genome.fa.s11.2.7.7.80.10.50.1000.20.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: Scaffold11
Parameters: 2 7 7 80 10 50 1000
Length:  5230303

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   

This is table  20  of  29  ( 3461 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)
3006705--3006772	6	12.3	6	75	17	58	57	2	0	39	1.14
3007638--3007677	19	2.2	19	86	4	55	37	0	0	62	0.95
3008535--3008568	17	1.9	18	88	5	52	47	2	0	50	1.16
3008830--3008859	2	15.0	2	100	0	60	50	0	0	50	1.00
3011741--3011783	19	2.3	19	80	11	54	51	0	0	48	1.00
3013031--3013062	2	16.0	2	100	0	64	50	0	0	50	1.00
3013658--3013849	98	2.0	98	98	1	377	28	23	6	40	1.80
3026601--3026788	49	4.0	49	79	10	185	25	19	13	40	1.89
3026671--3026788	48	2.6	43	84	11	132	22	22	15	39	1.91
3028034--3028104	34	2.1	34	91	0	115	26	8	19	45	1.79
3031463--3031512	25	2.0	25	100	0	100	28	32	8	32	1.86
3032364--3032555	50	3.8	50	90	0	285	31	18	19	30	1.96
3036939--3037100	50	3.2	51	78	6	161	34	18	16	30	1.93
3040552--3040600	25	2.0	24	88	4	71	36	0	2	61	1.08
3040850--3040877	2	14.0	2	100	0	56	50	0	0	50	1.00
3041499--3041529	3	10.3	3	100	0	62	0	35	0	64	0.94
3043827--3043870	18	2.4	19	80	3	54	31	0	0	68	0.90
3043819--3043874	20	2.8	19	78	10	51	37	0	0	62	0.95
3044391--3044415	2	12.5	2	100	0	50	48	0	0	52	1.00
3047736--3047781	24	1.9	24	86	8	67	63	0	0	36	0.95
3047731--3047782	16	3.5	16	73	23	51	61	0	0	38	0.96
3047770--3047814	18	2.7	18	76	13	51	46	0	0	53	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3048243--3048275	13	2.4	14	90	5	50	54	0	3	42	1.15
3048949--3048982	2	17.0	2	93	0	59	50	2	0	47	1.16
3049369--3049395	2	13.5	2	100	0	54	48	0	0	51	1.00
3053340--3053376	2	18.5	2	100	0	74	51	0	48	0	1.00
3053682--3053716	2	17.5	2	100	0	70	51	0	0	48	1.00
3055313--3055351	17	2.3	17	86	8	53	30	5	2	61	1.31
3057178--3057211	2	17.5	2	93	6	61	50	0	0	50	1.00
3057385--3057415	16	1.9	16	93	0	53	64	3	6	25	1.33
3065496--3065536	4	10.5	4	85	15	59	21	0	24	53	1.46
3066726--3066773	2	24.0	2	95	0	87	47	0	2	50	1.12
3067207--3067265	2	30.5	2	88	6	86	44	0	0	55	0.99
3067691--3067731	2	20.5	2	94	0	73	53	0	46	0	1.00
3069002--3069032	4	7.8	4	100	0	62	0	25	0	74	0.82
3070572--3070667	35	2.7	36	81	12	108	34	0	5	60	1.19
3070664--3070734	30	2.4	30	86	6	92	56	4	4	35	1.38
3071202--3071248	22	2.1	22	84	7	60	55	0	4	40	1.19
3071713--3071783	24	3.1	22	80	15	81	39	0	0	60	0.97
3071720--3071840	22	5.5	21	72	14	68	41	0	0	57	1.10
3071768--3071829	23	2.8	22	73	14	56	48	0	1	50	1.10
3073912--3073936	13	1.9	13	100	0	50	60	0	0	40	0.97
3073956--3073997	19	2.2	19	83	12	50	57	7	2	33	1.39
3074900--3074936	12	2.9	13	81	18	51	29	0	8	62	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3077473--3077505	2	16.5	2	93	0	57	51	0	0	48	1.00
3085166--3085227	22	2.9	21	76	16	65	56	0	0	43	0.99
3086141--3086198	22	2.6	22	79	17	59	60	0	0	39	0.97
3087834--3087867	3	11.3	3	87	12	52	32	35	2	29	1.73
3088115--3088147	2	17.5	2	87	12	52	48	0	0	51	1.00
3088118--3088149	16	2.0	16	100	0	64	50	0	0	50	1.00
3088595--3088630	8	4.4	8	89	3	54	86	0	13	0	0.58
3088599--3088628	14	2.1	14	93	0	51	90	0	10	0	0.47
3088597--3088630	17	2.0	17	88	0	50	88	0	11	0	0.52
3088994--3089027	2	17.0	2	100	0	68	50	0	0	50	1.00
3089027--3089056	2	15.0	2	100	0	60	50	0	50	0	1.00
3089575--3089655	41	2.0	41	92	0	135	46	13	6	33	1.68
3095548--3095633	24	3.6	25	72	10	81	62	1	3	32	1.19
3099021--3099105	18	4.7	18	98	0	161	50	10	0	38	1.37
3099004--3099106	22	4.9	22	87	9	151	49	10	0	39	1.38
3099013--3099106	4	23.5	4	91	0	107	50	9	0	40	1.35
3099122--3099219	46	2.2	45	90	5	153	38	14	17	29	1.89
3102292--3102682	193	2.0	193	100	0	782	29	12	18	39	1.87
3102931--3102983	2	26.5	2	100	0	106	49	0	0	50	1.00
3105743--3105770	7	4.0	7	100	0	56	28	0	28	42	1.56
3108988--3109231	52	4.7	52	90	4	379	30	16	18	34	1.93
3109271--3109337	33	2.0	33	88	0	98	40	13	11	34	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3109293--3109317	13	1.9	13	100	0	50	32	16	16	36	1.90
3111917--3111978	23	2.9	21	77	13	63	50	0	3	46	1.17
3121052--3121094	17	2.8	16	86	13	63	53	0	0	46	1.00
3121068--3121116	19	2.5	19	86	6	62	42	0	0	57	0.99
3127556--3127589	3	11.3	3	100	0	68	35	0	0	64	0.94
3133164--3133191	2	14.0	2	100	0	56	0	0	50	50	1.00
3135345--3135370	3	8.7	3	100	0	52	30	0	0	69	0.89
3137392--3137459	7	9.6	7	70	20	52	33	1	0	64	1.02
3137390--3137425	15	2.3	16	95	4	65	38	0	0	61	0.96
3137921--3137947	10	2.7	10	100	0	54	0	0	7	92	0.38
3139683--3139708	12	2.2	12	100	0	52	61	15	7	15	1.55
3140151--3140200	25	2.0	25	84	7	66	52	0	0	48	1.00
3142737--3142785	17	3.1	16	82	11	57	75	0	24	0	0.80
3142734--3142783	24	2.1	23	85	7	64	72	0	28	0	0.86
3142907--3142962	22	2.6	22	88	8	80	30	1	0	67	1.01
3142905--3142962	11	5.4	11	78	10	66	31	1	0	67	1.01
3142932--3143004	37	2.0	37	81	10	87	26	2	5	65	1.27
3143714--3143776	21	3.0	21	80	13	60	49	0	0	50	1.00
3146883--3146953	29	2.5	29	86	2	99	29	5	21	43	1.75
3147964--3148025	22	2.9	21	83	7	79	40	1	3	54	1.26
3147971--3148063	22	4.0	23	81	10	77	47	0	2	50	1.13
3147914--3148054	11	12.5	11	68	14	65	48	0	4	46	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3148949--3148982	5	7.0	5	86	6	52	0	23	0	76	0.79
3148949--3148982	14	2.3	15	95	5	61	0	23	0	76	0.79
3152180--3152211	2	16.0	2	100	0	64	50	0	0	50	1.00
3152415--3152446	2	16.0	2	100	0	64	50	0	0	50	1.00
3155824--3156107	148	1.9	148	98	0	550	36	24	11	27	1.90
3159778--3159806	9	3.3	9	95	4	51	24	0	0	75	0.80
3163140--3163208	32	2.4	28	80	19	95	43	5	4	46	1.47
3163150--3163212	32	2.0	32	100	0	126	41	6	4	47	1.50
3163757--3163833	26	2.9	27	78	20	81	49	0	0	50	1.00
3163758--3163833	25	2.8	25	79	16	73	50	0	0	50	1.00
3164053--3164139	31	2.8	31	100	0	174	19	18	13	48	1.81
3164598--3164630	17	1.9	17	93	0	57	57	0	0	42	0.98
3167132--3167186	29	2.0	27	89	7	83	60	0	3	36	1.15
3167267--3167312	20	2.3	21	78	17	53	63	2	0	34	1.07
3167643--3167671	15	1.9	15	100	0	58	51	0	0	48	1.00
3176104--3176174	27	2.6	27	88	6	99	45	26	7	21	1.77
3181087--3181135	19	2.7	18	78	6	55	53	2	2	42	1.24
3181616--3181641	2	13.0	2	100	0	52	50	0	0	50	1.00
3182966--3182994	1	29.0	1	100	0	58	100	0	0	0	0.00
3184288--3184326	18	2.2	18	85	0	51	35	0	2	61	1.10
3184663--3184692	2	15.0	2	92	0	51	46	0	0	53	1.00
3185155--3185188	17	1.9	18	88	5	52	70	2	8	17	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3185693--3185726	2	17.0	2	100	0	68	50	0	0	50	1.00
3195575--3195607	3	11.0	3	100	0	66	33	0	0	66	0.92
3195844--3195896	24	2.2	25	83	10	65	60	1	0	37	1.08
3195842--3195931	16	5.5	16	66	18	51	56	2	1	40	1.19
3195842--3195938	25	3.9	24	73	17	72	55	3	1	40	1.22
3201534--3201589	28	2.1	26	83	6	67	62	1	5	30	1.28
3203802--3203833	2	16.0	2	100	0	64	50	0	0	50	1.00
3204482--3204582	41	2.5	40	84	7	116	41	1	14	41	1.57
3204598--3204654	27	2.1	29	81	15	68	40	3	15	40	1.65
3205643--3205867	79	2.9	79	97	0	425	33	4	8	52	1.54

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