Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: VEPZ01009171.1 Hibiscus syriacus cultivar Beakdansim tig00112727_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: 53551 ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34 Found at i:7542 original size:42 final size:43 Alignment explanation
Indices: 7490--7573 Score: 116 Period size: 43 Copynumber: 2.0 Consensus size: 43 7480 TTAGCATTTC ** * * 7490 TGAGGAAAAATG-CACTATATGCATTATTATTAGTGGCGTTTG 1 TGAGGAAAAATGACACTATATAAATAATTATTAGTGACGTTTG * 7532 TGAGGGAAAATGACACTATATAAATAATTATTAGTGACGTTT 1 TGAGGAAAAATGACACTATATAAATAATTATTAGTGACGTTT 7574 CTATCAAAAT Statistics Matches: 36, Mismatches: 5, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 42 11 0.31 43 25 0.69 ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35 Consensus pattern (43 bp): TGAGGAAAAATGACACTATATAAATAATTATTAGTGACGTTTG Found at i:11699 original size:3 final size:3 Alignment explanation
Indices: 11686--11745 Score: 95 Period size: 3 Copynumber: 19.7 Consensus size: 3 11676 ATATTCTTTT 11686 TTC TTC TTTC TTC TTC TTC TTC TTTC TTC TTC -TC TTC TTC TTC TTC 1 TTC TTC -TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC 11732 TTC TTC TTC TTC TT 1 TTC TTC TTC TTC TT 11746 TACATTTCAC Statistics Matches: 54, Mismatches: 0, Indels: 6 0.90 0.00 0.10 Matches are distributed among these distances: 2 2 0.04 3 46 0.85 4 6 0.11 ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68 Consensus pattern (3 bp): TTC Found at i:11819 original size:15 final size:16 Alignment explanation
Indices: 11794--11825 Score: 57 Period size: 15 Copynumber: 2.1 Consensus size: 16 11784 TCATTAACTC 11794 TATTCTTTCTTCTTCT 1 TATTCTTTCTTCTTCT 11810 TATT-TTTCTTCTTCT 1 TATTCTTTCTTCTTCT 11825 T 1 T 11826 TTCACATTTC Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 12 0.75 16 4 0.25 ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72 Consensus pattern (16 bp): TATTCTTTCTTCTTCT Found at i:11856 original size:82 final size:84 Alignment explanation
Indices: 11712--11864 Score: 247 Period size: 82 Copynumber: 1.8 Consensus size: 84 11702 TTCTTCTTTC * * * 11712 TTCTTCTCTTCTTCTTCTTCTTCTTCTTCTTCTTTACATTTCACAAATTGTATAATTTTAAAACT 1 TTCTTCTCTTCTTCTTATTCTTCTTCTTCTTCTTCACATTTCACAAATTGCATAATTTTAAAACT 11777 ATGCATATCATTAACTCTA 66 ATGCATATCATTAACTCTA * * 11796 TTCTT-TCTTCTTCTTATTTTTCTTCTTCTT-TTCACATTTCACAAATTGCATAGTTTTAAAACT 1 TTCTTCTCTTCTTCTTATTCTTCTTCTTCTTCTTCACATTTCACAAATTGCATAATTTTAAAACT 11859 ATGCAT 66 ATGCAT 11865 TTACTGCCAA Statistics Matches: 64, Mismatches: 5, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 82 36 0.56 83 23 0.36 84 5 0.08 ACGTcount: A:0.23, C:0.22, G:0.03, T:0.52 Consensus pattern (84 bp): TTCTTCTCTTCTTCTTATTCTTCTTCTTCTTCTTCACATTTCACAAATTGCATAATTTTAAAACT ATGCATATCATTAACTCTA Found at i:13944 original size:17 final size:17 Alignment explanation
Indices: 13918--13955 Score: 51 Period size: 17 Copynumber: 2.3 Consensus size: 17 13908 TTCGAGCTTC * 13918 ATAA-ATAATAATATTT 1 ATAATATAATAATATTA * 13934 ATAATATAATATTATTA 1 ATAATATAATAATATTA 13951 ATAAT 1 ATAAT 13956 CATCACTCGG Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 16 4 0.21 17 15 0.79 ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45 Consensus pattern (17 bp): ATAATATAATAATATTA Found at i:14504 original size:46 final size:43 Alignment explanation
Indices: 14448--14596 Score: 141 Period size: 46 Copynumber: 3.5 Consensus size: 43 14438 TGGATTACTT 14448 CACTACTCTTTCGTGAAGTTCTCATACTTTGCTGAAAACTCTGTTC 1 CACTACTCTTTCGTGAAGTT-TCATACTTTGCTGAAAA-TC-GTTC * *** 14494 CACTACTCTTTCGTGGAG-TTCATA-TTTGCT-TTTA-C-TT- 1 CACTACTCTTTCGTGAAGTTTCATACTTTGCTGAAAATCGTTC 14531 CACTACTCTTAT-GTGAAGATTTCATACTTTGCTGAAAAATCCGTTC 1 CACTACTCTT-TCGTGAAG-TTTCATACTTTGCTG-AAAAT-CGTTC * 14577 CACTACTCTTTCGTGGAGTT 1 CACTACTCTTTCGTGAAGTT 14597 CAAATTTTAT Statistics Matches: 83, Mismatches: 9, Indels: 23 0.72 0.08 0.20 Matches are distributed among these distances: 37 15 0.18 38 3 0.04 39 6 0.07 40 7 0.08 42 2 0.02 43 6 0.07 44 6 0.07 45 6 0.07 46 32 0.39 ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41 Consensus pattern (43 bp): CACTACTCTTTCGTGAAGTTTCATACTTTGCTGAAAATCGTTC Found at i:14547 original size:83 final size:83 Alignment explanation
Indices: 14442--14603 Score: 265 Period size: 83 Copynumber: 2.0 Consensus size: 83 14432 CAAACTTGGA * * 14442 TTACTTCACTACTCTTTCGTGAAG-TTCTCATACTTTGCTGAAAACTCTGTTCCACTACTCTTTC 1 TTACTTCACTACTCTTTCGTGAAGATT-TCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTC * 14506 GTGGAGTTCATATTTGCTT 65 GTGGAGTTCAAATTTGCTT 14525 TTACTTCACTACTCTTAT-GTGAAGATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTC 1 TTACTTCACTACTCTT-TCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTC 14589 GTGGAGTTCAAATTT 65 GTGGAGTTCAAATTT 14604 TATTTTGCTC Statistics Matches: 74, Mismatches: 3, Indels: 4 0.91 0.04 0.05 Matches are distributed among these distances: 83 71 0.96 84 3 0.04 ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42 Consensus pattern (83 bp): TTACTTCACTACTCTTTCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTTCG TGGAGTTCAAATTTGCTT Found at i:15165 original size:22 final size:22 Alignment explanation
Indices: 15140--15207 Score: 127 Period size: 22 Copynumber: 3.1 Consensus size: 22 15130 AAAGCTTTCG 15140 TCTTTGAAAAGAGAATCTATCA 1 TCTTTGAAAAGAGAATCTATCA 15162 TCTTTGAAAAGAGAATCTATCA 1 TCTTTGAAAAGAGAATCTATCA * 15184 TCGTTGAAAAGAGAATCTATCA 1 TCTTTGAAAAGAGAATCTATCA 15206 TC 1 TC 15208 CTTGCAGAAT Statistics Matches: 45, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 22 45 1.00 ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31 Consensus pattern (22 bp): TCTTTGAAAAGAGAATCTATCA Found at i:15410 original size:56 final size:56 Alignment explanation
Indices: 15295--15411 Score: 175 Period size: 57 Copynumber: 2.1 Consensus size: 56 15285 GAAACAGATT * 15295 ACAAGAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCTAATCTTTTA 1 ACAAGAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCTAATCTTTGA * * 15351 ACAAGAATGATTTTATCTTAATTCCTTTCATGTCTCCACATCTAATC-AGAT-TTTGA 1 ACAAGAAGGA-TTTATCCTAATTCCTTTCATGTCTCCACATCTAATCTA-ATCTTTGA 15407 ACAAG 1 ACAAG 15412 GTTTTCCAAA Statistics Matches: 56, Mismatches: 3, Indels: 4 0.89 0.05 0.06 Matches are distributed among these distances: 56 19 0.34 57 37 0.66 ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38 Consensus pattern (56 bp): ACAAGAAGGATTTATCCTAATTCCTTTCATGTCTCCACATCTAATCTAATCTTTGA Found at i:23418 original size:65 final size:65 Alignment explanation
Indices: 23280--23439 Score: 209 Period size: 65 Copynumber: 2.5 Consensus size: 65 23270 TGTACTAAGA * * * * 23280 GTGCATCGATGCATAAAATGCACTCGATG-TTTCAAAATAGCCTGAGTGTATCGATGCATGGCTG 1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTAAGTGCATCGATGCATGGCTG * * 23344 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTAAGTGCATCGATGGATGG-T 1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTAAGTGCATCGATGCATGGCT * 23407 AT 65 -G * 23409 GTGCATCGATGCATGAAATGCATTCGATGTT 1 GTGCATCGATGCATAAAATGCATTCGATGTT 23440 CAATTTATTC Statistics Matches: 85, Mismatches: 8, Indels: 5 0.87 0.08 0.05 Matches are distributed among these distances: 64 28 0.33 65 54 0.64 66 3 0.04 ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30 Consensus pattern (65 bp): GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTAAGTGCATCGATGCATGGCTG Found at i:23478 original size:65 final size:62 Alignment explanation
Indices: 23280--23487 Score: 188 Period size: 65 Copynumber: 3.2 Consensus size: 62 23270 TGTACTAAGA * * * * * 23280 GTGCATCGATGCATAAAATGCACTCGATGTTTCAAAATAGCCTGAGTGTATCGATGCATGGCTG 1 GTGCATCGATGCATAAAATGCATTCGATGTTTC-AATTAACCTG-GTGCATCGATGCATGGTTG * * * * 23344 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACCCTAAGTGCATCGATGGATGGTA 1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAT-TAA-CCT-GGTGCATCGATGCATGGT- 23408 T- 61 TG * * 23409 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATGGTGCATCGATGCATGGATT 1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA-TTA-ACC-TGGTGCATCGATGCATGG-TT 23473 G 62 G * 23474 GTGCATCGGTGCAT 1 GTGCATCGATGCAT 23488 CACTTTGAAA Statistics Matches: 118, Mismatches: 15, Indels: 21 0.77 0.10 0.14 Matches are distributed among these distances: 63 4 0.03 64 48 0.41 65 65 0.55 66 1 0.01 ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31 Consensus pattern (62 bp): GTGCATCGATGCATAAAATGCATTCGATGTTTCAATTAACCTGGTGCATCGATGCATGGTTG Found at i:26119 original size:23 final size:22 Alignment explanation
Indices: 26089--26170 Score: 94 Period size: 23 Copynumber: 3.6 Consensus size: 22 26079 GCATGGCCTT 26089 GTGCATCGATGCACATTCAAGG 1 GTGCATCGATGCACATTCAAGG * * * 26111 CGTGCATCGGTGCACCTTC-ATG 1 -GTGCATCGATGCACATTCAAGG * 26133 GTGTATCGATGCACATTCAAAGG 1 GTGCATCGATGCACATTC-AAGG 26156 GATGCATCGATGCAC 1 G-TGCATCGATGCAC 26171 TGTTAAGTGT Statistics Matches: 48, Mismatches: 8, Indels: 5 0.79 0.13 0.08 Matches are distributed among these distances: 21 15 0.31 22 2 0.04 23 19 0.40 24 12 0.25 ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24 Consensus pattern (22 bp): GTGCATCGATGCACATTCAAGG Found at i:26181 original size:44 final size:44 Alignment explanation
Indices: 26093--26186 Score: 113 Period size: 44 Copynumber: 2.1 Consensus size: 44 26083 GGCCTTGTGC * * 26093 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGT 1 ATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATAGTGT * 26137 ATCGATGCACATTCAAAGG-GATGCATCGATGCA-CTGTTA-AGTGT 1 ATCGATGCACATTC-AAGGCG-TGCATCGATGCACCT-TCATAGTGT 26181 ATCGAT 1 ATCGAT 26187 ACACTAAGCA Statistics Matches: 44, Mismatches: 3, Indels: 6 0.83 0.06 0.11 Matches are distributed among these distances: 44 27 0.61 45 17 0.39 ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28 Consensus pattern (44 bp): ATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATAGTGT Found at i:32480 original size:23 final size:22 Alignment explanation
Indices: 32409--32490 Score: 94 Period size: 23 Copynumber: 3.6 Consensus size: 22 32399 ACACTTAACA 32409 GTGCATCGATGCATCCCTTTGAAT 1 GTGCATCGATGCA-CCC-TTGAAT * * * 32433 GTGCATCGATACA-CCATGAAG 1 GTGCATCGATGCACCCTTGAAT * 32454 GTGCACCGATGCACGCCTTGAAT 1 GTGCATCGATGCAC-CCTTGAAT 32477 GTGCATCGATGCAC 1 GTGCATCGATGCAC 32491 AAGGCCATGC Statistics Matches: 48, Mismatches: 8, Indels: 5 0.79 0.13 0.08 Matches are distributed among these distances: 21 15 0.31 22 2 0.04 23 19 0.40 24 12 0.25 ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24 Consensus pattern (22 bp): GTGCATCGATGCACCCTTGAAT Found at i:37592 original size:27 final size:27 Alignment explanation
Indices: 37561--37615 Score: 110 Period size: 27 Copynumber: 2.0 Consensus size: 27 37551 TTATGGCCTT 37561 ATTCTATCTATGTATAAAATATGATAA 1 ATTCTATCTATGTATAAAATATGATAA 37588 ATTCTATCTATGTATAAAATATGATAA 1 ATTCTATCTATGTATAAAATATGATAA 37615 A 1 A 37616 GGCCAATATT 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:0.45, C:0.07, G:0.07, T:0.40 Consensus pattern (27 bp): ATTCTATCTATGTATAAAATATGATAA Found at i:41864 original size:21 final size:20 Alignment explanation
Indices: 41835--41873 Score: 69 Period size: 21 Copynumber: 1.9 Consensus size: 20 41825 ACGCCTACGA 41835 AAAGATCGCTTGGATTTAAG 1 AAAGATCGCTTGGATTTAAG 41855 AAAGAGTCGCTTGGATTTA 1 AAAGA-TCGCTTGGATTTA 41874 TCCATGATTT Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 20 5 0.28 21 13 0.72 ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31 Consensus pattern (20 bp): AAAGATCGCTTGGATTTAAG Found at i:41908 original size:18 final size:18 Alignment explanation
Indices: 41885--41920 Score: 72 Period size: 18 Copynumber: 2.0 Consensus size: 18 41875 CCATGATTTC 41885 TTTATTCCTTATTTCTAA 1 TTTATTCCTTATTTCTAA 41903 TTTATTCCTTATTTCTAA 1 TTTATTCCTTATTTCTAA 41921 AAAGAATCCT 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:0.22, C:0.17, G:0.00, T:0.61 Consensus pattern (18 bp): TTTATTCCTTATTTCTAA Found at i:43599 original size:12 final size:12 Alignment explanation
Indices: 43584--43609 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 43574 TTTACAGTCT 43584 TATTTATTATGA 1 TATTTATTATGA 43596 TATTTATTATGA 1 TATTTATTATGA 43608 TA 1 TA 43610 AGAAAGCGCT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58 Consensus pattern (12 bp): TATTTATTATGA Found at i:43790 original size:14 final size:14 Alignment explanation
Indices: 43771--43824 Score: 53 Period size: 14 Copynumber: 4.1 Consensus size: 14 43761 TCTCCTTGGA * 43771 TTAAATTATTAAAT 1 TTAAATTATAAAAT 43785 TTAAATTATAAAAT 1 TTAAATTATAAAAT 43799 TT---TTATAAAA- 1 TTAAATTATAAAAT * 43809 TTAAAGATATAAAAT 1 TTAAA-TTATAAAAT 43824 T 1 T 43825 AAAGAATTAA Statistics Matches: 33, Mismatches: 2, Indels: 9 0.75 0.05 0.20 Matches are distributed among these distances: 10 2 0.06 11 8 0.24 14 22 0.67 15 1 0.03 ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44 Consensus pattern (14 bp): TTAAATTATAAAAT Found at i:43835 original size:14 final size:14 Alignment explanation
Indices: 43802--43829 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 43792 ATAAAATTTT 43802 TATAAAATTAAAGA 1 TATAAAATTAAAGA 43816 TATAAAATTAAAGA 1 TATAAAATTAAAGA 43830 ATTAAAGAAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29 Consensus pattern (14 bp): TATAAAATTAAAGA Found at i:46274 original size:14 final size:14 Alignment explanation
Indices: 46255--46283 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 46245 ATATATTTAA 46255 TATTTATATTTCTT 1 TATTTATATTTCTT 46269 TATTTATATTTCTT 1 TATTTATATTTCTT 46283 T 1 T 46284 TTTTTGGTTG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72 Consensus pattern (14 bp): TATTTATATTTCTT Found at i:46433 original size:25 final size:25 Alignment explanation
Indices: 46399--46449 Score: 102 Period size: 25 Copynumber: 2.0 Consensus size: 25 46389 TAAGTAAATC 46399 AAAAAAAAAATATCTATTATCTATT 1 AAAAAAAAAATATCTATTATCTATT 46424 AAAAAAAAAATATCTATTATCTATT 1 AAAAAAAAAATATCTATTATCTATT 46449 A 1 A 46450 TAAGTAAATC Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35 Consensus pattern (25 bp): AAAAAAAAAATATCTATTATCTATT Found at i:49514 original size:23 final size:23 Alignment explanation
Indices: 49487--49533 Score: 94 Period size: 23 Copynumber: 2.0 Consensus size: 23 49477 TTCTGAAGAA 49487 ACTTCAGTTTAGTTCTGCTATAG 1 ACTTCAGTTTAGTTCTGCTATAG 49510 ACTTCAGTTTAGTTCTGCTATAG 1 ACTTCAGTTTAGTTCTGCTATAG 49533 A 1 A 49534 AAAAAGGATT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 24 1.00 ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43 Consensus pattern (23 bp): ACTTCAGTTTAGTTCTGCTATAG Found at i:50771 original size:17 final size:17 Alignment explanation
Indices: 50749--50782 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 50739 TTCGTATATT 50749 ATACTAAATATATCTAA 1 ATACTAAATATATCTAA * * 50766 ATACTAAGTATTTCTAA 1 ATACTAAATATATCTAA 50783 GCGAGTCTAG Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38 Consensus pattern (17 bp): ATACTAAATATATCTAA Found at i:53490 original size:14 final size:14 Alignment explanation
Indices: 53471--53499 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 53461 AGTCTTTTAT 53471 TTTTGTATTTAAGA 1 TTTTGTATTTAAGA 53485 TTTTGTATTTAAGA 1 TTTTGTATTTAAGA 53499 T 1 T 53500 ATATCTAGAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59 Consensus pattern (14 bp): TTTTGTATTTAAGA Done.