genome.fa.s8428.2.7.7.80.10.50.1000.13.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: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6915314

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   

This is table  13  of  30  ( 3508 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)
3203435--3203484	21	2.5	20	87	9	68	32	26	14	28	1.94
3211805--3211849	22	2.1	22	84	12	58	42	2	0	55	1.12
3211822--3211956	42	3.3	42	91	4	204	52	0	0	46	1.05
3211889--3211988	28	3.6	28	73	9	105	53	0	0	47	1.00
3211875--3211951	19	3.8	20	70	20	63	57	0	0	42	0.99
3211846--3211955	12	10.3	11	65	26	58	53	0	0	46	1.00
3219957--3220022	3	22.3	3	90	3	98	37	1	0	60	1.06
3232625--3232688	15	4.4	16	79	18	70	82	0	17	0	0.66
3232628--3232690	16	3.9	16	76	19	69	82	0	17	0	0.67
3232624--3232686	12	5.2	12	85	12	85	80	0	19	0	0.70
3232628--3232683	25	2.1	25	90	9	85	83	0	16	0	0.64
3233824--3234646	83	10.0	83	97	1	1527	28	14	21	35	1.93
3235447--3235888	113	3.9	110	84	6	575	38	13	19	28	1.89
3235805--3236192	124	3.3	122	77	15	504	40	12	18	27	1.87
3235465--3236192	236	3.1	236	89	6	1025	39	13	19	27	1.89
3236444--3236504	3	20.3	3	93	0	104	36	1	0	62	1.05
3236434--3236513	9	7.5	11	78	18	57	40	1	0	58	1.06
3236922--3236963	15	2.9	14	80	16	50	80	2	16	0	0.81
3236930--3236969	18	2.2	19	86	4	55	72	7	20	0	1.08
3240281--3240327	17	2.8	17	75	12	51	17	25	6	51	1.69
3240362--3240427	17	4.0	16	74	18	55	22	13	3	60	1.47
3240973--3241094	62	2.0	62	98	0	235	32	17	0	49	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3241395--3241516	64	1.9	63	90	5	192	31	0	13	55	1.38
3242101--3242149	19	2.6	18	81	9	62	20	4	2	73	1.10
3245173--3245198	11	2.4	11	100	0	52	15	7	0	76	0.99
3247137--3247180	19	2.3	19	80	0	52	38	0	13	47	1.43
3248824--3248929	20	5.2	20	77	4	106	42	19	16	21	1.89
3248875--3248958	20	4.2	20	78	6	71	38	15	20	26	1.92
3248971--3249105	57	2.4	57	96	0	243	25	14	22	37	1.93
3249028--3249317	77	3.8	77	96	0	526	27	13	21	38	1.90
3248932--3249182	134	1.9	134	96	0	466	27	14	21	37	1.92
3249162--3249202	20	2.0	20	95	0	73	24	14	19	41	1.89
3249240--3249279	20	2.0	20	90	0	62	25	10	20	45	1.81
3249316--3249432	57	2.1	57	98	0	225	36	21	13	28	1.91
3249407--3249470	20	3.2	20	90	0	101	28	23	14	34	1.93
3249474--3249513	19	2.1	19	85	0	53	40	17	20	22	1.92
3249507--3249677	20	8.6	19	73	17	125	22	15	21	41	1.90
3249507--3249640	40	3.3	40	79	8	155	22	15	20	41	1.90
3249669--3249714	21	2.2	21	92	0	74	36	15	26	21	1.93
3250557--3250605	20	2.5	20	100	0	98	32	18	4	44	1.68
3254737--3254775	2	20.0	2	94	5	71	48	0	0	51	1.00
3260504--3260606	51	2.0	51	100	0	206	24	33	11	31	1.91
3263710--3263735	13	2.0	13	100	0	52	23	7	23	46	1.78
3274100--3274421	161	2.0	161	100	0	644	30	28	20	20	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3286507--3286543	15	2.2	18	86	13	53	40	13	10	35	1.80
3293726--3293965	124	1.9	126	98	1	466	35	16	18	29	1.93
3297373--3297430	22	2.6	22	100	0	116	39	17	5	37	1.72
3305475--3305509	17	2.1	17	94	0	61	25	22	34	17	1.96
3306089--3306119	16	1.9	16	93	0	53	19	12	19	48	1.81
3308130--3308212	20	3.8	20	71	24	62	71	4	4	19	1.23
3309720--3310280	84	6.8	84	77	8	526	25	20	24	29	1.99
3309732--3310280	164	3.3	163	86	3	726	25	20	24	29	1.99
3326252--3326315	28	2.2	29	86	2	85	29	14	6	50	1.67
3326290--3326573	130	2.2	129	91	4	446	24	17	13	45	1.84
3326663--3326699	16	2.3	16	90	0	56	29	29	5	35	1.80
3326670--3326726	16	3.6	16	74	9	53	29	24	1	43	1.64
3326875--3326909	16	2.2	16	90	5	54	25	11	5	57	1.56
3330821--3330889	24	3.1	21	80	13	75	72	5	18	2	1.18
3333542--3333731	102	1.9	102	85	4	267	36	16	12	34	1.86
3333908--3334018	30	3.5	30	70	20	98	30	18	11	39	1.86
3333937--3334055	37	3.4	37	68	19	101	28	19	12	39	1.88
3333679--3334159	200	2.4	201	88	1	707	29	16	13	40	1.86
3333680--3334178	67	7.5	67	87	0	660	29	16	13	40	1.87
3334383--3335298	139	6.6	139	80	2	857	31	26	17	24	1.97
3334534--3335298	277	2.8	278	81	1	827	32	26	16	24	1.96
3342565--3342607	2	21.5	2	90	0	68	51	0	2	46	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3342663--3342876	85	2.5	85	81	4	227	34	15	20	29	1.94
3342848--3342938	13	7.0	13	94	0	128	31	16	23	28	1.96
3343601--3343981	130	3.1	129	83	9	444	23	19	13	43	1.87
3343763--3343981	115	1.9	114	86	2	314	23	18	14	43	1.86
3343977--3344020	16	2.7	17	79	6	56	29	27	6	36	1.83
3345471--3345505	3	11.7	3	100	0	70	34	0	0	65	0.93
3351226--3351251	2	13.0	2	100	0	52	50	0	0	50	1.00
3353922--3353978	14	4.2	14	76	14	57	57	0	0	42	0.98
3357433--3357719	57	5.2	57	85	4	365	34	11	19	33	1.88
3357433--3357685	114	2.2	114	92	2	420	35	11	18	34	1.87
3359515--3359586	3	24.0	3	79	10	76	40	1	0	58	1.07
3360744--3360822	40	2.0	40	82	9	99	29	1	2	67	1.12
3360777--3360824	14	3.3	15	77	19	57	31	0	0	68	0.90
3360772--3360851	14	6.1	13	70	21	51	28	1	2	67	1.11
3360831--3360876	3	15.3	3	82	8	58	26	4	0	69	1.07
3360831--3360879	19	2.5	19	81	15	64	26	4	0	69	1.06
3360971--3361192	117	1.9	115	83	4	286	37	7	8	46	1.62
3361157--3361220	31	2.2	30	78	13	71	50	1	0	48	1.10
3361691--3361734	17	2.6	16	86	10	61	27	2	0	70	0.99
3366805--3366834	11	2.8	11	95	5	53	86	0	13	0	0.57
3371051--3371129	39	2.0	40	97	2	151	31	15	22	30	1.95
3371535--3371586	22	2.4	22	90	0	77	38	11	15	34	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3371974--3372646	114	5.9	114	92	3	1127	41	14	17	27	1.88
3371974--3372646	227	2.9	227	94	2	1132	41	14	17	27	1.88
3372585--3372686	40	2.5	40	92	3	161	52	7	21	17	1.69
3372625--3373483	113	7.5	114	92	1	1384	39	13	18	27	1.89
3373422--3373523	40	2.5	40	93	3	170	52	7	20	18	1.69
3373081--3373858	381	2.1	374	92	3	1276	40	13	18	26	1.88
3373196--3373750	267	2.1	266	93	2	936	41	13	18	26	1.88
3373462--3373972	114	4.5	114	90	5	781	41	13	18	27	1.87
3373462--3373972	227	2.3	225	90	4	793	41	13	18	27	1.87
3373911--3374012	40	2.5	40	92	3	161	52	7	20	18	1.69
3372965--3374125	489	2.4	493	96	1	2152	40	13	18	26	1.88
3374070--3374165	41	2.4	41	91	1	149	51	9	20	18	1.74
3373306--3373637	154	2.2	155	89	2	499	43	12	19	25	1.86
3373815--3374284	156	3.0	155	92	1	746	42	12	19	25	1.86
3374111--3374410	114	2.6	112	87	3	395	39	14	19	27	1.90
3374458--3374512	17	3.1	17	70	27	51	49	14	20	16	1.80
3374731--3374805	3	25.0	3	77	10	55	42	2	0	54	1.14
3375789--3375821	2	16.5	2	93	0	57	45	0	0	54	0.99
3381377--3381683	153	2.0	153	96	3	566	28	13	18	39	1.88
3382191--3382232	20	2.2	20	82	4	50	33	16	23	26	1.96
3382563--3383052	57	8.8	56	83	7	523	36	10	18	34	1.85
3382576--3383052	170	2.8	168	84	4	581	36	10	18	35	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3382570--3383042	113	4.2	113	85	6	565	36	10	17	34	1.84
3385296--3385350	28	2.0	28	82	13	69	14	9	10	65	1.47
3386698--3387034	168	2.0	169	92	1	568	31	16	20	31	1.95
3388081--3388115	16	2.2	16	100	0	70	28	28	25	17	1.97
3391278--3391474	97	2.0	97	97	0	367	36	19	13	30	1.90
3397264--3397296	14	2.4	14	90	10	50	78	0	9	12	0.95
3397266--3397310	18	2.4	18	85	3	54	75	0	11	13	1.05
3397425--3397463	13	3.1	13	85	7	53	79	0	2	17	0.84
3397425--3397463	6	6.3	6	82	5	51	79	0	2	17	0.84
3416374--3416433	27	2.2	27	100	0	120	13	28	33	25	1.93

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