genome.fa.s8.2.7.7.80.10.50.1000.20.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   

This is table  20  of  33  ( 3942 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)
3048095--3048215	62	2.0	62	88	3	181	23	10	17	48	1.78
3056225--3056249	3	8.3	3	100	0	50	64	0	0	36	0.94
3060299--3060350	16	3.2	16	81	10	70	48	0	0	51	1.00
3060306--3060359	16	3.3	16	76	21	58	55	0	0	44	0.99
3063377--3063419	15	2.8	15	82	3	50	74	2	0	23	0.93
3064515--3064539	2	12.5	2	100	0	50	52	0	0	48	1.00
3065321--3065347	2	13.5	2	100	0	54	48	0	0	51	1.00
3075188--3075224	10	3.7	10	88	0	56	48	8	0	43	1.32
3075851--3075877	2	13.5	2	100	0	54	51	0	0	48	1.00
3076718--3076759	21	2.0	21	90	9	68	40	0	7	52	1.29
3077411--3077443	16	2.0	17	88	5	50	54	0	0	45	0.99
3077466--3077512	19	2.3	21	78	10	62	31	8	0	59	1.27
3077473--3077520	19	2.5	20	86	6	64	41	10	0	47	1.37
3084041--3084279	50	4.8	50	86	3	336	33	18	19	28	1.96
3084041--3084273	101	2.3	100	86	0	349	33	18	19	28	1.96
3087247--3087301	16	3.4	16	79	20	69	58	1	0	40	1.09
3087230--3087302	32	2.2	33	87	4	103	57	1	0	41	1.07
3088675--3088734	21	2.9	21	84	0	75	35	23	5	36	1.77
3092079--3092118	21	1.9	21	94	0	71	40	22	0	37	1.54
3097125--3097287	80	2.0	81	90	1	256	36	7	20	35	1.81
3104562--3104602	2	20.5	2	85	9	57	48	2	2	46	1.28
3104987--3105030	17	2.3	20	85	11	58	50	4	4	40	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3107495--3107541	23	2.1	21	85	14	60	70	4	0	25	1.05
3108037--3108070	17	1.9	18	94	5	61	44	5	0	50	1.26
3108559--3108607	21	2.3	21	75	3	53	38	4	6	51	1.46
3112880--3112906	2	13.5	2	100	0	54	48	0	0	51	1.00
3113415--3113439	2	12.5	2	100	0	50	52	0	0	48	1.00
3115110--3115149	2	20.0	2	89	0	62	45	0	0	55	0.99
3115111--3115157	8	5.8	8	85	12	51	42	2	0	55	1.12
3116241--3116315	26	2.9	26	75	15	84	54	0	0	45	0.99
3116256--3116316	8	7.1	8	73	12	50	55	0	0	44	0.99
3116663--3116716	10	5.2	10	76	14	56	66	3	0	29	1.09
3116992--3117045	26	2.1	26	85	0	72	62	1	3	31	1.23
3117024--3117086	31	2.1	31	91	5	103	55	0	1	42	1.09
3117432--3117486	21	2.6	22	77	8	60	63	1	1	32	1.15
3117677--3117710	10	3.4	10	87	0	50	50	0	0	50	1.00
3119466--3119503	19	2.0	20	85	15	53	55	0	2	42	1.14
3127104--3127159	16	3.4	16	92	2	94	42	0	0	57	0.99
3127901--3127940	2	20.0	2	89	0	62	50	0	0	50	1.00
3127940--3127965	2	13.0	2	100	0	52	50	0	50	0	1.00
3128141--3128171	2	15.5	2	100	0	62	0	51	0	48	1.00
3128476--3128505	16	1.9	16	93	6	53	63	0	0	36	0.95
3128483--3128537	20	3.1	17	80	14	58	63	5	0	30	1.17
3129316--3129355	20	2.1	19	86	9	55	57	2	0	40	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3129453--3129530	32	2.3	32	77	12	77	34	2	0	62	1.09
3129606--3129652	18	2.6	18	89	0	67	44	6	2	46	1.40
3130600--3130694	44	2.2	44	96	0	172	26	9	9	54	1.63
3139245--3139271	2	13.5	2	100	0	54	48	0	0	51	1.00
3147843--3147876	3	11.3	3	100	0	68	64	0	0	35	0.94
3149932--3149978	17	2.7	18	80	12	53	27	0	2	70	0.99
3150254--3150297	22	2.0	21	82	4	52	65	2	2	29	1.16
3150516--3150621	9	10.7	10	68	22	55	46	0	0	53	1.00
3150516--3150619	16	5.7	19	70	25	66	46	0	0	53	1.00
3150512--3150619	28	4.1	28	74	16	97	45	0	0	54	0.99
3150516--3150594	20	4.2	20	75	19	73	48	0	0	51	1.00
3150582--3150641	23	2.5	24	84	10	79	36	1	0	61	1.06
3150539--3150630	29	3.1	29	75	13	80	43	0	0	56	0.99
3150603--3150657	20	2.6	21	77	5	58	29	3	0	67	1.08
3151286--3151329	2	22.0	2	85	0	61	45	2	4	47	1.35
3151384--3151443	30	2.1	30	87	6	88	35	1	1	61	1.16
3151741--3151843	34	3.0	33	79	13	84	58	2	0	38	1.13
3152595--3152684	37	2.4	37	83	10	103	57	2	2	37	1.23
3152631--3152725	11	8.1	11	69	18	50	62	0	0	37	0.96
3152627--3152729	21	5.0	21	75	15	83	61	0	0	38	0.96
3152629--3152735	37	3.0	35	78	20	116	59	0	0	40	0.97
3153976--3154017	22	2.0	21	85	4	57	54	0	2	42	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3160356--3160394	13	3.2	12	82	10	53	41	0	0	58	0.98
3160417--3160460	22	2.0	22	86	0	61	65	0	0	34	0.93
3160399--3160451	18	2.8	19	80	5	54	62	0	0	37	0.96
3161389--3161428	2	20.5	2	94	5	73	0	50	0	50	1.00
3166853--3166880	2	14.0	2	100	0	56	0	0	50	50	1.00
3170558--3170627	24	2.8	24	79	12	77	38	0	2	58	1.13
3170582--3170637	18	3.4	17	80	12	71	37	0	1	60	1.07
3170751--3170787	11	3.4	11	84	0	56	70	0	0	29	0.88
3170749--3170809	22	2.6	24	87	7	90	68	3	3	24	1.19
3170756--3170800	18	2.6	18	83	13	51	73	2	2	22	1.05
3170749--3170818	24	3.0	22	80	17	79	70	2	4	22	1.19
3173527--3173574	2	24.0	2	95	0	87	0	47	0	52	1.00
3173574--3173599	2	13.0	2	100	0	52	50	0	0	50	1.00
3177282--3177316	2	17.5	2	100	0	70	48	0	0	51	1.00
3178153--3178271	63	1.9	62	81	5	143	37	2	21	37	1.67
3186273--3186298	2	13.0	2	100	0	52	50	0	0	50	1.00
3188103--3188128	2	13.0	2	100	0	52	50	0	0	50	1.00
3191897--3191948	21	2.5	21	78	12	61	67	0	0	32	0.91
3191898--3191968	30	2.3	31	77	15	76	64	0	0	35	0.94
3191911--3191967	19	2.8	20	84	10	64	63	0	0	36	0.95
3192087--3192125	20	2.0	20	89	0	60	33	2	0	64	1.08
3192139--3192188	15	3.4	15	77	5	66	66	0	0	34	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3192142--3192191	14	3.5	14	83	5	73	66	0	0	34	0.92
3192129--3192191	29	2.1	31	91	5	103	60	0	0	39	0.97
3192439--3192463	11	2.3	11	100	0	50	48	0	0	52	1.00
3193885--3194067	34	5.4	34	88	0	260	25	7	26	39	1.83
3198456--3198640	34	5.5	34	88	0	264	25	7	26	40	1.82
3199387--3199453	24	2.9	23	80	10	75	47	0	0	52	1.00
3199397--3199459	12	5.5	12	75	16	53	46	1	0	52	1.10
3200443--3200479	12	3.1	13	85	14	53	67	0	0	32	0.91
3200431--3200478	25	1.9	25	83	8	62	66	2	0	31	1.03
3202840--3202920	40	2.0	40	97	0	153	40	23	9	25	1.85
3220366--3220412	2	23.5	2	95	0	85	46	0	0	53	1.00
3223411--3223439	12	2.3	13	94	5	51	0	17	0	82	0.66
3224772--3224803	15	2.1	16	94	5	57	78	3	12	6	1.06
3230513--3230568	29	1.9	29	88	0	85	41	10	19	28	1.85
3236887--3236915	13	2.1	14	93	6	51	34	0	0	65	0.93
3238108--3238164	26	2.1	27	93	3	98	14	17	3	64	1.41
3239421--3239449	15	1.9	15	100	0	58	37	6	0	55	1.27
3242627--3242668	15	2.9	15	85	3	50	42	0	0	57	0.99
3249718--3249755	2	19.0	2	100	0	76	0	50	0	50	1.00
3251018--3251089	31	2.4	29	80	15	76	41	4	4	50	1.41
3255272--3255303	16	2.1	15	94	5	55	21	12	28	37	1.90
3260704--3260748	2	22.5	2	90	0	72	46	48	4	0	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3261779--3261807	2	14.5	2	100	0	58	48	0	0	51	1.00
3261807--3261847	2	20.5	2	100	0	82	0	0	48	51	1.00
3269055--3269106	17	3.2	16	80	20	63	48	0	0	51	1.00
3269049--3269105	18	3.3	18	80	14	66	49	0	0	50	1.00
3271674--3271727	3	18.0	3	100	0	108	66	0	0	33	0.92
3272549--3272581	2	16.5	2	100	0	66	51	0	0	48	1.00
3273493--3273552	12	4.8	13	75	24	58	35	0	0	65	0.93
3273498--3273551	11	4.8	12	78	21	64	33	0	0	66	0.92
3273497--3273550	21	2.7	19	78	18	56	33	0	0	66	0.92
3273492--3273547	19	3.0	18	81	5	58	35	0	0	64	0.94

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