genome.fa.s16.2.7.7.80.10.50.1000.19.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  19  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)
2922648--2922701	8	6.8	8	81	12	58	85	11	1	1	0.76
2922636--2922689	10	5.8	10	80	14	55	85	12	1	0	0.69
2922633--2922701	12	5.8	11	77	14	66	84	13	1	1	0.77
2923917--2924415	28	17.5	28	86	4	667	29	31	18	20	1.96
2924494--2924616	49	2.6	46	81	8	140	21	26	19	31	1.97
2929213--2929252	21	1.9	21	85	10	55	17	12	12	57	1.65
2929270--2929310	21	2.0	21	85	9	57	19	21	0	58	1.39
2933368--2933402	7	5.0	7	96	0	61	14	2	0	82	0.77
2934798--2934844	15	3.1	15	87	6	69	23	0	0	76	0.78
2934778--2934845	22	3.0	22	78	2	64	26	1	0	72	0.94
2935332--2935559	42	5.4	41	72	9	147	37	19	26	16	1.92
2939639--2939663	13	1.9	13	100	0	50	36	16	16	32	1.90
2939726--2939750	13	1.9	13	100	0	50	32	16	16	36	1.90
2939704--2939770	33	2.0	33	85	0	89	41	14	10	32	1.80
2946473--2946591	42	2.8	42	90	0	184	9	46	1	42	1.46
2946506--2946581	12	6.9	11	78	15	61	10	48	1	39	1.46
2946501--2946561	9	7.1	9	72	10	56	11	44	1	42	1.50
2948238--2948347	42	2.6	42	91	0	175	41	2	45	10	1.52
2960041--2960103	30	2.1	30	93	0	108	30	17	20	31	1.96
2967174--2967222	20	2.5	20	86	0	62	4	14	6	75	1.14
2967264--2967327	28	2.3	28	94	0	110	9	23	23	43	1.82
2967604--2967696	15	6.3	15	71	20	63	24	0	1	74	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2967590--2967671	22	3.8	21	73	22	71	21	0	3	74	0.97
2967590--2967695	8	12.9	8	68	16	56	21	0	2	75	0.93
2967991--2968093	52	2.0	51	83	7	127	33	16	15	34	1.90
2968141--2968204	32	2.0	33	87	3	94	42	15	14	28	1.86
2968193--2968233	20	2.0	20	85	0	55	24	12	24	39	1.89
2969945--2970077	49	2.7	49	95	0	230	27	18	14	39	1.89
2972373--2972751	79	4.8	77	79	5	298	26	24	15	33	1.95
2972379--2972674	158	1.9	158	80	5	357	27	25	14	33	1.94
2972373--2972751	158	2.4	158	78	6	356	26	24	15	33	1.95
2974819--2974849	4	7.8	4	100	0	62	22	0	0	77	0.77
2978755--2978821	37	1.9	35	88	11	102	29	25	11	32	1.92
2979285--2979323	13	3.0	13	88	0	60	38	17	12	30	1.88
2979456--2979592	53	2.6	53	95	1	247	27	17	18	37	1.93
2979562--2979632	20	3.5	20	77	11	74	29	14	16	39	1.88
2979672--2979712	21	2.0	21	85	9	57	39	9	12	39	1.76
2987574--2988276	61	11.5	61	85	4	857	25	26	19	29	1.98
2987570--2988276	123	5.8	121	87	3	875	25	26	19	29	1.98
2988268--2988512	41	5.8	41	73	12	147	22	24	12	40	1.88
2989109--2989163	20	2.8	20	100	0	110	25	14	14	45	1.83
2989110--2989213	20	4.8	20	78	19	91	26	16	14	42	1.86
2991566--2991834	50	5.3	51	89	2	348	27	26	14	31	1.95
2995689--2996042	154	2.3	151	82	7	410	32	8	6	52	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2996472--2996577	55	1.9	56	96	1	196	53	13	16	16	1.72
3001843--3002236	152	2.6	152	78	4	391	25	17	18	39	1.91
3001998--3002466	154	3.1	151	77	6	442	27	18	16	37	1.92
3004234--3004341	42	2.6	42	92	0	180	10	46	2	40	1.52
3004249--3004319	18	3.6	18	69	20	52	9	43	2	43	1.52
3005641--3006279	319	2.0	319	96	0	1179	28	26	12	32	1.92
3009748--3010117	152	2.4	153	79	3	404	27	17	18	37	1.93
3009767--3010183	152	2.7	151	79	5	367	28	17	18	35	1.94
3010882--3011199	160	2.0	160	86	1	449	38	21	15	24	1.92
3016616--3016658	20	2.2	20	100	0	86	30	13	20	34	1.92
3019479--3019588	40	2.8	40	81	2	123	42	19	7	30	1.78
3020615--3020670	26	2.0	28	86	10	80	19	7	7	66	1.40
3026977--3027034	12	4.8	12	84	16	84	12	48	0	39	1.40
3026977--3027034	24	2.4	24	100	0	116	12	48	0	39	1.40
3030854--3030985	42	3.1	42	89	2	185	44	2	44	8	1.46
3038199--3038274	12	6.9	11	75	15	52	39	2	48	9	1.49
3038198--3038283	24	3.8	24	72	17	85	41	2	45	10	1.51
3038189--3038307	42	2.8	42	92	0	193	42	2	46	8	1.47
3043615--3043669	20	2.7	21	82	5	76	32	18	10	38	1.85
3045499--3045566	28	2.4	28	87	0	100	29	30	20	19	1.97
3046603--3046671	13	5.5	13	77	6	70	33	11	18	36	1.87
3046604--3046671	25	2.7	25	79	4	75	33	11	19	35	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3046604--3046662	12	4.7	13	72	8	50	33	11	16	37	1.86
3047228--3047284	28	2.0	28	86	0	78	35	33	22	8	1.85
3047195--3047465	97	2.8	97	85	0	364	31	32	18	16	1.94
3047732--3047917	80	2.3	80	76	3	212	26	26	17	29	1.98
3049437--3049849	226	1.8	225	94	0	736	29	17	13	39	1.88
3053182--3054161	159	6.2	159	79	5	925	37	12	18	32	1.88
3054075--3054249	88	2.0	86	85	2	233	36	8	20	34	1.83
3054389--3055019	159	4.0	159	73	8	437	37	12	17	32	1.87
3057201--3057276	12	6.9	11	75	15	52	39	2	48	9	1.49
3057200--3057285	24	3.8	24	72	17	85	41	2	45	10	1.51
3057191--3057309	42	2.8	42	92	0	193	42	2	46	8	1.47
3062622--3062918	158	1.9	159	81	3	366	36	11	18	34	1.87
3062631--3063217	296	2.0	296	78	6	618	35	12	20	32	1.89
3063046--3063336	159	1.8	159	80	4	354	37	11	19	30	1.88
3063417--3063695	149	1.9	150	83	3	366	41	10	18	29	1.85
3063962--3064256	144	2.0	146	81	5	339	38	11	16	33	1.84
3064108--3064554	159	2.8	159	79	6	446	37	11	19	31	1.87
3064538--3064601	32	2.0	32	96	0	119	34	7	18	39	1.80
3069334--3069409	12	6.9	11	75	15	52	39	2	48	9	1.49
3069333--3069418	24	3.8	24	72	17	85	41	2	45	10	1.51
3069324--3069442	42	2.8	42	90	0	184	43	2	45	8	1.47
3074889--3075007	42	2.8	42	92	0	193	8	46	2	42	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3074922--3074997	12	6.9	11	75	15	52	9	48	2	39	1.49
3074913--3074998	24	3.8	24	72	17	85	10	45	2	41	1.51
3074904--3074974	18	3.6	18	69	20	52	9	43	2	43	1.52
3080610--3080651	21	2.0	22	95	4	77	80	4	9	4	0.99
3081422--3081471	9	5.6	9	82	0	64	44	4	42	10	1.56
3081425--3081471	18	2.6	18	96	0	85	44	4	40	10	1.59
3081392--3081513	60	2.0	60	90	0	190	45	2	43	9	1.49
3081443--3081528	42	2.0	42	90	0	136	43	3	44	9	1.53
3088788--3088863	12	6.9	11	75	15	52	39	2	48	9	1.49
3088787--3088872	24	3.8	24	72	17	85	41	2	45	10	1.51
3088778--3088896	42	2.8	42	90	0	184	43	2	45	8	1.47
3097138--3097256	42	2.8	42	92	0	193	8	46	2	42	1.47
3097171--3097246	12	6.9	11	75	15	52	9	48	2	39	1.49
3097162--3097247	24	3.8	24	72	17	85	10	45	2	41	1.51
3097153--3097223	18	3.6	18	69	20	52	9	43	2	43	1.52
3099394--3099623	103	2.2	103	83	1	300	35	14	23	26	1.93
3102010--3102127	59	2.0	58	93	1	200	27	22	20	29	1.98
3102025--3102124	29	3.4	29	69	13	96	25	22	22	31	1.98
3108223--3108341	42	2.8	42	92	0	193	8	46	2	42	1.47
3108256--3108331	12	6.9	11	75	15	52	9	48	2	39	1.49
3108247--3108332	24	3.8	24	72	17	85	10	45	2	41	1.51
3108238--3108308	18	3.6	18	69	20	52	9	43	2	43	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3108818--3108850	12	2.5	14	90	9	52	66	6	15	12	1.42
3113052--3113133	33	2.5	33	91	0	128	45	0	42	12	1.41
3113061--3113133	21	3.3	22	76	16	71	42	0	43	13	1.44
3113062--3113128	12	5.9	11	77	18	66	40	0	46	13	1.43
3113082--3113161	42	1.9	42	92	0	133	41	1	46	11	1.48
3113064--3113142	12	6.9	12	73	20	55	43	0	43	13	1.44
3120133--3120755	310	2.0	310	92	0	1048	34	21	19	25	1.96
3122700--3123002	79	3.8	79	79	6	285	33	13	25	27	1.93
3122781--3122838	28	2.0	31	86	10	86	31	15	27	25	1.96
3128012--3128076	12	5.7	12	71	23	59	12	47	0	40	1.41

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