genome.fa.s8488.2.7.7.80.10.50.1000.41.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12876159

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   

This is table  41  of  54  ( 6450 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9824698--9824722	13	1.9	13	100	0	50	36	0	0	64	0.94
9827220--9827261	19	2.1	21	86	8	61	54	0	2	42	1.13
9828874--9828926	19	2.8	18	83	13	63	32	1	1	64	1.15
9829890--9829948	3	19.7	3	76	13	59	32	1	0	66	1.02
9829887--9829943	26	2.2	26	84	9	71	33	1	0	64	1.04
9830278--9830320	18	2.4	18	100	0	86	25	39	25	9	1.85
9831618--9831666	25	2.0	25	88	4	73	14	6	6	73	1.22
9832146--9832891	131	5.7	131	86	3	1018	32	11	16	39	1.84
9832121--9832891	262	2.9	262	88	1	1143	32	11	15	39	1.84
9832103--9832880	393	2.0	393	90	1	1238	33	11	15	39	1.83
9840610--9840639	14	2.1	14	100	0	60	20	30	26	23	1.98
9841620--9841685	29	2.3	29	89	5	98	40	9	3	46	1.51
9850355--9850642	125	2.3	125	91	0	459	32	15	26	25	1.96
9850355--9850677	126	2.6	125	87	1	477	33	15	27	24	1.95
9851475--9853374	216	8.9	216	89	3	2710	33	14	19	32	1.92
9852241--9852355	42	2.8	42	76	4	117	26	20	20	33	1.97
9852672--9852778	42	2.6	40	79	7	115	27	22	20	29	1.98
9852409--9853374	205	4.6	206	89	4	1353	32	15	19	32	1.94
9853079--9853196	42	2.8	43	72	7	109	27	22	19	30	1.98
9858743--9858797	18	2.8	19	81	8	58	78	1	10	9	1.05
9858743--9858807	31	2.1	32	85	8	89	78	1	9	10	1.03
9860160--9860354	89	2.1	92	84	3	252	26	21	20	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9860251--9860535	133	2.1	133	87	3	401	29	24	19	27	1.98
9860750--9860840	3	31.7	3	75	16	70	28	1	0	70	0.95
9860750--9860840	32	2.8	32	80	6	105	28	1	0	70	0.95
9860747--9860841	35	2.7	35	79	9	104	28	1	0	70	0.94
9862175--9862230	26	2.2	26	96	0	103	42	7	17	32	1.77
9863365--9863400	2	18.0	2	100	0	72	50	0	0	50	1.00
9865923--9865963	2	20.5	2	100	0	82	51	0	0	48	1.00
9877208--9877265	28	2.2	25	84	9	71	27	5	12	55	1.58
9883632--9883749	32	3.8	32	85	6	145	31	21	20	27	1.98
9887348--9887395	19	2.5	20	82	3	62	52	6	12	29	1.63
9899899--9899970	20	3.6	20	75	0	81	31	16	16	34	1.92
9899887--9899975	40	2.2	40	87	0	133	30	14	14	40	1.86
9899903--9899992	40	2.2	40	88	0	126	32	16	13	37	1.88
9902168--9902240	7	11.1	7	71	19	59	45	12	1	41	1.50
9905430--9905487	23	2.5	23	94	0	98	36	18	27	17	1.94
9906284--9906339	29	1.9	29	96	0	103	53	0	5	41	1.24
9909526--9909578	26	2.0	27	92	3	90	24	7	18	49	1.74
9912532--9912681	2	78.5	2	76	16	131	49	0	2	48	1.17
9912489--9912681	108	1.8	106	83	6	255	49	1	3	46	1.24
9913899--9913924	3	8.7	3	100	0	52	30	0	0	69	0.89
9927213--9927251	21	1.9	21	94	5	71	25	12	23	38	1.90
9932692--9932738	2	24.0	2	95	4	87	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9937353--9937382	2	15.0	2	100	0	60	50	0	0	50	1.00
9938429--9938503	2	37.5	2	100	0	150	49	0	0	50	1.00
9940265--9940317	21	2.5	21	84	0	70	32	28	18	20	1.97
9940325--9940599	21	13.3	21	72	11	174	21	20	23	35	1.96
9940332--9940590	42	6.3	40	85	3	329	20	19	23	36	1.95
9940332--9940590	82	3.1	80	87	5	347	20	19	23	36	1.95
9940330--9940590	124	2.1	123	88	2	380	20	19	23	36	1.95
9941204--9941234	6	5.2	6	92	0	53	0	19	48	32	1.49
9941324--9941467	21	6.9	20	70	13	96	35	21	20	22	1.96
9941327--9941461	42	3.3	42	93	2	220	36	22	19	22	1.95
9950105--9950136	16	2.0	16	93	0	55	34	18	9	37	1.83
9950968--9952006	522	2.0	518	91	1	1677	41	18	20	19	1.90
9952536--9952570	18	1.9	18	94	0	61	37	2	0	60	1.12
9969146--9969171	13	2.0	13	100	0	52	61	7	0	30	1.24
9970078--9970163	21	4.1	20	69	16	57	29	25	16	29	1.97
9978230--9978348	24	5.0	24	87	4	168	25	14	19	41	1.89
9978464--9978558	43	2.2	43	90	0	154	18	9	34	36	1.84
9980688--9980746	18	3.6	17	71	21	54	20	49	16	13	1.80
9980724--9980754	13	2.4	13	100	0	62	16	48	16	19	1.81
9983276--9983338	12	5.2	12	72	27	62	25	15	22	36	1.94
9983260--9983402	24	6.0	24	92	3	218	24	16	20	39	1.92
9983518--9983612	43	2.2	43	94	0	163	17	9	36	35	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9985740--9985798	18	3.6	17	73	21	63	20	49	18	11	1.79
9985744--9985820	13	5.3	13	73	18	55	18	44	19	18	1.87
9985780--9985840	8	7.5	8	77	17	56	14	37	24	22	1.92
9988292--9988370	24	3.3	24	87	0	113	24	15	22	37	1.92
9988271--9988331	19	3.2	19	66	25	56	21	14	22	40	1.90
9988485--9988580	43	2.2	43	92	0	156	15	10	34	39	1.82
9989391--9989424	2	17.0	2	100	0	68	50	0	0	50	1.00
9989927--9990096	91	1.9	91	97	0	322	34	7	12	45	1.70
9989950--9990091	44	3.2	44	63	23	105	33	6	13	46	1.68
9990915--9990998	2	43.5	2	81	11	104	48	1	0	50	1.08
9991180--9991209	2	15.0	2	100	0	60	50	0	0	50	1.00
9991372--9991428	9	6.3	9	80	13	64	57	0	0	42	0.98
9991372--9991428	18	3.2	20	79	20	72	57	0	0	42	0.98
9991384--9991428	9	5.0	9	84	10	65	57	0	0	42	0.98
9991372--9991428	27	2.1	27	100	0	114	57	0	0	42	0.98
9994601--9994640	21	1.9	21	84	0	53	37	5	17	40	1.72
9995843--9995875	17	1.9	17	88	11	50	18	27	9	45	1.79
10000430--10000729	111	2.7	111	95	0	537	37	6	10	45	1.65
10002588--10002652	3	21.7	3	80	0	67	33	23	35	7	1.83
10004387--10004501	3	38.0	3	81	6	126	38	0	2	59	1.12
10004389--10004506	14	8.1	14	77	12	98	38	0	2	58	1.12
10004402--10004501	38	2.7	37	86	11	134	37	0	3	60	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10004837--10005005	81	2.1	80	95	2	311	22	33	24	19	1.97
10011321--10011346	2	13.0	2	100	0	52	50	0	0	50	1.00
10011647--10011908	131	2.0	131	98	1	508	43	10	25	20	1.83
10013934--10014195	83	3.2	82	91	3	402	29	13	20	35	1.91
10017141--10017850	76	9.4	76	96	1	1309	21	21	21	34	1.96
10017979--10018095	3	39.3	3	83	8	150	35	0	2	61	1.10
10018035--10018108	18	4.1	18	86	8	53	39	0	0	60	0.97
10017991--10018108	28	4.2	27	71	16	78	38	0	2	59	1.11
10022448--10022473	13	2.0	13	100	0	52	46	15	15	23	1.83
10022898--10023006	30	3.7	29	79	10	114	32	8	0	58	1.34
10023004--10023046	15	3.0	13	83	16	50	48	2	0	48	1.14
10023011--10023053	14	3.1	14	84	15	54	48	2	0	48	1.14
10024000--10024070	29	2.4	29	97	0	133	50	2	8	38	1.47
10024899--10024949	25	2.0	25	81	7	59	64	1	7	25	1.31
10034400--10034471	2	37.0	2	91	5	103	44	2	0	52	1.15
10039644--10039690	23	2.1	22	84	4	58	63	0	31	4	1.13
10040757--10040792	2	18.0	2	100	0	72	50	0	0	50	1.00
10047870--10047918	24	2.0	24	84	7	64	59	6	0	34	1.22
10049446--10049516	3	23.7	3	73	21	60	59	0	1	39	1.06
10049436--10049516	31	2.5	32	88	7	112	56	0	1	41	1.07
10049734--10049843	41	2.7	41	82	4	105	37	20	18	23	1.94
10050006--10050096	42	2.2	42	91	0	146	38	19	17	24	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10050029--10050097	20	3.2	23	66	16	56	40	18	17	23	1.91
10057470--10057643	95	1.8	95	84	0	240	54	8	2	35	1.45
10058748--10058829	37	2.2	37	100	0	164	4	21	35	37	1.75
10058909--10058957	15	3.2	15	91	8	73	55	0	0	44	0.99
10058921--10058989	15	4.8	14	73	23	63	56	2	1	39	1.23
10060436--10060460	13	1.9	13	100	0	50	64	12	8	16	1.49
10060683--10060757	22	3.1	22	70	23	69	60	5	6	28	1.44
10061298--10061342	18	2.5	18	92	0	81	33	24	11	31	1.90
10061399--10061504	47	2.3	47	87	9	146	50	4	1	43	1.34
10061410--10061506	17	5.8	17	68	25	55	50	5	1	43	1.31

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54