genome.fa.s16.2.7.7.80.10.50.1000.34.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  34  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)
5068080--5068467	52	7.4	51	70	15	233	30	25	12	32	1.92
5068187--5068261	27	2.7	29	89	6	111	25	34	18	21	1.96
5068450--5068526	28	2.8	28	82	7	86	23	35	19	22	1.96
5068080--5068576	264	1.9	263	89	2	766	29	26	12	31	1.93
5068480--5068671	79	2.4	79	81	1	215	25	29	17	28	1.97
5072713--5072787	27	2.7	28	87	2	98	25	34	18	21	1.96
5072818--5072993	52	3.4	52	83	3	228	30	26	11	31	1.92
5072607--5072993	52	7.4	52	70	13	222	29	24	12	33	1.92
5072976--5073052	28	2.8	28	83	0	82	23	33	19	23	1.97
5072607--5073103	264	1.9	263	88	2	764	28	25	13	32	1.93
5073006--5073210	79	2.6	79	81	1	223	23	31	17	27	1.97
5074554--5074597	23	1.9	23	81	9	54	40	22	6	29	1.80
5075074--5075124	19	2.6	20	78	3	68	35	13	19	31	1.91
5075789--5075854	25	2.5	28	74	18	68	6	18	3	72	1.18
5077272--5077345	28	2.6	27	71	23	62	47	17	13	21	1.82
5077271--5077566	58	5.1	57	75	10	192	49	14	12	23	1.78
5077332--5077403	29	2.5	28	72	18	67	54	12	9	23	1.67
5077332--5077579	58	4.3	58	76	8	200	50	12	13	23	1.76
5077334--5077555	116	1.9	116	83	5	288	49	13	12	24	1.77
5079829--5079871	21	2.0	21	82	8	52	30	30	18	20	1.97
5079897--5080020	20	5.8	20	70	20	81	29	17	14	38	1.89
5082320--5082435	51	2.3	53	82	5	132	30	25	12	31	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5082377--5082594	76	2.8	77	82	5	235	27	28	13	30	1.94
5082418--5082592	76	2.3	78	85	3	237	27	27	14	30	1.95
5082526--5082644	51	2.3	51	89	0	184	31	24	11	32	1.91
5082577--5082859	79	3.6	77	82	5	334	26	24	13	34	1.93
5082450--5082723	130	2.1	127	86	2	377	28	24	13	33	1.94
5084165--5084202	15	2.5	15	82	0	58	26	5	7	60	1.46
5091023--5091048	13	2.0	13	100	0	52	38	15	15	30	1.88
5091319--5091432	51	2.3	50	92	1	183	27	17	14	41	1.88
5094233--5094266	15	2.3	15	100	0	68	55	8	23	11	1.63
5095282--5095323	21	2.0	21	90	0	66	30	26	0	42	1.55
5095403--5095473	34	2.1	34	84	5	90	16	32	1	49	1.55
5100177--5100305	52	2.5	52	98	0	249	30	17	17	34	1.93
5100379--5100445	33	2.0	33	88	0	98	40	14	11	32	1.83
5100401--5100425	13	1.9	13	100	0	50	32	16	16	36	1.90
5101217--5101345	67	1.9	67	81	6	154	39	12	25	22	1.89
5101510--5101795	52	5.7	52	87	6	380	34	19	23	22	1.97
5101608--5101800	95	2.1	96	83	3	241	34	18	24	22	1.96
5101661--5101800	43	3.1	44	78	9	147	32	18	25	23	1.97
5101788--5101855	32	2.2	31	87	7	102	16	20	35	27	1.94
5101816--5101943	56	2.2	56	85	9	161	23	17	30	28	1.97
5101848--5101969	29	4.3	29	85	6	171	25	17	27	29	1.97
5103115--5103167	1	53.0	1	80	0	61	1	1	5	90	0.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5103109--5103166	16	3.8	15	82	14	66	1	1	8	87	0.67
5103091--5103167	9	8.4	9	81	9	59	1	1	12	84	0.75
5116888--5117016	52	2.5	52	96	0	240	30	18	17	34	1.94
5117077--5117143	33	2.0	33	88	0	98	40	14	11	32	1.83
5117099--5117123	13	1.9	13	100	0	50	32	16	16	36	1.90
5122195--5122225	12	2.6	12	94	0	53	25	32	0	41	1.56
5123808--5123862	20	2.8	20	85	0	74	30	21	10	36	1.88
5123849--5123873	13	1.9	13	100	0	50	32	16	16	36	1.90
5125573--5125622	20	2.4	21	86	3	66	38	18	22	22	1.94
5125659--5125795	51	2.7	52	84	5	174	29	14	14	41	1.86
5130406--5130561	48	3.3	47	75	11	120	43	14	12	29	1.82
5130472--5130599	48	2.6	48	80	6	134	41	13	12	32	1.82
5130698--5130791	29	3.2	28	73	14	82	46	12	11	28	1.77
5130698--5130885	59	3.2	58	80	3	223	47	15	10	26	1.78
5132568--5132613	24	1.9	24	86	8	67	32	13	15	39	1.85
5132709--5132862	35	4.3	35	72	13	123	42	11	12	34	1.78
5143753--5143857	53	2.0	53	81	3	122	41	20	8	29	1.81
5144179--5144332	30	5.2	29	65	16	75	48	13	9	28	1.74
5144135--5144360	59	3.9	59	81	4	235	47	14	9	28	1.75
5144190--5144333	29	4.9	29	68	13	105	50	13	9	27	1.71
5144113--5144379	59	4.5	59	80	6	233	47	14	8	29	1.74
5144978--5145025	9	5.1	9	80	7	51	2	16	0	81	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5144978--5145019	19	2.2	19	87	8	59	0	19	0	80	0.70
5145476--5145525	20	2.5	20	90	0	73	38	16	20	26	1.92
5147854--5147905	19	2.6	19	78	6	59	44	0	0	55	0.99
5148328--5148441	31	3.6	32	68	26	82	32	2	2	62	1.23
5150197--5150226	13	2.2	14	94	5	53	50	0	0	50	1.00
5150753--5150787	13	2.7	13	90	0	52	40	5	0	54	1.24
5150759--5150822	13	5.2	12	78	14	51	45	4	1	48	1.32
5151512--5151552	21	2.0	21	90	9	66	46	2	0	51	1.14
5151777--5151812	16	2.3	15	86	13	54	50	5	5	38	1.49
5151780--5151812	17	2.0	16	94	5	57	48	6	6	39	1.53
5151924--5151962	18	2.1	19	86	13	55	51	2	2	43	1.29
5152077--5152157	25	3.3	24	70	19	60	43	0	0	56	0.99
5152068--5152158	16	5.8	16	71	22	61	42	0	0	57	0.99
5152071--5152192	17	7.4	16	72	17	81	39	0	0	59	1.03
5152068--5152158	48	1.9	47	84	8	123	42	0	0	57	0.99
5152092--5152165	24	3.1	24	77	11	80	43	0	0	56	0.99
5153182--5153298	59	2.0	59	100	0	234	23	19	15	41	1.90
5158161--5158199	6	6.5	6	100	0	78	17	0	82	0	0.68
5161197--5161226	10	3.0	10	95	0	51	0	13	0	86	0.57
5163954--5163987	15	2.2	16	94	5	61	64	2	17	14	1.40
5164323--5164596	95	2.9	95	98	0	539	33	7	12	46	1.69
5164585--5164626	16	2.6	16	88	0	66	21	9	23	45	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5164582--5164653	37	1.9	38	82	2	92	19	11	18	51	1.75
5164711--5164767	28	2.0	28	100	0	114	35	10	14	40	1.80
5164756--5164790	16	2.2	16	94	0	61	34	11	8	45	1.71
5164904--5164956	16	3.2	16	83	2	70	32	7	7	52	1.58
5167870--5167916	16	3.0	15	90	9	76	38	0	4	57	1.18
5167862--5167944	16	5.1	16	82	7	69	27	1	13	57	1.43
5168116--5168171	18	3.2	17	87	12	78	41	1	1	55	1.21
5168322--5168369	24	2.0	23	84	4	60	58	4	0	37	1.18
5169401--5169432	16	2.0	16	93	0	55	12	15	31	40	1.85
5172263--5172288	6	4.3	6	100	0	52	34	0	0	65	0.93
5173784--5173863	35	2.3	35	100	0	160	32	21	16	30	1.95
5174249--5174294	21	2.1	23	84	8	60	56	15	2	26	1.50
5174314--5174359	19	2.4	19	81	0	65	80	4	2	13	0.95
5174509--5174544	17	2.1	17	89	0	54	61	22	11	5	1.50
5174703--5174731	13	2.2	13	100	0	58	51	0	31	17	1.45
5174867--5174906	19	2.0	20	90	4	64	55	5	7	32	1.50
5174918--5174961	20	2.0	22	83	12	56	31	0	4	63	1.14
5175040--5175073	16	2.1	17	94	5	61	50	0	0	50	1.00
5176707--5176762	19	2.8	20	86	2	78	37	14	16	32	1.88
5177679--5177742	33	1.9	33	87	6	94	25	20	31	23	1.98
5179068--5179119	21	2.5	20	75	6	50	51	0	15	32	1.43
5179213--5179250	13	2.9	13	84	0	58	34	13	13	39	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5185437--5185492	19	2.8	20	91	2	87	37	16	16	30	1.90
5185477--5185503	13	2.1	13	100	0	54	40	14	14	29	1.86
5187712--5187759	24	2.0	25	83	4	62	20	8	16	54	1.68
5188777--5188830	20	2.7	20	91	5	83	35	18	12	33	1.89
5188859--5188911	19	2.7	19	85	2	61	33	16	18	30	1.94
5189514--5189555	22	1.9	22	90	0	66	21	33	4	40	1.74
5197464--5197497	16	2.1	16	94	0	59	47	0	8	44	1.34
5200264--5200370	41	2.6	40	76	8	99	21	24	12	42	1.87
5200298--5200411	41	2.8	41	86	0	138	18	25	15	40	1.90
5201282--5201329	24	2.0	25	83	4	62	31	8	6	54	1.55

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