Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11

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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 2600 characters in sequence are not A, C, G, or T


File 12 of 182

Found at i:4760568 original size:17 final size:19

Alignment explanation

Indices: 4760536--4760573 Score: 62 Period size: 17 Copynumber: 2.1 Consensus size: 19 4760526 TTTTGCTTTG 4760536 TTTGTTGATTCAATGTGTT 1 TTTGTTGATTCAATGTGTT 4760555 TTTGTTG-TTC-ATGTGTT 1 TTTGTTGATTCAATGTGTT 4760572 TT 1 TT 4760574 CTTTGTCTTA Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 17 9 0.47 18 3 0.16 19 7 0.37 ACGTcount: A:0.11, C:0.05, G:0.21, T:0.63 Consensus pattern (19 bp): TTTGTTGATTCAATGTGTT Found at i:4774075 original size:11 final size:11 Alignment explanation

Indices: 4774037--4774068 Score: 64 Period size: 11 Copynumber: 2.9 Consensus size: 11 4774027 CCAAATAAAT 4774037 TGTTTTGCTAC 1 TGTTTTGCTAC 4774048 TGTTTTGCTAC 1 TGTTTTGCTAC 4774059 TGTTTTGCTA 1 TGTTTTGCTA 4774069 TTATTTTATT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 21 1.00 ACGTcount: A:0.09, C:0.16, G:0.19, T:0.56 Consensus pattern (11 bp): TGTTTTGCTAC Found at i:4776038 original size:2 final size:2 Alignment explanation

Indices: 4776031--4776066 Score: 56 Period size: 2 Copynumber: 18.5 Consensus size: 2 4776021 GAAACTAATA * 4776031 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT TT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 4776067 AGCTCAACAT Statistics Matches: 31, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 1 1 0.03 2 30 0.97 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (2 bp): AT Found at i:4783909 original size:3 final size:3 Alignment explanation

Indices: 4783901--4783936 Score: 72 Period size: 3 Copynumber: 12.0 Consensus size: 3 4783891 AAAATAAAGA 4783901 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG 1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG 4783937 TGAAAGAGAG Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 33 1.00 ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00 Consensus pattern (3 bp): AAG Found at i:4786094 original size:16 final size:17 Alignment explanation

Indices: 4786064--4786095 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 4786054 TATTTTGTTT 4786064 AAAATTTGTATATAAAC 1 AAAATTTGTATATAAAC 4786081 AAAATTTG-ATATAAA 1 AAAATTTGTATATAAA 4786096 AATATAAAAA Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 7 0.47 17 8 0.53 ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34 Consensus pattern (17 bp): AAAATTTGTATATAAAC Found at i:4801796 original size:13 final size:13 Alignment explanation

Indices: 4801759--4801797 Score: 55 Period size: 13 Copynumber: 3.1 Consensus size: 13 4801749 TAACATTATT 4801759 TATTTATAAAAT- 1 TATTTATAAAATA 4801771 TATATTA-AAAATA 1 TAT-TTATAAAATA 4801784 TATTTATAAAATA 1 TATTTATAAAATA 4801797 T 1 T 4801798 TTATTCATTT Statistics Matches: 24, Mismatches: 0, Indels: 5 0.83 0.00 0.17 Matches are distributed among these distances: 12 11 0.46 13 13 0.54 ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46 Consensus pattern (13 bp): TATTTATAAAATA Found at i:4801798 original size:11 final size:11 Alignment explanation

Indices: 4801759--4801801 Score: 50 Period size: 12 Copynumber: 3.6 Consensus size: 11 4801749 TAACATTATT 4801759 TATTTATAAAA 1 TATTTATAAAA * 4801770 TTATATTAAAAATA 1 -TAT-TTATAAA-A 4801784 TATTTATAAAA 1 TATTTATAAAA 4801795 TATTTAT 1 TATTTAT 4801802 TCATTTAGTT Statistics Matches: 27, Mismatches: 2, Indels: 5 0.79 0.06 0.15 Matches are distributed among these distances: 11 8 0.30 12 9 0.33 13 9 0.33 14 1 0.04 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (11 bp): TATTTATAAAA Found at i:4802187 original size:31 final size:29 Alignment explanation

Indices: 4802120--4802188 Score: 77 Period size: 29 Copynumber: 2.3 Consensus size: 29 4802110 ATAATTACAT * * 4802120 AAGTGACTAAAATGTAACATTTCAAACAT 1 AAGTGACTAAAATGTAACATTACAAACAA * 4802149 AAGTGACTAAAATGTAAC-TTGAGACAAATAA 1 AAGTGACTAAAATGTAACATT---ACAAACAA 4802180 AAGTGACTA 1 AAGTGACTA 4802189 TTTTTACAGT Statistics Matches: 34, Mismatches: 3, Indels: 4 0.83 0.07 0.10 Matches are distributed among these distances: 28 2 0.06 29 18 0.53 31 14 0.41 ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25 Consensus pattern (29 bp): AAGTGACTAAAATGTAACATTACAAACAA Found at i:4817435 original size:21 final size:20 Alignment explanation

Indices: 4817402--4817524 Score: 74 Period size: 20 Copynumber: 5.7 Consensus size: 20 4817392 CAAAAAAAAA * 4817402 TAAAAATA-CATAAATATTTT 1 TAAAAATATAATAAATA-TTT * 4817422 TAAAAATATAAT-AATAAATT 1 TAAAAATATAATAAAT-ATTT 4817442 TAAAACATATAA-AAATATTGTT 1 TAAAA-ATATAATAAATA-T-TT 4817464 GATAAATAATAGTATATAAA-ATTT 1 --TAAA-AATA-TA-ATAAATATTT * 4817488 AAAAATATATAAAATAAATATTT 1 TAAAA-ATAT--AATAAATATTT 4817511 TAAAAATATAATAA 1 TAAAAATATAATAA 4817525 TTTAAATTTA Statistics Matches: 82, Mismatches: 5, Indels: 32 0.69 0.04 0.27 Matches are distributed among these distances: 20 24 0.29 21 14 0.17 22 17 0.21 23 9 0.11 24 9 0.11 25 4 0.05 26 2 0.02 27 3 0.04 ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36 Consensus pattern (20 bp): TAAAAATATAATAAATATTT Found at i:4817516 original size:15 final size:16 Alignment explanation

Indices: 4817498--4817530 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 4817488 AAAAATATAT * 4817498 AAAATA-AATATTTTA 1 AAAATATAATAATTTA 4817513 AAAATATAATAATTTA 1 AAAATATAATAATTTA 4817529 AA 1 AA 4817531 TTTAATATTA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 15 6 0.38 16 10 0.62 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (16 bp): AAAATATAATAATTTA Found at i:4817535 original size:22 final size:22 Alignment explanation

Indices: 4817420--4817520 Score: 66 Period size: 24 Copynumber: 4.5 Consensus size: 22 4817410 CATAAATATT * 4817420 TTTAAAAATATA-ATAAT-AAA 1 TTTAAAAATATATAAAATAAAA *** 4817440 TTTAAAACATATA-AAAATATTG 1 TTTAAAA-ATATATAAAATAAAA * * * 4817462 TTGATAAATA-ATAGTATATAAAA 1 TTTAAAAATATATA--AAATAAAA 4817485 TTTAAAAATATATAAAATAAATA 1 TTTAAAAATATATAAAATAAA-A 4817508 TTTTAAAAATATA 1 -TTTAAAAATATA 4817521 ATAATTTAAA Statistics Matches: 60, Mismatches: 13, Indels: 12 0.71 0.15 0.14 Matches are distributed among these distances: 20 8 0.13 21 13 0.22 22 11 0.18 23 13 0.22 24 15 0.25 ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37 Consensus pattern (22 bp): TTTAAAAATATATAAAATAAAA Found at i:4817567 original size:6 final size:6 Alignment explanation

Indices: 4817549--4817612 Score: 67 Period size: 6 Copynumber: 10.5 Consensus size: 6 4817539 TACTATTATT * * * 4817549 AATATTA AATATA AATATA AACAAA AATATA AGTATA AATA-A AATATA 1 AATA-TA AATATA AATATA AATATA AATATA AATATA AATATA AATATA * 4817597 AACATA AATATTA AAT 1 AATATA AATA-TA AAT 4817613 TAATAAAATT Statistics Matches: 47, Mismatches: 8, Indels: 4 0.80 0.14 0.07 Matches are distributed among these distances: 5 5 0.11 6 33 0.70 7 9 0.19 ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30 Consensus pattern (6 bp): AATATA Found at i:4817603 original size:17 final size:17 Alignment explanation

Indices: 4817555--4817606 Score: 68 Period size: 17 Copynumber: 3.0 Consensus size: 17 4817545 TATTAATATT * 4817555 AAATATAAATATAAACAA 1 AAATATAAATATAAA-TA * 4817573 AAATATAAGTATAAATA 1 AAATATAAATATAAATA * 4817590 AAATATAAACATAAATA 1 AAATATAAATATAAATA 4817607 TTAAATTAAT Statistics Matches: 30, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 17 16 0.53 18 14 0.47 ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25 Consensus pattern (17 bp): AAATATAAATATAAATA Found at i:4817625 original size:29 final size:29 Alignment explanation

Indices: 4817545--4817621 Score: 95 Period size: 29 Copynumber: 2.6 Consensus size: 29 4817535 ATATTACTAT 4817545 TATTAATATTAAATATAAATATAAACAAAAA 1 TATTAATATT-AATA-AAATATAAACAAAAA * * 4817576 TA-TAAGTATAAATAAAATATAAACATAAA 1 TATTAA-TATTAATAAAATATAAACAAAAA 4817605 TATTAA-ATTAATAAAAT 1 TATTAATATTAATAAAAT 4817622 TATATTGATA Statistics Matches: 41, Mismatches: 3, Indels: 7 0.80 0.06 0.14 Matches are distributed among these distances: 28 10 0.24 29 16 0.39 30 10 0.24 31 5 0.12 ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32 Consensus pattern (29 bp): TATTAATATTAATAAAATATAAACAAAAA Found at i:4818127 original size:21 final size:20 Alignment explanation

Indices: 4818093--4818148 Score: 60 Period size: 19 Copynumber: 2.8 Consensus size: 20 4818083 AATCTTTTAT * 4818093 TTTTTAAATTTATTATTATATA 1 TTTTTAAATATA-T-TTATATA * 4818115 TTTTTAAA-ATATTTATGTA 1 TTTTTAAATATATTTATATA * 4818134 TTTTTATATATATTT 1 TTTTTAAATATATTT 4818149 TTTGAATTAT Statistics Matches: 30, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 19 13 0.43 20 7 0.23 21 2 0.07 22 8 0.27 ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64 Consensus pattern (20 bp): TTTTTAAATATATTTATATA Found at i:4830190 original size:12 final size:12 Alignment explanation

Indices: 4830173--4830219 Score: 51 Period size: 12 Copynumber: 3.9 Consensus size: 12 4830163 ATCATTAATA 4830173 AATAAACGAGTC 1 AATAAACGAGTC * 4830185 AATAAACAAG-C 1 AATAAACGAGTC * 4830196 TTATAAACGAGTC 1 -AATAAACGAGTC * 4830209 AATAAATGAGT 1 AATAAACGAGT 4830220 TTATTCGTGA Statistics Matches: 28, Mismatches: 5, Indels: 4 0.76 0.14 0.11 Matches are distributed among these distances: 11 1 0.04 12 26 0.93 13 1 0.04 ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21 Consensus pattern (12 bp): AATAAACGAGTC Found at i:4837371 original size:31 final size:31 Alignment explanation

Indices: 4837312--4837371 Score: 75 Period size: 31 Copynumber: 1.9 Consensus size: 31 4837302 TGATGTAATC * * ** 4837312 ATATATATAAAATTTTGATTGTGGTTTAAAT 1 ATATACATAAAATTTTAATTGTAATTTAAAT * 4837343 ATATACATAAAATTTTAATTTTAATTTAA 1 ATATACATAAAATTTTAATTGTAATTTAA 4837372 TTGCATACAT Statistics Matches: 24, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 31 24 1.00 ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48 Consensus pattern (31 bp): ATATACATAAAATTTTAATTGTAATTTAAAT Found at i:4838789 original size:3 final size:3 Alignment explanation

Indices: 4838776--4838823 Score: 87 Period size: 3 Copynumber: 15.7 Consensus size: 3 4838766 AGTTTAATTC 4838776 ATT AGTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 4838822 AT 1 AT 4838824 CATTCGATTT Statistics Matches: 44, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 3 41 0.93 4 3 0.07 ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65 Consensus pattern (3 bp): ATT Found at i:4840204 original size:23 final size:23 Alignment explanation

Indices: 4840174--4840228 Score: 101 Period size: 23 Copynumber: 2.4 Consensus size: 23 4840164 ATACTCGTCA * 4840174 ATTCGATTTATTCAAAAAAATTC 1 ATTCGATTCATTCAAAAAAATTC 4840197 ATTCGATTCATTCAAAAAAATTC 1 ATTCGATTCATTCAAAAAAATTC 4840220 ATTCGATTC 1 ATTCGATTC 4840229 GATCGAATAC Statistics Matches: 31, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 23 31 1.00 ACGTcount: A:0.40, C:0.16, G:0.05, T:0.38 Consensus pattern (23 bp): ATTCGATTCATTCAAAAAAATTC Found at i:4842313 original size:19 final size:19 Alignment explanation

Indices: 4842289--4842335 Score: 51 Period size: 19 Copynumber: 2.5 Consensus size: 19 4842279 GTTGTTTGAA 4842289 TATTGTATAACTCTTATT-T 1 TATTGTATAA-TCTTATTAT * * 4842308 TATTGTTTAATTTTATTAT 1 TATTGTATAATCTTATTAT * 4842327 TATTTTATA 1 TATTGTATA 4842336 GTCATCTACT Statistics Matches: 23, Mismatches: 4, Indels: 2 0.79 0.14 0.07 Matches are distributed among these distances: 18 6 0.26 19 17 0.74 ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64 Consensus pattern (19 bp): TATTGTATAATCTTATTAT Found at i:4842990 original size:29 final size:30 Alignment explanation

Indices: 4842946--4843009 Score: 94 Period size: 30 Copynumber: 2.2 Consensus size: 30 4842936 CAACTTAACA * 4842946 AACAAATGCCTAT-AAATAGTAATAAAATT 1 AACAAATGCCTATAAAATAATAATAAAATT * * 4842975 AACAAATGCCTCTAAAATAATAATAATATT 1 AACAAATGCCTATAAAATAATAATAAAATT 4843005 AACAA 1 AACAA 4843010 TAAAATAAGT Statistics Matches: 31, Mismatches: 3, Indels: 1 0.89 0.09 0.03 Matches are distributed among these distances: 29 12 0.39 30 19 0.61 ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27 Consensus pattern (30 bp): AACAAATGCCTATAAAATAATAATAAAATT Found at i:4845086 original size:2 final size:2 Alignment explanation

Indices: 4845079--4845131 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 4845069 TTTATAAGTA 4845079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 4845121 AT AT AT AT AT A 1 AT AT AT AT AT A 4845132 AAGATGAAGA Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:4850458 original size:329 final size:331 Alignment explanation

Indices: 4849910--4850536 Score: 933 Period size: 329 Copynumber: 1.9 Consensus size: 331 4849900 CCGTGTTTGC * * 4849910 ATCATTTTCACCAATCAAAAGCTTTCCACTTTTTCTTTTACAATTTAATTTTTTTTTTCATGAAA 1 ATCATTTTCACCAATCAAAAGCTTTCCACTTTTTCTTCTACAATTTAA-TATTTTTTTCATGAAA * * * 4849975 CAATTTTGATAGTCATGAAATTTTATTGCTTTGTTTCCAAAATTTAATGCACTGAATTAATTAAT 65 CAATTTTCATAGCCATGAAATTTTATTGCTTTGTTTCCAAAATTTAATGCACTAAATTAATTAAT * * * 4850040 TCTTTTATAACAACTTGAATGTTGCTGTGGTGTAGAGGTTATCACGTTAGTATTACACATTAAAG 130 TCTTTTATAACAACATGAATGTTGCTGTGGTGTAGAGGTTATCACATTAGTATTACACACTAAAG * 4850105 GTCTCCAGTTCAATATTAGGCAACAACATATTTGTCTTGAAGATTTTTATTAATTATTATTAGAT 195 GTCTCCAGTTCAATACTAGGCAACAACATATTTGTCTTGAAGATTTTTATTAATTATTATTAGAT 4850170 TACTCAACTCCAAAAAAATTATAAAATGATCACTAAATTTTAAAATTGTTGTTGTATAGCTTTCA 260 TACTCAACTCC-AAAAAATTATAAAATGATCACTAAATTTTAAAATTGTTGTTGTATAGCTTTCA 4850235 GTATTTAT 324 GTATTTAT * * 4850243 ATCATTTTCACCAATCAAAAGCTTTTCA-TTTTT-TTCTACAATTTAA-ATTTTTTTCATGAAAT 1 ATCATTTTCACCAATCAAAAGCTTTCCACTTTTTCTTCTACAATTTAATATTTTTTTCATGAAAC * * 4850305 AATTTTCATCA-CCATG-AATTTTGATTGCTTTGTTTCCAAAATTTAATGCATTAAATTAATTAT 66 AATTTTCAT-AGCCATGAAATTTT-ATTGCTTTGTTTCCAAAATTTAATGCACTAAATTAATTAA * * * 4850368 TTCTTTTATCACAACATGAATGTTGTTGTGGTGTA-ATGGTTATCACATTAGTCTTACACACTAA 129 TTCTTTTATAACAACATGAATGTTGCTGTGGTGTAGA-GGTTATCACATTAGTATTACACACTAA * ** * * * 4850432 ATGTCTCCAGTTTGATCCTGGGCAACAACATATTTGTCTTGAGGATTTTTATTAATTATTATTAG 193 AGGTCTCCAGTTCAATACTAGGCAACAACATATTTGTCTTGAAGATTTTTATTAATTATTATTAG * * * * 4850497 GTTATTCAACTCCAAAAAATTATAAAATGATTATTAAATT 258 ATTACTCAACTCCAAAAAATTATAAAATGATCACTAAATT 4850537 ATTCAAAAGT Statistics Matches: 265, Mismatches: 26, Indels: 11 0.88 0.09 0.04 Matches are distributed among these distances: 328 32 0.12 329 188 0.71 330 1 0.00 331 12 0.05 332 5 0.02 333 27 0.10 ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43 Consensus pattern (331 bp): ATCATTTTCACCAATCAAAAGCTTTCCACTTTTTCTTCTACAATTTAATATTTTTTTCATGAAAC AATTTTCATAGCCATGAAATTTTATTGCTTTGTTTCCAAAATTTAATGCACTAAATTAATTAATT CTTTTATAACAACATGAATGTTGCTGTGGTGTAGAGGTTATCACATTAGTATTACACACTAAAGG TCTCCAGTTCAATACTAGGCAACAACATATTTGTCTTGAAGATTTTTATTAATTATTATTAGATT ACTCAACTCCAAAAAATTATAAAATGATCACTAAATTTTAAAATTGTTGTTGTATAGCTTTCAGT ATTTAT Found at i:4850873 original size:363 final size:361 Alignment explanation

Indices: 4850199--4851217 Score: 1488 Period size: 363 Copynumber: 2.8 Consensus size: 361 4850189 TATAAAATGA * * * * 4850199 TCACTAAATTTTAAAATTGTTGTTGTATAGCTTTCAGTATTTAT-ATCATTTTCACCAATCAAAA 1 TCACTAAATTTTAAAATTGCTGTTGTATAGCCTTCCGTGTTT-TCATCATTTTCACCAATCAAAA * * * * ** 4850263 GCTTTTCA-TTTTT-TTCTACAATTTAAATTTTTTTCATGAAATAATTTTCATCACCATGAATTT 65 GCTTTTCACTTTTTCTTCTACAATTTAATTTTTTTTCATGAAACAACTTTAATCGTCATGAATTT * * * * 4850326 TGATTGCTTTGTTTCCAAAATTTAATGCATTAAATTAATTATTTCTTTTATCACAACATGAATGT 130 TGATTGCTTTGTTTCCAAAATTTAATGCACTGAATTAATTAATTCTTTTATAACAACATGAATGT * * * * * * 4850391 TGTTGTGGTGTAATGGTTATCACATTAGTCTTACACACTAAATGTCTCCAGTTTGATCCTGGGCA 195 TGCTGTGGTGTAGTGGTTATCACATTAGTCTTACACACTAAAAGTCCCCAGATTGATCCTGGGTA * * * * * 4850456 ACAACATATTTGTCTTGAGGATTTTTATTAATTATTATTAGGTTATTCAACTCCAAAAAATTATA 260 GCAACATATATGTCTTGAAGATTTTTATTAATTATTATTAGGTTACTAAACTCCAAAAAATTATA * * 4850521 AAATGATTATTAAATTATTCAAAAGTTTTCATTTAAG 325 AAATGATCATTAAATTATTCAAAAATTTTCATTTAAG * 4850558 TCACTAAATTTTTAAAATTGCTATTGTATAGCCTTCCGTGTTTTCATCATTTTCACCAATCAAAA 1 TCACTAAA-TTTTAAAATTGCTGTTGTATAGCCTTCCGTGTTTTCATCATTTTCACCAATCAAAA * * 4850623 GCTTTCCACTTTTTCTTTTACAATTTAATTTTTTTTTCATGAAACAACTTTAATCGTCATGAATT 65 GCTTTTCACTTTTTCTTCTACAATTTAA-TTTTTTTTCATGAAACAACTTTAATCGTCATGAATT * * ** 4850688 TTGATTGTTTTGTTTCCAAAATTTAATGCACTGAATTAATTAATTATTTTATAACAATTTGAATG 129 TTGATTGCTTTGTTTCCAAAATTTAATGCACTGAATTAATTAATTCTTTTATAACAACATGAATG * * * 4850753 TTGCTATGGTGTAGTGGTTATCACGTTAGTCTTACACACTAAAAGTCCCCAGCTTGATCCTGGGT 194 TTGCTGTGGTGTAGTGGTTATCACATTAGTCTTACACACTAAAAGTCCCCAGATTGATCCTGGGT * * 4850818 AGTAACATATATGTCTTGAAGAATTTTATTAATTATTATTAGGTTACTAAACTCCAAAAAATTAT 259 AGCAACATATATGTCTTGAAGATTTTTATTAATTATTATTAGGTTACTAAACTCCAAAAAATTAT * * 4850883 AAATTGGTCATTAAATTATTCAAAAATTTTCATTTAAG 324 AAAATGATCATTAAATTATTCAAAAATTTTCATTTAAG * * * 4850921 TCATTAAACTTTTAAAATTGCTGTTGTATAGCCTTTCGTGTTTGCATCATTTTCACCAATCAAAA 1 TCACTAAA-TTTTAAAATTGCTGTTGTATAGCCTTCCGTGTTTTCATCATTTTCACCAATCAAAA * * 4850986 GCTTTTCACTTTTTCTTCTACAATTTAATTTTTTTTAATGAAACAACTTTGATCGTCATGAATTT 65 GCTTTTCACTTTTTCTTCTACAATTTAATTTTTTTTCATGAAACAACTTTAATCGTCATGAATTT 4851051 TGATTGCTTTGTTTCCAAAATTTAATGCACTGAATTAATTAATTCTTTTATAACAACATGAATGT 130 TGATTGCTTTGTTTCCAAAATTTAATGCACTGAATTAATTAATTCTTTTATAACAACATGAATGT * * * * 4851116 TGGTGTGGTGTAGTGGTTATCGCATTAGTCTTACACACTAAAGGTCCCTA-ATTCGATCCTGGGT 195 TGCTGTGGTGTAGTGGTTATCACATTAGTCTTACACACTAAAAGTCCCCAGATT-GATCCTGGGT * * * 4851180 AGCGACATATATGTTTTGAAGGTTTTTATTAATTATTA 259 AGCAACATATATGTCTTGAAGATTTTTATTAATTATTA 4851218 CTTGTTTACG Statistics Matches: 589, Mismatches: 65, Indels: 9 0.89 0.10 0.01 Matches are distributed among these distances: 359 9 0.02 360 56 0.10 361 7 0.01 362 195 0.33 363 322 0.55 ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43 Consensus pattern (361 bp): TCACTAAATTTTAAAATTGCTGTTGTATAGCCTTCCGTGTTTTCATCATTTTCACCAATCAAAAG CTTTTCACTTTTTCTTCTACAATTTAATTTTTTTTCATGAAACAACTTTAATCGTCATGAATTTT GATTGCTTTGTTTCCAAAATTTAATGCACTGAATTAATTAATTCTTTTATAACAACATGAATGTT GCTGTGGTGTAGTGGTTATCACATTAGTCTTACACACTAAAAGTCCCCAGATTGATCCTGGGTAG CAACATATATGTCTTGAAGATTTTTATTAATTATTATTAGGTTACTAAACTCCAAAAAATTATAA AATGATCATTAAATTATTCAAAAATTTTCATTTAAG Found at i:4852276 original size:2 final size:2 Alignment explanation

Indices: 4852269--4852297 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 4852259 AAAACTTTGT 4852269 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 4852298 TATTATCTCC Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:4863529 original size:17 final size:18 Alignment explanation

Indices: 4863507--4863542 Score: 56 Period size: 17 Copynumber: 2.1 Consensus size: 18 4863497 TTTTTCCAAA * 4863507 AACATTTAAT-ATTTTTT 1 AACATTAAATCATTTTTT 4863524 AACATTAAATCATTTTTT 1 AACATTAAATCATTTTTT 4863542 A 1 A 4863543 GAATTTTTAA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 17 9 0.53 18 8 0.47 ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53 Consensus pattern (18 bp): AACATTAAATCATTTTTT Found at i:4868556 original size:62 final size:59 Alignment explanation

Indices: 4868484--4868600 Score: 162 Period size: 62 Copynumber: 1.9 Consensus size: 59 4868474 AGTAATTATC * * * * 4868484 TTAATATTAAATTTAATTTAATATTTATTTTGTAGATAAATATTATTTTAATTTAATAAGAT 1 TTAATATTAAAATTAATCTAATATTTA-TCT-T-GATAAATATTATATTAATTTAATAAGAT * 4868546 TTAATATTAAAATTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATA 1 TTAATATTAAAATTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA 4868601 TTAAAGTGAT Statistics Matches: 50, Mismatches: 5, Indels: 3 0.86 0.09 0.05 Matches are distributed among these distances: 59 22 0.44 60 1 0.02 61 2 0.04 62 25 0.50 ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51 Consensus pattern (59 bp): TTAATATTAAAATTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAGAT Found at i:4872490 original size:18 final size:18 Alignment explanation

Indices: 4872467--4872509 Score: 61 Period size: 18 Copynumber: 2.4 Consensus size: 18 4872457 GTTCAATGTG 4872467 TAATTAATTTAAAATT-TT 1 TAATTAA-TTAAAATTATT * 4872485 TAATTAATTAAATTTATT 1 TAATTAATTAAAATTATT 4872503 TAATTAA 1 TAATTAA 4872510 AAATATATTC Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 17 7 0.30 18 16 0.70 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (18 bp): TAATTAATTAAAATTATT Found at i:4875817 original size:132 final size:132 Alignment explanation

Indices: 4875580--4875837 Score: 342 Period size: 132 Copynumber: 2.0 Consensus size: 132 4875570 CTTTCCCACC * * * * 4875580 GATTCGGATTTCACCTTGCTCGAATCATAATAGTGTACACCAGGCACAGTTTTTTCAGATTGCAA 1 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA * * 4875645 TGAACAAAAGGAGCTAGAACTCTTATGATCATCAATGGGAT-ATTTGAAGGAAGATTTGCTTCTC 66 CGAACAAAAGGAGCTAGAACTCTTATGATCATCAATGGGATGATTTG-AGGAAGACTTGCTTCTC 4875709 ACT 130 ACT * * 4875712 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTGCACCAGGCACAGGTTTTTCATATTCCAA 1 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA * * * * * * 4875777 CGAATC-AATGGA-ATCAGAAGTTTTATGATCATCGATGGGATGCTTTGAGGAAGACTTGCTT 66 CGAA-CAAAAGGAGCT-AGAACTCTTATGATCATCAATGGGATGATTTGAGGAAGACTTGCTT 4875838 GCCGTTGTCA Statistics Matches: 109, Mismatches: 14, Indels: 6 0.84 0.11 0.05 Matches are distributed among these distances: 131 1 0.01 132 103 0.94 133 5 0.05 ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31 Consensus pattern (132 bp): GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA CGAACAAAAGGAGCTAGAACTCTTATGATCATCAATGGGATGATTTGAGGAAGACTTGCTTCTCA CT Found at i:4875989 original size:150 final size:150 Alignment explanation

Indices: 4875713--4876047 Score: 422 Period size: 150 Copynumber: 2.2 Consensus size: 150 4875703 CTTCTCACTG * * 4875713 ATTCAGATTTCACCTTACTCGAATCATAATAGTGTGCACCAGGCACAGGTTTTTCATATTCCAAC 1 ATTCAGATTTCACCTTACTAGAATCATAATAGTGTACACCAGGCACAGGTTTTTCATATTCCAAC * * * * ** 4875778 GAATCAATGGAATCAGAAGTTTTATGATCATCGATGGGATGCTTTGAGGAAGACTTGCTTGCCGT 66 GAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGCTTGCCAC * * 4875843 TGTCAGAATCTTTCCCACCA 131 TGCCAAAATCTTTCCCACCA * * * 4875863 ATTCGGATTTTACCTTACTAGAATCATAATAGTGTACACCAGGCACA-GTTTGTTCGTATTCCAA 1 ATTCAGATTTCACCTTACTAGAATCATAATAGTGTACACCAGGCACAGGTTT-TTCATATTCCAA * ** * * 4875927 TGAAGCAATGGAATTGGAACTCTTATGGTCATCAATGGGATG-TTTGAAGGAAGATTTGCTTGCC 65 CGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTG-AGGAAGACTTGCTTGCC * * 4875991 ACTGCCAAAATCTTTCCCGCCG 129 ACTGCCAAAATCTTTCCCACCA * * * * 4876013 ATTCAGATTTCATCTTGCTTGAATCAAAATAGTGT 1 ATTCAGATTTCACCTTACTAGAATCATAATAGTGT 4876048 TTTGCCATAT Statistics Matches: 157, Mismatches: 26, Indels: 4 0.84 0.14 0.02 Matches are distributed among these distances: 149 8 0.05 150 149 0.95 ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32 Consensus pattern (150 bp): ATTCAGATTTCACCTTACTAGAATCATAATAGTGTACACCAGGCACAGGTTTTTCATATTCCAAC GAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGCTTGCCAC TGCCAAAATCTTTCCCACCA Found at i:4891670 original size:25 final size:27 Alignment explanation

Indices: 4891619--4891670 Score: 63 Period size: 26 Copynumber: 2.0 Consensus size: 27 4891609 TAATTATTTT * * 4891619 TTAATAATATATTTTCAAAGTTTTAAC 1 TTAATAATATATTTTAAAAGTTGTAAC * 4891646 TTAA-AATATTTTTTAAAAG-TGTAAC 1 TTAATAATATATTTTAAAAGTTGTAAC 4891671 ATATTTTATC Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 25 5 0.23 26 13 0.59 27 4 0.18 ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46 Consensus pattern (27 bp): TTAATAATATATTTTAAAAGTTGTAAC Found at i:4898209 original size:12 final size:12 Alignment explanation

Indices: 4898192--4898245 Score: 51 Period size: 12 Copynumber: 4.7 Consensus size: 12 4898182 TTGAATTCAA 4898192 AATTTTTATATT 1 AATTTTTATATT 4898204 AA-TTTTATCATT 1 AATTTTTAT-ATT * 4898216 AA-TTATAT-TT 1 AATTTTTATATT * 4898226 TATTTTTATATT 1 AATTTTTATATT * 4898238 ATTTTTTA 1 AATTTTTA 4898246 ATAAATTTGT Statistics Matches: 34, Mismatches: 5, Indels: 6 0.76 0.11 0.13 Matches are distributed among these distances: 10 3 0.09 11 11 0.32 12 20 0.59 ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67 Consensus pattern (12 bp): AATTTTTATATT Found at i:4898243 original size:11 final size:11 Alignment explanation

Indices: 4898193--4898243 Score: 57 Period size: 11 Copynumber: 4.5 Consensus size: 11 4898183 TGAATTCAAA 4898193 ATTTTTATATT 1 ATTTTTATATT * 4898204 AATTTTATCATT 1 ATTTTTAT-ATT * * * 4898216 AATTATATTTT 1 ATTTTTATATT 4898227 ATTTTTATATT 1 ATTTTTATATT 4898238 ATTTTT 1 ATTTTT 4898244 TAATAAATTT Statistics Matches: 33, Mismatches: 6, Indels: 2 0.80 0.15 0.05 Matches are distributed among these distances: 11 23 0.70 12 10 0.30 ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69 Consensus pattern (11 bp): ATTTTTATATT Found at i:4910483 original size:96 final size:96 Alignment explanation

Indices: 4910365--4910558 Score: 291 Period size: 96 Copynumber: 2.0 Consensus size: 96 4910355 GGGCTGTTGC * * * * * 4910365 TGCTGTGTAGGAGGCATTGGGAAGTGTTGACTTGGAGCCTCCTGAGTTTGGCCAGGCGGTGG-AT 1 TGCTGAGTAGGAGGCATCGGGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGG-GGGGGTAT 4910429 AGTAAGCATCTCGCTGAGGGACAGAAGGAACT 65 AGTAAGCATCTCGCTGAGGGACAGAAGGAACT * * * 4910461 TGCTGAGTAGGAGGCATCGGGAATTGCTGACTTGGAATCTCCTGAGTTTGGGCAGGGGGGGTATA 1 TGCTGAGTAGGAGGCATCGGGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGGGGGGTATA * 4910526 GTAAGCATCTCGTTGAGGGACAGAAGGAACT 66 GTAAGCATCTCGCTGAGGGACAGAAGGAACT 4910557 TG 1 TG 4910559 GCTCTGAGGG Statistics Matches: 88, Mismatches: 9, Indels: 2 0.89 0.09 0.02 Matches are distributed among these distances: 95 4 0.05 96 84 0.95 ACGTcount: A:0.23, C:0.15, G:0.38, T:0.24 Consensus pattern (96 bp): TGCTGAGTAGGAGGCATCGGGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGGGGGGTATA GTAAGCATCTCGCTGAGGGACAGAAGGAACT Found at i:4913524 original size:19 final size:19 Alignment explanation

Indices: 4913500--4913539 Score: 80 Period size: 19 Copynumber: 2.1 Consensus size: 19 4913490 TAGTTTGTCC 4913500 TTGCCAATGTCATTCTGTG 1 TTGCCAATGTCATTCTGTG 4913519 TTGCCAATGTCATTCTGTG 1 TTGCCAATGTCATTCTGTG 4913538 TT 1 TT 4913540 AATGACAAAA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 21 1.00 ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45 Consensus pattern (19 bp): TTGCCAATGTCATTCTGTG Found at i:4914834 original size:18 final size:19 Alignment explanation

Indices: 4914791--4914834 Score: 58 Period size: 18 Copynumber: 2.5 Consensus size: 19 4914781 TTAAATTTTT * 4914791 TATTA-AAATTTAATTTAA 1 TATTATAAATTTAATTAAA 4914809 TATT-TAAATTT-ATTAAA 1 TATTATAAATTTAATTAAA 4914826 TATTATAAA 1 TATTATAAA 4914835 AATTAAGTAA Statistics Matches: 23, Mismatches: 1, Indels: 4 0.82 0.04 0.14 Matches are distributed among these distances: 17 9 0.39 18 14 0.61 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (19 bp): TATTATAAATTTAATTAAA Found at i:4915078 original size:30 final size:29 Alignment explanation

Indices: 4915001--4915124 Score: 110 Period size: 30 Copynumber: 4.2 Consensus size: 29 4914991 GGACCCCTAA * * 4915001 AAGTTTAAGTACCAACTCAAAAAAAGTGTC 1 AAGTTTAAGTACCAAATTAAAAAAA-TGTC * 4915031 AAGTTTAGGTACCAAATTAGAAAAAATGTC 1 AAGTTTAAGTACCAAATTA-AAAAAATGTC * * 4915061 AAGTTTAAGTATCAAATTAAATCAAAA---A 1 AAGTTTAAGTACCAAATTAAA--AAAATGTC * * 4915089 AAGTTTTAAGTATCAAATTAAAAAAAATATC 1 AAG-TTTAAGTACCAAATT-AAAAAAATGTC 4915120 AAGTT 1 AAGTT 4915125 CGGATACCAA Statistics Matches: 79, Mismatches: 7, Indels: 16 0.77 0.07 0.16 Matches are distributed among these distances: 28 7 0.09 29 17 0.22 30 42 0.53 31 13 0.16 ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28 Consensus pattern (29 bp): AAGTTTAAGTACCAAATTAAAAAAATGTC Found at i:4918927 original size:13 final size:14 Alignment explanation

Indices: 4918909--4918938 Score: 53 Period size: 14 Copynumber: 2.2 Consensus size: 14 4918899 CATGAACGAG 4918909 AAAAA-TAAAGAAA 1 AAAAATTAAAGAAA 4918922 AAAAATTAAAGAAA 1 AAAAATTAAAGAAA 4918936 AAA 1 AAA 4918939 GAAGGAAGGC Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 13 5 0.31 14 11 0.69 ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10 Consensus pattern (14 bp): AAAAATTAAAGAAA Found at i:4920209 original size:16 final size:17 Alignment explanation

Indices: 4920178--4920211 Score: 52 Period size: 16 Copynumber: 2.1 Consensus size: 17 4920168 TAAGTGTTGA 4920178 ATTTATATTAAAAATTT 1 ATTTATATTAAAAATTT * 4920195 ATTTAT-TTTAAAATTT 1 ATTTATATTAAAAATTT 4920211 A 1 A 4920212 ATCTTACCAA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 16 10 0.62 17 6 0.38 ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56 Consensus pattern (17 bp): ATTTATATTAAAAATTT Found at i:4922790 original size:22 final size:22 Alignment explanation

Indices: 4922765--4922849 Score: 73 Period size: 22 Copynumber: 3.7 Consensus size: 22 4922755 CTAAATTTTC * 4922765 TATTTTGTTATTATTTTGCTGT 1 TATTTTGTTATTATTTTACTGT * * * 4922787 TATTTCGTTGTTGTTTTACTGT 1 TATTTTGTTATTATTTTACTGT * * 4922809 CATTTTGTTATTATATTATTATTGT 1 TATTTTGTTA-T-TATT-TTACTGT 4922834 T-TTATTGTTATTATTT 1 TATT-TTGTTATTATTT 4922850 GAATATTATA Statistics Matches: 49, Mismatches: 10, Indels: 8 0.73 0.15 0.12 Matches are distributed among these distances: 22 26 0.53 23 5 0.10 24 6 0.12 25 12 0.24 ACGTcount: A:0.16, C:0.05, G:0.12, T:0.67 Consensus pattern (22 bp): TATTTTGTTATTATTTTACTGT Found at i:4923831 original size:31 final size:30 Alignment explanation

Indices: 4923796--4923904 Score: 114 Period size: 30 Copynumber: 3.6 Consensus size: 30 4923786 AATTATGAGT * 4923796 AAATTTTCATTT-TGATCACTAAACTATTCAA 1 AAATTTTCATTTAAG-TCACTAAACTATTC-A * * * 4923827 AAATTTT-ATTTAAGTAACCAAACTATTTGA 1 AAATTTTCATTTAAGTCACTAAACTA-TTCA * 4923857 AAGTTTTCATTTAAGTCACTAAACTATTCA 1 AAATTTTCATTTAAGTCACTAAACTATTCA * * 4923887 AAAGTTTCATTCAAGTCA 1 AAATTTTCATTTAAGTCA 4923905 TTGGGCTATT Statistics Matches: 64, Mismatches: 11, Indels: 7 0.78 0.13 0.09 Matches are distributed among these distances: 30 38 0.59 31 26 0.41 ACGTcount: A:0.39, C:0.15, G:0.06, T:0.39 Consensus pattern (30 bp): AAATTTTCATTTAAGTCACTAAACTATTCA Found at i:4923903 original size:30 final size:30 Alignment explanation

Indices: 4923811--4923904 Score: 116 Period size: 30 Copynumber: 3.1 Consensus size: 30 4923801 TTCATTTTGA * * 4923811 TCACTAAACTATTCAAAAATTTTATTTAAG 1 TCACTAAACTATTCAAAAGTTTCATTTAAG * * ** 4923841 TAACCAAACTATTTGAAAGTTTTCATTTAAG 1 TCACTAAACTATTCAAAAG-TTTCATTTAAG * 4923872 TCACTAAACTATTCAAAAGTTTCATTCAAG 1 TCACTAAACTATTCAAAAGTTTCATTTAAG 4923902 TCA 1 TCA 4923905 TTGGGCTATT Statistics Matches: 52, Mismatches: 11, Indels: 2 0.80 0.17 0.03 Matches are distributed among these distances: 30 27 0.52 31 25 0.48 ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37 Consensus pattern (30 bp): TCACTAAACTATTCAAAAGTTTCATTTAAG Found at i:4931951 original size:18 final size:19 Alignment explanation

Indices: 4931928--4931972 Score: 83 Period size: 19 Copynumber: 2.4 Consensus size: 19 4931918 CGAAACAATT 4931928 AAAACAAATA-AAAAGAGA 1 AAAACAAATACAAAAGAGA 4931946 AAAACAAATACAAAAGAGA 1 AAAACAAATACAAAAGAGA 4931965 AAAACAAA 1 AAAACAAA 4931973 GCAAAAGTTT Statistics Matches: 26, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 18 10 0.38 19 16 0.62 ACGTcount: A:0.78, C:0.09, G:0.09, T:0.04 Consensus pattern (19 bp): AAAACAAATACAAAAGAGA Found at i:4931977 original size:18 final size:18 Alignment explanation

Indices: 4931928--4931979 Score: 70 Period size: 18 Copynumber: 2.8 Consensus size: 18 4931918 CGAAACAATT 4931928 AAAACAAATA-AAAAGAGA 1 AAAACAAA-ACAAAAGAGA 4931946 AAAACAAATACAAAAGAGA 1 AAAACAAA-ACAAAAGAGA * 4931965 AAAACAAAGCAAAAG 1 AAAACAAAACAAAAG 4931980 TTTAAGTAAA Statistics Matches: 32, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 18 16 0.50 19 16 0.50 ACGTcount: A:0.75, C:0.10, G:0.12, T:0.04 Consensus pattern (18 bp): AAAACAAAACAAAAGAGA Found at i:4933306 original size:18 final size:18 Alignment explanation

Indices: 4933283--4933324 Score: 59 Period size: 18 Copynumber: 2.3 Consensus size: 18 4933273 ATTCTAGGTG 4933283 TAATTAATTTAAAATT-TT 1 TAATTAA-TTAAAATTATT * 4933301 TAATTAATTAAATTTATT 1 TAATTAATTAAAATTATT 4933319 TAATTA 1 TAATTA 4933325 CAAACTTATT Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 17 7 0.32 18 15 0.68 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (18 bp): TAATTAATTAAAATTATT Found at i:4935809 original size:15 final size:15 Alignment explanation

Indices: 4935789--4935817 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 4935779 TTACATCAAT 4935789 TGAGTTTATAACTTA 1 TGAGTTTATAACTTA 4935804 TGAGTTTATAACTT 1 TGAGTTTATAACTT 4935818 TCTAAATTCA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48 Consensus pattern (15 bp): TGAGTTTATAACTTA Found at i:4969609 original size:20 final size:20 Alignment explanation

Indices: 4969586--4969624 Score: 69 Period size: 20 Copynumber: 1.9 Consensus size: 20 4969576 ATTCAAATTT * 4969586 AAACCTTAAACATTAAATCC 1 AAACCCTAAACATTAAATCC 4969606 AAACCCTAAACATTAAATC 1 AAACCCTAAACATTAAATC 4969625 ATGAACCCCC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23 Consensus pattern (20 bp): AAACCCTAAACATTAAATCC Found at i:4971351 original size:20 final size:18 Alignment explanation

Indices: 4971305--4971344 Score: 71 Period size: 18 Copynumber: 2.2 Consensus size: 18 4971295 GTTTTAAAAA 4971305 AATTAAAATATACTTGAC 1 AATTAAAATATACTTGAC * 4971323 AATTAAAATATATTTGAC 1 AATTAAAATATACTTGAC 4971341 AATT 1 AATT 4971345 TTAAAATTAA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38 Consensus pattern (18 bp): AATTAAAATATACTTGAC Found at i:4971528 original size:18 final size:19 Alignment explanation

Indices: 4971487--4971534 Score: 62 Period size: 18 Copynumber: 2.6 Consensus size: 19 4971477 TTATTTTTAA * 4971487 AAATTAAAATAGAATATAT 1 AAATTAAAATAGAAAATAT * 4971506 TAATTAAAAT-GAAAATAT 1 AAATTAAAATAGAAAATAT * 4971524 AAATTTAAATA 1 AAATTAAAATA 4971535 TTATATAATA Statistics Matches: 24, Mismatches: 4, Indels: 2 0.80 0.13 0.07 Matches are distributed among these distances: 18 15 0.62 19 9 0.38 ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33 Consensus pattern (19 bp): AAATTAAAATAGAAAATAT Found at i:4976415 original size:33 final size:36 Alignment explanation

Indices: 4976373--4976438 Score: 93 Period size: 33 Copynumber: 1.9 Consensus size: 36 4976363 TGTTTATGTG * * 4976373 AAATTGAAGAGAAA-GAGAAGAG-AG-GCAAGGATC 1 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGGATC 4976406 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGG 1 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGG 4976439 GGTAAAAGAG Statistics Matches: 28, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 33 13 0.46 34 7 0.25 35 2 0.07 36 6 0.21 ACGTcount: A:0.53, C:0.06, G:0.32, T:0.09 Consensus pattern (36 bp): AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGGATC Found at i:4977478 original size:23 final size:23 Alignment explanation

Indices: 4977452--4977613 Score: 151 Period size: 23 Copynumber: 7.2 Consensus size: 23 4977442 ACACTAGCGC 4977452 GCTCTCTGATTAGCACTGTGTGT 1 GCTCTCTGATTAGCACTGTGTGT * * 4977475 GCTCTCTGTTTAGCAC-GTCTCGT 1 GCTCTCTGATTAGCACTGTGT-GT 4977498 GCTCTCTGTTATTAGCACTGTGTGT 1 GCTCTCTG--ATTAGCACTGTGTGT * * 4977523 GCTCTCCGATTAGCACTTTGTGT 1 GCTCTCTGATTAGCACTGTGTGT * * 4977546 G--CTC-----AGTACTTTGTGT 1 GCTCTCTGATTAGCACTGTGTGT * 4977562 ACTCTCTGTTATTAGCACTGTGTGT 1 GCTCTCTG--ATTAGCACTGTGTGT * 4977587 GCTCTCTGATTAGCACTTTGTGT 1 GCTCTCTGATTAGCACTGTGTGT 4977610 GCTC 1 GCTC 4977614 AGTACTTTGT Statistics Matches: 114, Mismatches: 12, Indels: 26 0.75 0.08 0.17 Matches are distributed among these distances: 16 11 0.10 18 3 0.03 21 3 0.03 22 3 0.03 23 58 0.51 25 33 0.29 26 3 0.03 ACGTcount: A:0.12, C:0.23, G:0.23, T:0.41 Consensus pattern (23 bp): GCTCTCTGATTAGCACTGTGTGT Found at i:4977677 original size:64 final size:64 Alignment explanation

Indices: 4977499--4977656 Score: 284 Period size: 64 Copynumber: 2.5 Consensus size: 64 4977489 ACGTCTCGTG * 4977499 CTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTTGTGTGCTCAGTACTTTGTGTA 1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTTTGTGTA 4977563 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTTTGTGTA 1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTTTGTGTA * 4977627 CTCTCTG-T-TTAGCACTTTGTGTGCTCTCTG 1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTG 4977657 TTGCCCAGCA Statistics Matches: 92, Mismatches: 2, Indels: 2 0.96 0.02 0.02 Matches are distributed among these distances: 62 21 0.23 63 1 0.01 64 70 0.76 ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44 Consensus pattern (64 bp): CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTTTGTGTA Found at i:4979244 original size:17 final size:18 Alignment explanation

Indices: 4979219--4979255 Score: 51 Period size: 17 Copynumber: 2.1 Consensus size: 18 4979209 CTATTTAAAA 4979219 ATTATAAAT-ATATAAATT 1 ATTATAAATAATA-AAATT 4979237 ATTA-AAATAATAAAATT 1 ATTATAAATAATAAAATT 4979254 AT 1 AT 4979256 ATTTTTATTA Statistics Matches: 18, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 17 11 0.61 18 7 0.39 ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41 Consensus pattern (18 bp): ATTATAAATAATAAAATT Found at i:4979989 original size:23 final size:22 Alignment explanation

Indices: 4979953--4979998 Score: 58 Period size: 23 Copynumber: 2.0 Consensus size: 22 4979943 TAAATTAAGT 4979953 ATAAAAATTAAATTGCATAAATG 1 ATAAAAATTAAATT-CATAAATG * 4979976 ATAAAAA-TATAATTTATAAATG 1 ATAAAAATTA-AATTCATAAATG 4979998 A 1 A 4979999 ATTGTAATTT Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 22 10 0.48 23 11 0.52 ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33 Consensus pattern (22 bp): ATAAAAATTAAATTCATAAATG Found at i:4981209 original size:40 final size:40 Alignment explanation

Indices: 4981129--4981239 Score: 127 Period size: 40 Copynumber: 2.8 Consensus size: 40 4981119 TGAAAAGGTA * * * * * 4981129 TATCCGAAAGGAT-GT-TATGAAAAAGTTGAAAAGGATAT 1 TATCCGAAAGGATAATAAATGAAAAGGTTAAAAAGGACAT * * 4981167 TATCCGGAAGGATAATAAATGAAAAGGTTAAAAATGACAT 1 TATCCGAAAGGATAATAAATGAAAAGGTTAAAAAGGACAT * * 4981207 TATTCGAAAGGATAATAAATGAAAAGGTCAAAA 1 TATCCGAAAGGATAATAAATGAAAAGGTTAAAA 4981240 TGGTAAATTT Statistics Matches: 61, Mismatches: 10, Indels: 2 0.84 0.14 0.03 Matches are distributed among these distances: 38 12 0.20 39 1 0.02 40 48 0.79 ACGTcount: A:0.50, C:0.06, G:0.21, T:0.23 Consensus pattern (40 bp): TATCCGAAAGGATAATAAATGAAAAGGTTAAAAAGGACAT Found at i:4991274 original size:14 final size:15 Alignment explanation

Indices: 4991254--4991288 Score: 63 Period size: 14 Copynumber: 2.4 Consensus size: 15 4991244 AGAGGAGGAG 4991254 ATTTTTTACTTTTTT 1 ATTTTTTACTTTTTT 4991269 -TTTTTTACTTTTTT 1 ATTTTTTACTTTTTT 4991283 ATTTTT 1 ATTTTT 4991289 CCGCATAATA Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 14 14 0.74 15 5 0.26 ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83 Consensus pattern (15 bp): ATTTTTTACTTTTTT Found at i:4997992 original size:18 final size:18 Alignment explanation

Indices: 4997971--4998005 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 4997961 ACTTTACTAA * * 4997971 TCAAGTGATGCCTTCAAC 1 TCAAATGATGCCCTCAAC 4997989 TCAAATGATGCCCTCAA 1 TCAAATGATGCCCTCAA 4998006 ATTCTGTGAG Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26 Consensus pattern (18 bp): TCAAATGATGCCCTCAAC Found at i:5000019 original size:27 final size:27 Alignment explanation

Indices: 4999986--5000040 Score: 110 Period size: 27 Copynumber: 2.0 Consensus size: 27 4999976 TTATTTACTT 4999986 TCTTTTTTTTTTAATACAAAGTTTTAA 1 TCTTTTTTTTTTAATACAAAGTTTTAA 5000013 TCTTTTTTTTTTAATACAAAGTTTTAA 1 TCTTTTTTTTTTAATACAAAGTTTTAA 5000040 T 1 T 5000041 AAGAACGCGA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 28 1.00 ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60 Consensus pattern (27 bp): TCTTTTTTTTTTAATACAAAGTTTTAA Found at i:5002053 original size:40 final size:40 Alignment explanation

Indices: 5002009--5002119 Score: 97 Period size: 40 Copynumber: 2.8 Consensus size: 40 5001999 TCAGATAGTT * 5002009 CGAAGCAATAAAGTGACACCCAGTGTCTCATCG-GCCTAGC 1 CGAAG-AATAAAGTGACACCCAGTGTCTCATCGAACCTAGC ** ** * * 5002049 CGAAG--TAAAGTGGTACCCAGTACCTCATCGAATCTATC 1 CGAAGAATAAAGTGACACCCAGTGTCTCATCGAACCTAGC 5002087 CGAAGTAA-ATAA-TGACACCCAGTGTCTCATCGA 1 CGAAG-AATA-AAGTGACACCCAGTGTCTCATCGA 5002120 CTCATGGTCG Statistics Matches: 55, Mismatches: 11, Indels: 10 0.72 0.14 0.13 Matches are distributed among these distances: 37 21 0.38 38 9 0.16 40 23 0.42 41 2 0.04 ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21 Consensus pattern (40 bp): CGAAGAATAAAGTGACACCCAGTGTCTCATCGAACCTAGC Found at i:5002241 original size:6 final size:6 Alignment explanation

Indices: 5002222--5002266 Score: 81 Period size: 6 Copynumber: 7.5 Consensus size: 6 5002212 ACAATTCATA * 5002222 TCACTT TCAATT TCACTT TCACTT TCACTT TCACTT TCACTT TCA 1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA 5002267 ATTTTGATCA Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 6 37 1.00 ACGTcount: A:0.20, C:0.31, G:0.00, T:0.49 Consensus pattern (6 bp): TCACTT Found at i:5003285 original size:33 final size:36 Alignment explanation

Indices: 5003224--5003289 Score: 93 Period size: 33 Copynumber: 1.9 Consensus size: 36 5003214 CTCTTTTACC * * 5003224 CCTTGCTCTACTCTTTTCCTTTGTCTTCAATTTGAT 1 CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTTGAT 5003260 CCTTGC-CT-CTCTTCT-CTTTCTCTTCAATTT 1 CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTT 5003290 CACATAAACA Statistics Matches: 28, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 33 14 0.50 34 6 0.21 35 2 0.07 36 6 0.21 ACGTcount: A:0.09, C:0.32, G:0.06, T:0.53 Consensus pattern (36 bp): CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTTGAT Found at i:5009735 original size:31 final size:31 Alignment explanation

Indices: 5009700--5009792 Score: 74 Period size: 31 Copynumber: 3.2 Consensus size: 31 5009690 TTAAAAATTG 5009700 AAACTCATGGGTTAGGCAGATATATTGGATT 1 AAACTCATGGGTTAGGCAGATATATTGGATT * * *** 5009731 AAACT--TGGTGCT-GG-A-CT-TA-AAAATT 1 AAACTCATGG-GTTAGGCAGATATATTGGATT 5009756 GAAACTCATGGGTTAGGCAGATATATTGGATT 1 -AAACTCATGGGTTAGGCAGATATATTGGATT 5009788 AAACT 1 AAACT 5009793 TGGTCTTGGG Statistics Matches: 43, Mismatches: 10, Indels: 18 0.61 0.14 0.25 Matches are distributed among these distances: 25 3 0.07 26 7 0.16 27 3 0.07 28 6 0.14 29 6 0.14 30 3 0.07 31 12 0.28 32 3 0.07 ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31 Consensus pattern (31 bp): AAACTCATGGGTTAGGCAGATATATTGGATT Found at i:5009749 original size:57 final size:57 Alignment explanation

Indices: 5009683--5009796 Score: 228 Period size: 57 Copynumber: 2.0 Consensus size: 57 5009673 AGCAACCACA 5009683 GCTGGACTTAAAAATTGAAACTCATGGGTTAGGCAGATATATTGGATTAAACTTGGT 1 GCTGGACTTAAAAATTGAAACTCATGGGTTAGGCAGATATATTGGATTAAACTTGGT 5009740 GCTGGACTTAAAAATTGAAACTCATGGGTTAGGCAGATATATTGGATTAAACTTGGT 1 GCTGGACTTAAAAATTGAAACTCATGGGTTAGGCAGATATATTGGATTAAACTTGGT 5009797 CTTGGGTTGG Statistics Matches: 57, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 57 57 1.00 ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32 Consensus pattern (57 bp): GCTGGACTTAAAAATTGAAACTCATGGGTTAGGCAGATATATTGGATTAAACTTGGT Found at i:5013534 original size:16 final size:16 Alignment explanation

Indices: 5013508--5013540 Score: 50 Period size: 17 Copynumber: 2.1 Consensus size: 16 5013498 ATGGCTTTGG 5013508 AAAGAAAGGT-ATAAT 1 AAAGAAAGGTAATAAT 5013523 AAAGAGAAGGTAATAAT 1 AAAGA-AAGGTAATAAT 5013540 A 1 A 5013541 GAAACACCTA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 5 0.31 16 5 0.31 17 6 0.38 ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18 Consensus pattern (16 bp): AAAGAAAGGTAATAAT Found at i:5018165 original size:27 final size:27 Alignment explanation

Indices: 5018135--5018187 Score: 97 Period size: 27 Copynumber: 2.0 Consensus size: 27 5018125 CCCCTCCCAT 5018135 TCCTCCACCTTCACCCCCACCACCACC 1 TCCTCCACCTTCACCCCCACCACCACC * 5018162 TCCTCCACCTTCACCCCCACCTCCAC 1 TCCTCCACCTTCACCCCCACCACCAC 5018188 TCGGCATTTG Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 27 25 1.00 ACGTcount: A:0.17, C:0.66, G:0.00, T:0.17 Consensus pattern (27 bp): TCCTCCACCTTCACCCCCACCACCACC Found at i:5020118 original size:35 final size:35 Alignment explanation

Indices: 5020072--5020142 Score: 142 Period size: 35 Copynumber: 2.0 Consensus size: 35 5020062 TTAAACGTAT 5020072 ACAGTTTGAGTTACCTTTGCATGTAATCTCAAAAA 1 ACAGTTTGAGTTACCTTTGCATGTAATCTCAAAAA 5020107 ACAGTTTGAGTTACCTTTGCATGTAATCTCAAAAA 1 ACAGTTTGAGTTACCTTTGCATGTAATCTCAAAAA 5020142 A 1 A 5020143 TCTATTTAAC Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 35 36 1.00 ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34 Consensus pattern (35 bp): ACAGTTTGAGTTACCTTTGCATGTAATCTCAAAAA Found at i:5021052 original size:23 final size:23 Alignment explanation

Indices: 5021019--5021062 Score: 63 Period size: 23 Copynumber: 1.9 Consensus size: 23 5021009 ATATTTGCAT * 5021019 AAAAATGAAATTAAT-TAAAATAG 1 AAAAATAAAATT-ATCTAAAATAG 5021042 AAAAATAAAATTATCTAAAAT 1 AAAAATAAAATTATCTAAAAT 5021063 TTCAAGTTGA Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 22 2 0.11 23 17 0.89 ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27 Consensus pattern (23 bp): AAAAATAAAATTATCTAAAATAG Found at i:5024403 original size:16 final size:15 Alignment explanation

Indices: 5024376--5024408 Score: 57 Period size: 16 Copynumber: 2.1 Consensus size: 15 5024366 ATAACAACTA 5024376 AATTATTAAAATATT 1 AATTATTAAAATATT 5024391 AATTATATAAAATATT 1 AATTAT-TAAAATATT 5024407 AA 1 AA 5024409 AAAATATAAA Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 6 0.35 16 11 0.65 ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42 Consensus pattern (15 bp): AATTATTAAAATATT Found at i:5024417 original size:17 final size:16 Alignment explanation

Indices: 5024382--5024420 Score: 51 Period size: 17 Copynumber: 2.4 Consensus size: 16 5024372 ACTAAATTAT ** 5024382 TAAAATATTAATTATA 1 TAAAATATTAAAAATA 5024398 TAAAATATTAAAAAATA 1 TAAAATATT-AAAAATA 5024415 TAAAAT 1 TAAAAT 5024421 CACATAATTT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 16 9 0.45 17 11 0.55 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (16 bp): TAAAATATTAAAAATA Found at i:5025731 original size:22 final size:22 Alignment explanation

Indices: 5025689--5025758 Score: 63 Period size: 22 Copynumber: 3.2 Consensus size: 22 5025679 CTGTAACTTA * 5025689 TTTCTTTGTAAAAA-CTCAGGTT 1 TTTCATTGTAAAAATCT-AGGTT * 5025711 TTTCATTGTAAAAATCTAGGTA 1 TTTCATTGTAAAAATCTAGGTT * * * 5025733 ATTCACTTG-AAAAATCCAAGTT 1 TTTCA-TTGTAAAAATCTAGGTT 5025755 TTTC 1 TTTC 5025759 CTTGGTTATT Statistics Matches: 39, Mismatches: 7, Indels: 4 0.78 0.14 0.08 Matches are distributed among these distances: 22 34 0.87 23 5 0.13 ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41 Consensus pattern (22 bp): TTTCATTGTAAAAATCTAGGTT Found at i:5025956 original size:17 final size:18 Alignment explanation

Indices: 5025931--5025965 Score: 54 Period size: 17 Copynumber: 2.0 Consensus size: 18 5025921 TAATTCTAGG 5025931 AAATGAAAAAG-TAAAAT 1 AAATGAAAAAGATAAAAT * 5025948 AAATTAAAAAGATAAAAT 1 AAATGAAAAAGATAAAAT 5025966 TATTTTCCTA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 10 0.62 18 6 0.38 ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20 Consensus pattern (18 bp): AAATGAAAAAGATAAAAT Found at i:5026297 original size:32 final size:31 Alignment explanation

Indices: 5026260--5026323 Score: 83 Period size: 31 Copynumber: 2.0 Consensus size: 31 5026250 ATAATATTAA * 5026260 TTAATGATGGGTGTCTAAACTAAAAATAATTT 1 TTAATGAT-AGTGTCTAAACTAAAAATAATTT * * * 5026292 TTAATGGTAGTGTCTAAAGTGAAAATAATTT 1 TTAATGATAGTGTCTAAACTAAAAATAATTT 5026323 T 1 T 5026324 AATAACAGCG Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 31 21 0.75 32 7 0.25 ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39 Consensus pattern (31 bp): TTAATGATAGTGTCTAAACTAAAAATAATTT Found at i:5030252 original size:27 final size:26 Alignment explanation

Indices: 5030222--5030339 Score: 78 Period size: 27 Copynumber: 4.3 Consensus size: 26 5030212 AAAATAATTT * 5030222 AACTTTTAAAGG-TCAAATTTTTTTATC 1 AACTTTTAAAGGCT-AAATTTTTTT-CC * * 5030249 AACTTTTAAGAGGCCCAAATATTTTTT-T 1 AACTTTTAA-AGG-CTAAAT-TTTTTTCC * * * 5030277 AGCTTTTAAAAGCTTAATTTTTTTACC 1 AACTTTTAAAGGCTAAATTTTTTT-CC * * * 5030304 AATTTTTAAGGGACTTAATTTTTTTCC 1 AACTTTTAAAGG-CTAAATTTTTTTCC 5030331 AACTTTTAA 1 AACTTTTAA 5030340 GGAACTTAAA Statistics Matches: 72, Mismatches: 12, Indels: 14 0.73 0.12 0.14 Matches are distributed among these distances: 25 6 0.08 26 4 0.06 27 29 0.40 28 23 0.32 29 4 0.06 30 6 0.08 ACGTcount: A:0.31, C:0.13, G:0.08, T:0.47 Consensus pattern (26 bp): AACTTTTAAAGGCTAAATTTTTTTCC Found at i:5030340 original size:27 final size:28 Alignment explanation

Indices: 5030289--5030348 Score: 95 Period size: 27 Copynumber: 2.2 Consensus size: 28 5030279 CTTTTAAAAG * * 5030289 CTTAATTTTTTTACCAATTTTTAAGGGA 1 CTTAATTTTTTTACCAACTTTTAAGGAA 5030317 CTTAATTTTTTT-CCAACTTTTAAGGAA 1 CTTAATTTTTTTACCAACTTTTAAGGAA 5030344 CTTAA 1 CTTAA 5030349 AATTCCATTT Statistics Matches: 30, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 27 18 0.60 28 12 0.40 ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48 Consensus pattern (28 bp): CTTAATTTTTTTACCAACTTTTAAGGAA Found at i:5051132 original size:27 final size:27 Alignment explanation

Indices: 5051089--5051155 Score: 77 Period size: 27 Copynumber: 2.5 Consensus size: 27 5051079 ATTCATCACC * 5051089 TATTTTAAAATATTTTAATAAA-ATTAT 1 TATTTTAAAATAATTTAA-AAACATTAT 5051116 TATTTTCAAAA-AATTTAAAAATCATTAT 1 TATTTT-AAAATAATTTAAAAA-CATTAT 5051144 TA-TTTAAAATAA 1 TATTTTAAAATAA 5051156 CTTTGTAAGG Statistics Matches: 35, Mismatches: 1, Indels: 8 0.80 0.02 0.18 Matches are distributed among these distances: 26 7 0.20 27 17 0.49 28 11 0.31 ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46 Consensus pattern (27 bp): TATTTTAAAATAATTTAAAAACATTAT Found at i:5052219 original size:31 final size:30 Alignment explanation

Indices: 5052173--5052255 Score: 105 Period size: 31 Copynumber: 2.7 Consensus size: 30 5052163 TTATGGGACT 5052173 CATTATTAACTTAATTTAATTACATTATATAA 1 CATT-TTAA-TTAATTTAATTACATTATATAA * 5052205 CATTTTAATTTAATTTAATCACATTATATAA 1 CATTTTAA-TTAATTTAATTACATTATATAA * * 5052236 TA-ATTAATTAATTTAATTAC 1 CATTTTAATTAATTTAATTAC 5052256 CATACTATAT Statistics Matches: 46, Mismatches: 5, Indels: 3 0.85 0.09 0.06 Matches are distributed among these distances: 29 12 0.26 30 4 0.09 31 26 0.57 32 4 0.09 ACGTcount: A:0.43, C:0.08, G:0.00, T:0.48 Consensus pattern (30 bp): CATTTTAATTAATTTAATTACATTATATAA Found at i:5056983 original size:27 final size:28 Alignment explanation

Indices: 5056953--5057021 Score: 70 Period size: 28 Copynumber: 2.4 Consensus size: 28 5056943 TAATATTATT * 5056953 TTTTTTAATATTTAATAA-TTTTATATA- 1 TTTTTTAATATTGAA-AATTTTTATATAG * 5056980 TTTTTTATTTATTGAAAATTTTTATATAG 1 TTTTTTA-ATATTGAAAATTTTTATATAG * 5057009 TTATATTAATATT 1 TT-TTTTAATATT 5057022 ATTTTAATGT Statistics Matches: 34, Mismatches: 4, Indels: 6 0.77 0.09 0.14 Matches are distributed among these distances: 27 9 0.26 28 15 0.44 29 6 0.18 30 4 0.12 ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62 Consensus pattern (28 bp): TTTTTTAATATTGAAAATTTTTATATAG Found at i:5069216 original size:41 final size:38 Alignment explanation

Indices: 5069130--5069218 Score: 106 Period size: 39 Copynumber: 2.3 Consensus size: 38 5069120 GAAAATTATA * * * * * 5069130 TTTAATACAATAAATATTTATTATATTTATTTATGTTT 1 TTTAATATAATAAAAATTTATTATACTTATGTATGGTT 5069168 TTTAATATAATAAAAAATTTATTATACTTATGGTAGTGGTT 1 TTTAATATAAT-AAAAATTTATTATACTTAT-GTA-TGGTT 5069209 TTTAATATAA 1 TTTAATATAA 5069219 AGTTAAAAAA Statistics Matches: 43, Mismatches: 5, Indels: 3 0.84 0.10 0.06 Matches are distributed among these distances: 38 10 0.23 39 17 0.40 40 2 0.05 41 14 0.33 ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52 Consensus pattern (38 bp): TTTAATATAATAAAAATTTATTATACTTATGTATGGTT Found at i:5072439 original size:2 final size:2 Alignment explanation

Indices: 5072432--5072464 Score: 66 Period size: 2 Copynumber: 16.5 Consensus size: 2 5072422 AAATAGGTTA 5072432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 5072465 GGTATTTATG Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:5083736 original size:24 final size:24 Alignment explanation

Indices: 5083704--5083752 Score: 98 Period size: 24 Copynumber: 2.0 Consensus size: 24 5083694 TTATTAAAGC 5083704 TAAATATTATCCTAATTGTGATTT 1 TAAATATTATCCTAATTGTGATTT 5083728 TAAATATTATCCTAATTGTGATTT 1 TAAATATTATCCTAATTGTGATTT 5083752 T 1 T 5083753 TTCAAGGCTT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51 Consensus pattern (24 bp): TAAATATTATCCTAATTGTGATTT Found at i:5092187 original size:134 final size:136 Alignment explanation

Indices: 5092033--5092287 Score: 408 Period size: 134 Copynumber: 1.9 Consensus size: 136 5092023 CACTTACTTT 5092033 ATTTTTTTTATCATGTTTAATAAAAACTTAAATCTAATTACTTTCAAAAGCCAAATCTTTTAAAA 1 ATTTTTTTTATCATGTTTAATAAAAACTTAAATCTAATTACTTTCAAAAGCCAAATCTTTTAAAA * * * * 5092098 TAAAATAAATAAAATGATTA-AATATAAAAGTAGTACTCGAATTTATTTACTTTTTTAGGTTAAC 66 CAAAATAAATAAAAGGATTAGAAT-TAAAAGTAATACTCGAACTTATTTACTTTTTTAGGTTAAC 5092162 GTTCATA 130 GTTCATA 5092169 ATTTTTTTT-T-ATGTTTAATAAAAACTTAAATCTAATTACTTTCAAAAGCCAAATCTTTTAAAA 1 ATTTTTTTTATCATGTTTAATAAAAACTTAAATCTAATTACTTTCAAAAGCCAAATCTTTTAAAA ** * * 5092232 CAAAATAAATAAAAGGATTAGGGTTAAAAGTAATATTCGAACTTGTTTACTTTTTT 66 CAAAATAAATAAAAGGATTAGAATTAAAAGTAATACTCGAACTTATTTACTTTTTT 5092288 TCAGGTTGAT Statistics Matches: 110, Mismatches: 8, Indels: 4 0.90 0.07 0.03 Matches are distributed among these distances: 134 99 0.90 135 2 0.02 136 9 0.08 ACGTcount: A:0.42, C:0.09, G:0.07, T:0.41 Consensus pattern (136 bp): ATTTTTTTTATCATGTTTAATAAAAACTTAAATCTAATTACTTTCAAAAGCCAAATCTTTTAAAA CAAAATAAATAAAAGGATTAGAATTAAAAGTAATACTCGAACTTATTTACTTTTTTAGGTTAACG TTCATA Found at i:5092563 original size:47 final size:47 Alignment explanation

Indices: 5092505--5092598 Score: 161 Period size: 47 Copynumber: 2.0 Consensus size: 47 5092495 TGGCCGCCAC * 5092505 ACCAATTTCTTTCACTTTCCTCCCATCCAAACACCCACCACTCCATT 1 ACCAATTTCTTTCACTTTCCTCCCATCCAAACACCCACCACTACATT * * 5092552 ACCATTTTCTTTCACTTTCCTCCTATCCAAACACCCACCACTACATT 1 ACCAATTTCTTTCACTTTCCTCCCATCCAAACACCCACCACTACATT 5092599 CCCAGCAAAA Statistics Matches: 44, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 47 44 1.00 ACGTcount: A:0.26, C:0.43, G:0.00, T:0.32 Consensus pattern (47 bp): ACCAATTTCTTTCACTTTCCTCCCATCCAAACACCCACCACTACATT Found at i:5100848 original size:29 final size:28 Alignment explanation

Indices: 5100811--5100889 Score: 77 Period size: 29 Copynumber: 2.6 Consensus size: 28 5100801 AAATTTTAAA * 5100811 TTAATAATAATAAAATTATAATTTAATCCT 1 TTAA-AATAATAAAA-TATAACTTAATCCT * * 5100841 TTAAAATAATAAAAAATTAACTTAATCTT 1 TTAAAATAATAAAATA-TAACTTAATCCT * 5100870 TTAAAAATTATAAAAATATA 1 TT-AAAATAAT-AAAATATA 5100890 TATTATTAAA Statistics Matches: 41, Mismatches: 5, Indels: 6 0.79 0.10 0.12 Matches are distributed among these distances: 28 1 0.02 29 22 0.54 30 13 0.32 31 5 0.12 ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39 Consensus pattern (28 bp): TTAAAATAATAAAATATAACTTAATCCT Found at i:5100903 original size:24 final size:24 Alignment explanation

Indices: 5100873--5100921 Score: 80 Period size: 24 Copynumber: 2.0 Consensus size: 24 5100863 TAATCTTTTA 5100873 AAAATTATAAAAATATATATTATT 1 AAAATTATAAAAATATATATTATT * * 5100897 AAAATTATAAAATTATATTTTATT 1 AAAATTATAAAAATATATATTATT 5100921 A 1 A 5100922 TCATAAAAAT Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 24 23 1.00 ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45 Consensus pattern (24 bp): AAAATTATAAAAATATATATTATT Found at i:5102169 original size:22 final size:22 Alignment explanation

Indices: 5102119--5102171 Score: 61 Period size: 23 Copynumber: 2.4 Consensus size: 22 5102109 ATAAAATTTT * * 5102119 AATTTAATATTTTAAAAATTAC 1 AATTTAATATTGTAAAAATAAC * * 5102141 ATTTTTACTATTGTAAAAATAAC 1 A-ATTTAATATTGTAAAAATAAC 5102164 AATTTAAT 1 AATTTAAT 5102172 TTCGATACCT Statistics Matches: 24, Mismatches: 6, Indels: 2 0.75 0.19 0.06 Matches are distributed among these distances: 22 6 0.25 23 18 0.75 ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45 Consensus pattern (22 bp): AATTTAATATTGTAAAAATAAC Found at i:5105920 original size:23 final size:22 Alignment explanation

Indices: 5105861--5105938 Score: 79 Period size: 23 Copynumber: 3.5 Consensus size: 22 5105851 AGTGCTGGGA 5105861 AAACAGTAAGCACACAC-AGTGC- 1 AAACAGTAAG-A-ACACGAGTGCG * * * 5105883 AATCAGTAGGCACACGAGGTGCG 1 AAACAGTAAGAACACGA-GTGCG 5105906 AAACAGTAAGAACACGAAGTGCG 1 AAACAGTAAGAACACG-AGTGCG 5105929 AAACAGTAAG 1 AAACAGTAAG 5105939 CGTGCTAGTG Statistics Matches: 46, Mismatches: 6, Indels: 7 0.78 0.10 0.12 Matches are distributed among these distances: 20 4 0.09 21 1 0.02 22 12 0.26 23 28 0.61 24 1 0.02 ACGTcount: A:0.44, C:0.21, G:0.26, T:0.10 Consensus pattern (22 bp): AAACAGTAAGAACACGAGTGCG Found at i:5110571 original size:23 final size:23 Alignment explanation

Indices: 5110528--5110571 Score: 54 Period size: 23 Copynumber: 1.9 Consensus size: 23 5110518 AGTTTTAGAT * 5110528 ATAAAATTAAATTGATAAAATAA 1 ATAAAATTAAATGGATAAAATAA * 5110551 ATAAATATTAAA-GGATTAAAT 1 ATAAA-ATTAAATGGATAAAAT 5110572 TTATTATTTG Statistics Matches: 18, Mismatches: 2, Indels: 2 0.82 0.09 0.09 Matches are distributed among these distances: 23 12 0.67 24 6 0.33 ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32 Consensus pattern (23 bp): ATAAAATTAAATGGATAAAATAA Found at i:5110671 original size:28 final size:28 Alignment explanation

Indices: 5110635--5110697 Score: 85 Period size: 27 Copynumber: 2.3 Consensus size: 28 5110625 ACAAGGTGAC * * 5110635 TAAAATTTTAAAATGTTGA-TGA-TAAAA 1 TAAAATTTTTAAA-GTTAAGTGATTAAAA 5110662 TAAAATTTTTAAAGTTAAGTGATTAAAA 1 TAAAATTTTTAAAGTTAAGTGATTAAAA 5110690 TAAAATTT 1 TAAAATTT 5110698 ACCCAAAAGT Statistics Matches: 32, Mismatches: 2, Indels: 3 0.86 0.05 0.08 Matches are distributed among these distances: 26 4 0.12 27 15 0.47 28 13 0.41 ACGTcount: A:0.51, C:0.00, G:0.10, T:0.40 Consensus pattern (28 bp): TAAAATTTTTAAAGTTAAGTGATTAAAA Found at i:5121654 original size:6 final size:7 Alignment explanation

Indices: 5121637--5121662 Score: 52 Period size: 7 Copynumber: 3.7 Consensus size: 7 5121627 TTTTTACTTA 5121637 AAAAAGG 1 AAAAAGG 5121644 AAAAAGG 1 AAAAAGG 5121651 AAAAAGG 1 AAAAAGG 5121658 AAAAA 1 AAAAA 5121663 CAATTTGAGA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 19 1.00 ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00 Consensus pattern (7 bp): AAAAAGG Found at i:5136228 original size:17 final size:18 Alignment explanation

Indices: 5136197--5136233 Score: 58 Period size: 17 Copynumber: 2.1 Consensus size: 18 5136187 AAAACCCTTC 5136197 AAAATTATTAAAAAATAA 1 AAAATTATTAAAAAATAA * 5136215 AAAATT-TTAGAAAATAA 1 AAAATTATTAAAAAATAA 5136232 AA 1 AA 5136234 TCTTAAATAT Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 17 12 0.67 18 6 0.33 ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27 Consensus pattern (18 bp): AAAATTATTAAAAAATAA Found at i:5141630 original size:2 final size:2 Alignment explanation

Indices: 5141623--5141656 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 5141613 TAATATCAAA 5141623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 5141657 CTTTGTAACC Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:5142365 original size:24 final size:22 Alignment explanation

Indices: 5142338--5142387 Score: 55 Period size: 23 Copynumber: 2.2 Consensus size: 22 5142328 CAGCCTGACT * * 5142338 AATTAATAGGGACTTTCAATTTAC 1 AATTAATA-GCACATTCAATTT-C * 5142362 AATTCATAGCACATTCAATTTC 1 AATTAATAGCACATTCAATTTC 5142384 AATT 1 AATT 5142388 TTACTTATTA Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 22 5 0.22 23 11 0.48 24 7 0.30 ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38 Consensus pattern (22 bp): AATTAATAGCACATTCAATTTC Found at i:5143170 original size:26 final size:25 Alignment explanation

Indices: 5143137--5143185 Score: 71 Period size: 26 Copynumber: 1.9 Consensus size: 25 5143127 AAAAATACGA * 5143137 ATTAAATAATAATTTATATTATTAT 1 ATTAAATAATAATTTATAATATTAT * 5143162 ATTATAATATTAATTTATAATATT 1 ATTA-AATAATAATTTATAATATT 5143186 TTAAATCATG Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 25 4 0.19 26 17 0.81 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (25 bp): ATTAAATAATAATTTATAATATTAT Found at i:5143172 original size:13 final size:13 Alignment explanation

Indices: 5143141--5143185 Score: 56 Period size: 13 Copynumber: 3.5 Consensus size: 13 5143131 ATACGAATTA * 5143141 AATAATAATTTAT 1 AATATTAATTTAT * 5143154 ATTATT-ATATTAT 1 AATATTAAT-TTAT 5143167 AATATTAATTTAT 1 AATATTAATTTAT 5143180 AATATT 1 AATATT 5143186 TTAAATCATG Statistics Matches: 27, Mismatches: 3, Indels: 4 0.79 0.09 0.12 Matches are distributed among these distances: 12 2 0.07 13 23 0.85 14 2 0.07 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (13 bp): AATATTAATTTAT Found at i:5143912 original size:24 final size:24 Alignment explanation

Indices: 5143885--5143936 Score: 88 Period size: 24 Copynumber: 2.2 Consensus size: 24 5143875 CGGAAAACAC 5143885 CAGA-AAAAATCGTGTCATAAAAGA 1 CAGAGAAAAA-CGTGTCATAAAAGA 5143909 CAGAGAAAAACGTGTCATAAAAGA 1 CAGAGAAAAACGTGTCATAAAAGA 5143933 CAGA 1 CAGA 5143937 CAACTTCAGC Statistics Matches: 27, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 24 22 0.81 25 5 0.19 ACGTcount: A:0.54, C:0.13, G:0.19, T:0.13 Consensus pattern (24 bp): CAGAGAAAAACGTGTCATAAAAGA Found at i:5144137 original size:6 final size:7 Alignment explanation

Indices: 5144115--5144139 Score: 50 Period size: 7 Copynumber: 3.6 Consensus size: 7 5144105 TATGCTTTTA 5144115 TTTAATT 1 TTTAATT 5144122 TTTAATT 1 TTTAATT 5144129 TTTAATT 1 TTTAATT 5144136 TTTA 1 TTTA 5144140 CGTTTTTCTA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72 Consensus pattern (7 bp): TTTAATT Found at i:5146160 original size:59 final size:59 Alignment explanation

Indices: 5146068--5146230 Score: 220 Period size: 59 Copynumber: 2.8 Consensus size: 59 5146058 TTAATATAAC * * * * 5146068 ATTTGGTACTT-AAATTTAACACTTTTTTATAATTTGATACCTAAACTTTTTTTTATCTA 1 ATTTGGTACTTGAACTTT-ACACTTTTTCATAATTTGGTACCTAAACTTTTTTTTATCCA * * 5146127 ATTTGATACTTGAACTTTACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTATCCA 1 ATTTGGTACTTGAACTTTACACTTTTTCATAATTTGGTACCTAAACTTTTTTTTATCCA * * * * 5146186 ATTTGGTATTTGAACTTGACATTTTTTCTTAATTTGGTACCTAAA 1 ATTTGGTACTTGAACTTTACACTTTTTCATAATTTGGTACCTAAA 5146231 TTTATTAAAT Statistics Matches: 92, Mismatches: 11, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 59 87 0.95 60 5 0.05 ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50 Consensus pattern (59 bp): ATTTGGTACTTGAACTTTACACTTTTTCATAATTTGGTACCTAAACTTTTTTTTATCCA Found at i:5146162 original size:31 final size:31 Alignment explanation

Indices: 5146124--5146225 Score: 104 Period size: 31 Copynumber: 3.4 Consensus size: 31 5146114 TTTTTTTTAT * * 5146124 CTAATTTGATACTTGAACTTTACACTTTTTC 1 CTAATTTGGTACTTGAACTTTACATTTTTTC * * 5146155 CTAATTTGGTACCTAAACTTT---TTTTTATC 1 CTAATTTGGTACTTGAACTTTACATTTTT-TC * * 5146184 C-AATTTGGTATTTGAACTTGACATTTTTTC 1 CTAATTTGGTACTTGAACTTTACATTTTTTC * 5146214 TTAATTTGGTAC 1 CTAATTTGGTAC 5146226 CTAAATTTAT Statistics Matches: 56, Mismatches: 10, Indels: 10 0.74 0.13 0.13 Matches are distributed among these distances: 28 19 0.34 29 3 0.05 30 2 0.04 31 32 0.57 ACGTcount: A:0.25, C:0.16, G:0.10, T:0.50 Consensus pattern (31 bp): CTAATTTGGTACTTGAACTTTACATTTTTTC Found at i:5146193 original size:28 final size:28 Alignment explanation

Indices: 5146090--5146190 Score: 100 Period size: 28 Copynumber: 3.6 Consensus size: 28 5146080 AATTTAACAC 5146090 TTTTTTAT--AATTTGATACCTAAACTT 1 TTTTTTATCCAATTTGATACCTAAACTT * * * 5146116 TTTTTTATCTAATTTGATACTTGAACTT 1 TTTTTTATCCAATTTGATACCTAAACTT * * 5146144 TACACTTTT-TCCTAATTTGGTACCTAAACTT 1 T---TTTTTATCC-AATTTGATACCTAAACTT 5146175 TTTTTTATCCAATTTG 1 TTTTTTATCCAATTTG 5146191 GTATTTGAAC Statistics Matches: 60, Mismatches: 8, Indels: 12 0.75 0.10 0.15 Matches are distributed among these distances: 26 8 0.13 28 27 0.45 29 3 0.05 30 2 0.03 31 20 0.33 ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53 Consensus pattern (28 bp): TTTTTTATCCAATTTGATACCTAAACTT Found at i:5146201 original size:28 final size:28 Alignment explanation

Indices: 5146090--5146202 Score: 88 Period size: 28 Copynumber: 4.0 Consensus size: 28 5146080 AATTTAACAC * * * 5146090 TTTTTTAT--AATTTGATACCTAAACTT 1 TTTTTTATCCAATTTGGTACTTGAACTT * * 5146116 TTTTTTATCTAATTTGATACTTGAACTT 1 TTTTTTATCCAATTTGGTACTTGAACTT * * * 5146144 TACACTTTT-TCCTAATTTGGTACCTAAACTT 1 T---TTTTTATCC-AATTTGGTACTTGAACTT * 5146175 TTTTTTATCCAATTTGGTATTTGAACTT 1 TTTTTTATCCAATTTGGTACTTGAACTT 5146203 GACATTTTTT Statistics Matches: 69, Mismatches: 11, Indels: 12 0.75 0.12 0.13 Matches are distributed among these distances: 26 8 0.12 28 36 0.52 29 3 0.04 30 2 0.03 31 20 0.29 ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53 Consensus pattern (28 bp): TTTTTTATCCAATTTGGTACTTGAACTT Found at i:5146405 original size:31 final size:30 Alignment explanation

Indices: 5146371--5146542 Score: 138 Period size: 28 Copynumber: 5.7 Consensus size: 30 5146361 AAAAAATTAG * 5146371 GTACCAAATTAGAAAAAATAATCAAGTTTAG 1 GTACCAAATTAGAAAAAA-AATCAAGTTTAA * * **** 5146402 GTACCAATTTGGACCCCAAA--AAGTTTAA 1 GTACCAAATTAGAAAAAAAATCAAGTTTAA * 5146430 GTACCAATTTTA-AAAAAAAAGTGTCAAGTTTAA 1 GTACCAA-ATTAGAAAAAAAA---TCAAGTTTAA ** 5146463 GTACCAAATTAGGAAAAAATGTCAAGTTTAA 1 GTACCAAATTA-GAAAAAAAATCAAGTTTAA * * 5146494 GTATCAAATTAGATAAAAAA--AAGTTTAA 1 GTACCAAATTAGAAAAAAAATCAAGTTTAA * 5146522 GAACCAAATTAGAAAAAAAAT 1 GTACCAAATTAGAAAAAAAAT 5146543 ATCAAATTCA Statistics Matches: 110, Mismatches: 22, Indels: 20 0.72 0.14 0.13 Matches are distributed among these distances: 28 43 0.39 29 3 0.03 30 8 0.07 31 32 0.29 32 3 0.03 33 15 0.14 34 6 0.05 ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26 Consensus pattern (30 bp): GTACCAAATTAGAAAAAAAATCAAGTTTAA Found at i:5146529 original size:28 final size:27 Alignment explanation

Indices: 5146419--5146541 Score: 102 Period size: 31 Copynumber: 4.1 Consensus size: 27 5146409 TTTGGACCCC * * 5146419 AAAAAGTTTAAGTACCAATTTTAAAAAA 1 AAAAAGTTTAAGTACCAA-ATTAGAAAA 5146447 AAAGTGTCAAGTTTAAGTACCAAATTAGGAAAA 1 AAA-----AAGTTTAAGTACCAAATTA-GAAAA * * 5146480 AATGTCAAGTTTAAGTATCAAATTAGATAAA 1 AA---AAAGTTTAAGTACCAAATTAGA-AAA * 5146511 AAAAAGTTTAAGAACCAAATTAGAAAA 1 AAAAAGTTTAAGTACCAAATTAGAAAA 5146538 AAAA 1 AAAA 5146542 TATCAAATTC Statistics Matches: 78, Mismatches: 7, Indels: 21 0.74 0.07 0.20 Matches are distributed among these distances: 27 7 0.09 28 22 0.28 30 2 0.03 31 23 0.29 32 3 0.04 33 21 0.27 ACGTcount: A:0.55, C:0.07, G:0.12, T:0.25 Consensus pattern (27 bp): AAAAAGTTTAAGTACCAAATTAGAAAA Found at i:5152962 original size:18 final size:19 Alignment explanation

Indices: 5152917--5152967 Score: 50 Period size: 18 Copynumber: 2.7 Consensus size: 19 5152907 CTGATTTTTC * 5152917 TTCCTTTTGCTTTTTTGGGT 1 TTCCTTTTGC-TTTTTGGGA ** 5152937 TTAATTTTG-TTTTTGGGA 1 TTCCTTTTGCTTTTTGGGA * 5152955 TTCCTTTTTCTTT 1 TTCCTTTTGCTTT 5152968 CCATTGATGG Statistics Matches: 24, Mismatches: 6, Indels: 3 0.73 0.18 0.09 Matches are distributed among these distances: 18 14 0.58 19 3 0.12 20 7 0.29 ACGTcount: A:0.06, C:0.12, G:0.16, T:0.67 Consensus pattern (19 bp): TTCCTTTTGCTTTTTGGGA Found at i:5156972 original size:18 final size:19 Alignment explanation

Indices: 5156951--5156987 Score: 58 Period size: 19 Copynumber: 2.0 Consensus size: 19 5156941 GTATTGTCAC 5156951 AATTA-ATTATAAAAAAAT 1 AATTATATTATAAAAAAAT * 5156969 AATTATATTTTAAAAAAAT 1 AATTATATTATAAAAAAAT 5156988 TAAGAATTCT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 18 5 0.29 19 12 0.71 ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38 Consensus pattern (19 bp): AATTATATTATAAAAAAAT Found at i:5157798 original size:4 final size:4 Alignment explanation

Indices: 5157789--5157820 Score: 55 Period size: 4 Copynumber: 8.0 Consensus size: 4 5157779 CAGTTAATGT * 5157789 TATG TATG TATG TATG TATG TATG AATG TATG 1 TATG TATG TATG TATG TATG TATG TATG TATG 5157821 CTGGTGTTAT Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 4 26 1.00 ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47 Consensus pattern (4 bp): TATG Found at i:5169062 original size:26 final size:27 Alignment explanation

Indices: 5169012--5169062 Score: 77 Period size: 26 Copynumber: 1.9 Consensus size: 27 5169002 CGTTGAACAT * 5169012 CATGATTTATTTTTATTTTATTAATTA 1 CATGATTTATTTTCATTTTATTAATTA * 5169039 CATGTTTTA-TTTCATTTTATTAAT 1 CATGATTTATTTTCATTTTATTAAT 5169063 ATGAGTTGCT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 26 14 0.64 27 8 0.36 ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63 Consensus pattern (27 bp): CATGATTTATTTTCATTTTATTAATTA Found at i:5174658 original size:20 final size:22 Alignment explanation

Indices: 5174633--5174674 Score: 61 Period size: 21 Copynumber: 2.0 Consensus size: 22 5174623 CAATATATTA * 5174633 TTAATA-ATTAAATTTT-TAAT 1 TTAATAGAATAAATTTTATAAT 5174653 TTAATAGAATAAATTTTATAAT 1 TTAATAGAATAAATTTTATAAT 5174675 GTAAAATGTA Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 20 6 0.32 21 9 0.47 22 4 0.21 ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50 Consensus pattern (22 bp): TTAATAGAATAAATTTTATAAT Found at i:5187906 original size:57 final size:57 Alignment explanation

Indices: 5187818--5187932 Score: 212 Period size: 57 Copynumber: 2.0 Consensus size: 57 5187808 AAAGTTGAAA * 5187818 CTATTCTATTAATTATACTGAGTATTTATCACATAAAAGTCTTGATAAGTCAATCTC 1 CTATTCTATTAATTATACTGAGCATTTATCACATAAAAGTCTTGATAAGTCAATCTC * 5187875 CTATTCTATTAATTATAGTGAGCATTTATCACATAAAAGTCTTGATAAGTCAATCTC 1 CTATTCTATTAATTATACTGAGCATTTATCACATAAAAGTCTTGATAAGTCAATCTC 5187932 C 1 C 5187933 CAGTTGCTCC Statistics Matches: 56, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 57 56 1.00 ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39 Consensus pattern (57 bp): CTATTCTATTAATTATACTGAGCATTTATCACATAAAAGTCTTGATAAGTCAATCTC Found at i:5190075 original size:2 final size:2 Alignment explanation

Indices: 5190068--5190103 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 5190058 ACATAATTTA 5190068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 5190104 TGATATCTTC Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:5193347 original size:22 final size:23 Alignment explanation

Indices: 5193300--5193354 Score: 55 Period size: 22 Copynumber: 2.6 Consensus size: 23 5193290 CATGAACATG * * 5193300 AAAATTAAT-TAATAAATATTTC 1 AAAATTAATATAATAAACATATC * 5193322 AAAATTAATATAATAAGCATAT- 1 AAAATTAATATAATAAACATATC 5193344 AAAA--AATATAA 1 AAAATTAATATAA 5193355 AATACCCCAA Statistics Matches: 29, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 20 7 0.24 22 13 0.45 23 9 0.31 ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33 Consensus pattern (23 bp): AAAATTAATATAATAAACATATC Found at i:5193348 original size:23 final size:22 Alignment explanation

Indices: 5193300--5193348 Score: 53 Period size: 23 Copynumber: 2.2 Consensus size: 22 5193290 CATGAACATG * * * 5193300 AAAATTAATTAATAAATATTTC 1 AAAATTAATTAATAAACATATA * 5193322 AAAATTAATATAATAAGCATATA 1 AAAATTAAT-TAATAAACATATA 5193345 AAAA 1 AAAA 5193349 ATATAAAATA Statistics Matches: 22, Mismatches: 4, Indels: 1 0.81 0.15 0.04 Matches are distributed among these distances: 22 9 0.41 23 13 0.59 ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33 Consensus pattern (22 bp): AAAATTAATTAATAAACATATA Found at i:5206958 original size:18 final size:18 Alignment explanation

Indices: 5206935--5206970 Score: 72 Period size: 18 Copynumber: 2.0 Consensus size: 18 5206925 TATATTATTG 5206935 TTTAGAAACCAAACAATC 1 TTTAGAAACCAAACAATC 5206953 TTTAGAAACCAAACAATC 1 TTTAGAAACCAAACAATC 5206971 GGATCACCAC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22 Consensus pattern (18 bp): TTTAGAAACCAAACAATC Found at i:5210115 original size:23 final size:23 Alignment explanation

Indices: 5210089--5210209 Score: 113 Period size: 23 Copynumber: 5.2 Consensus size: 23 5210079 ACACTAGCGC 5210089 GCTCTCTGATTAGCATTGTGTGT 1 GCTCTCTGATTAGCATTGTGTGT * * * 5210112 GCTCTCTGTTTAGCA-CGTCTCGT 1 GCTCTCTGATTAGCATTGTGT-GT * * 5210135 GCTCTCTATTATTAGCACTGTGTGT 1 GCTCTC--TGATTAGCATTGTGTGT * * 5210160 GCTCTCCGATTAGCACTT-CGTGT 1 GCTCTCTGATTAGCA-TTGTGTGT 5210183 GCTCTCTGATTAGCACTT-TGTGT 1 GCTCTCTGATTAGCA-TTGTGTGT 5210206 GCTC 1 GCTC 5210210 AGTACTTTGT Statistics Matches: 80, Mismatches: 13, Indels: 10 0.78 0.13 0.10 Matches are distributed among these distances: 22 3 0.04 23 58 0.73 24 1 0.01 25 15 0.19 26 3 0.04 ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40 Consensus pattern (23 bp): GCTCTCTGATTAGCATTGTGTGT Found at i:5210141 original size:25 final size:24 Alignment explanation

Indices: 5210113--5210198 Score: 74 Period size: 25 Copynumber: 3.6 Consensus size: 24 5210103 ATTGTGTGTG * 5210113 CTCTCTGTTTAGCACGTCTCGTGCT 1 CTCTCTGATTAGCACGT-TCGTGCT * * 5210138 CTCTATTATTAGCACTGTGT-GTGCT 1 CTCTCTGATTAGCAC-GT-TCGTGCT 5210163 CTC-C-GATTAGCAC-TTCGTG-T 1 CTCTCTGATTAGCACGTTCGTGCT 5210183 GCTCTCTGATTAGCAC 1 -CTCTCTGATTAGCAC 5210199 TTTGTGTGCT Statistics Matches: 50, Mismatches: 6, Indels: 12 0.74 0.09 0.18 Matches are distributed among these distances: 20 2 0.04 21 7 0.14 22 1 0.02 23 17 0.34 25 20 0.40 26 3 0.06 ACGTcount: A:0.14, C:0.28, G:0.20, T:0.38 Consensus pattern (24 bp): CTCTCTGATTAGCACGTTCGTGCT Found at i:5210195 original size:46 final size:49 Alignment explanation

Indices: 5210089--5210209 Score: 160 Period size: 48 Copynumber: 2.6 Consensus size: 49 5210079 ACACTAGCGC * * * 5210089 GCTCTCTGATTAGCATTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCT 1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCT * * 5210138 -CTCTATTATTAGCACTGTGTGTGCTCTCCGATTAGCAC-T-TCGTG-T 1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCT * 5210183 GCTCTCTGATTAGCACTTTGTGTGCTC 1 GCTCTCTGATTAGCACTGTGTGTGCTC 5210210 AGTACTTTGT Statistics Matches: 63, Mismatches: 8, Indels: 5 0.83 0.11 0.07 Matches are distributed among these distances: 45 1 0.02 46 28 0.44 47 1 0.02 48 33 0.52 ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40 Consensus pattern (49 bp): GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCT Found at i:5210236 original size:14 final size:16 Alignment explanation

Indices: 5210197--5210237 Score: 82 Period size: 16 Copynumber: 2.6 Consensus size: 16 5210187 TCTGATTAGC 5210197 ACTTTGTGTGCTCAGT 1 ACTTTGTGTGCTCAGT 5210213 ACTTTGTGTGCTCAGT 1 ACTTTGTGTGCTCAGT 5210229 ACTTTGTGT 1 ACTTTGTGT 5210238 ACTCTCTGTT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 25 1.00 ACGTcount: A:0.12, C:0.17, G:0.24, T:0.46 Consensus pattern (16 bp): ACTTTGTGTGCTCAGT Found at i:5211727 original size:2 final size:2 Alignment explanation

Indices: 5211720--5211766 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 5211710 GTTAAAATGA 5211720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 5211762 AT AT A 1 AT AT A 5211767 AGCAAAACAA Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:5213136 original size:19 final size:19 Alignment explanation

Indices: 5213114--5213178 Score: 55 Period size: 21 Copynumber: 3.3 Consensus size: 19 5213104 TATTTTCCCC 5213114 ATTTTTGTATATTTTAATA 1 ATTTTTGTATATTTTAATA * 5213133 A-TTTTGATTGATTTTTTAAT- 1 ATTTTTG--T-ATATTTTAATA 5213153 ATTTTT-TATAATTATTAATA 1 ATTTTTGTAT-ATT-TTAATA 5213173 ATTTTT 1 ATTTTT 5213179 CTAAAATTTC Statistics Matches: 37, Mismatches: 2, Indels: 13 0.71 0.04 0.25 Matches are distributed among these distances: 17 2 0.05 18 8 0.22 19 6 0.16 20 8 0.22 21 13 0.35 ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65 Consensus pattern (19 bp): ATTTTTGTATATTTTAATA Found at i:5213533 original size:23 final size:24 Alignment explanation

Indices: 5213502--5213553 Score: 74 Period size: 23 Copynumber: 2.2 Consensus size: 24 5213492 TTTCAAATAA 5213502 ATAAGAAAAAATA-TTTTTAAAATT 1 ATAA-AAAAAATATTTTTTAAAATT 5213526 AT-AAAAAAATATTTTTTAAAATT 1 ATAAAAAAAATATTTTTTAAAATT 5213549 -TAAAA 1 ATAAAA 5213554 TTTTTAAAAA Statistics Matches: 26, Mismatches: 0, Indels: 5 0.84 0.00 0.16 Matches are distributed among these distances: 22 9 0.35 23 15 0.58 24 2 0.08 ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38 Consensus pattern (24 bp): ATAAAAAAAATATTTTTTAAAATT Found at i:5213535 original size:22 final size:22 Alignment explanation

Indices: 5213507--5213553 Score: 78 Period size: 22 Copynumber: 2.1 Consensus size: 22 5213497 AATAAATAAG 5213507 AAAAAATA-TTTTTAAAATTATA 1 AAAAAATATTTTTTAAAATT-TA 5213529 AAAAAATATTTTTTAAAATTTA 1 AAAAAATATTTTTTAAAATTTA 5213551 AAA 1 AAA 5213554 TTTTTAAAAA Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 22 13 0.54 23 11 0.46 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (22 bp): AAAAAATATTTTTTAAAATTTA Done.