Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01009493.1 Hibiscus syriacus cultivar Beakdansim tig00114653_pilon, whole genome shotgun sequence

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: 24170
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22


Found at i:8153 original size:33 final size:32

Alignment explanation

Indices: 8116--8204 Score: 115 Period size: 33 Copynumber: 2.8 Consensus size: 32 8106 GCGTGAGCCC * 8116 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT 1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT * ** * 8149 CGGTCACCATCGGCAAAACCATACGGGTGTCT 1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT * 8181 CGGTCACCATCGGCAACCCCAGGC 1 CGGTCACCATCGGCAAACCCAGGC 8205 CATTGGTGAG Statistics Matches: 47, Mismatches: 9, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 32 23 0.49 33 24 0.51 ACGTcount: A:0.20, C:0.37, G:0.28, T:0.15 Consensus pattern (32 bp): CGGTCACCATCGGCAAACCCAGGCGGGTGCCT Found at i:8335 original size:32 final size:32 Alignment explanation

Indices: 8250--8380 Score: 187 Period size: 32 Copynumber: 4.2 Consensus size: 32 8240 GTGCGTGAGG * * 8250 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC 1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT 8282 CTC-GTCACCATC-GCAAACCCAGACGGGTGT 1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT 8312 CTCGGTCACCATCGGCAAACCCAGACGGGTGT 1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT * * * 8344 CTCGGTCACCATCGGCAACCCCCGACGGGTGG 1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT 8376 CTCGG 1 CTCGG 8381 CAACCCCAGG Statistics Matches: 91, Mismatches: 5, Indels: 6 0.89 0.05 0.06 Matches are distributed among these distances: 30 6 0.07 31 30 0.33 32 55 0.60 ACGTcount: A:0.18, C:0.37, G:0.30, T:0.15 Consensus pattern (32 bp): CTCGGTCACCATCGGCAAACCCAGACGGGTGT Found at i:8503 original size:61 final size:63 Alignment explanation

Indices: 8427--8558 Score: 234 Period size: 61 Copynumber: 2.1 Consensus size: 63 8417 GCCGAGAGTT * 8427 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC-G-AACCCCAGGCCAC 1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC 8488 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC 1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC 8551 -GGTGCGGG 1 GGGTGCGGG 8559 AGTGCCGCAC Statistics Matches: 68, Mismatches: 1, Indels: 3 0.94 0.01 0.04 Matches are distributed among these distances: 61 46 0.68 62 9 0.13 63 13 0.19 ACGTcount: A:0.14, C:0.39, G:0.36, T:0.11 Consensus pattern (63 bp): GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC Found at i:8664 original size:31 final size:31 Alignment explanation

Indices: 8593--8724 Score: 158 Period size: 31 Copynumber: 4.2 Consensus size: 31 8583 GTGCGTGAGG * * * 8593 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC 1 CTCGGTCACCATCGGCAA-ACCAGACGGGT-GT * 8626 CTCGGTCACCATTGGCAAAGCCAGAC-GGTGT 1 CTCGGTCACCATCGGCAAA-CCAGACGGGTGT 8657 CTCGGTCACCATCGGCAAACCAGACGGGTGT 1 CTCGGTCACCATCGGCAAACCAGACGGGTGT * * * 8688 CTCGGTCACCATCGGCAACCCCCGACGGGTGC 1 CTCGGTCACCATCGGCAA-ACCAGACGGGTGT 8720 CTCGG 1 CTCGG 8725 CAACCCCAGG Statistics Matches: 88, Mismatches: 8, Indels: 7 0.85 0.08 0.07 Matches are distributed among these distances: 30 6 0.07 31 42 0.48 32 18 0.20 33 22 0.25 ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16 Consensus pattern (31 bp): CTCGGTCACCATCGGCAAACCAGACGGGTGT Found at i:8683 original size:156 final size:157 Alignment explanation

Indices: 8279--8692 Score: 495 Period size: 156 Copynumber: 2.7 Consensus size: 157 8269 CCAGGCGGGT * * 8279 GGCCTC-GTCACCATC-GCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAAACCCAGACGGGT 1 GGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCAT-GGCAAAGCCAGACGGGT * 8342 GTCTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGT 65 GTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGT * * * 8407 TCCGGACAGAGCCGAGAGTTGGGTGCGG 130 GCCGCACAGAACCGAGAGTTGGGTGCGG * * ** * * * *** * 8435 GGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGAACCCCA-GGCCACGGGTG-CGGGG 1 GG-CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATGGCAAAGCCAGACGGGT * 8498 GCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC-GGTGCGGGAGT 65 GTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGT * 8562 GCCGCACAGAACCGAGCGTT-GGTGCGTG 130 GCCGCACAGAACCGAGAGTTGGGTGCG-G * * 8590 AGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGAC-G 1 -GGCCTCGGTCACCATCGGCAAACCCAGACGGGT-GCCTCGGTCACCA-TGGCAAAGCCAGACGG * * * 8653 GTGTCTCGGTCACCATCGGCAA-ACCAGACGGGTGTCTCGG 63 GTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG 8693 TCACCATCGG Statistics Matches: 214, Mismatches: 35, Indels: 18 0.80 0.13 0.07 Matches are distributed among these distances: 154 33 0.15 155 38 0.18 156 74 0.35 157 36 0.17 158 10 0.05 159 23 0.11 ACGTcount: A:0.18, C:0.35, G:0.34, T:0.14 Consensus pattern (157 bp): GGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATGGCAAAGCCAGACGGGTG TCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTG CCGCACAGAACCGAGAGTTGGGTGCGG Found at i:8838 original size:343 final size:342 Alignment explanation

Indices: 8190--8839 Score: 1094 Period size: 343 Copynumber: 1.9 Consensus size: 342 8180 TCGGTCACCA * 8190 TCGGCAACCCCAGGCCATTGGTGAGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGG 1 TCGGCAACCCCAGGCCATCGGTGAGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGG 8255 TCACCATCGGCAACCCAGGCGGGTGGCCTCGTCACCATCGCAAACCCAGACGGGTGTCTCGGTCA 66 TCACCATCGGCAACCCAGGCGGGTGGCCTCGTCACCATCGCAAACCCAGACGGGTGTCTCGGTCA * 8320 CCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCAAC 131 CCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAAC * * * 8385 CCCAGGCCACGGGTGCGGGAGTTCCGGACAGAGCCGAGAGTTGGGTGCGGGGTCCTCGGTCACCA 196 CCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCACCA * 8450 TCGGCAACCCCCGACGGGTGCCTCGAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGG 261 TCGGCAACACCC-ACGGGTGCCTCGAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGG 8515 CAACCCCCGACGGGTGCC 325 CAACCCCCGACGGGTGCC * 8533 TCGGCAACCCCAGGCCA-CGGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG 1 TCGGCAACCCCAGGCCATCGGTG-AGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG * * 8597 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGAC-GGTGTCTCG 65 GTCACCATCGGCAA-CCCAGGCGGGTGGCCTC-GTCACCA-TCGCAAACCCAGACGGGTGTCTCG 8661 GTCACCATCGGCAAA-CCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG 127 GTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG 8725 CAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTT-GGTGCGGGGGCCTCGGTC 192 CAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTC * ** 8789 ACCATCGGCAACACCC-CGGGTGCCTCGGCAACCCCAGTCCATTGGTGCGGG 257 ACCATCGGCAACACCCACGGGTGCCTC-G-AACCCCAGGCCACGGGTGCGGG 8840 AGTGCCGCAC Statistics Matches: 289, Mismatches: 12, Indels: 12 0.92 0.04 0.04 Matches are distributed among these distances: 341 10 0.03 342 5 0.02 343 122 0.42 344 109 0.38 345 31 0.11 346 12 0.04 ACGTcount: A:0.18, C:0.35, G:0.34, T:0.13 Consensus pattern (342 bp): TCGGCAACCCCAGGCCATCGGTGAGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGG TCACCATCGGCAACCCAGGCGGGTGGCCTCGTCACCATCGCAAACCCAGACGGGTGTCTCGGTCA CCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAAC CCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCACCA TCGGCAACACCCACGGGTGCCTCGAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGGC AACCCCCGACGGGTGCC Found at i:8847 original size:92 final size:93 Alignment explanation

Indices: 8489--8858 Score: 310 Period size: 94 Copynumber: 4.0 Consensus size: 93 8479 CCAGGCCACG * 8489 GGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC-GG 1 GGTGCGGGGGCCTCGGTCACCATCGGCAACACCC-ACGGGTGCCTCGGCAACCCCAGGCCACGGG * 8553 TGCGGGAGTGCCGCACAGAACCGAGCGTT 65 TGCGGGAGTGCCGCACAGAACCGAGAGTT * * *** * 8582 GGTGCGTGAGG-CTCGGTCACCATCGGCAA-TCCCAGGCGGGTGGCCTCGGTC-ACCATTGGCAA 1 GGTGCG-GGGGCCTCGGTCACCATCGGCAACACCCA--CGGGT-GCCTCGG-CAACCCCAGGCCA * *** * * * * *** 8644 AGCCAGAC-GGTGT-CTCGGTCAC-CATCGGCA-AACC 61 CGGGTG-CGGGAGTGC-C-G-CACAGAACCG-AGAGTT * * * * * 8678 AG-ACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG 1 GGTGCGGGGGCCTCGGTCACCATCGGCAACACCC-ACGGGTGCCTCGGCAACCCCAGGCCACGGG * 8742 TGCGGGAGTGCCGCACAGAGCCGAGAGTT 65 TGCGGGAGTGCCGCACAGAACCGAGAGTT * ** 8771 GGTGCGGGGGCCTCGGTCACCATCGGCAACACCC-CGGGTGCCTCGGCAACCCCAGTCCATTGGT 1 GGTGCGGGGGCCTCGGTCACCATCGGCAACACCCACGGGTGCCTCGGCAACCCCAGGCCACGGGT 8835 GCGGGAGTGCCGCACAGAACCGAG 66 GCGGGAGTGCCGCACAGAACCGAG 8859 CGCTGGGTGC Statistics Matches: 210, Mismatches: 47, Indels: 41 0.70 0.16 0.14 Matches are distributed among these distances: 91 1 0.00 92 57 0.27 93 37 0.18 94 68 0.32 95 33 0.16 96 9 0.04 97 5 0.02 ACGTcount: A:0.18, C:0.35, G:0.35, T:0.13 Consensus pattern (93 bp): GGTGCGGGGGCCTCGGTCACCATCGGCAACACCCACGGGTGCCTCGGCAACCCCAGGCCACGGGT GCGGGAGTGCCGCACAGAACCGAGAGTT Found at i:17038 original size:31 final size:31 Alignment explanation

Indices: 17000--17084 Score: 100 Period size: 31 Copynumber: 2.7 Consensus size: 31 16990 GCGTGAGCCC * 17000 CGGTCACCATCGGCAATCCCAGGGGGTGCCT 1 CGGTCACCATCGGCAAACCCAGGGGGTGCCT * ** * 17031 CGGTCACCATCGGCAAAACCATACGGGTGTCT 1 CGGTCACCATCGGCAAACCCA-GGGGGTGCCT * 17063 CGGTCACCATC-GCAACCCCAGG 1 CGGTCACCATCGGCAAACCCAGG 17085 CCATTGGTGA Statistics Matches: 44, Mismatches: 9, Indels: 3 0.79 0.16 0.05 Matches are distributed among these distances: 31 26 0.59 32 18 0.41 ACGTcount: A:0.21, C:0.36, G:0.27, T:0.15 Consensus pattern (31 bp): CGGTCACCATCGGCAAACCCAGGGGGTGCCT Found at i:17229 original size:31 final size:32 Alignment explanation

Indices: 17132--17263 Score: 196 Period size: 32 Copynumber: 4.2 Consensus size: 32 17122 GTGCGTGAGG * * 17132 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC 1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT 17164 CTCGGTCACCATCGGCAAACCCAGACGGGTGT 1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT 17196 CTCGGTCACCATCGGCAAACCCAGAC-GGTGT 1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT * * * 17227 CTCGGTCACCATCGGCAACCCCCGACGGGTGG 1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT 17259 CTCGG 1 CTCGG 17264 CAACCCCAGG Statistics Matches: 93, Mismatches: 5, Indels: 4 0.91 0.05 0.04 Matches are distributed among these distances: 31 29 0.31 32 52 0.56 33 12 0.13 ACGTcount: A:0.18, C:0.37, G:0.30, T:0.14 Consensus pattern (32 bp): CTCGGTCACCATCGGCAAACCCAGACGGGTGT Found at i:17244 original size:63 final size:64 Alignment explanation

Indices: 17130--17263 Score: 200 Period size: 63 Copynumber: 2.1 Consensus size: 64 17120 TGGTGCGTGA * 17130 GGCTCGGTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT 1 GGCTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT * * * * 17194 GTCTCGGTCACCATCGGCAAACCCAGAC-GGT-GTCTCGGTCACCATCGGCAACCCCCGACGGGT 1 GGCTCGGTCACCATCGGC-AACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT 17257 GGCTCGG 1 GGCTCGG 17264 CAACCCCAGG Statistics Matches: 63, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 63 35 0.56 64 20 0.32 65 8 0.13 ACGTcount: A:0.18, C:0.37, G:0.31, T:0.14 Consensus pattern (64 bp): GGCTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT Found at i:17378 original size:61 final size:61 Alignment explanation

Indices: 17308--17438 Score: 230 Period size: 61 Copynumber: 2.1 Consensus size: 61 17298 GCCGAGAGTT 17308 GGGTGCGGGGTCCTCGGTCACCATC-GCAACCCCCGAC-GGTGCCTCGGCAACCCCAGGCCAC 1 GGGTGCGGGG-CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC-GCAACCCCAGGCCAC 17369 GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCAC 1 GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCAC 17430 GGGTGCGGG 1 GGGTGCGGG 17439 AGTGCCGCAC Statistics Matches: 68, Mismatches: 0, Indels: 4 0.94 0.00 0.06 Matches are distributed among these distances: 60 14 0.21 61 46 0.68 62 8 0.12 ACGTcount: A:0.14, C:0.40, G:0.35, T:0.11 Consensus pattern (61 bp): GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCAC Found at i:17548 original size:31 final size:32 Alignment explanation

Indices: 17473--17604 Score: 169 Period size: 31 Copynumber: 4.2 Consensus size: 32 17463 GTGCGTGAGG * * 17473 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC 1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC * * * 17506 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT 1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC * 17538 CTC-GTCACCATCGGCAAACCCAGAC-GGTGT 1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC * * 17568 CTCGGTCACCATCGGCAACCCCCGACGGGTGC 1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC 17600 CTCGG 1 CTCGG 17605 CAACCCCAGG Statistics Matches: 87, Mismatches: 10, Indels: 5 0.85 0.10 0.05 Matches are distributed among these distances: 30 8 0.09 31 40 0.46 32 13 0.15 33 26 0.30 ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16 Consensus pattern (32 bp): CTCGGTCACCATCGGCAAACCCAGACGGGTGC Found at i:17678 original size:94 final size:95 Alignment explanation

Indices: 17369--17752 Score: 340 Period size: 94 Copynumber: 4.1 Consensus size: 95 17359 CCCAGGCCAC 17369 GGGTGC-GGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC-GCAACCCCAGGCCACGG 1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG * 17432 GTGCGGGAGTGCCGCACAGAACCGAGCG-T 66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT * * * * * *** * 17461 TGGTGCGTGAGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTC-ACCATTGGCAA 1 GGGTGCG-GGGGCCTCGGTCACCATCGGCAACCCCCGACGGGT-GCCTCGG-CAACCCCAGGCCA * *** * * * * * * 17524 AGCCAGACGGGTGT-CTCGTCAC-CATCGGCA-AACC 63 CGGGTG-CGGGAGTGC-CG-CACAGAACCG-AGAGCT ** * * * 17558 CAG-AC-GGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG 1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG * * 17621 GTGC-GGAGTGCCGCACAGAGCCGAGAGTT 66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT * * ** 17650 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTG 1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG * 17715 GTGCGGGAGTGCCGCACAGAACCGAGCGCT 66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT 17745 GGGTGCGG 1 GGGTGCGG 17753 CAGCCTCGCA Statistics Matches: 219, Mismatches: 55, Indels: 33 0.71 0.18 0.11 Matches are distributed among these distances: 91 4 0.02 92 16 0.07 93 31 0.14 94 82 0.37 95 68 0.31 96 13 0.06 97 5 0.02 ACGTcount: A:0.17, C:0.34, G:0.35, T:0.13 Consensus pattern (95 bp): GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG GTGCGGGAGTGCCGCACAGAACCGAGAGCT Done.