genome.fa.s25.2.7.7.80.10.50.1000.53.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  53  of  56  ( 6609 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)
9093529--9093651	63	1.9	64	95	1	221	13	17	36	31	1.89
9093642--9094723	71	15.7	70	85	8	1240	34	12	33	20	1.89
9093662--9094723	34	30.9	35	85	9	1284	34	12	33	20	1.89
9093667--9094723	105	10.2	102	87	8	1343	34	12	33	20	1.90
9094569--9094746	34	6.0	28	83	11	173	28	14	35	20	1.92
9094536--9094773	61	3.9	59	78	15	220	30	14	34	20	1.92
9094665--9094752	27	3.2	27	91	3	131	27	14	35	22	1.93
9094727--9094902	31	5.7	31	83	5	187	27	17	28	25	1.98
9094727--9094902	62	2.8	62	84	5	207	27	17	28	25	1.98
9098841--9098918	21	3.7	21	84	3	104	38	12	14	34	1.84
9099029--9099054	13	2.0	13	100	0	52	30	15	15	38	1.88
9099009--9099074	33	2.0	33	87	0	96	25	15	16	42	1.87
9101523--9101596	27	2.7	28	89	6	107	24	32	20	22	1.98
9101581--9101802	52	4.3	51	80	2	219	29	25	12	32	1.93
9101410--9101912	263	1.9	263	88	2	767	28	26	13	31	1.94
9101736--9101940	107	1.9	108	81	1	250	26	27	16	30	1.96
9101815--9102020	80	2.6	79	82	3	236	23	30	16	28	1.97
9101815--9102048	80	2.9	77	77	6	234	25	29	14	30	1.95
9105651--9106548	28	30.9	29	84	7	1033	23	18	30	28	1.97
9105650--9106548	58	15.5	56	83	7	977	23	18	30	28	1.97
9107742--9107832	10	9.2	10	76	10	73	2	2	9	85	0.76
9107764--9107832	1	69.0	1	79	0	66	1	1	8	88	0.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9107742--9107832	26	3.7	23	82	15	94	2	2	9	85	0.76
9107740--9107832	32	3.0	32	81	9	95	2	2	10	84	0.78
9107742--9107832	27	3.3	28	79	11	98	2	2	9	85	0.76
9107742--9107832	11	8.4	11	78	8	80	2	2	9	85	0.76
9107764--9107830	25	2.7	26	81	6	75	1	1	8	88	0.65
9121121--9121162	6	6.8	6	81	13	50	78	0	19	2	0.86
9124120--9124250	43	3.2	41	80	9	131	16	21	19	41	1.90
9124146--9124268	41	3.0	41	78	7	122	17	22	18	41	1.90
9124342--9124657	66	4.8	66	83	1	346	18	22	18	40	1.92
9124446--9124547	32	3.1	32	63	25	77	19	25	17	37	1.94
9124554--9124684	32	4.0	31	71	20	106	16	25	16	41	1.89
9124342--9124657	132	2.4	132	84	0	416	18	22	18	40	1.92
9124635--9124703	32	2.2	32	87	7	97	18	27	14	39	1.90
9124697--9124806	41	2.6	42	76	8	116	20	18	16	45	1.86
9126838--9126867	7	4.1	7	95	4	51	80	0	3	16	0.85
9129361--9129436	34	2.3	32	77	14	84	36	0	3	59	1.16
9130787--9130816	9	3.4	9	90	9	53	10	10	0	80	0.92
9133720--9133771	24	2.3	23	83	6	61	51	7	5	34	1.54
9135970--9136060	45	2.0	45	89	0	137	27	23	20	28	1.99
9137334--9137385	23	2.2	23	82	3	59	63	0	1	34	1.06
9137896--9137934	19	2.0	20	90	5	62	41	2	5	51	1.38
9137918--9138149	122	1.9	122	86	5	335	52	12	6	28	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9138433--9138462	12	2.5	12	94	0	51	0	16	0	83	0.65
9139146--9139184	21	1.9	20	89	5	60	35	2	0	61	1.10
9140405--9140563	82	1.9	82	88	5	241	37	6	25	30	1.82
9144756--9144807	15	3.5	14	81	7	50	44	0	5	50	1.26
9144929--9145200	134	2.0	133	80	4	307	39	10	3	46	1.56
9146135--9146170	15	2.3	16	95	4	65	25	0	13	61	1.33
9146135--9146176	15	2.8	15	89	7	50	28	0	14	57	1.38
9146922--9146966	21	2.2	21	88	11	67	51	0	0	48	1.00
9147509--9147566	6	9.7	6	88	7	82	36	0	0	63	0.94
9147508--9147578	18	3.6	18	75	16	61	38	0	0	61	0.96
9147744--9147801	27	2.2	25	80	14	64	62	0	0	37	0.96
9147774--9147800	8	3.4	8	100	0	54	66	0	0	33	0.92
9148629--9148658	14	2.1	14	93	0	51	33	3	0	63	1.11
9148744--9148854	26	4.3	25	72	13	91	45	0	2	51	1.15
9148744--9148854	25	4.3	24	72	13	78	45	0	2	51	1.15
9148830--9148906	26	3.0	26	66	22	63	51	0	0	48	1.00
9152829--9152858	12	2.5	12	100	0	60	13	10	13	63	1.52
9158321--9158384	15	4.2	15	72	7	58	56	1	0	42	1.09
9161422--9161624	16	12.2	16	74	14	117	43	0	1	54	1.11
9161423--9161517	47	2.0	49	87	4	140	42	0	1	56	1.06
9161422--9161610	32	5.7	31	73	17	139	42	0	2	55	1.12
9161567--9161624	17	3.6	17	71	17	52	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9161909--9162042	40	3.3	40	87	4	155	34	12	24	28	1.92
9162285--9162329	18	2.5	18	83	16	58	48	0	35	15	1.45
9166307--9166411	40	2.6	40	92	3	176	31	10	28	29	1.90
9166427--9166465	20	2.0	20	84	0	51	35	7	23	33	1.83
9166663--9166707	18	2.5	18	83	16	58	48	0	35	15	1.45
9168804--9168829	13	2.0	13	100	0	52	38	15	15	30	1.88
9171047--9171091	21	2.1	21	84	8	56	53	4	20	22	1.63
9175052--9175172	52	2.3	52	97	0	224	28	18	18	34	1.94
9175052--9175192	52	2.7	51	90	4	212	30	17	18	33	1.94
9175181--9175205	13	1.9	13	100	0	50	36	16	16	32	1.90
9175271--9175295	13	1.9	13	100	0	50	32	16	16	36	1.90
9175249--9175315	33	2.0	33	91	0	107	41	11	11	34	1.79
9176192--9177077	49	18.7	49	82	9	1092	30	18	25	25	1.97
9176183--9177077	92	9.5	92	89	5	1122	31	17	25	25	1.97
9177077--9177146	33	2.1	35	94	5	126	20	17	37	25	1.94
9177131--9178270	34	34.6	36	78	16	830	32	12	34	20	1.90
9177260--9177313	27	2.0	27	92	0	90	22	14	40	22	1.90
9177220--9178264	61	16.1	61	76	15	508	31	12	34	20	1.90
9177653--9177768	27	4.0	26	75	20	115	25	14	37	21	1.92
9177225--9178259	455	2.3	438	88	10	1283	31	12	34	20	1.90
9178143--9178196	27	2.0	27	92	0	90	22	14	40	22	1.90
9177281--9178230	489	1.9	483	90	3	1510	31	12	35	20	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9179301--9179331	15	2.1	15	93	0	53	48	16	22	12	1.80
9181336--9181415	20	3.8	20	75	15	79	26	15	15	43	1.85
9181401--9181439	13	3.0	13	96	0	69	30	17	15	35	1.91
9183981--9184006	13	2.0	13	100	0	52	38	15	15	30	1.88
9185661--9185798	71	1.9	72	85	7	192	40	10	17	31	1.83
9186852--9187384	58	9.1	58	74	6	287	29	12	14	43	1.82
9186879--9187304	115	3.6	117	75	8	343	29	11	15	43	1.82
9187039--9187129	29	3.1	29	68	12	69	26	9	16	47	1.78
9187164--9187304	60	2.4	58	81	8	153	29	13	13	43	1.82
9191719--9191758	18	2.2	19	90	4	64	52	17	12	17	1.74
9197850--9197946	30	3.6	29	70	25	95	46	12	15	25	1.81
9197833--9197945	50	2.3	50	90	0	181	44	12	15	27	1.83
9198649--9198806	61	2.6	61	81	2	174	35	12	25	26	1.91
9198804--9199037	32	7.3	32	75	8	165	22	16	30	29	1.96
9198802--9199086	63	4.5	64	77	6	226	23	16	30	30	1.96
9199135--9199213	31	2.5	31	85	0	113	36	16	21	25	1.94
9199042--9199445	145	2.8	144	82	4	429	27	17	26	28	1.98
9199403--9199468	32	2.0	32	85	2	87	27	18	27	27	1.98
9199012--9199534	28	17.7	30	79	8	372	26	17	27	28	1.98
9199534--9199755	32	6.8	32	76	5	185	34	12	30	22	1.91
9199543--9199833	34	8.8	34	74	8	183	37	12	27	23	1.90
9199542--9199776	66	3.6	66	85	1	305	35	12	28	22	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9199606--9199833	100	2.3	100	80	6	264	38	11	25	24	1.89
9205821--9205929	51	2.2	51	89	1	166	47	9	15	27	1.76
9207111--9207249	56	2.5	56	83	3	163	39	20	19	20	1.93
9207079--9207405	56	5.9	54	74	6	147	39	17	18	24	1.91
9207376--9207484	55	2.0	55	90	0	173	36	16	20	26	1.93
9208577--9208620	11	3.9	11	80	14	54	2	18	2	77	0.98
9208576--9208618	23	2.0	23	90	9	72	2	18	2	76	1.00
9210002--9210051	16	3.1	16	85	2	64	48	30	16	6	1.70
9209977--9210040	32	2.0	32	81	9	76	45	29	18	6	1.74
9210839--9210872	17	2.1	17	88	5	52	58	0	2	38	1.13

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   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56