genome.fa.s40.2.7.7.80.10.50.1000.22.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: Scaffold40
Parameters: 2 7 7 80 10 50 1000
Length:  3440810

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   

This is table  22  of  24  ( 2833 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)
2922210--2922244	9	4.0	9	96	3	63	54	0	0	45	0.99
2923720--2923755	2	18.0	2	100	0	72	50	0	0	50	1.00
2927275--2927333	18	3.3	18	73	4	57	55	0	0	44	0.99
2929966--2930009	3	14.7	3	95	0	79	63	0	2	34	1.07
2930755--2930831	39	2.0	39	82	5	93	50	0	0	49	1.00
2931461--2931520	19	3.4	18	73	13	63	48	0	0	51	1.00
2931508--2931548	20	2.2	18	86	8	55	51	2	4	41	1.36
2931852--2931883	2	16.0	2	100	0	64	50	0	0	50	1.00
2932229--2932269	22	1.9	21	85	5	55	43	0	0	56	0.99
2933176--2933219	19	2.3	19	88	0	61	43	0	2	54	1.12
2933176--2933219	6	7.0	6	82	7	52	43	0	2	54	1.12
2934047--2934088	14	2.8	15	82	7	50	71	0	0	28	0.86
2939445--2939475	15	2.1	15	94	5	55	51	12	0	35	1.40
2940448--2940475	4	7.0	4	100	0	56	75	0	25	0	0.81
2940838--2940881	20	2.2	20	84	8	54	40	2	2	54	1.25
2941285--2941314	9	3.3	9	95	0	51	70	10	0	20	1.16
2941532--2941561	16	1.9	15	93	6	51	6	10	3	80	1.01
2944605--2944629	3	8.3	3	100	0	50	36	0	0	64	0.94
2945029--2945115	32	2.4	37	83	12	103	33	0	0	66	0.92
2945027--2945117	16	5.6	16	72	16	71	32	0	0	67	0.91
2945134--2945158	13	1.9	13	100	0	50	28	0	0	72	0.86
2945134--2945231	19	5.3	19	69	20	55	34	1	2	62	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2945203--2945293	24	3.7	24	72	12	69	27	1	4	67	1.17
2945594--2945674	34	2.4	34	78	17	87	33	2	1	62	1.16
2946091--2946151	28	2.1	30	81	6	72	47	0	1	50	1.10
2946078--2946157	43	1.9	41	82	10	99	45	0	1	53	1.08
2948727--2948813	42	2.1	42	93	4	149	18	14	28	37	1.91
2950386--2950410	1	25.0	1	100	0	50	0	100	0	0	0.00
2950490--2950523	2	17.0	2	100	0	68	50	0	0	50	1.00
2950621--2950663	22	1.9	23	85	4	61	51	0	0	48	1.00
2950633--2950674	14	2.8	15	82	10	50	42	0	0	57	0.99
2951619--2951647	2	14.5	2	100	0	58	51	0	0	48	1.00
2952179--2952239	18	3.1	19	77	20	63	36	0	0	63	0.94
2952299--2952383	27	3.3	26	74	15	68	31	8	0	60	1.26
2952566--2952613	18	2.8	17	81	18	55	43	0	0	56	0.99
2952575--2952635	19	3.2	19	79	6	61	45	1	1	50	1.21
2956467--2956498	2	16.0	2	100	0	64	50	0	0	50	1.00
2956629--2956844	34	6.4	34	88	1	292	24	7	27	40	1.83
2956629--2956846	67	3.2	67	88	1	319	24	7	27	40	1.82
2961258--2961475	34	6.5	34	88	1	296	24	7	27	40	1.82
2961258--2961477	67	3.3	67	88	1	323	24	7	27	40	1.82
2961908--2961946	3	13.0	3	100	0	78	66	0	0	33	0.92
2963537--2963570	2	17.0	2	93	0	59	52	0	0	47	1.00
2964115--2964164	22	2.3	22	79	6	57	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2965409--2965461	19	2.8	20	78	16	58	45	0	0	54	0.99
2965834--2965887	23	2.5	21	77	17	56	53	1	3	40	1.29
2972411--2972447	3	12.3	3	100	0	74	67	0	0	32	0.91
2975015--2975059	21	2.1	21	84	15	58	40	0	0	60	0.97
2975664--2975702	3	13.0	3	100	0	78	33	0	0	66	0.92
2976459--2976494	18	2.0	18	89	10	56	41	2	0	55	1.14
2976975--2977012	2	19.0	2	100	0	76	50	0	0	50	1.00
2977732--2977759	7	4.0	7	100	0	56	42	14	14	28	1.84
2977867--2977905	17	2.4	16	86	4	51	33	0	0	66	0.92
2977648--2978013	179	2.0	183	90	7	578	43	3	7	45	1.49
2981463--2981499	3	12.3	3	94	0	65	64	0	2	32	1.07
2981802--2981833	2	16.0	2	93	0	55	50	3	0	46	1.17
2983913--2983960	2	24.0	2	100	0	96	50	0	0	50	1.00
2985327--2985366	2	20.0	2	100	0	80	50	0	0	50	1.00
2986032--2986097	27	2.4	27	90	7	98	46	22	7	22	1.77
2987981--2988026	21	2.1	22	84	4	58	19	30	19	30	1.97
2992487--2992522	2	19.5	2	83	16	51	55	0	0	44	0.99
2992706--2992736	4	7.8	4	100	0	62	25	48	0	25	1.52
2993010--2993036	4	6.8	4	100	0	54	51	22	0	25	1.48
2994371--2994508	49	2.8	49	88	1	195	28	18	17	35	1.93
2994372--2994531	50	3.2	50	89	0	214	28	17	20	33	1.95
2996751--2997010	50	5.2	50	91	0	412	28	20	19	32	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2997232--2997282	25	2.0	25	96	0	93	33	15	9	41	1.80
2999117--2999151	2	17.5	2	100	0	70	0	48	0	51	1.00
3000158--3000185	3	9.3	3	100	0	56	67	0	0	32	0.91
3001019--3001048	2	15.0	2	92	0	51	46	0	3	50	1.18
3001322--3001359	20	2.0	20	84	5	51	52	2	0	44	1.14
3004092--3004153	27	2.3	26	80	5	61	38	3	3	54	1.32
3004797--3004844	16	3.0	16	79	8	53	58	2	0	39	1.10
3004822--3004847	2	13.0	2	100	0	52	50	0	0	50	1.00
3007134--3007177	21	2.2	19	84	15	54	38	0	0	61	0.96
3010428--3010458	6	5.0	6	96	4	53	80	0	0	19	0.71
3011024--3011066	13	3.5	13	78	12	54	53	0	0	46	1.00
3012692--3012723	16	2.0	16	100	0	64	56	0	6	37	1.25
3013502--3013684	34	5.4	34	88	0	260	25	7	26	39	1.83
3013989--3014051	19	3.3	19	90	0	90	28	17	19	34	1.94
3018117--3018301	34	5.5	34	88	0	264	25	7	26	40	1.82
3019402--3019435	2	17.0	2	93	0	59	52	0	0	47	1.00
3020294--3020337	20	2.1	22	83	8	56	43	0	6	50	1.29
3021061--3021091	2	15.5	2	100	0	62	48	0	0	51	1.00
3021501--3021558	30	1.9	30	83	13	75	13	18	3	63	1.43
3025659--3025699	20	2.0	20	95	0	73	43	4	7	43	1.53
3025681--3025840	30	5.1	30	77	8	158	59	5	6	28	1.45
3025674--3025790	15	7.8	15	67	13	62	54	5	5	34	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3025785--3025824	20	2.0	20	90	4	64	67	5	5	22	1.30
3025681--3025841	65	2.6	60	84	6	196	59	5	6	28	1.44
3028961--3028997	2	18.5	2	100	0	74	48	0	0	51	1.00
3030068--3030097	2	15.0	2	92	0	51	46	0	0	53	1.00
3030279--3030304	2	13.0	2	100	0	52	50	0	0	50	1.00
3030653--3030684	3	10.7	3	100	0	64	68	0	0	31	0.90
3031919--3032008	29	3.1	28	71	17	69	38	0	1	60	1.04
3031939--3032012	28	2.5	31	75	14	75	41	0	1	56	1.07
3032025--3032085	32	1.9	33	83	6	81	37	3	0	59	1.14
3032067--3032115	25	2.0	25	84	8	64	53	2	2	42	1.24
3032514--3032560	18	2.6	17	78	15	51	72	4	0	23	1.02
3033044--3033113	27	2.5	28	80	13	83	24	7	22	45	1.77
3035687--3035732	21	2.1	22	84	4	58	30	19	30	19	1.97
3045521--3045552	2	16.5	2	93	6	57	50	0	0	50	1.00
3047416--3047481	2	33.0	2	100	0	132	50	0	0	50	1.00
3050408--3050471	27	2.3	27	86	7	85	25	7	20	46	1.77
3050480--3050530	24	2.1	24	92	3	84	17	9	25	47	1.78
3054998--3055122	27	4.9	24	74	13	97	21	7	24	46	1.76
3055000--3055065	27	2.4	27	90	7	98	22	7	22	46	1.77
3055055--3055124	24	2.8	25	87	6	90	22	8	24	44	1.81
3056534--3056579	24	1.9	24	95	0	83	45	28	6	19	1.75
3056584--3056666	28	3.0	28	96	0	148	49	19	10	20	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3058570--3058615	21	2.1	22	84	4	58	19	30	19	30	1.97
3061161--3061206	24	1.9	24	95	0	83	45	28	6	19	1.75
3061211--3061293	28	3.0	28	96	0	148	49	19	10	20	1.78
3061942--3061971	13	2.4	12	89	10	51	23	0	3	73	0.98
3065870--3065896	12	2.2	12	100	0	54	0	37	0	62	0.95
3066965--3067015	26	1.9	27	84	4	68	17	15	3	62	1.47
3069222--3069406	34	5.5	34	87	3	257	40	26	7	25	1.82
3073820--3074003	34	5.4	34	86	3	246	40	26	7	25	1.81
3075555--3075592	2	19.0	2	88	0	58	50	0	2	47	1.15
3076191--3076224	17	2.0	17	88	0	50	47	11	23	17	1.81

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