genome.fa.s16.2.7.7.80.10.50.1000.20.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: Scaffold16
Parameters: 2 7 7 80 10 50 1000
Length:  5287347

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   34   35   

This is table  20  of  35  ( 4175 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)
3128004--3128085	33	2.5	33	91	0	128	10	43	1	43	1.47
3129736--3129809	28	2.6	28	85	4	96	27	22	25	24	2.00
3129764--3130001	79	3.0	78	79	4	269	32	14	25	27	1.94
3129797--3130001	81	2.6	79	81	6	234	33	12	24	28	1.92
3149590--3150284	157	4.4	154	73	8	472	32	16	12	38	1.86
3151556--3151674	42	2.8	42	92	0	193	8	46	2	42	1.47
3151589--3151664	12	6.9	11	75	15	52	9	48	2	39	1.49
3151580--3151665	24	3.8	24	72	17	85	10	45	2	41	1.51
3151571--3151641	18	3.6	18	69	20	52	9	43	2	43	1.52
3155225--3155769	147	3.7	147	89	1	803	30	18	12	38	1.88
3155667--3157664	158	12.6	158	74	6	1348	31	18	12	36	1.88
3155648--3157466	632	2.9	629	86	3	2316	31	18	12	36	1.88
3158294--3158745	157	2.9	154	73	7	408	37	12	18	31	1.88
3158673--3158984	104	3.0	104	96	0	563	32	11	22	34	1.89
3158884--3159948	159	6.8	159	73	9	758	36	11	19	32	1.87
3160276--3160364	16	5.6	16	75	4	72	40	29	13	16	1.87
3160269--3160395	32	4.0	32	82	6	134	39	27	15	17	1.90
3160275--3160396	48	2.5	48	83	0	136	39	27	15	17	1.90
3160309--3160395	16	5.4	16	81	0	111	39	29	17	13	1.88
3160350--3160474	56	2.2	56	88	1	180	43	26	12	17	1.85
3161471--3161575	22	4.8	22	97	0	201	34	28	16	20	1.94
3161450--3161575	44	2.9	43	88	4	119	34	30	15	19	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3161570--3161691	16	7.6	16	77	7	113	40	32	13	13	1.82
3161570--3161694	48	2.6	47	82	5	144	42	32	12	12	1.81
3161747--3161857	16	7.0	16	72	9	66	43	33	11	11	1.78
3161546--3161886	166	2.0	167	96	1	632	42	30	12	15	1.83
3161736--3161797	32	2.0	31	87	3	88	46	33	11	8	1.69
3161880--3161914	15	2.3	15	95	0	61	45	40	5	8	1.58
3162011--3162435	158	2.7	157	79	8	450	39	10	19	31	1.85
3163480--3163549	34	2.1	34	94	0	122	31	12	11	44	1.78
3163701--3164235	156	3.4	158	76	7	391	38	11	18	31	1.86
3163932--3164236	157	1.9	157	83	5	393	37	11	17	32	1.86
3168403--3168451	23	2.0	25	84	7	66	73	0	0	26	0.83
3168816--3168857	12	3.3	12	87	12	66	54	11	23	9	1.66
3173914--3173956	23	2.0	20	86	13	59	74	0	18	6	1.04
3174236--3174265	16	1.9	15	93	6	51	80	3	10	6	1.01
3175701--3175929	89	2.6	87	80	6	246	30	24	14	30	1.95
3176254--3177262	42	23.9	42	74	7	558	20	29	17	33	1.95
3176295--3178407	126	16.6	126	74	8	1193	18	29	18	33	1.95
3176245--3177270	85	12.1	84	77	6	771	19	29	17	33	1.95
3176245--3178407	168	12.8	169	74	8	1134	18	29	18	33	1.95
3177214--3177331	59	2.0	59	86	3	166	21	28	16	33	1.95
3177286--3178409	42	26.9	42	71	9	430	17	29	19	33	1.95
3177268--3178409	84	13.7	83	78	6	857	17	29	19	33	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3178005--3178453	163	2.7	163	81	7	403	16	28	19	35	1.93
3178978--3179037	14	4.5	14	71	25	58	70	1	1	26	1.07
3178978--3179037	27	2.3	25	81	16	68	70	1	1	26	1.07
3179386--3179427	12	3.3	12	81	12	57	52	11	26	9	1.68
3179494--3179563	30	2.4	28	86	9	95	52	11	20	15	1.73
3180588--3180642	23	2.3	22	79	14	56	72	7	12	7	1.26
3183766--3184149	152	2.5	153	78	10	363	37	11	18	32	1.86
3186749--3186831	37	2.3	37	85	2	105	22	9	14	53	1.70
3187691--3187715	13	1.9	13	100	0	50	32	16	16	36	1.90
3187670--3187733	32	2.0	33	87	3	94	29	17	14	39	1.88
3187701--3187753	19	2.7	19	82	2	61	33	16	13	35	1.88
3189754--3189804	17	2.8	18	79	5	59	41	0	7	50	1.31
3190508--3190562	28	2.0	28	100	0	110	43	14	12	29	1.82
3195479--3195523	17	2.6	17	85	3	54	42	2	4	51	1.34
3198173--3198207	11	3.1	11	92	8	61	40	34	0	25	1.56
3198692--3198814	42	2.9	42	88	1	174	8	47	2	41	1.46
3198729--3198804	12	6.9	11	75	15	52	9	50	2	38	1.49
3206315--3206443	59	2.2	61	88	6	194	21	18	12	47	1.81
3208334--3208360	13	2.1	13	100	0	54	29	14	14	40	1.86
3219067--3219096	2	15.0	2	100	0	60	50	0	0	50	1.00
3220238--3220268	13	2.4	13	94	0	53	35	12	16	35	1.87
3220217--3220284	33	2.1	33	88	5	102	36	17	13	32	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3220313--3220368	19	2.9	19	91	2	85	35	17	16	30	1.92
3220353--3220379	13	2.1	13	100	0	54	40	14	14	29	1.86
3220923--3220999	22	3.5	22	87	3	111	24	33	3	37	1.74
3222888--3222912	13	1.9	13	100	0	50	40	16	16	28	1.89
3229154--3229181	13	2.2	13	100	0	56	42	14	14	28	1.84
3233887--3234831	81	11.6	81	80	2	822	42	12	21	23	1.87
3233922--3234812	163	5.5	163	83	1	923	42	12	21	23	1.86
3233925--3234831	244	3.7	243	81	4	934	42	12	21	23	1.86
3234950--3234974	12	2.1	12	100	0	50	32	0	8	60	1.26
3235398--3235725	91	3.6	92	80	4	376	29	12	28	29	1.93
3237263--3237316	11	5.2	10	82	10	56	1	12	1	83	0.81
3237261--3237299	11	3.5	11	89	6	60	2	12	0	84	0.72
3237263--3237316	14	3.9	14	77	15	58	1	12	1	83	0.81
3241338--3241810	155	3.0	157	79	4	440	38	20	17	23	1.93
3242807--3242871	33	2.0	33	84	6	87	35	13	13	36	1.85
3242903--3242962	20	3.0	20	82	7	86	36	18	13	31	1.89
3242903--3242958	19	2.8	20	91	2	87	37	17	14	30	1.90
3242943--3242969	13	2.1	13	100	0	54	40	14	14	29	1.86
3245469--3245495	13	2.1	13	100	0	54	40	14	14	29	1.86
3249339--3249381	21	2.1	21	87	12	63	27	13	4	53	1.60
3251664--3251717	19	2.8	20	88	2	74	37	16	14	31	1.89
3255630--3255830	52	3.9	52	92	0	321	29	16	18	34	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3255819--3255843	13	1.9	13	100	0	50	36	16	16	32	1.90
3255884--3255950	33	2.0	33	88	0	98	40	14	11	32	1.83
3255906--3255930	13	1.9	13	100	0	50	32	16	16	36	1.90
3256815--3257256	52	9.0	49	81	10	458	33	16	24	26	1.96
3256886--3257261	95	3.9	93	80	13	415	32	16	24	26	1.96
3256886--3257261	147	2.6	143	91	3	603	32	16	24	26	1.96
3257249--3257323	33	2.4	32	88	6	118	18	17	36	28	1.94
3257256--3257319	33	1.9	34	96	3	121	17	18	35	28	1.93
3257310--3257569	37	7.4	36	87	7	335	33	11	35	20	1.88
3257431--3257593	37	5.0	30	83	11	141	30	13	33	22	1.92
3257312--3257569	141	1.8	141	88	3	394	33	11	34	20	1.88
3259035--3259146	1	112.0	1	76	0	89	0	0	13	86	0.57
3259038--3259139	6	17.5	6	79	17	117	0	0	13	86	0.58
3259035--3259146	43	2.6	44	85	9	167	0	0	13	86	0.57
3268833--3268857	10	2.5	10	100	0	50	80	20	0	0	0.72
3272978--3273106	52	2.5	52	98	0	249	28	17	17	35	1.93
3273115--3273139	13	1.9	13	100	0	50	36	16	16	32	1.90
3273180--3273246	33	2.0	33	88	0	98	40	14	11	32	1.83
3273202--3273226	13	1.9	13	100	0	50	32	16	16	36	1.90
3274458--3274813	165	2.2	165	82	4	414	48	10	10	31	1.70
3276877--3276924	25	2.0	25	84	12	64	54	2	0	43	1.12
3277199--3277548	154	2.3	155	84	3	470	39	21	16	23	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3277452--3277631	95	1.9	95	87	0	261	36	23	17	22	1.95
3279213--3279443	117	2.0	117	91	0	372	30	13	11	44	1.79
3279741--3280234	165	3.0	165	79	7	425	49	9	10	30	1.70
3279816--3280244	165	2.6	164	81	8	508	50	9	10	29	1.68
3281734--3281838	42	2.5	42	78	6	113	41	17	18	22	1.89
3281688--3282929	44	28.6	44	72	7	506	40	15	23	20	1.91
3281697--3282929	88	14.2	87	74	8	660	40	15	23	20	1.91
3281690--3282804	132	8.5	131	75	7	654	40	15	23	20	1.90
3282650--3282806	43	3.6	44	78	9	133	37	15	24	21	1.93
3282945--3283190	48	5.1	48	86	2	343	41	19	20	18	1.91

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   34   35