Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011725.1 Kokia drynarioides strain JFW-HI SEQ_126719, 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: 19970
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30

Warning! 27 characters in sequence are not A, C, G, or T


Found at i:3481 original size:29 final size:29

Alignment explanation

Indices: 3434--3638 Score: 277 Period size: 29 Copynumber: 6.9 Consensus size: 29 3424 GAGGTCCACA 3434 AACTATCCAAAAATTCCATTTTCACCCCCG 1 AACT-TCCAAAAATTCCATTTTCACCCCCG * *** 3464 AACTTCCAAAAATTCCATTTTTGACCCAAA 1 AACTTCCAAAAATTCCA-TTTTCACCCCCG * 3494 AACTTCCAAAAATTCCATTTT-ACCCCCTA 1 AACTTCCAAAAATTCCATTTTCACCCCC-G 3523 AACTTCCAAAAATTCCATTTTCACCCCCG 1 AACTTCCAAAAATTCCATTTTCACCCCCG * * * 3552 AACTTCCAAGAATTCCACTTTCAACCCCG 1 AACTTCCAAAAATTCCATTTTCACCCCCG 3581 AAACTTCCAAAAATTCCATTTTCACCCCCG 1 -AACTTCCAAAAATTCCATTTTCACCCCCG * 3611 AACTTCCAAAAATTCCACTTTTAACCCC 1 AACTTCCAAAAATTCCA-TTTTCACCCC 3639 GAAACTTTAA Statistics Matches: 156, Mismatches: 14, Indels: 10 0.87 0.08 0.06 Matches are distributed among these distances: 28 4 0.03 29 82 0.53 30 70 0.45 ACGTcount: A:0.34, C:0.35, G:0.03, T:0.28 Consensus pattern (29 bp): AACTTCCAAAAATTCCATTTTCACCCCCG Found at i:3531 original size:59 final size:59 Alignment explanation

Indices: 3432--3645 Score: 290 Period size: 59 Copynumber: 3.6 Consensus size: 59 3422 TGGAGGTCCA * * * 3432 CAAACTATCCAAAAATTCCA-TTTTCACCCCCG-AACTTCCAAAAATTCCATTTTTGACCCA 1 CAAACT-TCCAAAAATTCCACTTTT-AACCCCGAAACTTCCAAAAATTCCA-TTTTCACCCC * * * 3492 AAAACTTCCAAAAATTCCA-TTTTACCCCCTAAACTTCCAAAAATTCCATTTTCACCCC 1 CAAACTTCCAAAAATTCCACTTTTAACCCCGAAACTTCCAAAAATTCCATTTTCACCCC * * * 3550 CGAACTTCCAAGAATTCCACTTTCAACCCCGAAACTTCCAAAAATTCCATTTTCACCCC 1 CAAACTTCCAAAAATTCCACTTTTAACCCCGAAACTTCCAAAAATTCCATTTTCACCCC * 3609 CGAACTTCCAAAAATTCCACTTTTAACCCCGAAACTT 1 CAAACTTCCAAAAATTCCACTTTTAACCCCGAAACTT 3646 TAAAATCGAG Statistics Matches: 140, Mismatches: 12, Indels: 5 0.89 0.08 0.03 Matches are distributed among these distances: 58 30 0.21 59 105 0.75 60 5 0.04 ACGTcount: A:0.35, C:0.35, G:0.03, T:0.28 Consensus pattern (59 bp): CAAACTTCCAAAAATTCCACTTTTAACCCCGAAACTTCCAAAAATTCCATTTTCACCCC Found at i:3588 original size:88 final size:88 Alignment explanation

Indices: 3432--3638 Score: 308 Period size: 88 Copynumber: 2.3 Consensus size: 88 3422 TGGAGGTCCA * ** 3432 CAAACTATCCAAAAATTCCATTTTCACCCCCGAACTTCCAAAAATTCCATTTTTGACCCAAAAAC 1 CAAACT-TCCAAAAATTCCATTTTCACCCCCGAACTTCCAAAAATTCCACTTTCAACCCAAAAAC 3497 TTCCAAAAATTCCATTTT-ACCCC 65 TTCCAAAAATTCCATTTTCACCCC * ** 3520 CTAAACTTCCAAAAATTCCATTTTCACCCCCGAACTTCCAAGAATTCCACTTTCAACCCCGAAAC 1 C-AAACTTCCAAAAATTCCATTTTCACCCCCGAACTTCCAAAAATTCCACTTTCAACCCAAAAAC 3585 TTCCAAAAATTCCATTTTCACCCC 65 TTCCAAAAATTCCATTTTCACCCC * * 3609 CGAACTTCCAAAAATTCCACTTTTAACCCC 1 CAAACTTCCAAAAATTCCA-TTTTCACCCC 3639 GAAACTTTAA Statistics Matches: 108, Mismatches: 8, Indels: 5 0.89 0.07 0.04 Matches are distributed among these distances: 88 88 0.81 89 20 0.19 ACGTcount: A:0.34, C:0.35, G:0.03, T:0.28 Consensus pattern (88 bp): CAAACTTCCAAAAATTCCATTTTCACCCCCGAACTTCCAAAAATTCCACTTTCAACCCAAAAACT TCCAAAAATTCCATTTTCACCCC Found at i:7628 original size:22 final size:21 Alignment explanation

Indices: 7587--7629 Score: 52 Period size: 22 Copynumber: 2.0 Consensus size: 21 7577 CCTAGACAAA * 7587 TAGAGGAAAAATACAGGCGAT 1 TAGAGGAAAAATACACGCGAT 7608 TAGAGGAGAAAAT-CGACGCGAT 1 TAGAGGA-AAAATAC-ACGCGAT 7630 GCAAGGAATT Statistics Matches: 19, Mismatches: 1, Indels: 3 0.83 0.04 0.13 Matches are distributed among these distances: 21 8 0.42 22 11 0.58 ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14 Consensus pattern (21 bp): TAGAGGAAAAATACACGCGAT Found at i:11751 original size:122 final size:123 Alignment explanation

Indices: 11529--11806 Score: 416 Period size: 122 Copynumber: 2.3 Consensus size: 123 11519 ATGCGGTCAT * * * * * * * * 11529 CTTCTTGATGAGATACCGATAAGAAGACCGAATCAATGAAACGAGGCTCGATGTGAGCAAATCTT 1 CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACGAGGCTCAAAGCGAGCAAATCTT 11594 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATAAT-AAAATGTTAG 66 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATAATAAAAATGTTAG * * 11651 CTTCCTGATGAGATACTGAGGAGTAGACCAAATCAATGAAAC-ATGGTTCAAAGCGAGCAAATCT 1 CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACGA-GGCTCAAAGCGAGCAAATCT * * 11715 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAAATGTTAG 65 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATAATAAAAATGTTAG * 11774 CTTCCTGATGAGATACTGAGAAGTGGACCAAAT 1 CTTCCTGATGAGATACTGAGAAGTAGACCAAAT 11807 TCGTCTTCCT Statistics Matches: 140, Mismatches: 14, Indels: 3 0.89 0.09 0.02 Matches are distributed among these distances: 121 1 0.01 122 98 0.70 123 41 0.29 ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23 Consensus pattern (123 bp): CTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACGAGGCTCAAAGCGAGCAAATCTT CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATAATAAAAATGTTAG Found at i:11842 original size:13 final size:13 Alignment explanation

Indices: 11824--11850 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 11814 CCTGATGAGG 11824 TACAGTAGCAAAT 1 TACAGTAGCAAAT 11837 TACAGTAGCAAAT 1 TACAGTAGCAAAT 11850 T 1 T 11851 TTGTCTTTTT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26 Consensus pattern (13 bp): TACAGTAGCAAAT Found at i:12128 original size:17 final size:17 Alignment explanation

Indices: 12089--12140 Score: 61 Period size: 17 Copynumber: 3.1 Consensus size: 17 12079 GCCCAACAAG * 12089 ATTTAAATTCATTTTAA 1 ATTTAAATTTATTTTAA * 12106 AATTAAATTTATTTTAA 1 ATTTAAATTTATTTTAA * * 12123 GTTTAAATCTA-TTTAA 1 ATTTAAATTTATTTTAA 12139 AT 1 AT 12141 CAAGTCCAAT Statistics Matches: 29, Mismatches: 6, Indels: 1 0.81 0.17 0.03 Matches are distributed among these distances: 16 6 0.21 17 23 0.79 ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52 Consensus pattern (17 bp): ATTTAAATTTATTTTAA Found at i:12803 original size:9 final size:9 Alignment explanation

Indices: 12781--12948 Score: 65 Period size: 9 Copynumber: 17.8 Consensus size: 9 12771 TCAAAACGTT 12781 TTAATAACTA 1 TTAATAA-TA 12791 TTAATAATA 1 TTAATAATA * 12800 TTAATAATTGTT 1 TTAATAA---TA 12812 TTAATAATAA 1 TTAATAAT-A 12822 TAATAATAATA 1 T--TAATAATA * 12833 TTATTAATA 1 TTAATAATA * * 12842 TTAATGACA 1 TTAATAATA 12851 TTAATAATAA 1 TTAATAAT-A * * * 12861 TAAACAATTTT 1 TTAATAA--TA 12872 TTAATAATCA 1 TTAATAAT-A 12882 TTAATAATA 1 TTAATAATA * * 12891 AT-A-AATG 1 TTAATAATA * 12898 TT-TTAATGA 1 TTAATAAT-A * 12907 -TGATAATA 1 TTAATAATA * 12915 ATAATAATA 1 TTAATAATA * 12924 ATAATAATA 1 TTAATAATA * * 12933 TTAATTATT 1 TTAATAATA 12942 TTAATAA 1 TTAATAA 12949 AGAAAAAAAG Statistics Matches: 119, Mismatches: 25, Indels: 29 0.69 0.14 0.17 Matches are distributed among these distances: 7 4 0.03 8 6 0.05 9 64 0.54 10 22 0.18 11 7 0.06 12 16 0.13 ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43 Consensus pattern (9 bp): TTAATAATA Found at i:12817 original size:21 final size:21 Alignment explanation

Indices: 12782--12948 Score: 94 Period size: 21 Copynumber: 8.1 Consensus size: 21 12772 CAAAACGTTT 12782 TAATAACTATTAATAATATTAA 1 TAATAA-TATTAATAATATTAA ** * * 12804 TAATTGTTTTAATAATAATAA 1 TAATAATATTAATAATATTAA * 12825 TAATAATATTATTAATATTAA 1 TAATAATATTAATAATATTAA * * * * 12846 TGACATTAATAATAATA--AA 1 TAATAATATTAATAATATTAA * * * 12865 CAAT-TTTTTAATAATCATTAA 1 TAATAATATTAATAAT-ATTAA * * 12886 TAATAATA--AAT-GTTTTAA 1 TAATAATATTAATAATATTAA * * * * 12904 TGATGATAATAATAATAATAA 1 TAATAATATTAATAATATTAA * * 12925 TAATAATATTAATTATTTTAA 1 TAATAATATTAATAATATTAA 12946 TAA 1 TAA 12949 AGAAAAAAAG Statistics Matches: 103, Mismatches: 35, Indels: 15 0.67 0.23 0.10 Matches are distributed among these distances: 18 19 0.18 19 5 0.05 20 6 0.06 21 68 0.66 22 5 0.05 ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43 Consensus pattern (21 bp): TAATAATATTAATAATATTAA Found at i:12819 original size:3 final size:3 Alignment explanation

Indices: 12813--12937 Score: 56 Period size: 3 Copynumber: 41.3 Consensus size: 3 12803 ATAATTGTTT * * * * * * 12813 TAA TAA TAA TAA TAA TAA TAT TAT TAA TAT TAA TGA CAT TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA * * ** * * ** * 12861 TAAA CAA T-T TTT TAA TAA TCAT TAA TAA TAA TAA -ATG TTT TAA TGA 1 T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA * * 12907 TGA TAA TAA TAA TAA TAA TAA TAA TAT TAA T 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T 12938 TATTTTAATA Statistics Matches: 91, Mismatches: 26, Indels: 10 0.72 0.20 0.08 Matches are distributed among these distances: 2 2 0.02 3 85 0.93 4 4 0.04 ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41 Consensus pattern (3 bp): TAA Found at i:13929 original size:29 final size:29 Alignment explanation

Indices: 13879--14283 Score: 344 Period size: 29 Copynumber: 14.0 Consensus size: 29 13869 TGGAGGTCCA * 13879 CAAACTATCAAAAAATTCCATTTTTACCCC 1 CAAACT-TCCAAAAATTCCATTTTTACCCC * * 13909 CGAACTTTCAAAAATTCCATTTTTGACCCC 1 CAAACTTCCAAAAATTCCATTTTT-ACCCC * * 13939 AAAACTTCCAAAAATTCAATTTTTACCCC 1 CAAACTTCCAAAAATTCCATTTTTACCCC * 13968 TAAACTTCCAAAAATTCCATTTTTAACCCC 1 CAAACTTCCAAAAATTCCATTTTT-ACCCC * * 13998 AAAACTTCCAAAAATTCCATTTTCACCCC 1 CAAACTTCCAAAAATTCCATTTTTACCCC * ** * 14027 CAAACTTCCAAGAATTCCACTTTCGACCTC 1 CAAACTTCCAAAAATTCCA-TTTTTACCCC * * * * 14057 GAAACTTTCAAAAATTCCATTTTCA-CCT 1 CAAACTTCCAAAAATTCCATTTTTACCCC * * 14085 CGAACTTCCAAAAATTCCATTTTTGACCTC 1 CAAACTTCCAAAAATTCCATTTTT-ACCCC * ** 14115 GAAACTTCCAAAAATTCCATTTTTTTCCC 1 CAAACTTCCAAAAATTCCATTTTTACCCC * 14144 CAAACTTCCAAAAATTCCCTTTTT----- 1 CAAACTTCCAAAAATTCCATTTTTACCCC * 14168 --GACTT-CAAAAATTCCATTTTTGA-CCC 1 CAAACTTCCAAAAATTCCATTTTT-ACCCC * * * * 14194 TAAAATTCCAAAAACTCCATTTTTGACCCT 1 CAAACTTCCAAAAATTCCATTTTT-ACCCC * * 14224 AAAACTTTCAAAAAAATTCCATTTTTACCCC 1 CAAAC-TTC-CAAAAATTCCATTTTTACCCC * * * ** 14255 TAAACCTCTAAAGTTTCCATTTTTGACCC 1 CAAACTTCCAAAAATTCCATTTTT-ACCC 14284 TAAAACTTTT Statistics Matches: 306, Mismatches: 52, Indels: 34 0.78 0.13 0.09 Matches are distributed among these distances: 21 15 0.05 22 4 0.01 28 24 0.08 29 124 0.41 30 114 0.37 31 11 0.04 32 14 0.05 ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33 Consensus pattern (29 bp): CAAACTTCCAAAAATTCCATTTTTACCCC Found at i:13974 original size:59 final size:59 Alignment explanation

Indices: 13880--14309 Score: 425 Period size: 59 Copynumber: 7.4 Consensus size: 59 13870 GGAGGTCCAC * ** * 13880 AAACTATCAAAAAATTCCATTTTTACCCCCGAACTTTCAAAAATTCCATTTTTGACCCCA 1 AAACT-TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA * * 13940 AAACTTCCAAAAATTCAATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCCA 1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA * * * * * * * 13999 AAACTTCCAAAAATTCCATTTTCACCCCCAAACTTCCAAGAATTCCACTTTCGACCTCG 1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA * * * * * * 14058 AAACTTTCAAAAATTCCATTTTCACCTC-GAACTTCCAAAAATTCCATTTTTGACCTCG 1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA * * 14116 AAACTTCCAAAAATTCCATTTTTTTCCCC-AAACTTCCAAAAATTCCCTTTTTG------ 1 AAACTTCCAAAAATTCCA-TTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA * * * 14169 --ACTT-CAAAAATTCCATTTTTGA-CCCTAAAATTCCAAAAACTCCATTTTTGACCCTA 1 AAACTTCCAAAAATTCCATTTTT-ACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA * * * ** * 14225 AAACTTTCAAAAAAATTCCATTTTTACCCCTAAACCTCTAAAGTTTCCATTTTTGACCCTA 1 AAAC-TTC-CAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA *** 14286 AAACTTTTGAAAATTACCATTTTT 1 AAACTTCCAAAAATT-CCATTTTT 14310 CCCTTGAATG Statistics Matches: 313, Mismatches: 41, Indels: 32 0.81 0.11 0.08 Matches are distributed among these distances: 49 8 0.03 50 32 0.10 51 4 0.01 58 45 0.14 59 161 0.51 60 16 0.05 61 47 0.15 ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34 Consensus pattern (59 bp): AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA Found at i:14177 original size:21 final size:22 Alignment explanation

Indices: 14147--14203 Score: 75 Period size: 21 Copynumber: 2.7 Consensus size: 22 14137 TTTTCCCCAA * 14147 ACTTCCAAAAATTCCCTTTTTG 1 ACTTCCAAAAATTCCATTTTTG 14169 ACTT-CAAAAATTCCATTTTTG 1 ACTTCCAAAAATTCCATTTTTG * 14190 AC--CCTAAAATTCCA 1 ACTTCCAAAAATTCCA 14204 AAAACTCCAT Statistics Matches: 32, Mismatches: 2, Indels: 4 0.84 0.05 0.11 Matches are distributed among these distances: 20 10 0.31 21 18 0.56 22 4 0.12 ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37 Consensus pattern (22 bp): ACTTCCAAAAATTCCATTTTTG Found at i:14177 original size:50 final size:51 Alignment explanation

Indices: 14118--14220 Score: 145 Period size: 50 Copynumber: 2.0 Consensus size: 51 14108 TGACCTCGAA ** * * * 14118 ACTTCCAAAAATTCCATTTTTTTCCCCAAACTTCCAAAAATTCCCTTTTTG 1 ACTTCCAAAAATTCCATTTTTGACCCCAAAATTCCAAAAACTCCATTTTTG * 14169 ACTT-CAAAAATTCCATTTTTGACCCTAAAATTCCAAAAACTCCATTTTTG 1 ACTTCCAAAAATTCCATTTTTGACCCCAAAATTCCAAAAACTCCATTTTTG 14219 AC 1 AC 14221 CCTAAAACTT Statistics Matches: 46, Mismatches: 6, Indels: 1 0.87 0.11 0.02 Matches are distributed among these distances: 50 42 0.91 51 4 0.09 ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37 Consensus pattern (51 bp): ACTTCCAAAAATTCCATTTTTGACCCCAAAATTCCAAAAACTCCATTTTTG Found at i:14244 original size:61 final size:61 Alignment explanation

Indices: 14174--14292 Score: 168 Period size: 61 Copynumber: 2.0 Consensus size: 61 14164 TTTTGACTTC * 14174 AAAAATTCCATTTTTGA-CCCTAAAATTCCAAAAACTCCATTTTTGACCCTAAAACTTTCAA 1 AAAAATTCCATTTTT-ACCCCTAAAACTCCAAAAACTCCATTTTTGACCCTAAAACTTTCAA * * *** 14235 AAAAATTCCATTTTTACCCCTAAACCTCTAAAGTTTCCATTTTTGACCCTAAAACTTT 1 AAAAATTCCATTTTTACCCCTAAAACTCCAAAAACTCCATTTTTGACCCTAAAACTTT 14293 TGAAAATTAC Statistics Matches: 51, Mismatches: 6, Indels: 2 0.86 0.10 0.03 Matches are distributed among these distances: 60 1 0.02 61 50 0.98 ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35 Consensus pattern (61 bp): AAAAATTCCATTTTTACCCCTAAAACTCCAAAAACTCCATTTTTGACCCTAAAACTTTCAA Found at i:16136 original size:15 final size:15 Alignment explanation

Indices: 16116--16147 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 16106 TAATTAATTT 16116 TTTAAAATTAAAAAA 1 TTTAAAATTAAAAAA * 16131 TTTAAAATTATAAAA 1 TTTAAAATTAAAAAA 16146 TT 1 TT 16148 ATTTTTAAAA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41 Consensus pattern (15 bp): TTTAAAATTAAAAAA Found at i:16157 original size:27 final size:27 Alignment explanation

Indices: 16127--16193 Score: 64 Period size: 27 Copynumber: 2.4 Consensus size: 27 16117 TTAAAATTAA * 16127 AAAATTTAAAATTATAAAAT-TATTTTT 1 AAAATTTAAAATTAAAAAATATA-TTTT * * * 16154 AAAAATAAAAAATAAAAAATATATTTT 1 AAAATTTAAAATTAAAAAATATATTTT * 16181 AATATTTTAAAAT 1 AA-AATTTAAAAT 16194 GGAATTGAAA Statistics Matches: 30, Mismatches: 8, Indels: 3 0.73 0.20 0.07 Matches are distributed among these distances: 27 22 0.73 28 8 0.27 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (27 bp): AAAATTTAAAATTAAAAAATATATTTT Done.