genome.fa.s48.2.7.7.80.10.50.1000.20.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: Scaffold48
Parameters: 2 7 7 80 10 50 1000
Length:  4619657

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   

This is table  20  of  27  ( 3212 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)
2942300--2942325	3	8.7	3	100	0	52	34	0	0	65	0.93
2942393--2942423	2	15.0	2	93	6	53	48	0	3	48	1.17
2942816--2942858	16	2.8	16	89	3	70	46	0	0	53	1.00
2943689--2943749	18	3.2	19	77	11	63	36	0	4	59	1.19
2945058--2945092	7	5.0	7	96	0	61	42	17	0	40	1.49
2945161--2945192	16	2.0	16	100	0	64	18	25	0	56	1.42
2959914--2959942	2	14.5	2	100	0	58	0	0	48	51	1.00
2960398--2960424	2	13.5	2	100	0	54	51	0	0	48	1.00
2963332--2963384	9	6.3	9	78	12	60	41	0	1	56	1.10
2974121--2974414	100	2.9	100	99	0	579	35	10	8	45	1.69
2978594--2978641	19	2.4	21	80	16	57	33	2	0	64	1.05
2987962--2987992	15	2.1	15	93	0	53	70	0	0	29	0.87
2987967--2988014	15	3.1	17	80	19	52	58	0	0	41	0.98
2988162--2988232	26	2.6	28	72	17	76	54	2	0	42	1.14
2988644--2988769	21	6.0	21	68	18	68	60	0	0	38	1.03
2988647--2988677	16	1.9	16	93	0	53	67	0	0	32	0.91
2988689--2988736	14	3.4	14	80	8	62	56	0	0	43	0.99
2988647--2988783	48	3.0	46	78	15	133	59	1	0	38	1.06
2989919--2989945	3	9.0	3	100	0	54	33	0	0	66	0.92
2996526--2996563	18	2.1	19	90	5	60	44	0	0	55	0.99
2997898--2997979	32	2.5	32	83	13	89	36	0	1	62	1.03
2997898--2997979	34	2.5	31	83	13	94	36	0	1	62	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2999419--2999468	2	25.0	2	100	0	100	50	0	0	50	1.00
2999468--2999494	2	13.5	2	100	0	54	51	48	0	0	1.00
3004770--3004799	8	3.8	8	90	0	51	86	0	3	10	0.67
3004770--3004800	16	1.9	16	100	0	62	83	0	6	9	0.79
3014373--3014405	6	5.5	6	96	0	57	81	0	3	15	0.80
3015284--3015317	17	2.0	17	88	0	50	26	0	2	70	1.01
3015292--3015317	12	2.2	12	100	0	52	26	0	0	73	0.84
3015379--3015411	2	16.5	2	100	0	66	0	0	48	51	1.00
3015949--3015987	20	2.0	20	84	0	51	33	0	10	56	1.33
3016040--3016088	15	3.2	16	80	8	57	51	4	0	44	1.20
3016039--3016109	18	4.0	18	75	13	67	47	2	0	49	1.16
3016337--3016369	9	3.7	9	92	8	50	24	0	0	75	0.80
3016457--3016541	25	3.2	25	74	15	73	52	0	0	47	1.00
3017334--3017446	58	1.9	59	94	1	201	33	21	8	36	1.84
3017971--3018004	16	2.0	16	88	11	50	76	5	0	17	0.98
3018640--3018766	64	2.0	64	87	9	188	37	23	13	25	1.92
3022569--3022599	2	15.5	2	100	0	62	48	0	0	51	1.00
3023615--3023657	2	22.0	2	95	4	79	51	0	0	48	1.00
3028819--3028877	21	2.8	21	84	5	75	59	1	0	38	1.08
3028819--3028881	20	3.0	20	76	4	63	57	1	0	41	1.08
3028929--3028963	2	17.5	2	93	0	61	51	0	0	48	1.00
3033390--3033424	10	3.4	10	88	7	52	74	0	0	25	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3033384--3033424	21	2.0	21	90	0	64	68	0	0	31	0.90
3033384--3033426	11	4.0	11	81	6	52	67	0	0	32	0.91
3037662--3037729	11	6.0	11	75	13	66	58	0	0	41	0.98
3037679--3037737	11	5.4	11	84	8	75	59	0	1	38	1.08
3037661--3037729	22	3.1	21	82	14	77	59	0	0	40	0.97
3039081--3039105	10	2.5	10	100	0	50	20	8	16	56	1.65
3039674--3039719	19	2.4	19	92	7	76	63	10	15	10	1.53
3043798--3043854	28	2.1	26	90	6	87	64	7	0	28	1.19
3043804--3043866	28	2.2	28	85	2	81	63	4	0	31	1.15
3043871--3043992	59	2.1	56	92	4	199	40	1	6	50	1.38
3044022--3044101	19	4.2	20	73	20	57	26	2	0	71	0.99
3044052--3044111	31	2.0	30	83	3	75	33	0	1	65	1.03
3046080--3046118	18	2.2	18	95	0	69	17	23	7	51	1.71
3056335--3056390	17	3.2	18	80	12	64	33	0	0	66	0.92
3058572--3058651	11	7.4	11	74	20	55	68	0	0	31	0.90
3058578--3058654	27	2.9	26	86	3	109	68	0	0	31	0.90
3058606--3058667	19	3.4	17	75	18	61	69	0	0	30	0.89
3058578--3058667	27	3.5	27	80	10	98	67	0	0	32	0.91
3058612--3058675	20	3.3	19	74	24	62	65	0	0	34	0.93
3058584--3058647	26	2.7	22	76	19	74	68	0	0	31	0.90
3058573--3058711	38	3.5	39	80	10	133	64	0	0	35	0.94
3059029--3059105	27	2.9	26	76	3	73	46	1	1	50	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3063961--3063994	15	2.3	15	89	0	50	47	17	32	2	1.63
3064070--3064155	44	2.0	44	92	0	145	36	16	6	40	1.75
3071987--3072676	138	5.0	138	93	2	1154	44	19	11	24	1.83
3076798--3076838	21	2.1	20	82	13	50	58	2	2	36	1.24
3076965--3077028	20	3.3	19	70	16	51	45	3	0	51	1.17
3076999--3077040	18	2.3	18	84	8	59	50	2	0	47	1.14
3077877--3077903	2	13.5	2	100	0	54	51	0	48	0	1.00
3078273--3078345	22	3.1	23	81	15	71	49	1	0	49	1.09
3078288--3078347	15	4.0	15	72	19	54	46	1	0	51	1.10
3099338--3099384	25	1.9	24	82	4	58	42	4	6	46	1.48
3099882--3099936	2	26.5	2	82	14	67	45	1	3	49	1.30
3102628--3102698	38	1.9	38	83	11	94	54	0	1	43	1.08
3103416--3103443	2	14.0	2	100	0	56	50	0	0	50	1.00
3104044--3104068	2	12.5	2	100	0	50	48	0	0	52	1.00
3104478--3104519	2	21.0	2	100	0	84	50	0	0	50	1.00
3108902--3108941	2	20.0	2	89	0	62	45	0	2	52	1.14
3111361--3111397	2	18.5	2	94	0	65	48	2	0	48	1.15
3111361--3111403	8	5.4	8	88	0	50	46	4	2	46	1.36
3113555--3113597	23	2.0	21	86	9	59	41	4	0	53	1.21
3113794--3113838	2	22.5	2	95	0	81	48	0	0	51	1.00
3117247--3117351	37	2.9	36	78	13	110	34	0	3	60	1.21
3117263--3117337	33	2.3	34	79	9	84	33	1	2	62	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3118379--3118420	22	1.9	22	85	9	59	28	4	4	61	1.36
3119096--3119151	8	7.0	8	72	8	51	39	3	0	57	1.16
3119250--3119323	27	2.7	26	78	14	78	43	0	0	56	0.99
3119299--3119341	16	2.7	16	82	13	61	44	0	0	55	0.99
3119740--3119809	28	2.5	28	78	13	74	50	0	1	48	1.09
3119872--3119930	25	2.4	25	81	13	61	40	0	0	59	0.97
3121778--3121843	34	1.9	35	82	14	84	54	1	0	43	1.09
3121716--3121867	38	3.9	40	66	20	104	47	1	1	50	1.18
3121874--3121927	21	2.5	22	75	6	56	42	7	0	50	1.30
3121671--3121899	117	2.0	118	84	7	308	47	2	2	48	1.28
3121880--3121921	22	2.0	21	85	4	57	45	9	0	45	1.36
3121943--3121984	15	2.8	15	75	13	50	40	0	4	54	1.21
3121997--3122089	41	2.3	39	80	16	100	37	4	0	58	1.18
3122091--3122135	20	2.5	19	77	22	53	42	6	0	51	1.28
3122227--3122257	16	1.9	16	93	0	53	58	12	0	29	1.35
3123326--3123454	32	4.1	32	80	7	149	43	1	3	51	1.29
3123670--3123732	31	2.0	31	100	0	126	31	6	12	49	1.66
3130786--3130848	29	2.2	27	78	16	65	53	0	1	44	1.10
3130835--3130887	19	2.7	20	77	11	56	50	0	5	43	1.25
3131398--3131427	2	15.0	2	92	0	51	50	3	0	46	1.18
3137190--3137255	26	2.7	24	83	4	78	24	4	21	50	1.67
3137219--3137264	24	1.9	24	90	0	74	21	4	28	45	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3141834--3141916	41	2.0	41	100	0	166	26	7	24	42	1.80
3142514--3142547	17	2.0	17	88	0	50	29	2	0	67	1.05
3145708--3145732	9	2.8	9	100	0	50	24	20	0	56	1.43
3150583--3150620	13	2.8	14	84	4	51	42	0	0	57	0.98
3151243--3151311	33	2.0	35	86	10	99	47	7	1	43	1.39
3155218--3155245	2	14.0	2	100	0	56	50	0	0	50	1.00
3157654--3157705	18	3.1	18	70	27	51	38	1	1	57	1.21
3157638--3157705	32	2.1	33	86	10	95	38	1	5	54	1.34
3157686--3157759	28	2.5	29	80	8	87	40	5	0	54	1.24
3161516--3161567	14	3.7	14	82	5	52	51	0	0	48	1.00

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