genome.fa.s58.2.7.7.80.10.50.1000.7.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: Scaffold58
Parameters: 2 7 7 80 10 50 1000
Length:  1582273

Tables:   1   2   3   4   5   6   7   8   9   10   

This is table  7  of  10  ( 1168 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)
1021451--1021561	27	4.0	29	75	15	101	63	0	0	36	0.95
1021467--1021549	27	3.2	25	83	10	103	66	0	0	33	0.92
1021479--1021566	30	2.9	30	73	9	81	61	0	0	38	0.96
1025885--1026059	87	2.0	86	93	3	298	38	16	18	26	1.91
1027532--1027586	25	2.4	21	82	14	65	52	0	0	47	1.00
1027734--1027802	22	3.0	22	76	18	61	57	1	1	39	1.16
1028114--1028143	2	15.0	2	100	0	60	50	0	0	50	1.00
1029116--1029140	1	25.0	1	100	0	50	100	0	0	0	0.00
1031311--1031430	27	4.2	27	72	23	86	42	0	0	57	0.98
1031334--1031428	16	6.1	16	65	28	53	42	0	0	57	0.98
1032722--1032792	34	2.1	34	81	5	81	50	1	0	47	1.09
1032776--1032814	19	2.0	20	90	5	62	38	0	0	61	0.96
1033472--1033507	19	1.9	19	94	5	65	52	2	0	44	1.15
1034056--1034088	16	2.0	17	88	5	50	21	3	3	72	1.11
1040345--1040472	39	3.3	39	94	2	220	61	15	8	14	1.55
1040351--1040472	40	3.1	40	96	1	219	61	15	9	13	1.56
1041968--1042004	2	18.5	2	100	0	74	51	0	0	48	1.00
1047545--1047579	6	5.8	6	93	0	61	45	0	2	51	1.16
1047647--1047686	21	1.9	21	90	10	64	42	0	0	57	0.98
1047678--1047740	23	2.6	23	85	7	81	50	1	1	46	1.20
1047629--1047740	51	2.3	49	78	19	119	51	0	0	46	1.13
1057065--1057089	3	8.3	3	100	0	50	32	0	0	68	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1057686--1057752	28	2.4	26	79	18	73	43	0	1	55	1.09
1057717--1057774	22	2.8	21	80	12	66	50	0	1	48	1.11
1057881--1057921	16	2.6	16	82	14	50	36	0	2	60	1.10
1059199--1059237	20	2.0	20	89	0	60	41	0	0	58	0.98
1059303--1059367	19	3.4	19	75	12	78	24	24	21	29	1.99
1059296--1059387	39	2.4	39	100	0	184	23	22	22	30	1.99
1059296--1059387	20	4.7	20	71	14	84	23	22	22	30	1.99
1060597--1060665	29	2.3	30	87	5	95	34	10	1	53	1.44
1060586--1060666	29	2.8	29	78	12	85	37	9	1	51	1.43
1060699--1060763	27	2.3	29	81	7	80	66	3	0	30	1.07
1064298--1064343	24	1.9	24	81	0	56	43	0	2	54	1.12
1065814--1065873	5	10.8	6	81	13	51	71	1	25	1	1.04
1080044--1080099	20	2.8	20	83	0	67	37	16	10	35	1.83
1085098--1085139	3	14.0	3	89	0	57	59	0	7	33	1.25
1088987--1089041	27	2.0	27	85	0	74	43	1	5	49	1.36
1089631--1089674	23	2.0	23	86	4	63	40	0	2	56	1.11
1090060--1090123	32	2.0	32	81	6	76	50	3	4	42	1.39
1090618--1090665	22	2.2	22	88	7	71	60	0	0	39	0.97
1090633--1090688	16	3.4	16	80	11	69	58	3	1	35	1.26
1090777--1090814	19	1.9	19	89	5	58	57	0	2	39	1.12
1094167--1094240	25	3.0	25	82	2	78	58	0	1	40	1.07
1094178--1094235	8	7.1	8	82	3	71	62	0	0	37	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1094251--1094311	27	2.2	28	83	13	83	55	0	0	44	0.99
1094745--1094802	29	2.0	30	83	10	75	53	5	1	39	1.33
1095131--1095181	15	3.4	14	76	12	57	54	1	0	43	1.11
1095136--1095183	14	3.3	14	75	11	51	54	2	0	43	1.12
1095134--1095192	30	2.1	28	81	12	68	52	3	0	44	1.17
1097658--1097704	21	2.3	21	85	3	60	42	6	10	40	1.65
1098090--1098153	31	2.1	31	90	0	101	40	15	7	35	1.76
1098931--1098965	4	8.8	4	93	0	61	25	25	0	48	1.51
1101072--1101111	21	2.0	20	85	5	53	50	0	2	47	1.14
1101424--1101505	29	2.8	30	78	12	89	58	7	0	34	1.26
1101438--1101524	29	3.1	29	75	12	85	60	5	0	33	1.20
1109428--1109635	104	2.0	104	91	1	337	49	19	10	20	1.77
1114536--1114575	15	2.5	16	88	8	55	57	0	0	42	0.98
1114536--1114578	16	2.6	17	85	10	63	55	0	0	44	0.99
1114645--1114698	24	2.3	24	84	9	67	64	3	0	31	1.11
1114979--1115036	15	4.0	14	76	12	55	0	22	0	77	0.77
1114979--1115035	22	2.6	23	78	10	66	0	21	0	78	0.74
1114979--1115035	8	7.7	7	74	18	53	0	21	0	78	0.74
1115215--1115293	31	2.4	32	81	8	79	54	5	7	32	1.51
1115378--1115419	17	2.6	16	82	14	50	61	7	4	26	1.42
1115506--1115548	16	2.7	15	83	13	52	9	11	0	79	0.95
1116198--1116242	22	2.0	24	83	16	60	66	6	0	26	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1116452--1116502	24	2.2	24	86	6	70	68	1	3	25	1.17
1116511--1116571	4	15.5	4	80	10	72	0	22	0	77	0.78
1116511--1116571	17	3.6	17	82	13	81	0	22	0	77	0.78
1117371--1117413	17	2.6	17	88	3	61	60	0	4	34	1.17
1117487--1117557	26	2.8	26	91	8	112	59	2	4	33	1.31
1119157--1119200	15	3.1	14	80	6	54	47	4	0	47	1.22
1119267--1119308	18	2.4	17	81	18	50	50	0	0	50	1.00
1119256--1119324	19	3.5	19	81	16	63	52	0	0	47	1.00
1119437--1119477	16	2.5	17	85	14	59	56	2	0	41	1.13
1119582--1119627	18	2.6	18	83	12	60	47	0	2	50	1.13
1120534--1120575	21	2.0	21	90	9	68	54	0	0	45	0.99
1124510--1124548	14	2.8	14	81	14	53	61	0	0	38	0.96
1124510--1124562	13	3.9	13	80	7	52	60	0	1	37	1.08
1124510--1124558	16	3.3	16	75	16	52	61	0	2	36	1.08
1124510--1124659	76	2.0	76	85	5	207	59	2	2	35	1.26
1131657--1131736	27	3.1	26	76	16	62	25	5	7	62	1.42
1131693--1131747	23	2.5	22	91	8	85	25	0	3	70	1.03
1132050--1132099	16	3.1	17	80	8	59	54	0	0	46	1.00
1132873--1132971	30	3.3	31	77	14	107	54	0	1	44	1.06
1132876--1132978	31	3.4	31	77	10	95	54	0	0	44	1.06
1133037--1133099	30	2.1	30	85	5	83	53	0	0	46	1.00
1133362--1133395	11	3.1	11	82	0	50	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1133493--1133602	46	2.4	46	93	0	184	28	19	12	40	1.88
1133705--1133741	11	3.4	11	84	0	56	37	0	0	62	0.96
1134325--1134370	24	2.0	24	86	4	67	43	0	0	56	0.99
1135876--1135913	19	2.0	19	85	10	51	39	2	0	57	1.12
1136902--1136951	22	2.3	22	89	0	73	70	0	24	6	1.10
1137479--1137532	23	2.4	21	80	17	63	20	3	11	64	1.40
1137716--1137754	21	1.9	21	84	5	53	23	12	5	58	1.54
1137967--1138049	45	2.0	41	81	11	96	39	7	18	34	1.78
1138513--1138547	18	1.9	18	88	0	52	28	5	5	60	1.43
1139156--1139203	11	4.5	11	80	12	55	29	2	2	66	1.14
1140674--1140716	22	2.0	22	85	0	59	72	0	6	20	1.08
1141157--1141201	2	22.5	2	81	0	54	46	0	0	53	1.00
1141169--1141211	20	2.2	20	86	0	59	48	0	0	51	1.00
1141165--1141213	24	2.0	24	84	0	62	51	0	0	48	1.00
1149922--1149946	2	12.5	2	100	0	50	52	48	0	0	1.00
1152995--1153036	12	3.3	13	83	12	52	61	0	0	38	0.96
1153891--1153979	32	2.7	32	76	10	99	53	4	2	39	1.33
1156462--1156511	22	2.3	23	76	20	61	48	0	0	52	1.00
1156546--1156622	38	2.0	36	85	14	100	49	0	0	50	1.00
1157008--1157047	12	3.2	12	89	7	53	47	5	0	47	1.24
1157257--1157283	2	13.5	2	100	0	54	48	0	0	51	1.00
1160591--1160630	21	1.9	21	85	10	55	37	0	0	62	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1164110--1164157	25	1.9	25	100	0	96	45	8	20	25	1.79
1164029--1164260	125	1.9	125	100	0	464	36	12	23	27	1.90
1166757--1166790	2	17.0	2	100	0	68	50	0	0	50	1.00
1166886--1166925	20	2.0	20	85	9	55	47	0	5	47	1.24
1167915--1167968	16	3.3	16	75	12	56	44	0	0	55	0.99
1177222--1177438	109	2.0	109	87	0	310	42	3	4	49	1.39
1177509--1177568	26	2.5	23	74	17	59	61	10	0	28	1.28
1178330--1178392	28	2.2	30	85	5	85	31	7	7	52	1.59
1179735--1179762	3	9.3	3	100	0	56	67	0	0	32	0.91
1179968--1179992	5	5.0	5	100	0	50	20	0	0	80	0.72

Tables:   1   2   3   4   5   6   7   8   9   10