genome.fa.s2.2.7.7.80.10.50.1000.28.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  28  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)
4246827--4247043	58	3.7	57	78	3	209	26	26	13	33	1.93
4248296--4248869	164	3.5	163	79	8	500	30	11	8	50	1.67
4249311--4249361	11	4.8	11	77	15	54	70	0	25	3	1.04
4249311--4249368	21	2.7	22	81	10	66	70	0	24	5	1.07
4249565--4249643	39	2.0	39	97	0	149	24	18	12	44	1.85
4251246--4251675	155	2.8	155	82	3	501	24	16	20	39	1.92
4253496--4253567	20	3.6	20	71	14	76	36	15	16	31	1.90
4253497--4253588	40	2.3	40	94	0	157	32	15	18	33	1.92
4262638--4262662	13	1.9	13	100	0	50	32	16	20	32	1.94
4264708--4264737	15	2.0	15	93	0	51	13	23	13	50	1.77
4271105--4271178	38	1.9	38	97	0	139	39	9	28	22	1.85
4272261--4272341	19	4.2	18	71	13	54	40	13	14	30	1.85
4272372--4272397	13	2.0	13	100	0	52	30	15	15	38	1.88
4272384--4272442	21	2.9	21	89	2	93	25	16	15	42	1.88
4285684--4285733	9	5.9	8	81	11	55	84	10	6	0	0.79
4285693--4285734	17	2.5	17	81	18	52	80	9	9	0	0.89
4285693--4285748	9	6.6	8	76	11	58	80	7	12	0	0.90
4285684--4285734	26	2.0	26	92	0	84	82	9	7	0	0.85
4286802--4287539	61	12.4	61	85	6	783	25	27	20	26	1.99
4286707--4286898	100	1.9	100	79	4	217	26	28	17	28	1.97
4286831--4287544	116	6.0	118	84	7	774	25	27	20	26	1.99
4287520--4287685	42	3.8	43	81	12	180	19	27	12	39	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4287520--4287685	89	1.9	85	85	7	226	19	27	12	39	1.88
4288456--4288488	13	2.5	13	100	0	66	33	15	18	33	1.92
4288505--4288546	21	2.0	21	100	0	84	42	9	19	28	1.82
4288533--4288558	13	2.0	13	100	0	52	30	15	15	38	1.88
4288545--4288603	21	2.9	21	89	2	93	25	16	15	42	1.88
4290932--4291075	52	2.8	52	88	0	216	30	26	10	32	1.90
4291052--4291148	27	3.6	27	84	5	126	24	31	18	24	1.97
4291101--4291362	79	3.3	78	80	4	285	27	25	15	32	1.95
4294038--4294115	32	2.5	31	76	10	79	23	15	30	30	1.95
4294097--4294557	28	16.5	28	75	9	251	24	18	30	27	1.98
4294247--4294405	84	1.9	84	94	0	282	25	19	30	24	1.98
4295811--4295853	1	43.0	1	80	0	50	4	0	4	90	0.54
4295811--4295853	16	2.8	15	89	10	61	4	0	4	90	0.54
4295812--4295855	21	2.0	21	86	4	61	4	0	6	88	0.62
4303929--4304057	52	2.5	52	98	0	249	28	17	17	35	1.93
4304066--4304090	13	1.9	13	100	0	50	36	16	16	32	1.90
4304134--4304197	33	2.0	32	90	3	101	40	14	12	32	1.83
4305117--4305770	52	12.7	52	82	3	743	33	17	23	25	1.96
4305109--4305770	104	6.4	104	91	2	1038	33	17	24	25	1.96
4305790--4305913	28	4.3	29	84	9	157	17	16	29	36	1.92
4305904--4305978	35	2.2	34	83	9	98	36	9	33	21	1.85
4305958--4306132	29	6.1	29	77	7	160	26	17	28	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4305957--4306132	57	3.1	59	79	9	193	27	17	27	27	1.97
4307016--4307041	13	2.0	13	100	0	52	30	15	15	38	1.88
4307080--4307155	21	3.7	21	80	3	100	28	17	11	42	1.84
4307101--4307173	20	3.6	20	81	3	101	31	19	13	35	1.91
4307080--4307173	41	2.3	41	98	0	179	29	18	12	39	1.88
4308763--4308802	18	2.4	17	83	8	55	0	0	17	82	0.67
4322023--4322151	52	2.5	52	90	0	213	28	16	18	36	1.93
4322160--4322184	13	1.9	13	100	0	50	36	16	16	32	1.90
4322245--4322271	13	2.1	13	100	0	54	40	14	14	29	1.86
4323190--4323802	52	11.8	52	83	1	800	34	17	23	24	1.96
4323183--4323815	104	6.1	104	94	0	1124	34	17	23	24	1.96
4331196--4331359	20	7.7	20	79	12	139	40	13	12	32	1.82
4331275--4331369	50	1.9	50	95	0	172	44	10	16	28	1.81
4334007--4334083	23	3.3	24	83	7	97	10	22	16	50	1.75
4334252--4334454	82	2.5	82	82	0	235	7	20	15	56	1.64
4336698--4336822	20	5.7	20	69	18	88	30	18	11	40	1.85
4351961--4352454	28	17.5	28	85	4	575	29	30	17	21	1.96
4352942--4353436	28	17.5	28	85	4	593	29	30	17	22	1.96
4354349--4354425	20	3.8	20	89	0	127	31	18	12	37	1.88
4355567--4355607	21	2.0	21	85	9	57	39	12	9	39	1.76
4355994--4356019	13	2.0	13	100	0	52	38	15	15	30	1.88
4355976--4356039	32	2.0	33	90	3	103	39	18	14	28	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4358227--4358271	21	2.1	21	84	8	56	53	4	20	22	1.63
4360073--4360103	15	2.1	15	93	0	53	48	16	22	12	1.80
4362178--4362203	13	2.0	13	100	0	52	30	15	15	38	1.88
4363974--4364040	33	2.0	33	88	0	98	34	11	13	40	1.81
4363994--4364018	13	1.9	13	100	0	50	36	16	16	32	1.90
4364081--4364105	13	1.9	13	100	0	50	32	16	16	36	1.90
4364114--4364237	52	2.4	52	94	1	214	35	18	17	28	1.94
4367472--4367514	21	2.0	21	100	0	86	27	23	20	27	1.99
4372506--4372685	31	5.7	31	82	10	224	24	30	17	27	1.97
4372505--4372716	63	3.4	62	82	9	252	24	30	16	29	1.96
4372505--4372749	31	7.8	31	81	8	219	23	30	16	30	1.96
4372506--4372685	94	1.9	94	90	2	290	24	30	17	27	1.97
4372662--4373160	33	15.0	34	79	13	497	20	31	12	35	1.90
4372789--4372840	27	1.9	27	96	0	95	23	38	17	21	1.93
4372665--4373159	70	7.4	70	86	6	547	20	31	12	34	1.91
4373159--4373357	32	6.2	32	92	0	317	27	37	18	17	1.93
4372819--4373208	105	3.8	102	81	11	268	21	33	11	33	1.90
4373363--4374416	43	22.7	47	86	6	1280	25	26	18	30	1.98
4373363--4374416	373	2.8	367	90	5	1625	25	26	18	30	1.98
4374429--4374555	67	1.9	68	85	1	175	24	25	12	37	1.90
4379833--4379884	21	2.4	21	77	3	59	23	9	3	63	1.41
4382086--4382136	20	2.6	20	90	3	77	25	13	17	43	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4382529--4382561	12	2.9	11	91	8	57	81	0	18	0	0.68
4386101--4386393	79	3.7	78	79	8	290	32	12	26	28	1.92
4386152--4386393	79	3.1	80	85	4	298	32	13	26	28	1.93
4386261--4386318	28	2.0	28	86	6	80	34	17	25	22	1.96
4386355--4386421	28	2.4	28	100	0	134	29	14	28	26	1.96
4386276--4386504	107	2.1	107	89	1	352	30	15	27	27	1.96
4386370--4386581	79	2.7	75	80	8	244	33	14	24	27	1.94
4386302--4386476	51	3.3	51	68	16	149	29	14	28	28	1.95
4386198--4386767	186	3.1	185	83	7	699	33	13	24	28	1.93
4386461--4386690	107	2.1	107	84	2	309	33	15	22	27	1.95
4386543--4386611	28	2.5	28	82	0	93	36	21	17	24	1.95
4386569--4386953	159	2.5	157	80	8	421	34	13	23	29	1.93
4386566--4386953	78	5.0	78	81	7	389	34	13	23	28	1.93
4389958--4390139	75	2.4	74	77	4	186	40	15	23	20	1.91
4390153--4390776	59	10.5	59	84	4	691	27	18	26	26	1.98
4391723--4391758	16	2.2	16	95	0	63	0	19	0	80	0.71
4391718--4391778	7	8.6	7	84	10	54	0	13	4	81	0.83
4391737--4391815	29	2.7	28	86	5	95	0	3	13	82	0.81
4391744--4391809	20	3.3	19	85	4	78	0	3	15	81	0.80
4395380--4395753	184	2.0	184	99	0	739	35	15	18	30	1.92
4398651--4398681	13	2.4	13	94	0	53	32	16	12	38	1.86
4398633--4398746	33	3.5	33	87	4	167	27	14	14	43	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4398686--4398746	13	5.2	13	75	22	71	27	14	14	42	1.85
4398697--4398734	20	1.9	20	100	0	76	26	18	15	39	1.91
4401086--4401205	51	2.4	51	85	2	152	30	21	13	34	1.92
4401271--4401325	28	2.0	28	85	7	76	21	20	18	40	1.92
4401334--4401500	51	3.3	50	80	5	201	30	29	10	29	1.90
4416849--4416898	19	2.6	19	93	0	82	36	20	10	34	1.86
4417341--4417390	8	5.9	8	81	9	55	84	12	2	2	0.80
4417342--4417410	21	3.4	19	78	11	66	82	10	5	1	0.89
4417342--4417399	27	2.1	29	87	12	86	82	10	5	1	0.89
4417343--4417410	17	3.8	17	79	16	66	82	10	5	1	0.90

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