGGATAAAATTATATGAAGGAAAATTT 1 AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTC-CCAAGGACAAAATTATACGAAGGAAAATTT * * 2854511 AAATTTTTGATAGAACAAGGGTTAG 65 AAATTTTTAATAAAACAAGGGTTAG * * * 2854536 AGTATCCCCTCGGAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAGATTTG 1 AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAAATTTA 2854601 AATTTTTAATAAAACA 66 AATTTTTAATAAAACA 2854617 GAGTTGGAGT Statistics Matches: 70, Mismatches: 10, Indels: 2 0.85 0.12 0.02 Matches are distributed among these distances: 89 66 0.94 90 4 0.06 ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28 Consensus pattern (89 bp): AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAAATTTA AATTTTTAATAAAACAAGGGTTAG Found at i:2861914 original size:12 final size:12 Alignment explanation
Indices: 2861897--2861921 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 2861887 TTAAGATTAC 2861897 GGAGTTAGTTTA 1 GGAGTTAGTTTA 2861909 GGAGTTAGTTTA 1 GGAGTTAGTTTA 2861921 G 1 G 2861922 TGAAAACCTT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40 Consensus pattern (12 bp): GGAGTTAGTTTA Found at i:2863691 original size:3 final size:3 Alignment explanation
Indices: 2863683--2863713 Score: 53 Period size: 3 Copynumber: 10.3 Consensus size: 3 2863673 CAATTATCTC * 2863683 ATG ATG ATG ATG ATG ATG ATG ATT ATG ATG A 1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A 2863714 AATAATGCAT Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 3 26 1.00 ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35 Consensus pattern (3 bp): ATG Found at i:2866108 original size:89 final size:89 Alignment explanation
Indices: 2865997--2866166 Score: 234 Period size: 89 Copynumber: 1.9 Consensus size: 89 2865987 ATGAGGTTGA * * * * * 2865997 AGTATCCCCTCGAAGTAGTGGGGATGAAG-TTTCTCCAAGGATAAAATTATATGAAGGAAAATTT 1 AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTC-CCAAGGACAAAATTATACGAAGGAAAATTT * * 2866061 AAATTTTTGATAGAACAAGGGTTAG 65 AAATTTTTAATAAAACAAGGGTTAG * * * 2866086 AGTATCCCCTCGGAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAGATTTG 1 AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAAATTTA 2866151 AATTTTTAATAAAACA 66 AATTTTTAATAAAACA 2866167 GAGTTGGAGT Statistics Matches: 70, Mismatches: 10, Indels: 2 0.85 0.12 0.02 Matches are distributed among these distances: 89 66 0.94 90 4 0.06 ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28 Consensus pattern (89 bp): AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAAATTTA AATTTTTAATAAAACAAGGGTTAG Found at i:2873465 original size:12 final size:12 Alignment explanation
Indices: 2873448--2873472 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 2873438 TTAAGATTAC 2873448 GGAGTTAGTTTA 1 GGAGTTAGTTTA 2873460 GGAGTTAGTTTA 1 GGAGTTAGTTTA 2873472 G 1 G 2873473 TGAAAACCTT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40 Consensus pattern (12 bp): GGAGTTAGTTTA Found at i:2874863 original size:20 final size:20 Alignment explanation
Indices: 2874792--2874883 Score: 85 Period size: 20 Copynumber: 4.6 Consensus size: 20 2874782 AAAAACCCAA * * * 2874792 AATGTATTGATACATTGAGT 1 AATGTATCGATACATTAACT * * 2874812 AATTTATCGATACATTAAGT 1 AATGTATCGATACATTAACT * * 2874832 AATATATCGATACATTTACT 1 AATGTATCGATACATTAACT * * * 2874852 TATGTATTGATACATTCACT 1 AATGTATCGATACATTAACT * 2874872 TATGTATCGATA 1 AATGTATCGATA 2874884 TAATTTTTCC Statistics Matches: 61, Mismatches: 11, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 61 1.00 ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41 Consensus pattern (20 bp): AATGTATCGATACATTAACT Found at i:2874985 original size:20 final size:21 Alignment explanation
Indices: 2874946--2874991 Score: 67 Period size: 20 Copynumber: 2.2 Consensus size: 21 2874936 ATAAGCCTGA * 2874946 GTATCAATACATTCACTTA-T 1 GTATCAATACATTAACTTATT * 2874966 GTATCAATACATTAATTTATT 1 GTATCAATACATTAACTTATT 2874987 GTATC 1 GTATC 2874992 GATATAAATT Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 20 17 0.74 21 6 0.26 ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43 Consensus pattern (21 bp): GTATCAATACATTAACTTATT Found at i:2876042 original size:29 final size:29 Alignment explanation
Indices: 2875957--2876203 Score: 243 Period size: 29 Copynumber: 8.6 Consensus size: 29 2875947 TGCCAGCTAG * 2875957 TATGGGCTTTAAAAA-GGTGCCATTGACT 1 TATGGGCTTTAAAAAGGGTGCCACTGACT * * * * * * 2875985 TGTAGTCTTT-GAAAGAGTGCCATTGACT 1 TATGGGCTTTAAAAAGGGTGCCACTGACT * * 2876013 TGTGGGCTTTAAAAAGGGTGCCACTAACT 1 TATGGGCTTTAAAAAGGGTGCCACTGACT * * 2876042 TGTGGGCTTTGAAAAGGGTGCCACTGACT 1 TATGGGCTTTAAAAAGGGTGCCACTGACT * * * 2876071 TATGGGCTTTGAAAAGGGTGCCATTAACT 1 TATGGGCTTTAAAAAGGGTGCCACTGACT * * 2876100 TATGGGCTTT-GAAAGTGGTGCCACTTACT 1 TATGGGCTTTAAAAAG-GGTGCCACTGACT ** 2876129 TATGGGCTTTGAAAAA-GGTGCCACTGGTT 1 TATGGGCTTT-AAAAAGGGTGCCACTGACT * 2876158 TATGGGC-TTAGAAAAGGGTGCCACTAACT 1 TATGGGCTTTA-AAAAGGGTGCCACTGACT * * 2876187 TGTGGGCTTTGAAAAGG 1 TATGGGCTTTAAAAAGG 2876204 TTCAACTCCC Statistics Matches: 183, Mismatches: 28, Indels: 15 0.81 0.12 0.07 Matches are distributed among these distances: 27 4 0.02 28 37 0.20 29 137 0.75 30 2 0.01 31 3 0.02 ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30 Consensus pattern (29 bp): TATGGGCTTTAAAAAGGGTGCCACTGACT Found at i:2876086 original size:58 final size:57 Alignment explanation
Indices: 2875957--2876203 Score: 280 Period size: 58 Copynumber: 4.3 Consensus size: 57 2875947 TGCCAGCTAG * * * * * * * * 2875957 TATGGGCTTT-AAAAAGGTGCCATTGACTTGTAGTCTTTGAAAGAGTGCCATTGACT 1 TATGGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTGACT * * * 2876013 TGTGGGCTTTAAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACT 1 TATGGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTG-AAAGGGTGCCACTGACT * * 2876071 TATGGGCTTTGAAAAGGGTGCCATTAACTTATGGGCTTTGAAAGTGGTGCCACTTACT 1 TATGGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTGAAAG-GGTGCCACTGACT * *** * * 2876129 TATGGGCTTTGAAAAAGGTGCCACTGGTTTATGGGCTTAGAAAAGGGTGCCACTAACT 1 TATGGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTG-AAAGGGTGCCACTGACT * 2876187 TGTGGGCTTTGAAAAGG 1 TATGGGCTTTGAAAAGG 2876204 TTCAACTCCC Statistics Matches: 165, Mismatches: 22, Indels: 6 0.85 0.11 0.03 Matches are distributed among these distances: 56 9 0.05 57 28 0.17 58 124 0.75 59 4 0.02 ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30 Consensus pattern (57 bp): TATGGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTGACT Found at i:2876109 original size:87 final size:86 Alignment explanation
Indices: 2875957--2876203 Score: 318 Period size: 87 Copynumber: 2.9 Consensus size: 86 2875947 TGCCAGCTAG * * * * * * 2875957 TATGGGCTTT-AAAAAGGTGCCATTGACTTGTAGTCTTTG-AAAGAGTGCCATTGACTTGTGGGC 1 TATGGGCTTTGAAAAAGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCATTAACTTGTGGGC 2876020 TTTAAAAAGGGTGCCACTAACT 66 TTT-AAAAGGGTGCCACTAACT * * * 2876042 TGTGGGCTTTGAAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCATTAACTTATGGGC 1 TATGGGCTTTGAAAAAGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCATTAACTTGTGGGC * * 2876107 TTTGAAAGTGGTGCCACTTACT 66 TTTAAAAG-GGTGCCACTAACT ** * * 2876129 TATGGGCTTTGAAAAAGGTGCCACTGGTTTATGGGCTTAGAAAAGGGTGCCACTAACTTGTGGGC 1 TATGGGCTTTGAAAAAGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCATTAACTTGTGGGC 2876194 TTTGAAAAGG 66 TTT-AAAAGG 2876204 TTCAACTCCC Statistics Matches: 139, Mismatches: 19, Indels: 6 0.85 0.12 0.04 Matches are distributed among these distances: 85 9 0.06 86 28 0.20 87 98 0.71 88 4 0.03 ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30 Consensus pattern (86 bp): TATGGGCTTTGAAAAAGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCATTAACTTGTGGGC TTTAAAAGGGTGCCACTAACT Found at i:2876623 original size:24 final size:24 Alignment explanation
Indices: 2876591--2876636 Score: 67 Period size: 24 Copynumber: 1.9 Consensus size: 24 2876581 AGTTTCCTAA 2876591 TGAAAAAA-TCTTAACACAAGTTCT 1 TGAAAAAATTCTTAACA-AAGTTCT * 2876615 TGAAAAAATTCTTGACAAAGTT 1 TGAAAAAATTCTTAACAAAGTT 2876637 TCTGACAAAT Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 24 13 0.65 25 7 0.35 ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30 Consensus pattern (24 bp): TGAAAAAATTCTTAACAAAGTTCT Found at i:2882607 original size:32 final size:33 Alignment explanation
Indices: 2882544--2882608 Score: 87 Period size: 32 Copynumber: 2.0 Consensus size: 33 2882534 CAGACCCAGA * 2882544 TGTATCAATACATTATGCTTTGTATCAATACAT 1 TGTATCAATACATTATGCATTGTATCAATACAT * * * 2882577 TGTATCGATACA-TATTCATTGTATCGATACAT 1 TGTATCAATACATTATGCATTGTATCAATACAT 2882609 GGATAATTGT Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 32 17 0.61 33 11 0.39 ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42 Consensus pattern (33 bp): TGTATCAATACATTATGCATTGTATCAATACAT Found at i:2882619 original size:20 final size:20 Alignment explanation
Indices: 2882575--2882630 Score: 71 Period size: 19 Copynumber: 2.9 Consensus size: 20 2882565 GTATCAATAC * 2882575 ATTGTATCGATACAT-ATTC 1 ATTGTATCGATACATGATTA 2882594 ATTGTATCGATACATGGA-TA 1 ATTGTATCGATACAT-GATTA * 2882614 ATTGTATCAATACATGA 1 ATTGTATCGATACATGA 2882631 AACTGGCAGT Statistics Matches: 33, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 19 17 0.52 20 15 0.45 21 1 0.03 ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38 Consensus pattern (20 bp): ATTGTATCGATACATGATTA Found at i:2884215 original size:20 final size:20 Alignment explanation
Indices: 2884190--2884246 Score: 96 Period size: 20 Copynumber: 2.9 Consensus size: 20 2884180 TTTTACCCAG * * 2884190 ATGTATTGATACATTTTTCA 1 ATGTATCGATACATTCTTCA 2884210 ATGTATCGATACATTCTTCA 1 ATGTATCGATACATTCTTCA 2884230 ATGTATCGATACATTCT 1 ATGTATCGATACATTCT 2884247 GTCTTTTTTC Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 35 1.00 ACGTcount: A:0.30, C:0.16, G:0.11, T:0.44 Consensus pattern (20 bp): ATGTATCGATACATTCTTCA Found at i:2890802 original size:19 final size:19 Alignment explanation
Indices: 2890756--2890809 Score: 72 Period size: 19 Copynumber: 2.8 Consensus size: 19 2890746 TGCTAGTTTC ** 2890756 ATGTATCGATACAATTGTCT 1 ATGTATCGATACAA-TGAAT * 2890776 ATGCATCGATACAATGAAT 1 ATGTATCGATACAATGAAT 2890795 ATGTATCGATACAAT 1 ATGTATCGATACAAT 2890810 TTATTGATAC Statistics Matches: 30, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 19 17 0.57 20 13 0.43 ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33 Consensus pattern (19 bp): ATGTATCGATACAATGAAT Found at i:2891435 original size:22 final size:22 Alignment explanation
Indices: 2891407--2891448 Score: 66 Period size: 22 Copynumber: 1.9 Consensus size: 22 2891397 ATCGAAATAT 2891407 ATTTCTCCCACTTTATCAAAGC 1 ATTTCTCCCACTTTATCAAAGC * * 2891429 ATTTCTCCCATTTTGTCAAA 1 ATTTCTCCCACTTTATCAAA 2891449 TCTTAAAAAA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.26, C:0.29, G:0.05, T:0.40 Consensus pattern (22 bp): ATTTCTCCCACTTTATCAAAGC Found at i:2893379 original size:33 final size:33 Alignment explanation
Indices: 2893337--2893402 Score: 123 Period size: 33 Copynumber: 2.0 Consensus size: 33 2893327 ATAGTAACCC * 2893337 ATGTATCGATACAAGGAATGTTGTATTGATACA 1 ATGTATCGATACAAGGAATGTTGTATCGATACA 2893370 ATGTATCGATACAAGGAATGTTGTATCGATACA 1 ATGTATCGATACAAGGAATGTTGTATCGATACA 2893403 TTTGGGTTTT Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 33 32 1.00 ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32 Consensus pattern (33 bp): ATGTATCGATACAAGGAATGTTGTATCGATACA Found at i:2893396 original size:20 final size:20 Alignment explanation
Indices: 2893338--2893402 Score: 72 Period size: 20 Copynumber: 3.6 Consensus size: 20 2893328 TAGTAACCCA 2893338 TGTATCGATACAAGGAATGT 1 TGTATCGATACAAGGAATGT * 2893358 TGTATTGATAC----AA--- 1 TGTATCGATACAAGGAATGT 2893371 TGTATCGATACAAGGAATGT 1 TGTATCGATACAAGGAATGT 2893391 TGTATCGATACA 1 TGTATCGATACA 2893403 TTTGGGTTTT Statistics Matches: 36, Mismatches: 2, Indels: 14 0.69 0.04 0.27 Matches are distributed among these distances: 13 10 0.28 16 2 0.06 17 2 0.06 20 22 0.61 ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32 Consensus pattern (20 bp): TGTATCGATACAAGGAATGT Found at i:2896131 original size:139 final size:139 Alignment explanation
Indices: 2895873--2896153 Score: 508 Period size: 139 Copynumber: 2.0 Consensus size: 139 2895863 GCTTTCGCCC * 2895873 AAAAATATCTTGGTAAATTATTTTCGCAAAGCATGGTTCTAGCCATTTCTTCCAAAGTCCAATTT 1 AAAAATATCTTGGTAAATTATTTTCACAAAGCATGGTTCTAGCCATTTCTTCCAAAGTCCAATTT 2895938 TTCCTCTCAACAACTCTATTTTGTTGAGGAGTTCTAGGAGCTGAAAAATCATGGCTAATACTATT 66 TTCCTCTCAACAACTCTATTTTGTTGAGGAGTTCTAGGAGCTGAAAAATCATGGCTAATACTATT 2896003 TTCATTACA 131 TTCATTACA * * 2896012 AAAAATATCTTGGTAAATTATTTTCACAAAGCATGGTTCTAGCCATTTCTTCGAAAGTCCGATTT 1 AAAAATATCTTGGTAAATTATTTTCACAAAGCATGGTTCTAGCCATTTCTTCCAAAGTCCAATTT * * * 2896077 TTCCTCTCAACAACTCTATTTTGTTGAGGAGTTCTAGGAGCTGAGAAATTATGGCTAATACTGTT 66 TTCCTCTCAACAACTCTATTTTGTTGAGGAGTTCTAGGAGCTGAAAAATCATGGCTAATACTATT 2896142 TTCATTACA 131 TTCATTACA 2896151 AAA 1 AAA 2896154 TTTATCAAAA Statistics Matches: 136, Mismatches: 6, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 139 136 1.00 ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37 Consensus pattern (139 bp): AAAAATATCTTGGTAAATTATTTTCACAAAGCATGGTTCTAGCCATTTCTTCCAAAGTCCAATTT TTCCTCTCAACAACTCTATTTTGTTGAGGAGTTCTAGGAGCTGAAAAATCATGGCTAATACTATT TTCATTACA Found at i:2899710 original size:20 final size:20 Alignment explanation
Indices: 2899685--2899734 Score: 57 Period size: 20 Copynumber: 2.5 Consensus size: 20 2899675 CAAGCAATGT * 2899685 ATCGATATAAT-TCATCATGC 1 ATCGATATAATGT-ACCATGC * * 2899705 ATCGATACAATGTACCATGT 1 ATCGATATAATGTACCATGC 2899725 ATCGATATAA 1 ATCGATATAA 2899735 ACATTGGTAG Statistics Matches: 25, Mismatches: 4, Indels: 2 0.81 0.13 0.06 Matches are distributed among these distances: 20 24 0.96 21 1 0.04 ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32 Consensus pattern (20 bp): ATCGATATAATGTACCATGC Found at i:2899802 original size:13 final size:13 Alignment explanation
Indices: 2899784--2899843 Score: 69 Period size: 13 Copynumber: 5.1 Consensus size: 13 2899774 ACAATTGTCC 2899784 ATGTATCGATACA 1 ATGTATCGATACA 2899797 ATGTATCGATACA 1 ATGTATCGATACA * 2899810 A---AGC-AT--A 1 ATGTATCGATACA 2899817 ATGTATCGATACA 1 ATGTATCGATACA 2899830 ATGTATCGATACA 1 ATGTATCGATACA 2899843 A 1 A 2899844 AGCATTCTGG Statistics Matches: 39, Mismatches: 2, Indels: 12 0.74 0.04 0.23 Matches are distributed among these distances: 7 2 0.05 9 2 0.05 10 4 0.10 11 2 0.05 13 29 0.74 ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28 Consensus pattern (13 bp): ATGTATCGATACA Found at i:2899848 original size:33 final size:33 Alignment explanation
Indices: 2899784--2899848 Score: 130 Period size: 33 Copynumber: 2.0 Consensus size: 33 2899774 ACAATTGTCC 2899784 ATGTATCGATACAATGTATCGATACAAAGCATA 1 ATGTATCGATACAATGTATCGATACAAAGCATA 2899817 ATGTATCGATACAATGTATCGATACAAAGCAT 1 ATGTATCGATACAATGTATCGATACAAAGCAT 2899849 TCTGGGTGTG Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 33 32 1.00 ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28 Consensus pattern (33 bp): ATGTATCGATACAATGTATCGATACAAAGCATA Found at i:2905549 original size:17 final size:17 Alignment explanation
Indices: 2905527--2905561 Score: 70 Period size: 17 Copynumber: 2.1 Consensus size: 17 2905517 TTGTTTGCTT 2905527 AAAAATACTCTAAAAAC 1 AAAAATACTCTAAAAAC 2905544 AAAAATACTCTAAAAAC 1 AAAAATACTCTAAAAAC 2905561 A 1 A 2905562 TGTTCTAAGT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17 Consensus pattern (17 bp): AAAAATACTCTAAAAAC Found at i:2914698 original size:34 final size:33 Alignment explanation
Indices: 2914642--2914846 Score: 211 Period size: 34 Copynumber: 6.5 Consensus size: 33 2914632 ATGATGCAAA 2914642 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGG 1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGG * 2914675 AGTTGTGGGCTTTGAAAAGAAGAAAGTGCCACGG 1 AGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGG * 2914709 AGTTGTGGGC-TT--AA-ACG--GGTGCCACGG 1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGG * * * 2914736 AGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACGG 1 AGTTGTGGGCTTTAAA-A-GAAGAAGGTGCCACGG * 2914770 AATTGTGGGCTTT--AA-AAG--GGTGCCACGG 1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGG * * 2914798 AGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGG 1 AGTTGTGGGCTTTAAAA-GAAGAAGGTGCCACGG 2914831 AGTTGTGGGCTTTAAA 1 AGTTGTGGGCTTTAAA 2914847 GAAAAAATGC Statistics Matches: 141, Mismatches: 15, Indels: 31 0.75 0.08 0.17 Matches are distributed among these distances: 27 22 0.16 28 17 0.12 29 5 0.04 30 5 0.04 31 2 0.01 32 2 0.01 33 35 0.25 34 51 0.36 35 2 0.01 ACGTcount: A:0.30, C:0.13, G:0.35, T:0.22 Consensus pattern (33 bp): AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGG Found at i:2914738 original size:27 final size:26 Alignment explanation
Indices: 2914700--2914812 Score: 100 Period size: 27 Copynumber: 3.9 Consensus size: 26 2914690 AAAGAAGAAA * 2914700 GTGCCACGGAGTTGTGGGCTTAAACGG 1 GTGCCACGGAGTTGTGGACTTAAA-GG 2914727 GTGCCACGGAGTTGTGGACTTAAAGATG 1 GTGCCACGGAGTTGTGGACTTAAAG--G * * 2914755 AAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGG 1 ------GTGCCACGGAGTTGTGGAC-TT-AAAGG 2914789 GTGCCACGGAGTTGTGGACTTAAA 1 GTGCCACGGAGTTGTGGACTTAAA 2914813 AGGAACAAGG Statistics Matches: 71, Mismatches: 5, Indels: 21 0.73 0.05 0.22 Matches are distributed among these distances: 26 4 0.06 27 25 0.35 28 18 0.25 34 18 0.25 35 2 0.03 36 4 0.06 ACGTcount: A:0.27, C:0.15, G:0.35, T:0.23 Consensus pattern (26 bp): GTGCCACGGAGTTGTGGACTTAAAGG Found at i:2914740 original size:61 final size:60 Alignment explanation
Indices: 2914665--2914847 Score: 251 Period size: 61 Copynumber: 3.0 Consensus size: 60 2914655 AAAAGAAGAA * * * 2914665 GGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAAGTGCCACGGAGTTGTGGGCTTAAACG 1 GGTGCCACGGAGTTGTGGAC-TT-AAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAG * * 2914726 GGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAG 1 GGTGCCACGGAGTTGTGGACTTAAA-AGGAAAAAAGTGCCACGGAGTTGTGGGC-TTAAAAG * * * 2914788 GGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAG 1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAG 2914848 AAAAAATGCC Statistics Matches: 110, Mismatches: 9, Indels: 7 0.87 0.07 0.06 Matches are distributed among these distances: 59 3 0.03 60 9 0.08 61 67 0.61 62 31 0.28 ACGTcount: A:0.28, C:0.14, G:0.36, T:0.22 Consensus pattern (60 bp): GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAG Found at i:2914885 original size:30 final size:31 Alignment explanation
Indices: 2914790--2914907 Score: 112 Period size: 30 Copynumber: 3.8 Consensus size: 31 2914780 TTTAAAAGGG * * * ** 2914790 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGG 1 TGCCACTGAGTCGTGGACTTTAAA-GAA-AAAA * * * 2914823 TGCCACGGAGTTGTGGGCTTTAAAGAAAAAA 1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA * * 2914854 TGCCACTGAGTCGTGGACTTT-GAGACAAAA 1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA * 2914884 TGCCACTGAGTCGTGGACGTTAAA 1 TGCCACTGAGTCGTGGACTTTAAA 2914908 AAGGTATTTG Statistics Matches: 73, Mismatches: 11, Indels: 4 0.83 0.12 0.05 Matches are distributed among these distances: 30 27 0.37 31 21 0.29 32 3 0.04 33 22 0.30 ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22 Consensus pattern (31 bp): TGCCACTGAGTCGTGGACTTTAAAGAAAAAA Found at i:2914907 original size:122 final size:122 Alignment explanation
Indices: 2914665--2914908 Score: 257 Period size: 122 Copynumber: 2.0 Consensus size: 122 2914655 AAAAGAAGAA * * ** 2914665 GGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAAGTGCCACGGAGTTGTGGGCTTAAACGGGTG 1 GGTGCCACGGAGTTGTGGACTTTGAAAAGAACAAAGTGCCACGGAGTTGTGGGCTTAAACGAATG * * * * 2914730 CCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAG 66 CCACGGAGTCGTGGACTT-AAGATGAAAAAAGTGCCACGGAATCGTGGACGTTAAAAG * 2914788 GGTGCCACGGAGTTGTGGAC-TT-AAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAA-GAA 1 GGTGCCACGGAGTTGTGGACTTTGAAAA-GAACAAAGTGCCACGGAGTTGTGGGC-TTAAACG-- * * * * * 2914850 AAAATGCCACTGAGTCGTGGACTT-TGA-GACAAAA-TGCCACTGAGTCGTGGACGTTAAAA 62 --AATGCCACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACGGAATCGTGGACGTTAAAA 2914909 AGGTATTTGA Statistics Matches: 101, Mismatches: 14, Indels: 13 0.79 0.11 0.10 Matches are distributed among these distances: 121 4 0.04 122 47 0.47 123 30 0.30 124 2 0.02 126 18 0.18 ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22 Consensus pattern (122 bp): GGTGCCACGGAGTTGTGGACTTTGAAAAGAACAAAGTGCCACGGAGTTGTGGGCTTAAACGAATG CCACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACGGAATCGTGGACGTTAAAAG Found at i:2916219 original size:14 final size:14 Alignment explanation
Indices: 2916202--2916241 Score: 62 Period size: 14 Copynumber: 2.9 Consensus size: 14 2916192 CCTTTGCACT 2916202 TTTTTTTTGTTTTG 1 TTTTTTTTGTTTTG * 2916216 TTTTTTTTTTTTTG 1 TTTTTTTTGTTTTG * 2916230 TTTTTTGTGTTT 1 TTTTTTTTGTTT 2916242 ACTTTTGACT Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 14 23 1.00 ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88 Consensus pattern (14 bp): TTTTTTTTGTTTTG Found at i:2916223 original size:9 final size:9 Alignment explanation
Indices: 2916202--2916241 Score: 53 Period size: 9 Copynumber: 4.3 Consensus size: 9 2916192 CCTTTGCACT 2916202 TTTTTTTTG 1 TTTTTTTTG * 2916211 TTTTGTTTTT 1 TTTT-TTTTG 2916221 TTTTTTTTG 1 TTTTTTTTG * 2916230 TTTTTTGTG 1 TTTTTTTTG 2916239 TTT 1 TTT 2916242 ACTTTTGACT Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 9 19 0.70 10 8 0.30 ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88 Consensus pattern (9 bp): TTTTTTTTG Found at i:2923215 original size:52 final size:52 Alignment explanation
Indices: 2923134--2923254 Score: 224 Period size: 52 Copynumber: 2.3 Consensus size: 52 2923124 TGAAAAGTTA * 2923134 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC 1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC * 2923186 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC 1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC 2923238 CTGCATGTATCGATACA 1 CTGCATGTATCGATACA 2923255 AAGATCAGTG Statistics Matches: 67, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 52 67 1.00 ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35 Consensus pattern (52 bp): CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC Found at i:2923267 original size:52 final size:51 Alignment explanation
Indices: 2923134--2923274 Score: 212 Period size: 52 Copynumber: 2.7 Consensus size: 51 2923124 TGAAAAGTTA 2923134 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC 1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC * * 2923186 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC 1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC * 2923238 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA 1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA 2923275 ATGTATCGAT Statistics Matches: 82, Mismatches: 5, Indels: 4 0.90 0.05 0.04 Matches are distributed among these distances: 51 2 0.02 52 80 0.98 ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33 Consensus pattern (51 bp): CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC Found at i:2923281 original size:13 final size:13 Alignment explanation
Indices: 2923263--2923287 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 2923253 CAAAGATCAG 2923263 TGTATCGATACAA 1 TGTATCGATACAA 2923276 TGTATCGATACA 1 TGTATCGATACA 2923288 TGTGAGTAAT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:2923369 original size:33 final size:33 Alignment explanation
Indices: 2923327--2923396 Score: 104 Period size: 33 Copynumber: 2.1 Consensus size: 33 2923317 GGCAGTAGCT 2923327 TACATTGTATCGATACAAAAAAATATGTATCGA 1 TACATTGTATCGATACAAAAAAATATGTATCGA * *** 2923360 TACATTGTATCGATACAACATTTTATGTATCGA 1 TACATTGTATCGATACAAAAAAATATGTATCGA 2923393 TACA 1 TACA 2923397 AATCGTTGAA Statistics Matches: 33, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 33 33 1.00 ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34 Consensus pattern (33 bp): TACATTGTATCGATACAAAAAAATATGTATCGA Found at i:2923370 original size:13 final size:13 Alignment explanation
Indices: 2923352--2923376 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 2923342 CAAAAAAATA 2923352 TGTATCGATACAT 1 TGTATCGATACAT 2923365 TGTATCGATACA 1 TGTATCGATACA 2923377 ACATTTTATG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:2928851 original size:39 final size:39 Alignment explanation
Indices: 2928797--2928875 Score: 149 Period size: 39 Copynumber: 2.0 Consensus size: 39 2928787 CGCCAACGGT * 2928797 GCCCGACGAAAAAGTACTTTTAGATTTTTTGAGCTTTTC 1 GCCCGACGAAAAAGTACTTTTAGATTTTTTAAGCTTTTC 2928836 GCCCGACGAAAAAGTACTTTTAGATTTTTTAAGCTTTTC 1 GCCCGACGAAAAAGTACTTTTAGATTTTTTAAGCTTTTC 2928875 G 1 G 2928876 GCTAATACGA Statistics Matches: 39, Mismatches: 1, Indels: 0 0.98 0.03 0.00 Matches are distributed among these distances: 39 39 1.00 ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38 Consensus pattern (39 bp): GCCCGACGAAAAAGTACTTTTAGATTTTTTAAGCTTTTC Found at i:2935175 original size:32 final size:33 Alignment explanation
Indices: 2935113--2935176 Score: 94 Period size: 32 Copynumber: 2.0 Consensus size: 33 2935103 TACACCCAGA * 2935113 TGTATCGATACATATTGCTTAGTATCGATACAT 1 TGTATCAATACATATTGCTTAGTATCGATACAT * * 2935146 TGTATCAATACATGTT-CTTGGTATCGATACA 1 TGTATCAATACATATTGCTTAGTATCGATACA 2935177 CAATGAATTG Statistics Matches: 28, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 32 14 0.50 33 14 0.50 ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39 Consensus pattern (33 bp): TGTATCAATACATATTGCTTAGTATCGATACAT Found at i:2935262 original size:13 final size:13 Alignment explanation
Indices: 2935225--2935262 Score: 58 Period size: 13 Copynumber: 2.9 Consensus size: 13 2935215 AACTTACTCA * 2935225 GTATCGATACAGT 1 GTATCGATACATT * 2935238 GTATTGATACATT 1 GTATCGATACATT 2935251 GTATCGATACAT 1 GTATCGATACAT 2935263 GGTGAAATGT Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 13 22 1.00 ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37 Consensus pattern (13 bp): GTATCGATACATT Found at i:2943281 original size:16 final size:16 Alignment explanation
Indices: 2943262--2943311 Score: 55 Period size: 16 Copynumber: 3.0 Consensus size: 16 2943252 ATAAATTTGT 2943262 AAAAAAAGGAGAGATA 1 AAAAAAAGGAGAGATA * * 2943278 AAAAAAAGGGGGGAGAGA 1 AAAAAAA--GGAGAGATA * 2943296 AAAAAAGGGAGAGATA 1 AAAAAAAGGAGAGATA 2943312 TTTTGAAATA Statistics Matches: 27, Mismatches: 5, Indels: 4 0.75 0.14 0.11 Matches are distributed among these distances: 16 14 0.52 18 13 0.48 ACGTcount: A:0.62, C:0.00, G:0.34, T:0.04 Consensus pattern (16 bp): AAAAAAAGGAGAGATA Found at i:2947991 original size:13 final size:13 Alignment explanation
Indices: 2947973--2947997 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 2947963 TCAAAGAGCT 2947973 TTTGTATTCTTTA 1 TTTGTATTCTTTA 2947986 TTTGTATTCTTT 1 TTTGTATTCTTT 2947998 GAAAGCTCAT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.12, C:0.08, G:0.08, T:0.72 Consensus pattern (13 bp): TTTGTATTCTTTA Found at i:2948683 original size:18 final size:19 Alignment explanation
Indices: 2948646--2948683 Score: 60 Period size: 19 Copynumber: 2.1 Consensus size: 19 2948636 GTTGTTCAAA * 2948646 TCCACTACTTTAATTAACT 1 TCCACGACTTTAATTAACT 2948665 TCCACGACTTTAA-TAACT 1 TCCACGACTTTAATTAACT 2948683 T 1 T 2948684 TATCAAGTTA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 18 6 0.33 19 12 0.67 ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39 Consensus pattern (19 bp): TCCACGACTTTAATTAACT Found at i:2948953 original size:20 final size:19 Alignment explanation
Indices: 2948930--2948984 Score: 62 Period size: 20 Copynumber: 2.9 Consensus size: 19 2948920 TTTTTATTAA 2948930 TTATTTGTTATATTTAACAC 1 TTATTTGTTATATTTAA-AC * 2948950 TTA-TT-TAATA-TTAAAC 1 TTATTTGTTATATTTAAAC 2948966 TTATTTGTTAATATTTAAA 1 TTATTTGTT-ATATTTAAA 2948985 ACTATTTTAA Statistics Matches: 29, Mismatches: 2, Indels: 8 0.74 0.05 0.21 Matches are distributed among these distances: 16 5 0.17 17 6 0.21 18 5 0.17 19 5 0.17 20 8 0.28 ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55 Consensus pattern (19 bp): TTATTTGTTATATTTAAAC Found at i:2948972 original size:36 final size:35 Alignment explanation
Indices: 2948930--2949001 Score: 101 Period size: 36 Copynumber: 2.0 Consensus size: 35 2948920 TTTTTATTAA * 2948930 TTATTTGTT-ATATTTAACACTTATTTAATATTAAAC 1 TTATTTGTTAATATTTAAAAC-TATTTAA-ATTAAAC * 2948966 TTATTTGTTAATATTTAAAACTATTTTAATTAAAC 1 TTATTTGTTAATATTTAAAACTATTTAAATTAAAC 2949001 T 1 T 2949002 GATCAATAAA Statistics Matches: 33, Mismatches: 2, Indels: 3 0.87 0.05 0.08 Matches are distributed among these distances: 35 8 0.24 36 15 0.45 37 10 0.30 ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53 Consensus pattern (35 bp): TTATTTGTTAATATTTAAAACTATTTAAATTAAAC Found at i:2948990 original size:20 final size:20 Alignment explanation
Indices: 2948931--2948991 Score: 60 Period size: 18 Copynumber: 3.2 Consensus size: 20 2948921 TTTTATTAAT * 2948931 TATTTGTT-ATATTTAACAC 1 TATTTGTTAATATTTAAAAC * 2948950 T-TAT-TTAATA-TT-AAAC 1 TATTTGTTAATATTTAAAAC 2948966 TTATTTGTTAATATTTAAAAC 1 -TATTTGTTAATATTTAAAAC 2948987 TATTT 1 TATTT 2948992 TAATTAAACT Statistics Matches: 33, Mismatches: 3, Indels: 11 0.70 0.06 0.23 Matches are distributed among these distances: 16 3 0.09 17 5 0.15 18 7 0.21 19 7 0.21 20 7 0.21 21 4 0.12 ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54 Consensus pattern (20 bp): TATTTGTTAATATTTAAAAC Found at i:2949454 original size:13 final size:13 Alignment explanation
Indices: 2949436--2949466 Score: 53 Period size: 13 Copynumber: 2.4 Consensus size: 13 2949426 TGATACATGG * 2949436 TACATTGTATCGA 1 TACATTATATCGA 2949449 TACATTATATCGA 1 TACATTATATCGA 2949462 TACAT 1 TACAT 2949467 GATCAATTGT Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39 Consensus pattern (13 bp): TACATTATATCGA Found at i:2955469 original size:13 final size:13 Alignment explanation
Indices: 2955451--2955489 Score: 78 Period size: 13 Copynumber: 3.0 Consensus size: 13 2955441 TACAGCAAGT 2955451 ATGTATCGATACA 1 ATGTATCGATACA 2955464 ATGTATCGATACA 1 ATGTATCGATACA 2955477 ATGTATCGATACA 1 ATGTATCGATACA 2955490 CAAAAAATTG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 26 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:2957741 original size:21 final size:21 Alignment explanation
Indices: 2957708--2957752 Score: 56 Period size: 21 Copynumber: 2.1 Consensus size: 21 2957698 TTGCAAGTTG * 2957708 AAATAAAGAAGTTGGCTAATGA 1 AAATAAAGAAGTTAGCTAA-GA * 2957730 AAATAATG-AGTTAGCTAAGA 1 AAATAAAGAAGTTAGCTAAGA 2957750 AAA 1 AAA 2957753 ATGAAAACTT Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 20 5 0.24 21 9 0.43 22 7 0.33 ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22 Consensus pattern (21 bp): AAATAAAGAAGTTAGCTAAGA Found at i:2959576 original size:15 final size:15 Alignment explanation
Indices: 2959556--2959586 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 2959546 TAAAAATGTC * 2959556 CAAAATGAGGAAGCT 1 CAAAATGAAGAAGCT 2959571 CAAAATGAAGAAGCT 1 CAAAATGAAGAAGCT 2959586 C 1 C 2959587 CAAACGAAAT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13 Consensus pattern (15 bp): CAAAATGAAGAAGCT Found at i:2961683 original size:13 final size:13 Alignment explanation
Indices: 2961665--2961703 Score: 78 Period size: 13 Copynumber: 3.0 Consensus size: 13 2961655 ACATTTTTCT 2961665 TTGTATCGATACA 1 TTGTATCGATACA 2961678 TTGTATCGATACA 1 TTGTATCGATACA 2961691 TTGTATCGATACA 1 TTGTATCGATACA 2961704 GGCTGATTAT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 26 1.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TTGTATCGATACA Found at i:2964269 original size:13 final size:13 Alignment explanation
Indices: 2964251--2964276 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 2964241 TACAGCAAGT 2964251 ATGTATCGATACA 1 ATGTATCGATACA 2964264 ATGTATCGATACA 1 ATGTATCGATACA 2964277 CAAAAAATTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:2965950 original size:20 final size:20 Alignment explanation
Indices: 2965925--2965981 Score: 89 Period size: 19 Copynumber: 2.9 Consensus size: 20 2965915 TACTGCCAGT 2965925 TTCATGTATCGATACAATTG 1 TTCATGTATCGATACAATTG 2965945 TTCATGTATCGATACAA-TG 1 TTCATGTATCGATACAATTG ** 2965964 AACATGTATCGATACAAT 1 TTCATGTATCGATACAAT 2965982 GTATCTATAC Statistics Matches: 34, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 19 17 0.50 20 17 0.50 ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35 Consensus pattern (20 bp): TTCATGTATCGATACAATTG Found at i:2974206 original size:13 final size:13 Alignment explanation
Indices: 2974188--2974213 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 2974178 CAATTTTTTG 2974188 TGTATCGATACAT 1 TGTATCGATACAT 2974201 TGTATCGATACAT 1 TGTATCGATACAT 2974214 ACTTGCTGTA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:2976778 original size:13 final size:13 Alignment explanation
Indices: 2976760--2976798 Score: 60 Period size: 13 Copynumber: 3.0 Consensus size: 13 2976750 ATAATCACCC * 2976760 TGTATCGATACAG 1 TGTATCGATACAA * 2976773 TGTATCGATAGAA 1 TGTATCGATACAA 2976786 TGTATCGATACAA 1 TGTATCGATACAA 2976799 AGAAAAATGT Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 13 23 1.00 ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31 Consensus pattern (13 bp): TGTATCGATACAA Found at i:2976809 original size:20 final size:20 Alignment explanation
Indices: 2976784--2976862 Score: 77 Period size: 20 Copynumber: 3.7 Consensus size: 20 2976774 GTATCGATAG 2976784 AATGTATCGATACAAAGAAA 1 AATGTATCGATACAAAGAAA * 2976804 AATGTATCGATACATAGAATTTCCA 1 AATGTATCGATACAAAGAA-----A * * 2976829 GATGTATCGATACACAGAAA 1 AATGTATCGATACAAAGAAA * 2976849 CATGTATCGATACA 1 AATGTATCGATACA 2976863 TTTTGGACAT Statistics Matches: 50, Mismatches: 4, Indels: 10 0.78 0.06 0.16 Matches are distributed among these distances: 20 32 0.64 25 18 0.36 ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25 Consensus pattern (20 bp): AATGTATCGATACAAAGAAA Found at i:2980741 original size:21 final size:21 Alignment explanation
Indices: 2980712--2980756 Score: 56 Period size: 21 Copynumber: 2.1 Consensus size: 21 2980702 AAGTTTTCAT * 2980712 TTTTCTTAGCTAAC-TCATTA 1 TTTTCTTAGCCAACTTCATTA * 2980732 TTTTCATTAGCCAACTTCTTTA 1 TTTTC-TTAGCCAACTTCATTA 2980754 TTT 1 TTT 2980757 CAACTTGCAA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 20 5 0.24 21 8 0.38 22 8 0.38 ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53 Consensus pattern (21 bp): TTTTCTTAGCCAACTTCATTA Found at i:2982996 original size:13 final size:13 Alignment explanation
Indices: 2982978--2983003 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 2982968 CAATTTTTTG 2982978 TGTATCGATACAT 1 TGTATCGATACAT 2982991 TGTATCGATACAT 1 TGTATCGATACAT 2983004 ACTTGCTGTA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:2984598 original size:13 final size:13 Alignment explanation
Indices: 2984580--2984607 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 2984570 TACAATTATT 2984580 AATGTATCGATAC 1 AATGTATCGATAC 2984593 AATGTATCGATAC 1 AATGTATCGATAC 2984606 AA 1 AA 2984608 AGCATAATGT 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:0.43, C:0.14, G:0.14, T:0.29 Consensus pattern (13 bp): AATGTATCGATAC Found at i:2984603 original size:33 final size:33 Alignment explanation
Indices: 2984561--2984626 Score: 98 Period size: 33 Copynumber: 2.0 Consensus size: 33 2984551 TGCCAGTTTC ** 2984561 ATGTATCGATAC-AATTATTAATGTATCGATACA 1 ATGTATCGATACAAAGCA-TAATGTATCGATACA 2984594 ATGTATCGATACAAAGCATAATGTATCGATACA 1 ATGTATCGATACAAAGCATAATGTATCGATACA 2984627 TTTGAAAGTG Statistics Matches: 30, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 33 27 0.90 34 3 0.10 ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32 Consensus pattern (33 bp): ATGTATCGATACAAAGCATAATGTATCGATACA Found at i:2986012 original size:20 final size:20 Alignment explanation
Indices: 2985987--2986037 Score: 68 Period size: 20 Copynumber: 2.5 Consensus size: 20 2985977 CCACTGTTTA * 2985987 TATCGATACATGGT-ACATTG 1 TATCGATACATGATGA-ATTG 2986007 TATCGATACATGATGAATTG 1 TATCGATACATGATGAATTG * 2986027 TATTGATACAT 1 TATCGATACAT 2986038 TGCTTCTAAC Statistics Matches: 28, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 20 27 0.96 21 1 0.04 ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37 Consensus pattern (20 bp): TATCGATACATGATGAATTG Found at i:2988155 original size:21 final size:22 Alignment explanation
Indices: 2988131--2988191 Score: 76 Period size: 21 Copynumber: 2.9 Consensus size: 22 2988121 GAATTAAAGG 2988131 AGAAAATGAATGAGTTAG-AAA 1 AGAAAATGAATGAGTTAGCAAA 2988152 AGAAAA-GAAATGAGTT-GCAAA 1 AGAAAATG-AATGAGTTAGCAAA 2988173 ATGAAAATG-ATGAGTTAGC 1 A-GAAAATGAATGAGTTAGC 2988192 TAATAAACAT Statistics Matches: 35, Mismatches: 0, Indels: 9 0.80 0.00 0.20 Matches are distributed among these distances: 20 2 0.06 21 25 0.71 22 7 0.20 23 1 0.03 ACGTcount: A:0.52, C:0.03, G:0.25, T:0.20 Consensus pattern (22 bp): AGAAAATGAATGAGTTAGCAAA Found at i:2990207 original size:31 final size:31 Alignment explanation
Indices: 2990172--2990231 Score: 120 Period size: 31 Copynumber: 1.9 Consensus size: 31 2990162 GGAGAGATTG 2990172 TTGTTCATAAATTTGGTTTTATCAAACTTTA 1 TTGTTCATAAATTTGGTTTTATCAAACTTTA 2990203 TTGTTCATAAATTTGGTTTTATCAAACTT 1 TTGTTCATAAATTTGGTTTTATCAAACTT 2990232 AGCTTATAAC Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 31 29 1.00 ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52 Consensus pattern (31 bp): TTGTTCATAAATTTGGTTTTATCAAACTTTA Found at i:2991133 original size:20 final size:20 Alignment explanation
Indices: 2991081--2991136 Score: 103 Period size: 20 Copynumber: 2.8 Consensus size: 20 2991071 CACACCCATA * 2991081 TGTATCGATACACTATGCTT 1 TGTATCGATACATTATGCTT 2991101 TGTATCGATACATTATGCTT 1 TGTATCGATACATTATGCTT 2991121 TGTATCGATACATTAT 1 TGTATCGATACATTAT 2991137 ATTGATACAT Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 20 35 1.00 ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43 Consensus pattern (20 bp): TGTATCGATACATTATGCTT Found at i:2991249 original size:13 final size:13 Alignment explanation
Indices: 2991231--2991294 Score: 86 Period size: 13 Copynumber: 5.4 Consensus size: 13 2991221 CGATACATGG 2991231 TACATTGTATCGA 1 TACATTGTATCGA 2991244 TACATTGTATCGA 1 TACATTGTATCGA 2991257 TACA-TG-AT-G- 1 TACATTGTATCGA 2991266 -A-ATTGTATCGA 1 TACATTGTATCGA 2991277 TACATTGTATCGA 1 TACATTGTATCGA 2991290 TACAT 1 TACAT 2991295 GCTTCTAACG Statistics Matches: 45, Mismatches: 0, Indels: 12 0.79 0.00 0.21 Matches are distributed among these distances: 7 1 0.02 8 3 0.07 9 2 0.04 10 2 0.04 11 2 0.04 12 3 0.07 13 32 0.71 ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38 Consensus pattern (13 bp): TACATTGTATCGA Found at i:2991255 original size:33 final size:33 Alignment explanation
Indices: 2991215--2991295 Score: 137 Period size: 33 Copynumber: 2.5 Consensus size: 33 2991205 TTACCATTGT * 2991215 TTGTATCGATACATGGT-ACATTGTATCGATACA 1 TTGTATCGATACATGATGA-ATTGTATCGATACA 2991248 TTGTATCGATACATGATGAATTGTATCGATACA 1 TTGTATCGATACATGATGAATTGTATCGATACA 2991281 TTGTATCGATACATG 1 TTGTATCGATACATG 2991296 CTTCTAACGG Statistics Matches: 46, Mismatches: 1, Indels: 2 0.94 0.02 0.04 Matches are distributed among these distances: 33 45 0.98 34 1 0.02 ACGTcount: A:0.31, C:0.14, G:0.19, T:0.37 Consensus pattern (33 bp): TTGTATCGATACATGATGAATTGTATCGATACA Found at i:2991370 original size:13 final size:13 Alignment explanation
Indices: 2991352--2991386 Score: 61 Period size: 13 Copynumber: 2.7 Consensus size: 13 2991342 ATCGATACAT 2991352 GGTACATTGTATC 1 GGTACATTGTATC 2991365 GGTACATTGTATC 1 GGTACATTGTATC * 2991378 GATACATTG 1 GGTACATTG 2991387 CTTCTAACGG Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 13 21 1.00 ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37 Consensus pattern (13 bp): GGTACATTGTATC Found at i:2991484 original size:52 final size:53 Alignment explanation
Indices: 2991372--2991491 Score: 197 Period size: 52 Copynumber: 2.3 Consensus size: 53 2991362 ATCGGTACAT * * * * 2991372 TGTATCGATACATTGCTTCTAACGGCTATAAAATGGCTATAATTTTAAATGCA 1 TGTATCGATACATTACTTCTAACGACTATAAAACGGCTATAATTTCAAATGCA 2991425 TGTATCGATACATTACTTCTAACGACTAT-AAACGGCTATAATTTCAAATGCA 1 TGTATCGATACATTACTTCTAACGACTATAAAACGGCTATAATTTCAAATGCA 2991477 TGTATCGATACATTA 1 TGTATCGATACATTA 2991492 TGAATTGTAT Statistics Matches: 63, Mismatches: 4, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 52 36 0.57 53 27 0.43 ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35 Consensus pattern (53 bp): TGTATCGATACATTACTTCTAACGACTATAAAACGGCTATAATTTCAAATGCA Found at i:2993667 original size:21 final size:21 Alignment explanation
Indices: 2993641--2993685 Score: 56 Period size: 21 Copynumber: 2.1 Consensus size: 21 2993631 ATCTTTTATT * 2993641 AATTTAAAAAACGT-AATAAAA 1 AATTT-AAAAACATAAATAAAA * 2993662 AATTTAATAACATAAATAAAA 1 AATTTAAAAACATAAATAAAA 2993683 AAT 1 AAT 2993686 ACTAATAGTT Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 20 6 0.29 21 15 0.71 ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27 Consensus pattern (21 bp): AATTTAAAAACATAAATAAAA Found at i:2993804 original size:41 final size:42 Alignment explanation
Indices: 2993697--2993789 Score: 109 Period size: 43 Copynumber: 2.2 Consensus size: 42 2993687 CTAATAGTTA * * * 2993697 TATAA-AAT-TAACAATAATAATATAAATAAAAATATTAACAT 1 TATAATAATATAA-AATAAGAATATAAATAAAAATAATAACAC * 2993738 TATAATAATATAAAATTAAGAATATAAATAAATATTAATAACAC 1 TATAATAATATAAAA-TAAGAATATAAATAAA-AATAATAACAC 2993782 TATAATAA 1 TATAATAA 2993790 GTTTAATAAA Statistics Matches: 44, Mismatches: 4, Indels: 5 0.83 0.08 0.09 Matches are distributed among these distances: 41 5 0.11 42 5 0.11 43 18 0.41 44 16 0.36 ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32 Consensus pattern (42 bp): TATAATAATATAAAATAAGAATATAAATAAAAATAATAACAC Found at i:3000103 original size:17 final size:17 Alignment explanation
Indices: 3000081--3000131 Score: 59 Period size: 17 Copynumber: 3.0 Consensus size: 17 3000071 ATAATTAATT * 3000081 TAAAATATTATATATAA 1 TAAAATATTTTATATAA 3000098 TAAAAT-TTTTAATATAA 1 TAAAATATTTT-ATATAA ** 3000115 TAATTTATTTTATATAA 1 TAAAATATTTTATATAA 3000132 ATTTTAATTT Statistics Matches: 29, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 16 3 0.10 17 22 0.76 18 4 0.14 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (17 bp): TAAAATATTTTATATAA Found at i:3000111 original size:24 final size:24 Alignment explanation
Indices: 3000058--3000112 Score: 58 Period size: 24 Copynumber: 2.3 Consensus size: 24 3000048 TTATTTTTTA * * 3000058 TTAATATTTTATTATAATTAATTT 1 TTAATATTATATTATAATAAATTT ** 3000082 AAAATATTATA-TATAATAAAATTT 1 TTAATATTATATTATAAT-AAATTT 3000106 TTAATAT 1 TTAATAT 3000113 AATAATTTAT Statistics Matches: 24, Mismatches: 6, Indels: 2 0.75 0.19 0.06 Matches are distributed among these distances: 23 6 0.25 24 18 0.75 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (24 bp): TTAATATTATATTATAATAAATTT Found at i:3000157 original size:10 final size:9 Alignment explanation
Indices: 3000138--3000179 Score: 50 Period size: 10 Copynumber: 4.4 Consensus size: 9 3000128 ATAAATTTTA 3000138 ATTTATTTAT 1 ATTTA-TTAT 3000148 ATATTATTAT 1 AT-TTATTAT 3000158 ATTT-TTAT 1 ATTTATTAT 3000166 ATTATATTAT 1 ATT-TATTAT 3000176 ATTT 1 ATTT 3000180 TAATTATTTT Statistics Matches: 29, Mismatches: 0, Indels: 7 0.81 0.00 0.19 Matches are distributed among these distances: 8 7 0.24 9 4 0.14 10 15 0.52 11 3 0.10 ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67 Consensus pattern (9 bp): ATTTATTAT Found at i:3000160 original size:16 final size:15 Alignment explanation
Indices: 3000141--3000187 Score: 51 Period size: 17 Copynumber: 2.9 Consensus size: 15 3000131 AATTTTAATT 3000141 TATTTATATATTATTA 1 TATTT-TATATTATTA 3000157 TATTTTTATATTATATTA 1 TA-TTTTATA-T-TATTA 3000175 TATTTTA-ATTATT 1 TATTTTATATTATT 3000188 TTTTTGTGTC Statistics Matches: 28, Mismatches: 0, Indels: 8 0.78 0.00 0.22 Matches are distributed among these distances: 14 4 0.14 15 1 0.04 16 7 0.25 17 9 0.32 18 7 0.25 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (15 bp): TATTTTATATTATTA Found at i:3000164 original size:18 final size:18 Alignment explanation
Indices: 3000143--3000180 Score: 60 Period size: 18 Copynumber: 2.1 Consensus size: 18 3000133 TTTTAATTTA 3000143 TTTATA-TATTATTATATT 1 TTTATATTA-TATTATATT 3000161 TTTATATTATATTATATT 1 TTTATATTATATTATATT 3000179 TT 1 TT 3000181 AATTATTTTT Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 18 17 0.89 19 2 0.11 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (18 bp): TTTATATTATATTATATT Found at i:3000408 original size:16 final size:16 Alignment explanation
Indices: 3000352--3000410 Score: 50 Period size: 16 Copynumber: 3.7 Consensus size: 16 3000342 TAATTTGTAT * 3000352 ATTTTAAATTCAGATTA 1 ATTTTAAATTAAGA-TA * 3000369 A-TTTAAATTTAA-ATC 1 ATTTTAAA-TTAAGATA * * 3000384 GTTTCAAATTAAGATA 1 ATTTTAAATTAAGATA 3000400 ATTTTAAATTA 1 ATTTTAAATTA 3000411 TTAACTTTAA Statistics Matches: 32, Mismatches: 7, Indels: 7 0.70 0.15 0.15 Matches are distributed among these distances: 15 5 0.16 16 23 0.72 17 4 0.12 ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46 Consensus pattern (16 bp): ATTTTAAATTAAGATA Found at i:3000903 original size:30 final size:28 Alignment explanation
Indices: 3000848--3000919 Score: 87 Period size: 30 Copynumber: 2.6 Consensus size: 28 3000838 AATAAATAAA 3000848 ATATTATATATTTTATATAAATTTTAAT 1 ATATTATATATTTTATATAAATTTTAAT * 3000876 ATATTA-ATAATTTATATTATAATTTTTAAT 1 ATATTATAT-ATTT-TA-TATAAATTTTAAT 3000906 ATATT-T-TATTTTAT 1 ATATTATATATTTTAT 3000920 TTTATTTTAT Statistics Matches: 39, Mismatches: 1, Indels: 10 0.78 0.02 0.20 Matches are distributed among these distances: 26 1 0.03 27 4 0.10 28 14 0.36 29 3 0.08 30 17 0.44 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (28 bp): ATATTATATATTTTATATAAATTTTAAT Found at i:3000917 original size:15 final size:15 Alignment explanation
Indices: 3000899--3000953 Score: 64 Period size: 15 Copynumber: 3.9 Consensus size: 15 3000889 ATATTATAAT 3000899 TTTTAATATATTTTA 1 TTTTAATATATTTTA * * 3000914 TTTTATTTTATTTTA 1 TTTTAATATATTTTA 3000929 TTTT--TATA-TTTA 1 TTTTAATATATTTTA 3000941 TTTTAAT-TATTTT 1 TTTTAATATATTTT 3000954 TTATTATATT Statistics Matches: 34, Mismatches: 3, Indels: 7 0.77 0.07 0.16 Matches are distributed among these distances: 12 8 0.24 13 5 0.15 14 4 0.12 15 17 0.50 ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75 Consensus pattern (15 bp): TTTTAATATATTTTA Found at i:3000933 original size:21 final size:21 Alignment explanation
Indices: 3000899--3000963 Score: 71 Period size: 22 Copynumber: 3.1 Consensus size: 21 3000889 ATATTATAAT * 3000899 TTTTAA-TATATTTTATTTTA 1 TTTTAATTATTTTTTATTTTA * 3000919 TTTT-ATTTTATTTTTATATTTA 1 TTTTAATTAT-TTTTTAT-TTTA * 3000941 TTTTAATTATTTTTTATTATA 1 TTTTAATTATTTTTTATTTTA 3000962 TT 1 TT 3000964 CATTAAAATT Statistics Matches: 37, Mismatches: 4, Indels: 7 0.77 0.08 0.15 Matches are distributed among these distances: 19 1 0.03 20 6 0.16 21 11 0.30 22 15 0.41 23 4 0.11 ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74 Consensus pattern (21 bp): TTTTAATTATTTTTTATTTTA Found at i:3000935 original size:6 final size:5 Alignment explanation
Indices: 3000907--3000963 Score: 62 Period size: 5 Copynumber: 10.8 Consensus size: 5 3000897 ATTTTTAATA 3000907 TATTT TATTT TATTT TATTT TATTTT TATATT TATTT TAATTAT T-TTT 1 TATTT TATTT TATTT TATTT TA-TTT TAT-TT TATTT T-ATT-T TATTT * 3000955 TATTA TATT 1 TATTT TATT 3000964 CATTAAAATT Statistics Matches: 46, Mismatches: 1, Indels: 10 0.81 0.02 0.18 Matches are distributed among these distances: 4 2 0.04 5 29 0.63 6 13 0.28 7 2 0.04 ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75 Consensus pattern (5 bp): TATTT Found at i:3000973 original size:25 final size:26 Alignment explanation
Indices: 3000921--3000975 Score: 67 Period size: 25 Copynumber: 2.2 Consensus size: 26 3000911 TTATTTTATT * * ** 3000921 TTATTTTATTTTTATATTTATTTTAA 1 TTATTTTATTATTATATTCATTAAAA 3000947 TTATTTT-TTATTATATTCATTAAAA 1 TTATTTTATTATTATATTCATTAAAA 3000972 TTAT 1 TTAT 3000976 ATGATCCATA Statistics Matches: 25, Mismatches: 4, Indels: 1 0.83 0.13 0.03 Matches are distributed among these distances: 25 18 0.72 26 7 0.28 ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67 Consensus pattern (26 bp): TTATTTTATTATTATATTCATTAAAA Found at i:3002180 original size:17 final size:17 Alignment explanation
Indices: 3002126--3002192 Score: 57 Period size: 17 Copynumber: 3.8 Consensus size: 17 3002116 AGTTTAATTA 3002126 AAATAAA-TTTAAATATT 1 AAATAAATTTTAAATA-T * * 3002143 AAATAAGTAATTAAAATTAT 1 AAATAA--ATTTTAAA-TAT 3002163 AAATAAATTTTAAATAT 1 AAATAAATTTTAAATAT 3002180 -AATAAATATTTAA 1 AAATAAAT-TTTAA 3002193 TAAATTATGT Statistics Matches: 42, Mismatches: 3, Indels: 10 0.76 0.05 0.18 Matches are distributed among these distances: 16 7 0.17 17 14 0.33 18 6 0.14 19 1 0.02 20 12 0.29 21 2 0.05 ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39 Consensus pattern (17 bp): AAATAAATTTTAAATAT Found at i:3002184 original size:20 final size:19 Alignment explanation
Indices: 3002126--3002187 Score: 58 Period size: 20 Copynumber: 3.3 Consensus size: 19 3002116 AGTTTAATTA 3002126 AAATAAA-TTTAAATAT-T 1 AAATAAATTTTAAATATAT * * 3002143 AAATAAGTAATTAAA-ATTAT 1 AAATAAAT-TTTAAATA-TAT 3002163 AAATAAATTTTAAATATAAT 1 AAATAAATTTTAAATAT-AT 3002183 AAATA 1 AAATA 3002188 TTTAATAAAT Statistics Matches: 35, Mismatches: 4, Indels: 9 0.73 0.08 0.19 Matches are distributed among these distances: 17 6 0.17 18 1 0.03 19 12 0.34 20 16 0.46 ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37 Consensus pattern (19 bp): AAATAAATTTTAAATATAT Found at i:3003368 original size:2 final size:2 Alignment explanation
Indices: 3003361--3003404 Score: 52 Period size: 2 Copynumber: 22.0 Consensus size: 2 3003351 TCTGTGATTT * * * * 3003361 TA TA TA TA TA TA TA TA TA TA TA TG TT TA TA TT TA TA TT TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 3003403 TA 1 TA 3003405 AGTATATTTA Statistics Matches: 35, Mismatches: 7, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57 Consensus pattern (2 bp): TA Found at i:3004364 original size:2 final size:2 Alignment explanation
Indices: 3004316--3004350 Score: 52 Period size: 2 Copynumber: 16.5 Consensus size: 2 3004306 TTAGACTTGT 3004316 AG AG AG AG AG AG AG AG AG AG AG AG TAG AG TAG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG -AG AG -AG AG A 3004351 AGGTTTGAGA Statistics Matches: 31, Mismatches: 0, Indels: 4 0.89 0.00 0.11 Matches are distributed among these distances: 2 27 0.87 3 4 0.13 ACGTcount: A:0.49, C:0.00, G:0.46, T:0.06 Consensus pattern (2 bp): AG Found at i:3004811 original size:22 final size:22 Alignment explanation
Indices: 3004796--3004839 Score: 88 Period size: 22 Copynumber: 2.0 Consensus size: 22 3004786 AAATAGTAAT 3004796 TTATCAAAAAATAAATTATATC 1 TTATCAAAAAATAAATTATATC 3004818 TTATCAAAAAATAAATTATATC 1 TTATCAAAAAATAAATTATATC 3004840 ATGAGCTTTA Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36 Consensus pattern (22 bp): TTATCAAAAAATAAATTATATC Found at i:3005257 original size:13 final size:13 Alignment explanation
Indices: 3005239--3005269 Score: 62 Period size: 13 Copynumber: 2.4 Consensus size: 13 3005229 ATAAAGTACT 3005239 TTCAAAAACTATA 1 TTCAAAAACTATA 3005252 TTCAAAAACTATA 1 TTCAAAAACTATA 3005265 TTCAA 1 TTCAA 3005270 TACTATAATG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 18 1.00 ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32 Consensus pattern (13 bp): TTCAAAAACTATA Found at i:3006354 original size:21 final size:20 Alignment explanation
Indices: 3006328--3006378 Score: 66 Period size: 20 Copynumber: 2.5 Consensus size: 20 3006318 TCTACAATTG * 3006328 TATCGATATAAACAGTGAATA 1 TATCGATACAAA-AGTGAATA * * 3006349 TATCGATACATAAGTGAATG 1 TATCGATACAAAAGTGAATA 3006369 TATCGATACA 1 TATCGATACA 3006379 TGTCTGAAAT Statistics Matches: 27, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 20 17 0.63 21 10 0.37 ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29 Consensus pattern (20 bp): TATCGATACAAAAGTGAATA Found at i:3006386 original size:20 final size:20 Alignment explanation
Indices: 3006343--3006399 Score: 69 Period size: 20 Copynumber: 2.8 Consensus size: 20 3006333 ATATAAACAG * * 3006343 TGAATATATCGATACATAAG 1 TGAATGTATCGATACATAAC ** 3006363 TGAATGTATCGATACATGTC 1 TGAATGTATCGATACATAAC 3006383 TGAAATGTATCGATACA 1 TG-AATGTATCGATACA 3006400 AAACCATGTC Statistics Matches: 32, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 20 18 0.56 21 14 0.44 ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32 Consensus pattern (20 bp): TGAATGTATCGATACATAAC Found at i:3006464 original size:20 final size:20 Alignment explanation
Indices: 3006437--3006491 Score: 101 Period size: 20 Copynumber: 2.8 Consensus size: 20 3006427 CTGGAAAGAA 3006437 AATGTATCGATACATTTTTC 1 AATGTATCGATACATTTTTC * 3006457 ATTGTATCGATACATTTTTC 1 AATGTATCGATACATTTTTC 3006477 AATGTATCGATACAT 1 AATGTATCGATACAT 3006492 GTAGCCTATT Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 33 1.00 ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44 Consensus pattern (20 bp): AATGTATCGATACATTTTTC Found at i:3010240 original size:16 final size:15 Alignment explanation
Indices: 3010219--3010248 Score: 51 Period size: 16 Copynumber: 1.9 Consensus size: 15 3010209 TTATTACACT 3010219 TAGAATAGTAATATAG 1 TAGAATAG-AATATAG 3010235 TAGAATAGAATATA 1 TAGAATAGAATATA 3010249 AAGTTAACAT Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 6 0.43 16 8 0.57 ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30 Consensus pattern (15 bp): TAGAATAGAATATAG Found at i:3013102 original size:24 final size:23 Alignment explanation
Indices: 3013074--3013121 Score: 69 Period size: 24 Copynumber: 2.0 Consensus size: 23 3013064 TTTAGTTAAG * 3013074 ATTAAATAAATTTTTAAATATTTT 1 ATTAAATAAATTTTAAAAT-TTTT * 3013098 ATTAAATATATTTTAAAATTTTT 1 ATTAAATAAATTTTAAAATTTTT 3013121 A 1 A 3013122 AATATTAAGT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 23 5 0.23 24 17 0.77 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (23 bp): ATTAAATAAATTTTAAAATTTTT Found at i:3013120 original size:9 final size:10 Alignment explanation
Indices: 3013083--3013127 Score: 56 Period size: 11 Copynumber: 4.3 Consensus size: 10 3013073 GATTAAATAA 3013083 ATTTTTAAAT 1 ATTTTTAAAT 3013093 ATTTTATTAAAT 1 A-TTT-TTAAAT 3013105 ATATTTTAAA- 1 AT-TTTTAAAT 3013115 ATTTTTAAAT 1 ATTTTTAAAT 3013125 ATT 1 ATT 3013128 AAGTCGGTGT Statistics Matches: 31, Mismatches: 0, Indels: 8 0.79 0.00 0.21 Matches are distributed among these distances: 9 7 0.23 10 6 0.19 11 9 0.29 12 9 0.29 ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58 Consensus pattern (10 bp): ATTTTTAAAT Found at i:3013568 original size:16 final size:17 Alignment explanation
Indices: 3013523--3013597 Score: 77 Period size: 16 Copynumber: 4.6 Consensus size: 17 3013513 CTCAAAAAAA 3013523 CCCGAACCCG-TATAAG 1 CCCGAACCCGATATAAG ** * * 3013539 ATCGAGCTCG-TATAAG 1 CCCGAACCCGATATAAG 3013555 CCCGAACCC-ATATAAG 1 CCCGAACCCGATATAAG * 3013571 CCCGAACCCGA-ATGAG 1 CCCGAACCCGATATAAG 3013587 CCCGAACCCGA 1 CCCGAACCCGA 3013598 ACCCGAACGA Statistics Matches: 48, Mismatches: 9, Indels: 4 0.79 0.15 0.07 Matches are distributed among these distances: 16 47 0.98 17 1 0.02 ACGTcount: A:0.32, C:0.36, G:0.20, T:0.12 Consensus pattern (17 bp): CCCGAACCCGATATAAG Found at i:3013596 original size:22 final size:22 Alignment explanation
Indices: 3013571--3013616 Score: 74 Period size: 22 Copynumber: 2.1 Consensus size: 22 3013561 CCCATATAAG * * 3013571 CCCGAACCCGAATGAGCCCGAA 1 CCCGAACCCGAACGAGCCCAAA 3013593 CCCGAACCCGAACGAGCCCAAA 1 CCCGAACCCGAACGAGCCCAAA 3013615 CC 1 CC 3013617 AGAATGAACT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.33, C:0.46, G:0.20, T:0.02 Consensus pattern (22 bp): CCCGAACCCGAACGAGCCCAAA Found at i:3016088 original size:20 final size:22 Alignment explanation
Indices: 3016059--3016101 Score: 72 Period size: 22 Copynumber: 2.0 Consensus size: 22 3016049 ATTAGCTGTC 3016059 GTATA-TTTT-TACTGATACTT 1 GTATAGTTTTATACTGATACTT 3016079 GTATAGTTTTATACTGATACTT 1 GTATAGTTTTATACTGATACTT 3016101 G 1 G 3016102 CCACAAAAAA Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 20 5 0.24 21 4 0.19 22 12 0.57 ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51 Consensus pattern (22 bp): GTATAGTTTTATACTGATACTT Found at i:3017173 original size:13 final size:13 Alignment explanation
Indices: 3017155--3017179 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3017145 CATTATGCTT 3017155 TGTATCGATACAA 1 TGTATCGATACAA 3017168 TGTATCGATACA 1 TGTATCGATACA 3017180 TGATCATTGT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:3017176 original size:33 final size:32 Alignment explanation
Indices: 3017134--3017196 Score: 99 Period size: 33 Copynumber: 1.9 Consensus size: 32 3017124 ACACATCCAG * * 3017134 ATGTATCGATACATTATGCTTTGTATCGATACA 1 ATGTATCGATACATGAT-CATTGTATCGATACA 3017167 ATGTATCGATACATGATCATTGTATCGATA 1 ATGTATCGATACATGATCATTGTATCGATA 3017197 TATGAAACTA Statistics Matches: 28, Mismatches: 2, Indels: 1 0.90 0.06 0.03 Matches are distributed among these distances: 32 12 0.43 33 16 0.57 ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38 Consensus pattern (32 bp): ATGTATCGATACATGATCATTGTATCGATACA Found at i:3017264 original size:13 final size:13 Alignment explanation
Indices: 3017246--3017272 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 3017236 GATAAATGGC 3017246 ACATTGTATCGAT 1 ACATTGTATCGAT 3017259 ACATTGTATCGAT 1 ACATTGTATCGAT 3017272 A 1 A 3017273 GATTCATAAT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37 Consensus pattern (13 bp): ACATTGTATCGAT Found at i:3017331 original size:95 final size:95 Alignment explanation
Indices: 3017154--3017357 Score: 284 Period size: 95 Copynumber: 2.1 Consensus size: 95 3017144 ACATTATGCT * * * * * * 3017154 TTGTATCGATACAATGTATCGATACATGATCATTGTATCGATATATGAAACTAGCAGTAGCTACC 1 TTGTATCGATACATTGTATCGATACATCATAATTATATCGATACATAAAACTAGCAGTAGCTACC * * 3017219 GTACCGCTGTTTGTATCGATAAATGGCACA 66 CTACCACTGTTTGTATCGATAAATGGCACA * * 3017249 TTGTATCGATACATTGTATCGATAGATTCATAATTATATCGATACATAAAACTGGCAGTAGCTAC 1 TTGTATCGATACATTGTATCGATACA-TCATAATTATATCGATACATAAAACTAGCAGTAGCTAC * 3017314 CCTACCATTGTTT-TATCGATAAATGGCACA 65 CCTACCACTGTTTGTATCGATAAATGGCACA * 3017344 TTTTATCGATACAT 1 TTGTATCGATACAT 3017358 GAAGAATTGT Statistics Matches: 96, Mismatches: 12, Indels: 2 0.87 0.11 0.02 Matches are distributed among these distances: 95 54 0.56 96 42 0.44 ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34 Consensus pattern (95 bp): TTGTATCGATACATTGTATCGATACATCATAATTATATCGATACATAAAACTAGCAGTAGCTACC CTACCACTGTTTGTATCGATAAATGGCACA Found at i:3018953 original size:21 final size:21 Alignment explanation
Indices: 3018927--3018968 Score: 84 Period size: 21 Copynumber: 2.0 Consensus size: 21 3018917 CAAGAGCCAC 3018927 CAAAGAAAGCAAGTGTCACCT 1 CAAAGAAAGCAAGTGTCACCT 3018948 CAAAGAAAGCAAGTGTCACCT 1 CAAAGAAAGCAAGTGTCACCT 3018969 TCAAGTCAGC Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 21 1.00 ACGTcount: A:0.43, C:0.24, G:0.19, T:0.14 Consensus pattern (21 bp): CAAAGAAAGCAAGTGTCACCT Found at i:3025734 original size:13 final size:13 Alignment explanation
Indices: 3025716--3025742 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 3025706 ATATTATGCT 3025716 TTGTATCGATACA 1 TTGTATCGATACA 3025729 TTGTATCGATACA 1 TTGTATCGATACA 3025742 T 1 T 3025743 GCATAATTGT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41 Consensus pattern (13 bp): TTGTATCGATACA Found at i:3027085 original size:11 final size:11 Alignment explanation
Indices: 3027069--3027105 Score: 58 Period size: 11 Copynumber: 3.5 Consensus size: 11 3027059 AAACTTGGAG 3027069 AAAAAAAGAGA 1 AAAAAAAGAGA 3027080 AAAAAAAGAGA 1 AAAAAAAGAGA * 3027091 GAAAAAAGA-A 1 AAAAAAAGAGA 3027101 AAAAA 1 AAAAA 3027106 TCTAAATTCT Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 10 5 0.21 11 19 0.79 ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00 Consensus pattern (11 bp): AAAAAAAGAGA Found at i:3027090 original size:21 final size:20 Alignment explanation
Indices: 3027066--3027105 Score: 62 Period size: 20 Copynumber: 1.9 Consensus size: 20 3027056 TGGAAACTTG 3027066 GAGAAAAAAAGAGAAAAAAAA 1 GAGAAAAAAA-AGAAAAAAAA * 3027087 GAGAGAAAAAAGAAAAAAA 1 GAGAAAAAAAAGAAAAAAA 3027106 TCTAAATTCT Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 20 9 0.50 21 9 0.50 ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00 Consensus pattern (20 bp): GAGAAAAAAAAGAAAAAAAA Found at i:3028512 original size:16 final size:17 Alignment explanation
Indices: 3028486--3028519 Score: 52 Period size: 16 Copynumber: 2.1 Consensus size: 17 3028476 TCTTGTCTGA 3028486 AAAATTAAAAAAATAAT 1 AAAATTAAAAAAATAAT * 3028503 AAAA-TAAAAATATAAT 1 AAAATTAAAAAAATAAT 3028519 A 1 A 3028520 TTCTTTAAAA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 16 12 0.75 17 4 0.25 ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24 Consensus pattern (17 bp): AAAATTAAAAAAATAAT Found at i:3030885 original size:2 final size:2 Alignment explanation
Indices: 3030878--3030920 Score: 86 Period size: 2 Copynumber: 21.5 Consensus size: 2 3030868 TCTTTTCTTT 3030878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 3030920 T 1 T 3030921 TACTGAAAGC Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 41 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:3031771 original size:20 final size:21 Alignment explanation
Indices: 3031726--3031778 Score: 72 Period size: 20 Copynumber: 2.6 Consensus size: 21 3031716 CTGCCAAGAA * ** 3031726 ATGTATCGATACATCTTTTTC 1 ATGTATCGATACATCTGTAAC 3031747 ATGTATCGATACAT-TGTAAC 1 ATGTATCGATACATCTGTAAC 3031767 ATGTATCGATAC 1 ATGTATCGATAC 3031779 TTTGAATTGT Statistics Matches: 29, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 20 15 0.52 21 14 0.48 ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40 Consensus pattern (21 bp): ATGTATCGATACATCTGTAAC Done.