genome.fa.s116.2.7.7.80.10.50.1000.4.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: Scaffold116
Parameters: 2 7 7 80 10 50 1000
Length:  1263769

Tables:   1   2   3   4   5   

This is table  4  of  5  ( 557 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)
846849--846906	23	2.6	23	80	2	64	25	1	3	68	1.14
847810--847859	16	3.1	17	75	13	52	48	0	0	52	1.00
848714--848774	30	2.1	29	82	14	72	50	0	1	47	1.10
848840--848904	19	3.3	18	71	24	60	47	1	1	49	1.20
852549--852578	2	15.0	2	100	0	60	50	0	0	50	1.00
855264--855319	20	2.6	22	77	8	62	51	1	0	46	1.11
855639--855663	2	12.5	2	100	0	50	0	52	0	48	1.00
855756--855799	23	1.9	23	85	0	61	43	4	0	52	1.22
867672--867710	5	7.8	5	97	0	51	89	0	10	0	0.48
877483--877513	9	3.4	9	90	0	53	9	0	90	0	0.46
879724--879758	3	11.7	3	87	0	52	31	5	0	62	1.18
879724--879758	12	2.9	12	95	0	61	31	5	0	62	1.18
895527--895604	27	3.1	27	65	24	80	32	14	3	50	1.61
895508--895604	47	2.0	48	98	2	187	32	12	4	50	1.59
902013--902050	2	19.5	2	94	5	69	50	0	0	50	1.00
904068--904105	2	19.0	2	94	0	67	47	0	2	50	1.15
916814--916847	2	17.0	2	100	0	68	50	0	0	50	1.00
918232--918278	19	2.5	19	80	10	53	53	0	0	46	1.00
918277--918327	20	2.5	20	84	6	68	62	0	1	35	1.06
918410--918438	2	14.5	2	100	0	58	51	0	0	48	1.00
919477--919508	2	16.0	2	100	0	64	50	0	0	50	1.00
922176--922243	29	2.4	28	80	9	75	55	1	2	39	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
944078--944141	27	2.4	27	81	0	83	10	21	31	35	1.88
947912--948004	47	2.0	47	91	0	150	30	21	15	33	1.94
961653--961677	2	12.5	2	100	0	50	48	0	0	52	1.00
967412--967439	2	14.0	2	100	0	56	50	0	0	50	1.00
974359--974388	3	10.0	3	100	0	60	33	0	0	66	0.92
978348--978391	22	2.0	22	95	0	79	22	25	13	38	1.91
980626--980738	1	113.0	1	79	0	82	1	7	4	85	0.78
980626--980739	32	3.7	32	81	12	157	1	8	4	85	0.81
988436--988465	7	4.3	7	95	0	51	90	0	10	0	0.47
997427--997472	16	3.0	16	84	6	51	60	0	0	39	0.97
998720--998777	17	3.4	17	88	7	64	46	0	0	53	1.00
998832--998861	12	2.5	12	100	0	60	60	0	0	40	0.97
1000349--1000391	2	21.5	2	95	0	77	48	2	0	48	1.14
1000955--1001198	124	2.0	118	90	6	382	36	17	12	33	1.87
1001312--1001336	2	12.5	2	100	0	50	48	0	0	52	1.00
1001586--1001610	2	12.5	2	100	0	50	52	0	0	48	1.00
1005281--1005318	2	19.5	2	86	5	51	52	5	0	42	1.24
1006706--1006743	2	19.0	2	100	0	76	50	0	0	50	1.00
1007499--1007527	2	15.0	2	92	7	51	48	0	0	51	1.00
1008679--1008722	4	11.0	4	100	0	88	75	0	25	0	0.81
1010362--1010397	19	2.0	17	89	10	54	19	8	0	72	1.10
1010541--1010572	14	2.3	14	100	0	64	43	0	6	50	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1012942--1013090	73	2.0	73	100	0	298	38	10	19	31	1.86
1017548--1017586	2	19.5	2	100	0	78	51	0	0	48	1.00
1018001--1018032	15	2.1	15	100	0	64	0	40	0	59	0.97
1017999--1018029	3	10.3	3	92	0	53	0	35	0	64	0.94
1018067--1018092	2	13.0	2	100	0	52	50	0	50	0	1.00
1018652--1018715	32	2.0	32	93	0	110	21	20	25	32	1.97
1022182--1022228	2	23.5	2	95	0	85	0	46	0	53	1.00
1023224--1023261	3	12.7	3	100	0	76	65	0	0	34	0.93
1023403--1023434	2	16.5	2	93	6	57	50	0	0	50	1.00
1024137--1024167	3	10.3	3	92	0	53	0	35	0	64	0.94
1024301--1024344	2	22.0	2	100	0	88	50	0	0	50	1.00
1031243--1031273	2	15.5	2	100	0	62	51	0	48	0	1.00
1035900--1035939	2	20.0	2	100	0	80	50	0	0	50	1.00
1043216--1043245	2	15.0	2	92	0	51	53	0	0	46	1.00
1047476--1047505	2	15.0	2	92	0	51	50	0	3	46	1.18
1059286--1059320	7	5.1	7	96	3	63	0	14	45	40	1.45
1059570--1059611	2	21.0	2	100	0	84	50	0	0	50	1.00
1059878--1059918	12	3.3	13	80	10	50	14	9	0	75	1.04
1060528--1060586	13	4.5	13	73	10	50	50	0	0	49	1.00
1060546--1060616	35	2.1	34	86	7	99	50	0	0	49	1.00
1060924--1060996	37	2.0	37	86	0	101	16	23	5	54	1.62
1063639--1063681	3	14.3	3	95	0	77	30	0	2	67	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1074175--1074209	2	17.5	2	87	0	52	51	0	2	45	1.16
1074885--1074909	2	12.5	2	100	0	50	48	0	0	52	1.00
1078818--1078849	2	16.0	2	93	0	55	46	0	0	53	1.00
1088331--1088397	33	2.0	33	88	0	98	34	11	13	40	1.81
1088351--1088375	13	1.9	13	100	0	50	36	16	16	32	1.90
1088443--1088467	13	1.9	13	100	0	50	32	16	16	36	1.90
1095756--1095789	15	2.3	15	89	0	50	85	5	8	0	0.75
1095829--1095853	13	1.9	13	100	0	50	92	8	0	0	0.40
1096823--1097164	31	10.8	32	84	10	339	23	30	15	30	1.95
1096823--1097091	62	4.3	62	92	1	407	24	28	16	30	1.97
1096852--1097975	33	33.9	33	84	5	1028	21	32	12	33	1.91
1097062--1097970	199	4.5	200	89	6	1209	20	33	11	33	1.90
1097979--1098049	33	2.2	33	94	2	126	26	35	16	21	1.95
1098049--1098847	49	16.7	49	85	6	1043	24	25	17	31	1.97
1098049--1098910	190	4.5	192	90	4	1125	24	25	17	32	1.97
1098049--1098910	239	3.6	237	86	5	1150	24	25	17	32	1.97
1098757--1098906	52	2.8	54	81	4	178	26	23	16	34	1.95
1099723--1099789	33	2.0	33	88	0	98	34	11	13	40	1.81
1099743--1099767	13	1.9	13	100	0	50	36	16	16	32	1.90
1099835--1099859	13	1.9	13	100	0	50	32	16	16	36	1.90
1108833--1108914	41	2.0	41	92	0	137	24	17	17	41	1.89
1112172--1112222	20	2.6	19	81	9	57	52	7	3	35	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1124248--1124289	5	8.4	5	100	0	84	21	0	19	59	1.38
1124917--1124961	16	2.8	16	77	12	56	53	8	2	35	1.45
1125424--1125466	16	2.7	16	85	0	59	51	11	9	27	1.69
1125519--1125559	16	2.5	17	77	22	52	51	7	0	41	1.30
1131080--1131121	3	14.0	3	100	0	84	66	0	0	33	0.92
1136196--1136242	19	2.5	19	90	10	71	40	2	0	57	1.11
1137732--1137772	19	2.2	19	91	4	66	31	0	2	65	1.05
1138955--1138990	18	2.0	18	89	10	56	61	0	5	33	1.19
1140010--1140066	25	2.3	26	79	11	75	50	0	0	49	1.00
1140048--1140098	16	3.3	15	81	10	50	49	0	0	50	1.00
1140487--1140576	24	3.5	24	73	16	74	65	0	2	32	1.05
1140492--1140532	13	3.3	13	80	13	50	70	0	2	26	0.99
1141524--1141552	3	9.7	3	100	0	58	31	0	0	68	0.89
1142224--1142262	2	19.5	2	83	0	51	46	2	0	51	1.14
1146879--1146913	18	1.9	18	88	11	54	51	0	11	37	1.38
1149934--1149958	2	12.5	2	100	0	50	52	0	0	48	1.00
1153582--1153611	16	1.9	15	93	6	51	63	0	0	36	0.95
1158470--1158522	26	2.0	27	82	10	65	47	1	0	50	1.12
1161672--1161712	3	14.0	3	89	5	66	31	0	0	68	0.90
1167613--1167643	2	15.5	2	100	0	62	51	0	0	48	1.00
1168716--1168755	19	2.0	20	85	4	55	42	12	0	45	1.42
1169809--1169866	25	2.4	25	82	2	73	43	3	3	50	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1179610--1179639	9	3.2	9	90	9	51	0	13	0	86	0.57
1179618--1179649	16	1.9	17	93	6	57	0	15	0	84	0.63
1179610--1179649	17	2.2	19	86	8	57	0	15	0	85	0.61
1179758--1179804	22	2.0	24	84	12	62	0	21	23	55	1.44
1179766--1179819	24	2.3	24	81	12	60	0	25	18	55	1.43
1179788--1179831	22	2.0	22	81	0	52	2	25	11	61	1.41
1179828--1179931	36	2.9	36	90	4	158	3	19	21	55	1.58
1179877--1179932	18	3.1	18	65	10	51	5	17	23	53	1.64
1180084--1180280	93	2.1	93	85	3	263	11	27	14	46	1.79
1180853--1180893	14	2.9	15	82	10	50	29	0	2	68	1.03

Tables:   1   2   3   4   5