Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.009G254600.2-JGI_221_v2.1

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: 3147
ACGTcount: A:0.41, C:0.15, G:0.27, T:0.17


Found at i:756 original size:117 final size:117

Alignment explanation

Indices: 605--1526 Score: 1004 Period size: 117 Copynumber: 7.9 Consensus size: 117 595 GCAGCTGAAG * * * * 605 CTGAAGCTGCA-AAGGCATCAAAACTGAAGTTGGCTGAAGAGAAGAAACCCGAAGAGGTACCCAA 1 CTGAAGCTG-AGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA * ** * *** * 669 GGAGAAAAGTGTTGAGCAAGTGGTGCCAAAACCAATGCCAGTTGAAAAGGAGA 65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA ** 722 CTGAAGCTGAGAAGGTACTGAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG 1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG * * * * 787 GAGGAAAGTGTTAAGCAAAAGGTGCAAAAACCAAAGCTGGTCCAAAAGGAGGATGAA 66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT-CGAAA--AGGA-G-A * ** * 844 GCTGAACCTGAGAATTTACCAAAACTGAAGTTTGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA 1 -CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA * * * * * 909 GGAGAAAAGTGTTGAGCAAATGGTGCCAAAACCAAAGTTAGTCGTAAAGGAGG 65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA * * * 962 CTGAAGCTGAAAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAG 1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG ** * * * 1027 GAGGAAAGCATTGAGCAAAAGGTGCCCAAACCAAATTTGGTCGAAAAGGAGG 66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA * * * ** * * * 1079 CTGAAGCTGAGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAAGAGATAACCAAG 1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG * * 1144 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCACAGTTGCTC---AA--AG- 66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA ** ** * * * * 1190 CTGAAGAAGAGAAGGTACCGCAATTGATA-TTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAA 1 CTGAAGCTGAGAAGGTACCAAAACTGA-AGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA **** 1254 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGACGCTGA-A 65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA * * * * * * 1306 GCTGAAGCTGAGAAAGTACCAAAACTGATGTTGTCCGAAAAGAAGAAACCTAAAGAGGTAACC-- 1 -CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA ** * * * * 1369 -GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGG 65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA * * * * * * 1421 CTGAACCTGAGAAGGTGCCAAAACAGATGATGGCTGCAAAGAAGAAACCTGAAGAGGTACCCAAG 1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG 1486 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT 66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT 1527 TGAGAAGAAG Statistics Matches: 671, Mismatches: 114, Indels: 40 0.81 0.14 0.05 Matches are distributed among these distances: 111 90 0.13 112 2 0.00 114 95 0.14 116 2 0.00 117 371 0.55 118 3 0.00 119 1 0.00 120 8 0.01 121 1 0.00 122 4 0.01 123 94 0.14 ACGTcount: A:0.41, C:0.16, G:0.28, T:0.15 Consensus pattern (117 bp): CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA Found at i:1028 original size:240 final size:237 Alignment explanation

Indices: 600--1526 Score: 1044 Period size: 240 Copynumber: 4.0 Consensus size: 237 590 AAACTGCAGC * * * * * 600 TGAAGCTGAAGCTGCA-AAGGCATCAAAACTGAAGTTGGCTGAAGAGAAGAAACCCGAAGAGGTA 1 TGAAGCTGAAGCTG-AGAAAGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTA * ** * ** * * 664 CCCAAGGAGAAAAGTGTTGAGCAAGTGGTGCCAAAACCAATGCCAGTTGAAAAGGAGACTGAAGC 65 ACCAAGGAGAAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTAGTCGAAAAGGAGGCTGAAGC ** * 729 TGAGAAGGTACTGAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAA 130 TGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAA * * * 794 GTGTTAAGCAAAAGGTGCAAAAACCAAAGCTGGTCCAAAAGGAGGA 195 GTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT-C-AAA-GAGGA * ** * * 840 TGAAGCTGAACCTGAGAATTTACCAAAACTGAAGTTTGCTGAAAAGAAGAAACCTGAAGAGGTAC 1 TGAAGCTGAAGCTGAGAAAGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAA * * 905 CCAAGGAGAAAAGTGTTGAGCAAATGGTGCCAAAACCAAAGTTAGTCGTAAAGGAGGCTGAAGCT 66 CCAAGGAGAAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTAGTCGAAAAGGAGGCTGAAGCT * * * 970 GAAAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAG 131 GAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG ** * * 1035 CATTGAGCAAAAGGTGCCCAAACCAAATTTGGTCGAAA-AGGA 196 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTC-AAAGAGGA * * * * ** * * 1077 -G--GCTGAAGCTGAGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAAGAGATAA 1 TGAAGCTGAAGCTGAGAAAGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAA * * * 1139 CCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCACAGTT-GCTC---AA--A-GCTGAAGA 66 CCAAGGAGAAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTAG-TCGAAAAGGAGGCTGAAGC * ** * * * * * 1197 AGAGAAGGTACCGCAATTGATATTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGGAAA 130 TGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAA * * 1262 GTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTC---GACGC 195 GTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCAAAGAGGA * * * * 1302 TGAAGCTGAAGCTGAGAAAGTACCAAAACTGATGTTGTCCGAAAAGAAGAAACCTAAAGAGGTAA 1 TGAAGCTGAAGCTGAGAAAGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAA * ** * * * * * 1367 CC---GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAACCT 66 CCAAGGAGAAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTAGTCGAAAAGGAGGCTGAAGCT * * * * 1429 GAGAAGGTGCCAAAACAGATGATGGCTGCAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG 131 GAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG 1494 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT 196 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT 1527 TGAGAAGAAG Statistics Matches: 583, Mismatches: 91, Indels: 35 0.82 0.13 0.05 Matches are distributed among these distances: 225 36 0.06 226 2 0.00 228 147 0.25 229 1 0.00 230 1 0.00 231 95 0.16 233 1 0.00 234 91 0.16 236 1 0.00 237 4 0.01 239 5 0.01 240 199 0.34 ACGTcount: A:0.41, C:0.16, G:0.28, T:0.15 Consensus pattern (237 bp): TGAAGCTGAAGCTGAGAAAGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAA CCAAGGAGAAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTAGTCGAAAAGGAGGCTGAAGCT GAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCAAAGAGGA Found at i:1499 original size:342 final size:347 Alignment explanation

Indices: 601--1524 Score: 1067 Period size: 357 Copynumber: 2.6 Consensus size: 347 591 AACTGCAGCT * * * * * * ** * 601 GAAGCTGAAGCTGCAAAGGCATCAAAACTGAAGTTGGCTGAAGAGAAGAAACCCGAAGAGGTACC 1 GAAGCTGAAGCTGAAAAGGTACCAAAACTGACGTTGGCCGAAAAGAAGAAACCTAAAGAGGTAAC * ** * ** * * * *** * * 666 CAAGGAGAAAAGTGTTGAGCAAGTGGTGCCAAAACCAATGCCAGTTGAAAAGGAGACTGAAGCTG 66 C-A-GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAAGCTG ** * * * 731 AGAAGGTACTGAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGT 129 AGAAGGTACCAAAACAGATGATGGCTG-AAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGT * * * * ** 796 GTTAAGCAAAAGGTGCAAAAACCAAAGCTGGTCCAAAAGGAGGATGAAGCTGAACCTGAGAATTT 193 GTTGAGCAAAAGGTGCCAAAACCAAAGTTGCTCC-AAA-GAGGATGAA-C-GAA-C-GAGAAGGT * * * * 861 ACCAAAACTGAAGTTTGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGAAAAGTGTTGAGC 252 ACCAAAACTGAAGTTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGAAAAGTGTTGAGC * 926 AAATGGTGCCAAAACCAAAGTTAGTCGTAAAG 317 AAAAGGTGCCAAAACCAAAGTTAGTCG-AAAG * * * 958 GAGGCTGAAGCTGAAAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAAC 1 GAAGCTGAAGCTGAAAAGGTACCAAAACTGACGTTGGCCGAAAAGAAGAAACCTAAAGAGGTAAC * * * 1023 CAAGGAGGAAAGCATTGAGCAAAAGGTGCCCAAACCAAATTTGGTCGAAAAGGAGGCTGAAGCTG 66 C-A-GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAAGCTG * * * * 1088 AGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAAGAGATAACCAAGGAGGAAAGT 129 AGAAGGTACCAAAACAGATGATGGCTGAA-AGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGT * * ** 1153 GTTGAGCAAAAGGTGCCAAAACCACAGTTGCT-C-AA-A-GCTGAA-GAA-GAGAAGGTACCGCA 193 GTTGAGCAAAAGGTGCCAAAACCAAAGTTGCTCCAAAGAGGATGAACGAACGAGAAGGTACCAAA * * 1212 ATTGATA-TTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGGAAAGTGTTGAGCAAAAG 258 ACTGA-AGTTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGAAAAGTGTTGAGCAAAAG * * 1276 GTGCCAAAACCAAAGTTGGTCG-ACG 322 GTGCCAAAACCAAAGTTAGTCGAAAG * * 1301 CTGAAGCTGAAGCTGAGAAA-GTACCAAAACTGATGTTGTCCGAAAAGAAGAAACCTAAAGAGGT 1 --GAAGCTGAAGCTGA-AAAGGTACCAAAACTGACGTTGGCCGAAAAGAAGAAACCTAAAGAGGT * 1365 AACC-GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAACCT 63 AACCAGAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAAGCT * 1429 GAGAAGGTGCCAAAACAGATGATGGCTGCAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG 128 GAGAAGGTACCAAAACAGATGATGGCTG-AAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG 1494 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTG 192 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTG 1525 GTTGAGAAGA Statistics Matches: 497, Mismatches: 64, Indels: 27 0.85 0.11 0.05 Matches are distributed among these distances: 342 143 0.29 343 4 0.01 345 143 0.29 346 4 0.01 348 3 0.01 351 5 0.01 352 1 0.00 354 2 0.00 356 3 0.01 357 189 0.38 ACGTcount: A:0.42, C:0.16, G:0.28, T:0.15 Consensus pattern (347 bp): GAAGCTGAAGCTGAAAAGGTACCAAAACTGACGTTGGCCGAAAAGAAGAAACCTAAAGAGGTAAC CAGAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAAGCTGAG AAGGTACCAAAACAGATGATGGCTGAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTT GAGCAAAAGGTGCCAAAACCAAAGTTGCTCCAAAGAGGATGAACGAACGAGAAGGTACCAAAACT GAAGTTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGAAAAGTGTTGAGCAAAAGGTGC CAAAACCAAAGTTAGTCGAAAG Found at i:1510 original size:72 final size:72 Alignment explanation

Indices: 1459--2206 Score: 671 Period size: 72 Copynumber: 10.4 Consensus size: 72 1449 GATGGCTGCA * * * * * * 1459 AAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTT 1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT 1524 GGTTGAG 66 GGTTGAG * * * 1531 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGTGAGTGTTGAGGAAAAGGTATCAAAACCAAAGTT 1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT 1596 GGTTGAG 66 GGTTGAG * * * 1603 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTT 1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT 1668 GGTTGAG 66 GGTTGAG * * * * * ** * 1675 AAAAAGGAACCTGAAGAGATACCCAAGGTGGAGGGTGTTGA-AAAGAAATTACCGAAACCAAAGT 1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAA-AAGGTACCAAAACCAAAGT * 1739 TGATTGAG 65 TGGTTGAG * * * ** * * 1747 AATAAGGAACCTAAAGAGTTACCCAAGGTGGAGACCGATGAGGAAAAGGTACCAAAACCAAAGTT 1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT 1812 GGTTGAG 66 GGTTGAG * * * * * ** * * * 1819 AAGCAGAAACCTGATGAGGCACCCAAGGAAGAGAGGGTTGAGGAAAAA-GCACCAAAATCAAAGT 1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGA-GAAAAAGGTACCAAAACCAAAGT 1883 TGGTTGAG 65 TGGTTGAG * ** * * * * * * *** 1891 AAGAAGGAACTTGGAGAGATACCTAAGGTGGAGAGTATTAAGAAGAAGGTATGGAAACCAAAGTT 1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT * * 1956 GATCGAG 66 GGTTGAG * *** * * * * * * 1963 AAGAAGGAACCTGAAGACACACCCAAGAAGGG-GAGTGTTGAGGAAAATGTACCAAAATCAAGGC 1 AAGAAGGAACCTAAAGAGGTACCCAAG-GGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGT 2027 TGGTTGA- 65 TGGTTGAG * * * * * * * 2034 AACTAAGGAACCTGAAGAGGAACCCAAAGGGGAGAGTATTGAGGAAAAGGTACCAAAACTAAAGT 1 AA-GAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGT 2099 TGGTTGAG 65 TGGTTGAG * * * * * * * 2107 AAGAAGGAACCTGGAA-AGGCAACCAAAGAGGAAAG-GCTTGAGGAAAAGGTACCAAAACCAAAG 1 AAGAAGGAACCT-AAAGAGGTACCCAAGGGGGAGAGTG-TTGAGAAAAAGGTACCAAAACCAAAG * 2170 TTGGTTGAA 64 TTGGTTGAG * * * * 2179 AATAAGGAACTTGAAGAGGTACCTAAGG 1 AAGAAGGAACCTAAAGAGGTACCCAAGG 2207 AGAAGACTGT Statistics Matches: 547, Mismatches: 118, Indels: 22 0.80 0.17 0.03 Matches are distributed among these distances: 71 16 0.03 72 517 0.95 73 14 0.03 ACGTcount: A:0.42, C:0.13, G:0.30, T:0.15 Consensus pattern (72 bp): AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT GGTTGAG Found at i:1692 original size:144 final size:144 Alignment explanation

Indices: 1459--2226 Score: 763 Period size: 144 Copynumber: 5.3 Consensus size: 144 1449 GATGGCTGCA * * * * * 1459 AAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTT 1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT * * * * * * 1524 GGTTGAGAAGAAGGAACCTAAAGAGGTACCCAAGGGGGTGAGTGTTGAGGAAAAGGTATCAAAAC 66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC 1589 CAAAGTTGGTTGAG 131 CAAAGTTGGTTGAG * * * * 1603 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTT 1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT * ** * * * * * 1668 GGTTGAGAAAAAGGAACCTGAAGAGATACCCAAGGTGGAGGGTGTTGA-AAAGAAATTACCGAAA 66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAA-AAAGTACCAAAA * 1732 CCAAAGTTGATTGAG 130 CCAAAGTTGGTTGAG * * * * * * * 1747 AATAAGGAACCTAAAGAGTTACCCAAGGTGGAGACCGATGAGGAAAAGGTACCAAAACCAAAGTT 1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT * * * * * * * 1812 GGTTGAGAAGCAGAAACCTGATGAGGCACCCAAGGAAGAGAGGGTTGAGGAAAAAGCACCAAAAT 66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC 1877 CAAAGTTGGTTGAG 131 CAAAGTTGGTTGAG * * * * * * * * * *** 1891 AAGAAGGAACTTGGAGAGATACCTAAGGTGGAGAGTATTAAGAAGAAGGTATGGAAACCAAAGTT 1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT * * ** * * * * 1956 GATCGAGAAGAAGGAACCTGAAGACACACCCAAGAAGGGGAGTGTTGAGGAAAATGTACCAAAAT 66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC * * 2021 CAAGGCTGGTTGA- 131 CAAAGTTGGTTGAG * * * * * * 2034 AACTAAGGAACCTGAAGAGGAACCCAAAGG-GGAGAGTATTGAGGAAAAGGTACCAAAACTAAAG 1 AA-GAAGGAACCTGAAGAGGTACCC-AAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAG * * * * 2098 TTGGTTGAGAAGAAGGAACCTGGAA-AGGCAACCAAAGAGGAAAG-GCTTGAGGAAAAGGTACCA 64 TTGGTTGAGAAGAAGGAACCT-GAAGAGGCACCCAAGGAGGAGAGTG-TTGAGGAAAAAGTACCA * 2161 AAACCAAAGTTGGTTGAA 127 AAACCAAAGTTGGTTGAG * * * * * * 2179 AATAAGGAACTTGAAGAGGTACCTAAGGAGAAGACTGTCGAGAGAAAG 1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAG 2227 ATTCAAAGTA Statistics Matches: 505, Mismatches: 111, Indels: 16 0.80 0.18 0.03 Matches are distributed among these distances: 143 9 0.02 144 485 0.96 145 11 0.02 ACGTcount: A:0.42, C:0.13, G:0.30, T:0.15 Consensus pattern (144 bp): AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC CAAAGTTGGTTGAG Found at i:1845 original size:216 final size:216 Alignment explanation

Indices: 1459--2119 Score: 747 Period size: 216 Copynumber: 3.1 Consensus size: 216 1449 GATGGCTGCA * * * * * * * * * 1459 AAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTTGAGCAA-AAGGTGCCAAAACCAAAGT 1 AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATTAAG-AAGAAAGTACCGAAACCAAAGT * * * * * 1523 TGGTTGAGAAGAAGGAACCTAAAGAGGTACCCAAGGGGGTGAGTGTTGAGGAAAAGGTATCAAAA 65 TGATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAA * * * * * 1588 CCAAAGTTGGTTGAGAAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGT 130 CCAAAGTTGGTTGAGAAGCAGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAGT 1653 ACCAAAATCAAAGTTGGTTGAG 195 ACCAAAATCAAAGTTGGTTGAG * * * * 1675 AAAAAGGAACCTGAAGAGATACCCAAGGTGGAGGGTGTTGAA-AAGAAATTACCGAAACCAAAGT 1 AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATT-AAGAAGAAAGTACCGAAACCAAAGT * * * ** * 1739 TGATTGAGAATAAGGAACCTAAAGAGTTACCCAAGGTGGAGACCGATGAGGAAAAGGTACCAAAA 65 TGATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAA * * * ** * * 1804 CCAAAGTTGGTTGAGAAGCAGAAACCTGATGAGGCACCCAAGGAAGAGAGGGTTGAGGAAAAAGC 130 CCAAAGTTGGTTGAGAAGCAGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAGT 1869 ACCAAAATCAAAGTTGGTTGAG 195 ACCAAAATCAAAGTTGGTTGAG * * * * ** 1891 AAGAAGGAACTTGGAGAGATACCTAAGGTGGAGAGTATTAAGAAGAAGGTATGGAAACCAAAGTT 1 AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATTAAGAAGAAAGTACCGAAACCAAAGTT * * * * * * * * 1956 GATCGAGAAGAAGGAACCTGAAGACACACCCAAGAAGGGGAGTGTTGAGGAAAATGTACCAAAAT 66 GATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAAC * * * * * 2021 CAAGGCTGGTTGA-AA-CTAAGGAACCTGAAGAGGAACCCAAAGGGGAGAGTATTGAGGAAAAGG 131 CAAAGTTGGTTGAGAAGC--AGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAG 2084 TACCAAAA-CTAAAGTTGGTTGAG 194 TACCAAAATC-AAAGTTGGTTGAG 2107 AAGAAGGAACCTG 1 AAGAAGGAACCTG 2120 GAAAGGCAAC Statistics Matches: 371, Mismatches: 68, Indels: 12 0.82 0.15 0.03 Matches are distributed among these distances: 214 1 0.00 215 7 0.02 216 362 0.98 217 1 0.00 ACGTcount: A:0.42, C:0.13, G:0.30, T:0.15 Consensus pattern (216 bp): AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATTAAGAAGAAAGTACCGAAACCAAAGTT GATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAAC CAAAGTTGGTTGAGAAGCAGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAGTA CCAAAATCAAAGTTGGTTGAG Done.