Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01007415.1 Hibiscus syriacus cultivar Beakdansim tig00020041_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: 69580
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:2630 original size:18 final size:18

Alignment explanation

Indices: 2602--2647 Score: 65 Period size: 18 Copynumber: 2.6 Consensus size: 18 2592 TTCACGAAAT * * 2602 ATAATATTACCGGTGGGA 1 ATAAGATTACCGGCGGGA * 2620 ATAGGATTACCGGCGGGA 1 ATAAGATTACCGGCGGGA 2638 ATAAGATTAC 1 ATAAGATTAC 2648 TGGGAATGCT Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 18 24 1.00 ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24 Consensus pattern (18 bp): ATAAGATTACCGGCGGGA Found at i:4336 original size:2 final size:2 Alignment explanation

Indices: 4329--4373 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 4319 TTTAATCTTC 4329 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 4371 AT A 1 AT A 4374 ATGGTTCTTA Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:5854 original size:22 final size:22 Alignment explanation

Indices: 5812--5855 Score: 54 Period size: 22 Copynumber: 2.0 Consensus size: 22 5802 TCTAATAATT * 5812 TTTGTAAAAATATTTAATTCAA 1 TTTGTAAAAATATTCAATTCAA * 5834 TTTG-AAAATATATTCATTTCAA 1 TTTGTAAAA-ATATTCAATTCAA 5856 GTAAATCGGA Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 21 4 0.21 22 15 0.79 ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45 Consensus pattern (22 bp): TTTGTAAAAATATTCAATTCAA Found at i:10745 original size:2 final size:2 Alignment explanation

Indices: 10738--10780 Score: 86 Period size: 2 Copynumber: 21.5 Consensus size: 2 10728 ATTTTATAAA 10738 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 10780 A 1 A 10781 AATTTTATTA Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 41 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:11821 original size:27 final size:27 Alignment explanation

Indices: 11768--11823 Score: 78 Period size: 27 Copynumber: 2.1 Consensus size: 27 11758 CAGTTATATG * * 11768 GTTTCTGAAGTTTTTTTTGGATATGTA 1 GTTTCTGAAGTTTTGTTTGCATATGTA 11795 GTTTCTGAAGTTTTGTTTGCACT-TGTA 1 GTTTCTGAAGTTTTGTTTGCA-TATGTA 11822 GT 1 GT 11824 CATGATATTT Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 27 25 0.96 28 1 0.04 ACGTcount: A:0.16, C:0.07, G:0.23, T:0.54 Consensus pattern (27 bp): GTTTCTGAAGTTTTGTTTGCATATGTA Found at i:14086 original size:16 final size:16 Alignment explanation

Indices: 14046--14087 Score: 50 Period size: 16 Copynumber: 2.6 Consensus size: 16 14036 AATTTTTTTC * 14046 AAATAATCATATATAA 1 AAATAATTATATATAA * 14062 AAATTATTATATATTAA 1 AAATAATTATATA-TAA 14079 AAA-AATTAT 1 AAATAATTAT 14088 CTTACAACGA Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 16 16 0.73 17 6 0.27 ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38 Consensus pattern (16 bp): AAATAATTATATATAA Found at i:19872 original size:110 final size:106 Alignment explanation

Indices: 19675--19892 Score: 357 Period size: 110 Copynumber: 2.0 Consensus size: 106 19665 TAATTACAAA * * 19675 ATTTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAAT 1 ATTTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAAT * 19740 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGAT 66 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGAT 19781 ATTTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAAT 1 ATTTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAA--T---T 19845 TAAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGAT 61 TAAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGAT 19891 AT 1 AT 19893 ATGATTTCCA Statistics Matches: 104, Mismatches: 3, Indels: 6 0.92 0.03 0.05 Matches are distributed among these distances: 105 18 0.17 106 37 0.36 107 1 0.01 110 48 0.46 ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36 Consensus pattern (106 bp): ATTTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAAT TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGAT Found at i:20595 original size:30 final size:30 Alignment explanation

Indices: 20561--20618 Score: 82 Period size: 30 Copynumber: 1.9 Consensus size: 30 20551 GTGTTTTGTA * * 20561 TTTATATTGTTTTTATTTTTA-ATAATTTAT 1 TTTATATT-TATTTATATTTATATAATTTAT 20591 TTTATATTTATTTATATTTATATAATTT 1 TTTATATTTATTTATATTTATATAATTT 20619 TTTGTGTATG Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 29 10 0.40 30 15 0.60 ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69 Consensus pattern (30 bp): TTTATATTTATTTATATTTATATAATTTAT Found at i:20962 original size:17 final size:17 Alignment explanation

Indices: 20935--20967 Score: 50 Period size: 17 Copynumber: 1.9 Consensus size: 17 20925 TTATAGATGA 20935 ATAAATTTTAC-TAAAT 1 ATAAATTTTACATAAAT 20951 ATAAATTTTTACATAAA 1 ATAAA-TTTTACATAAA 20968 ATATTTGGGC Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 5 0.33 17 6 0.40 18 4 0.27 ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42 Consensus pattern (17 bp): ATAAATTTTACATAAAT Found at i:21353 original size:16 final size:17 Alignment explanation

Indices: 21332--21370 Score: 62 Period size: 16 Copynumber: 2.4 Consensus size: 17 21322 CATTTAGCCT 21332 TTTTTTCTTTTT-AAAA 1 TTTTTTCTTTTTGAAAA * 21348 TTTTTTCTTTTTGATAA 1 TTTTTTCTTTTTGAAAA 21365 TTTTTT 1 TTTTTT 21371 GAATTTTTTT Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 16 12 0.57 17 9 0.43 ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74 Consensus pattern (17 bp): TTTTTTCTTTTTGAAAA Found at i:22434 original size:2 final size:2 Alignment explanation

Indices: 22427--22460 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 22417 ACATACAGAC 22427 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 22461 TCCTTTATTG 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:25021 original size:10 final size:10 Alignment explanation

Indices: 25008--25055 Score: 55 Period size: 9 Copynumber: 5.0 Consensus size: 10 24998 TTTAATTTAA 25008 AAAAAATTAG 1 AAAAAATTAG * 25018 AAAAAA-TAC 1 AAAAAATTAG * 25027 AAAAAATCAG 1 AAAAAATTAG * 25037 -AAAAATTAC 1 AAAAAATTAG 25046 AAAAAATTAG 1 AAAAAATTAG 25056 TATGATTATT Statistics Matches: 30, Mismatches: 6, Indels: 4 0.75 0.15 0.10 Matches are distributed among these distances: 9 15 0.50 10 15 0.50 ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17 Consensus pattern (10 bp): AAAAAATTAG Found at i:25032 original size:19 final size:19 Alignment explanation

Indices: 25008--25055 Score: 78 Period size: 19 Copynumber: 2.5 Consensus size: 19 24998 TTTAATTTAA 25008 AAAAAATTAGAAAAAATAC 1 AAAAAATTAGAAAAAATAC * * 25027 AAAAAATCAGAAAAATTAC 1 AAAAAATTAGAAAAAATAC 25046 AAAAAATTAG 1 AAAAAATTAG 25056 TATGATTATT Statistics Matches: 26, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 19 26 1.00 ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17 Consensus pattern (19 bp): AAAAAATTAGAAAAAATAC Found at i:25103 original size:113 final size:114 Alignment explanation

Indices: 24912--25126 Score: 369 Period size: 113 Copynumber: 1.9 Consensus size: 114 24902 TTTGAATTTA * * 24912 AAAAAATCAGAAAAATTACAAAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTAT 1 AAAAAATCAGAAAAATTAC-AAAAAAATTAGTATGATTATTTATCTAATTTCAATATATTTTTAT * * 24977 CTATCTTACAATTTAATCTACTTTAATTTAAAAAAAATTAGAAAAAATAC 65 CTATATTACAATTTAATATACTTTAATTTAAAAAAAATTAGAAAAAATAC 25027 AAAAAATCAGAAAAATTAC-AAAAAATTAGTATGATTATTTATCTAATTTCAATATATTTTTATC 1 AAAAAATCAGAAAAATTACAAAAAAATTAGTATGATTATTTATCTAATTTCAATATATTTTTATC * 25091 TATATTATAATTTAATATACTTTAATTTAAAAAAAA 66 TATATTACAATTTAATATACTTTAATTTAAAAAAAA 25127 CAAATGTAGT Statistics Matches: 95, Mismatches: 5, Indels: 2 0.93 0.05 0.02 Matches are distributed among these distances: 113 76 0.80 115 19 0.20 ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40 Consensus pattern (114 bp): AAAAAATCAGAAAAATTACAAAAAAATTAGTATGATTATTTATCTAATTTCAATATATTTTTATC TATATTACAATTTAATATACTTTAATTTAAAAAAAATTAGAAAAAATAC Found at i:30735 original size:14 final size:14 Alignment explanation

Indices: 30710--30744 Score: 54 Period size: 14 Copynumber: 2.6 Consensus size: 14 30700 ATCAAAAATC 30710 ATTTTA-TATTTAA 1 ATTTTATTATTTAA 30723 ATTTTATTATTTAA 1 ATTTTATTATTTAA * 30737 AATTTATT 1 ATTTTATT 30745 GAGGGTTATC Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 13 6 0.30 14 14 0.70 ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63 Consensus pattern (14 bp): ATTTTATTATTTAA Found at i:48988 original size:20 final size:20 Alignment explanation

Indices: 48963--49008 Score: 65 Period size: 20 Copynumber: 2.3 Consensus size: 20 48953 AAAATTATAA * * 48963 ATTAAATTAAGTTTTTTAAT 1 ATTAAATTAAATTATTTAAT 48983 ATTAAATTAAATTATTTAAT 1 ATTAAATTAAATTATTTAAT * 49003 TTTAAA 1 ATTAAA 49009 GTCGGGTCGA Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 23 1.00 ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52 Consensus pattern (20 bp): ATTAAATTAAATTATTTAAT Found at i:52376 original size:12 final size:12 Alignment explanation

Indices: 52346--52379 Score: 59 Period size: 12 Copynumber: 2.8 Consensus size: 12 52336 CTATACGGTA * 52346 TGAACAATACCG 1 TGAACAGTACCG 52358 TGAACAGTACCG 1 TGAACAGTACCG 52370 TGAACAGTAC 1 TGAACAGTAC 52380 TGAATGTTAA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 21 1.00 ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18 Consensus pattern (12 bp): TGAACAGTACCG Found at i:54300 original size:63 final size:62 Alignment explanation

Indices: 54216--54333 Score: 182 Period size: 63 Copynumber: 1.9 Consensus size: 62 54206 TTGTTCAAGG * * * * 54216 TGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA 1 TGTATCGATGAACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA * 54279 TGTATCGATGAACAAGTAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAAT 1 TGTATCGATGAACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAAT 54334 AAGATTTATG Statistics Matches: 50, Mismatches: 5, Indels: 1 0.89 0.09 0.02 Matches are distributed among these distances: 62 17 0.34 63 33 0.66 ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25 Consensus pattern (62 bp): TGTATCGATGAACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCCATCA Found at i:54345 original size:63 final size:62 Alignment explanation

Indices: 54216--54375 Score: 180 Period size: 63 Copynumber: 2.5 Consensus size: 62 54206 TTGTTCAAGG * * * * ** 54216 TGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA 1 TGTATCGATG-ACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATAACATCA * * 54279 TGTATCGATGAACAAGTAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATAAGATTTA 1 TGTATCGATG-ACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATAACA-TCA * 54342 TGTATCGATG-CATAGATAGTGCATCGATGTACCC 1 TGTATCGATGACA-AG-TAGTGCATCGATGCACCC 54376 GTCAAGGGAT Statistics Matches: 84, Mismatches: 10, Indels: 6 0.84 0.10 0.06 Matches are distributed among these distances: 61 2 0.02 62 20 0.24 63 62 0.74 ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26 Consensus pattern (62 bp): TGTATCGATGACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATAACATCA Found at i:55050 original size:23 final size:23 Alignment explanation

Indices: 55020--55086 Score: 107 Period size: 23 Copynumber: 2.9 Consensus size: 23 55010 CTTATATGGT * 55020 ACTTCGGTGCAATTCTACGTGGC 1 ACTTCGGTGCAATTCTACGAGGC 55043 ACTTCGGTGCAATTCTACGAGGC 1 ACTTCGGTGCAATTCTACGAGGC * * 55066 ACTTCGGTGCATTTATACGAG 1 ACTTCGGTGCAATTCTACGAG 55087 CTGTGGTGAC Statistics Matches: 41, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 23 41 1.00 ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30 Consensus pattern (23 bp): ACTTCGGTGCAATTCTACGAGGC Found at i:61252 original size:64 final size:63 Alignment explanation

Indices: 61182--61301 Score: 168 Period size: 64 Copynumber: 1.9 Consensus size: 63 61172 ATTGTTCAAG * * * * 61182 GTGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA 1 GTGTATCAATGCACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA * * * 61246 GTGTATCAATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAATATCGAAT 1 GTGTATCAATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAAT 61302 AGGATTTCTG Statistics Matches: 49, Mismatches: 7, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 63 15 0.31 64 34 0.69 ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25 Consensus pattern (63 bp): GTGTATCAATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCCATCA Found at i:61321 original size:63 final size:64 Alignment explanation

Indices: 61183--61343 Score: 166 Period size: 63 Copynumber: 2.5 Consensus size: 64 61173 TTGTTCAAGG * * * * * 61183 TGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAG 1 TGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCAC * * * * ** 61247 TGTATCAATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAATATCGAATAG-GATTTC 1 TGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAAT-GCCATCAC * * 61310 TGTATCGATGCA-TAGATAGTGCATCGATCCACCC 1 TGTATCGATGCACAAG-TAGTGCATCGATGCACCC 61344 GTCAAGGGAT Statistics Matches: 81, Mismatches: 14, Indels: 5 0.81 0.14 0.05 Matches are distributed among these distances: 62 2 0.02 63 45 0.56 64 34 0.42 ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26 Consensus pattern (64 bp): TGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCAC Found at i:62015 original size:23 final size:23 Alignment explanation

Indices: 61985--62044 Score: 93 Period size: 23 Copynumber: 2.6 Consensus size: 23 61975 CATCTTATAT * 61985 GGCACTTCGGTGTAATTCTACGC 1 GGCACTTCGGTGCAATTCTACGC * * 62008 GGCACTTCGATGCAATTCTACGT 1 GGCACTTCGGTGCAATTCTACGC 62031 GGCACTTCGGTGCA 1 GGCACTTCGGTGCA 62045 TTTATGCGAG Statistics Matches: 33, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 23 33 1.00 ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28 Consensus pattern (23 bp): GGCACTTCGGTGCAATTCTACGC Found at i:66129 original size:12 final size:12 Alignment explanation

Indices: 66112--66167 Score: 57 Period size: 12 Copynumber: 5.0 Consensus size: 12 66102 CTATACGGTA * 66112 TGAACAGTACCG 1 TGAACAATACCG * 66124 TGAACAATA--A 1 TGAACAATACCG * 66134 TGAACAGTA--G 1 TGAACAATACCG 66144 TGAACAATACCG 1 TGAACAATACCG 66156 TGAACAATACCG 1 TGAACAATACCG 66168 AATGTTAAAT Statistics Matches: 37, Mismatches: 5, Indels: 4 0.80 0.11 0.09 Matches are distributed among these distances: 10 16 0.43 12 21 0.57 ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18 Consensus pattern (12 bp): TGAACAATACCG Found at i:66161 original size:22 final size:21 Alignment explanation

Indices: 66111--66152 Score: 68 Period size: 20 Copynumber: 2.0 Consensus size: 21 66101 ACTATACGGT 66111 ATGAACAGTACCGTGAACAATA 1 ATGAACAGTA-CGTGAACAATA 66133 ATGAACAGTA-GTGAACAATA 1 ATGAACAGTACGTGAACAATA 66153 CCGTGAACAA Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 20 10 0.50 22 10 0.50 ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19 Consensus pattern (21 bp): ATGAACAGTACGTGAACAATA Found at i:66234 original size:20 final size:21 Alignment explanation

Indices: 66199--66238 Score: 64 Period size: 20 Copynumber: 2.0 Consensus size: 21 66189 TGCTTCAGGG 66199 GTATCGATACCCCTGCTACAT 1 GTATCGATACCCCTGCTACAT * 66220 GTATCGAT-TCCCTGCTACA 1 GTATCGATACCCCTGCTACA 66239 GTAACTTTCG Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 20 10 0.56 21 8 0.44 ACGTcount: A:0.23, C:0.33, G:0.15, T:0.30 Consensus pattern (21 bp): GTATCGATACCCCTGCTACAT Done.