genome.fa.s48.2.7.7.80.10.50.1000.21.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  21  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)
3161544--3161585	21	2.0	21	85	0	57	57	0	2	40	1.12
3162142--3162331	64	3.0	64	96	0	344	17	15	10	56	1.67
3162307--3162355	3	16.3	3	100	0	98	32	0	0	67	0.91
3165061--3165127	28	2.3	31	73	17	72	47	0	0	52	1.00
3171670--3171698	13	2.1	14	93	6	51	13	0	0	86	0.58
3171670--3171698	7	4.3	7	91	8	51	13	0	0	86	0.58
3172823--3172851	2	14.5	2	100	0	58	48	0	0	51	1.00
3173235--3173264	6	5.0	6	95	0	51	63	0	0	36	0.95
3173336--3173378	3	14.3	3	100	0	86	32	0	0	67	0.91
3173500--3173566	26	2.6	26	75	0	71	35	1	1	61	1.15
3173547--3173585	17	2.4	17	87	12	55	41	0	0	58	0.98
3174132--3174173	19	2.2	19	86	4	57	50	2	0	47	1.14
3177260--3177378	34	3.5	33	86	8	177	42	28	6	22	1.79
3181785--3181903	34	3.5	33	84	8	168	42	27	6	23	1.79
3182590--3182685	31	2.9	32	84	9	106	67	5	2	25	1.22
3182627--3182665	19	2.1	18	86	13	53	71	2	0	25	0.98
3182625--3182677	10	5.2	10	76	10	54	75	1	0	22	0.90
3184728--3184762	2	17.5	2	93	0	61	48	2	0	48	1.16
3185127--3185160	17	2.0	17	88	11	52	52	0	0	47	1.00
3186171--3186226	14	4.4	14	70	21	50	51	0	7	41	1.29
3186181--3186224	23	1.9	23	100	0	88	50	0	6	43	1.29
3187939--3187985	13	3.4	13	81	16	58	63	0	0	36	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3187930--3187997	29	2.3	29	87	2	91	52	0	0	47	1.00
3192907--3192936	14	2.1	14	93	0	51	76	0	0	23	0.78
3193398--3193440	17	2.5	18	85	7	54	72	0	0	27	0.85
3193759--3193819	12	5.1	12	78	13	54	60	0	0	39	0.97
3193800--3193854	23	2.4	25	82	14	73	60	0	0	40	0.97
3193800--3193861	23	2.7	22	80	9	70	58	0	0	41	0.98
3193816--3193898	32	2.5	33	79	13	98	53	0	0	46	1.00
3193834--3193882	14	3.2	14	76	18	53	51	0	0	48	1.00
3193835--3193897	17	3.9	16	76	17	58	50	0	0	49	1.00
3194071--3194320	123	2.0	123	95	0	446	33	19	24	23	1.97
3194342--3194381	2	20.0	2	100	0	80	50	0	50	0	1.00
3196802--3196830	2	14.5	2	100	0	58	51	48	0	0	1.00
3196830--3196872	2	22.0	2	85	4	61	48	2	2	46	1.27
3198632--3198671	19	2.0	21	85	9	57	62	0	0	37	0.95
3199172--3199238	2	34.0	2	87	3	91	50	1	2	44	1.26
3199164--3199229	33	2.0	33	100	0	132	51	3	6	39	1.42
3200511--3200555	13	3.2	13	79	14	54	55	0	0	44	0.99
3208240--3208307	21	3.1	21	75	12	57	45	0	0	54	0.99
3208236--3208300	19	3.3	19	68	10	51	47	0	0	52	1.00
3208313--3208359	15	2.9	16	81	9	51	53	0	0	46	1.00
3208425--3208449	12	2.1	12	100	0	50	64	0	16	20	1.30
3208456--3208488	11	3.0	11	83	16	50	27	0	0	72	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3208571--3208626	22	2.5	22	85	5	69	25	0	5	69	1.09
3208590--3208628	11	3.5	11	89	0	51	25	0	2	71	0.98
3208877--3208922	22	2.0	24	87	8	69	34	0	0	65	0.93
3208951--3209005	17	3.4	16	80	11	67	38	3	3	54	1.36
3210126--3210167	17	2.4	18	84	11	61	54	4	0	40	1.21
3210287--3210311	13	1.9	13	100	0	50	36	0	0	64	0.94
3210948--3211017	8	7.9	8	71	20	50	37	0	0	62	0.95
3210955--3210997	10	4.1	11	79	8	54	30	0	0	69	0.88
3210948--3211017	19	3.8	19	80	12	74	37	0	0	62	0.95
3210948--3210989	13	3.0	15	80	16	54	33	0	0	66	0.92
3210972--3211020	18	2.8	16	84	12	53	42	0	0	57	0.99
3211005--3211085	20	4.0	21	80	13	82	45	0	0	54	0.99
3211038--3211095	30	2.0	28	83	6	71	39	0	0	60	0.97
3211385--3211426	2	21.5	2	90	4	68	52	0	0	47	1.00
3211547--3211595	15	3.3	15	73	21	50	53	0	2	44	1.12
3214805--3214845	12	3.6	11	84	15	57	46	0	0	53	1.00
3215369--3215407	16	2.4	17	84	16	55	48	0	0	51	1.00
3219490--3219575	43	2.0	43	100	0	172	30	9	13	46	1.75
3219499--3219568	22	3.2	22	63	25	58	34	8	14	42	1.76
3219496--3219587	43	2.1	43	92	4	150	35	10	11	41	1.77
3221033--3221066	15	2.3	15	94	0	59	61	11	14	11	1.56
3221113--3221154	20	2.2	19	91	4	66	52	0	11	35	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3224551--3224637	35	2.4	37	81	13	108	42	0	0	57	0.98
3224564--3224661	35	2.8	35	81	9	112	36	1	0	62	1.02
3231887--3231914	13	2.2	13	100	0	56	39	17	14	28	1.89
3231869--3231934	33	2.0	33	85	5	89	40	13	15	30	1.85
3232983--3233054	32	2.3	31	81	11	83	45	0	1	52	1.09
3232497--3233071	284	2.0	283	92	0	961	34	7	6	50	1.57
3232974--3233061	20	4.9	19	68	25	66	43	1	1	54	1.15
3233329--3233381	20	2.6	22	80	17	69	50	0	5	43	1.25
3233329--3233380	21	2.6	19	82	8	59	51	0	5	42	1.25
3233342--3233413	35	2.1	34	82	7	85	48	4	5	41	1.45
3233439--3233490	20	2.7	20	82	11	72	51	11	1	34	1.49
3233538--3233574	13	2.7	15	80	20	53	35	0	0	64	0.94
3244528--3244590	28	2.3	27	82	12	76	52	1	1	44	1.20
3247159--3247268	55	2.0	55	92	0	184	39	13	20	27	1.90
3247357--3247390	16	2.1	17	94	5	61	41	0	0	58	0.98
3247515--3247567	26	2.0	26	100	0	106	45	11	7	35	1.69
3252809--3252871	20	3.1	20	81	2	72	57	4	1	36	1.30
3252834--3252871	11	3.7	10	83	16	51	60	2	0	36	1.11
3252836--3252908	31	2.3	32	77	15	80	56	6	1	35	1.35
3256907--3256953	2	23.5	2	100	0	94	51	0	0	48	1.00
3257209--3257253	22	2.0	23	91	8	74	64	0	0	35	0.94
3257218--3257255	11	3.3	12	78	14	53	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3269120--3269144	2	12.5	2	100	0	50	48	0	52	0	1.00
3269865--3269935	36	2.0	36	100	0	142	53	7	19	19	1.68
3272262--3272286	10	2.5	10	100	0	50	0	8	0	92	0.40
3275534--3275569	13	2.8	13	91	0	54	55	0	0	44	0.99
3276941--3276983	17	2.4	18	84	3	52	25	0	9	65	1.22
3277018--3277087	23	3.1	22	73	15	63	45	0	0	54	0.99
3280066--3280114	2	24.5	2	100	0	98	51	48	0	0	1.00
3284342--3284376	2	17.5	2	100	0	70	48	0	0	51	1.00
3288487--3288597	22	5.1	21	72	15	82	63	0	0	35	1.00
3288487--3288556	11	6.1	11	73	15	61	65	0	1	32	1.01
3288521--3288575	17	3.1	18	76	10	60	69	0	0	30	0.89
3288521--3288635	8	13.8	8	72	17	58	61	0	0	38	0.96
3288521--3288604	19	4.9	18	72	16	63	64	0	0	35	0.94
3288521--3288635	32	3.4	34	81	13	121	61	0	0	38	0.96
3294149--3294282	38	3.5	38	87	0	187	30	26	11	32	1.91
3294460--3294530	17	4.4	17	79	10	78	36	0	1	61	1.05
3295996--3296028	3	11.0	3	100	0	66	66	0	0	33	0.92
3298112--3298186	32	2.5	29	77	12	89	41	4	1	53	1.28
3298112--3298193	33	2.5	32	80	13	94	40	3	2	53	1.32
3300245--3300278	2	17.0	2	93	0	59	47	0	2	50	1.16
3305505--3305550	20	2.3	18	80	20	56	65	0	0	34	0.93
3305487--3305552	22	3.2	22	75	16	61	60	1	0	37	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3306051--3306102	17	3.2	16	78	7	61	51	0	1	46	1.12
3307868--3307893	2	13.0	2	100	0	52	50	0	0	50	1.00
3309398--3309477	39	2.1	39	97	0	151	42	28	7	21	1.80
3311074--3311098	2	12.5	2	100	0	50	52	0	0	48	1.00
3313046--3313107	23	2.7	22	78	14	63	46	4	1	46	1.33
3313194--3313246	3	17.7	3	90	0	79	35	0	1	62	1.06
3317062--3317139	26	3.1	26	72	5	70	43	0	1	55	1.08
3321111--3321153	18	2.6	16	81	7	50	58	0	0	41	0.98
3321111--3321148	18	2.2	18	86	9	53	60	0	0	39	0.97
3321484--3321511	13	2.2	13	100	0	56	57	0	0	42	0.99

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