genome.fa.s2.2.7.7.80.10.50.1000.20.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   36   37   38   

This is table  20  of  38  ( 4457 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)
3033399--3033786	101	3.8	99	76	10	315	23	26	17	32	1.96
3033404--3033732	153	2.2	152	86	3	428	23	25	17	32	1.97
3034245--3034321	20	3.8	20	72	6	75	32	19	9	38	1.83
3046600--3046673	21	3.5	21	83	10	98	37	12	16	33	1.85
3046768--3046822	20	2.8	20	82	0	74	23	14	16	45	1.84
3049368--3049436	28	2.5	28	86	11	97	21	31	20	26	1.98
3049205--3049493	107	2.7	108	83	4	352	27	27	15	29	1.96
3049393--3049596	78	2.6	79	82	2	232	24	29	17	28	1.97
3061902--3061953	12	4.2	13	85	9	65	84	9	5	0	0.77
3061900--3061959	29	2.1	28	84	9	77	85	8	6	0	0.76
3062938--3064047	55	19.4	54	81	10	1056	26	28	20	24	1.99
3063197--3063286	29	3.2	29	62	15	71	27	30	18	23	1.98
3062937--3064047	288	3.9	283	85	6	1340	26	28	20	24	1.99
3062963--3064024	343	3.1	342	89	3	1550	26	28	20	24	1.99
3064778--3064854	21	3.7	21	83	10	95	37	12	15	33	1.86
3064965--3064990	13	2.0	13	100	0	52	30	15	15	38	1.88
3064945--3065011	33	2.0	33	88	0	98	25	14	16	43	1.86
3067449--3067517	27	2.5	28	85	2	86	26	31	20	21	1.98
3067558--3067629	28	2.6	28	89	8	103	22	33	19	25	1.97
3067395--3067683	107	2.7	108	85	4	370	27	28	14	28	1.96
3067583--3067785	77	2.6	79	81	3	241	24	29	17	29	1.97
3070378--3070449	18	3.9	17	77	13	72	83	11	4	1	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3070377--3070455	19	4.2	18	73	15	70	82	11	5	1	0.89
3070396--3070449	15	3.4	15	82	14	56	83	12	1	1	0.81
3071667--3072220	28	19.5	28	81	3	561	31	29	16	22	1.96
3072315--3072469	48	3.2	48	87	0	211	21	27	14	36	1.92
3073024--3073240	20	10.3	20	71	15	143	29	18	11	39	1.87
3073024--3073237	40	5.6	39	75	13	187	29	18	12	39	1.87
3074157--3074195	20	2.1	19	85	9	53	23	10	10	56	1.63
3083209--3083302	20	4.7	20	79	19	106	41	11	18	28	1.85
3086947--3087691	47	15.8	47	73	5	446	39	15	22	22	1.92
3086947--3087696	141	5.3	141	74	6	550	39	15	22	22	1.92
3086942--3087696	94	8.0	94	78	4	549	39	15	22	22	1.92
3089620--3089650	15	2.0	15	93	6	53	0	16	0	83	0.64
3091895--3092232	130	2.6	131	81	4	389	42	12	25	19	1.86
3092002--3092907	86	10.8	84	77	8	826	42	12	25	18	1.86
3091949--3092238	131	2.2	130	83	1	357	43	12	25	18	1.85
3092015--3092907	168	5.3	168	85	3	1091	42	12	25	19	1.86
3091890--3092908	44	24.1	43	72	13	535	42	12	25	19	1.86
3092919--3093621	62	11.4	62	83	3	826	30	20	26	23	1.98
3094015--3094058	23	1.9	24	86	9	65	40	22	6	29	1.80
3100193--3100226	15	2.2	16	89	5	52	26	14	2	55	1.53
3103516--3103575	32	1.9	31	86	3	84	3	11	6	78	1.06
3105267--3105304	20	1.9	20	94	0	67	39	13	13	34	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3111989--3112566	79	7.5	79	76	6	439	35	13	24	26	1.92
3111990--3112402	226	1.8	224	84	4	553	35	14	23	26	1.93
3112243--3112587	159	2.2	157	81	3	361	36	12	23	27	1.91
3115249--3115310	19	3.6	19	71	24	73	32	14	19	33	1.92
3115267--3115291	13	1.9	13	100	0	50	32	20	16	32	1.94
3115249--3115323	32	2.3	32	95	0	132	32	16	18	33	1.93
3115340--3115395	20	2.8	20	97	0	103	37	14	8	39	1.77
3115362--3115460	33	3.0	33	89	2	146	30	16	13	40	1.86
3115382--3115442	13	5.2	13	74	22	62	29	16	14	39	1.88
3115394--3115460	20	3.7	20	70	25	76	28	16	13	41	1.86
3116920--3116958	21	1.9	20	85	15	53	53	5	0	41	1.23
3122298--3122651	152	2.3	152	80	3	406	38	19	16	24	1.92
3123061--3123525	159	2.9	158	84	3	594	40	13	11	34	1.81
3124367--3124726	140	2.6	142	84	2	451	42	13	12	31	1.81
3126158--3126229	34	2.1	35	84	7	94	55	12	13	18	1.69
3126597--3126623	13	2.1	13	100	0	54	40	14	14	29	1.86
3126579--3126642	33	2.0	32	90	3	101	40	15	15	28	1.88
3129714--3129791	20	3.9	19	76	6	75	34	12	14	38	1.84
3129714--3129791	40	2.0	39	84	2	102	34	12	14	38	1.84
3130701--3130754	22	2.5	22	96	3	101	18	11	9	61	1.55
3136716--3136740	13	1.9	13	100	0	50	36	16	16	32	1.90
3138350--3138383	3	11.3	3	93	0	59	35	0	35	29	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3142112--3142152	21	2.0	21	85	9	57	39	12	9	39	1.76
3147756--3147781	13	2.0	13	100	0	52	38	15	15	30	1.88
3147738--3147802	32	2.0	32	87	6	94	43	15	13	27	1.85
3153413--3153487	38	2.0	38	97	0	141	32	20	28	20	1.97
3153929--3153989	19	3.1	19	75	13	61	29	13	13	44	1.81
3154351--3154413	33	1.9	33	83	6	83	33	11	15	39	1.83
3157686--3157739	20	2.8	20	88	2	74	33	22	11	33	1.89
3158336--3158801	167	2.9	164	83	6	569	50	9	12	28	1.70
3159727--3159761	16	2.2	16	94	0	61	14	20	25	40	1.90
3160882--3160925	22	2.0	22	95	0	79	36	2	9	52	1.46
3161634--3161701	20	3.5	19	76	13	57	58	1	0	39	1.07
3161649--3161713	27	2.4	27	80	17	80	55	1	0	43	1.09
3161627--3161759	29	4.5	28	68	22	76	57	0	0	40	1.09
3161645--3161784	29	4.9	27	69	19	72	57	0	0	41	1.09
3162243--3162289	22	2.1	22	88	7	69	61	0	0	38	0.96
3162781--3162842	29	2.1	29	82	11	74	35	0	1	62	1.05
3166929--3166985	30	1.9	29	82	10	71	42	0	1	56	1.10
3169484--3169538	15	3.7	15	80	7	58	38	0	0	61	0.96
3169618--3169669	18	2.9	19	77	11	56	59	1	0	38	1.08
3171709--3171937	20	10.8	20	66	14	109	31	15	13	39	1.86
3171840--3171889	24	2.1	24	84	0	64	30	14	14	42	1.84
3171800--3171928	64	2.0	63	90	1	204	31	14	14	38	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3172849--3172901	23	2.3	23	100	0	106	16	13	9	60	1.58
3185928--3185983	1	56.0	1	81	0	58	89	10	0	0	0.49
3185928--3186013	10	8.3	10	84	13	104	84	11	2	1	0.76
3185928--3185984	29	2.0	29	96	0	105	87	12	0	0	0.54
3187246--3188769	28	52.6	28	84	6	1684	28	29	18	23	1.98
3187246--3188769	114	13.2	113	84	6	1704	28	29	18	23	1.98
3187246--3188769	142	10.5	140	86	4	1718	28	29	18	23	1.98
3188848--3188973	49	2.7	47	84	7	157	20	26	20	31	1.98
3191562--3191664	33	3.1	33	88	0	161	37	12	19	30	1.89
3191597--3191681	20	4.6	19	76	21	83	38	14	17	29	1.89
3191614--3191644	13	2.4	13	88	0	53	38	12	16	32	1.86
3191697--3191751	20	2.8	20	85	0	74	43	9	16	30	1.79
3192394--3192575	42	4.2	43	75	12	158	43	13	25	17	1.85
3192565--3192906	61	5.7	61	84	5	446	27	19	29	24	1.98
3192565--3192906	121	2.9	122	86	4	457	27	19	29	24	1.98
3192565--3192906	182	1.9	178	87	3	506	27	19	29	24	1.98
3194263--3194329	33	2.0	33	85	0	89	35	11	11	40	1.79
3194283--3194307	13	1.9	13	100	0	50	36	16	16	32	1.90
3194370--3194395	13	2.0	13	100	0	52	30	15	15	38	1.88
3194383--3194511	52	2.5	52	90	0	204	34	17	17	31	1.92
3202695--3202902	79	2.6	79	84	3	276	34	10	24	30	1.89
3202842--3202953	51	2.2	50	82	6	127	37	5	21	35	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3203048--3203120	28	2.6	29	82	12	98	24	19	31	24	1.98
3202893--3203169	107	2.6	107	78	6	328	33	13	24	28	1.93
3205525--3205644	20	5.6	20	75	21	109	43	15	15	25	1.86
3208166--3208292	49	2.6	49	97	0	236	33	18	26	20	1.96
3208433--3209072	28	22.5	28	81	5	685	24	17	29	29	1.97
3208403--3209072	57	11.7	57	82	5	705	24	17	29	28	1.97
3208401--3209072	200	3.4	200	84	4	831	24	17	29	28	1.97
3217137--3217162	13	2.0	13	100	0	52	30	15	15	38	1.88
3217117--3217181	32	2.0	33	87	3	96	27	13	16	41	1.87
3223147--3223194	24	2.0	25	83	4	62	27	6	16	50	1.69

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   36   37   38