genome.fa.s246.2.7.7.80.10.50.1000.7.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: Scaffold246
Parameters: 2 7 7 80 10 50 1000
Length:  1425817

Tables:   1   2   3   4   5   6   7   8   

This is table  7  of  8  ( 935 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)
1004679--1004726	21	2.3	21	88	0	69	62	4	6	27	1.38
1009107--1009141	17	2.1	17	94	0	61	62	2	0	34	1.10
1010443--1010518	18	4.1	19	76	15	70	43	0	0	56	0.99
1016244--1016270	3	9.0	3	100	0	54	66	0	0	33	0.92
1022213--1022353	70	2.0	70	100	0	282	30	18	7	43	1.76
1022475--1022512	17	2.2	17	86	9	51	42	2	0	55	1.14
1026563--1026588	5	5.2	5	100	0	52	19	0	0	80	0.71
1026833--1026877	18	2.5	18	82	10	56	37	0	0	62	0.96
1026917--1026957	17	2.5	17	80	11	50	29	2	0	68	1.03
1026946--1026998	20	3.0	17	75	17	54	64	0	0	35	0.94
1029626--1029660	2	17.5	2	100	0	70	48	0	0	51	1.00
1030457--1030486	6	5.0	6	95	0	51	36	0	0	63	0.95
1031105--1031327	115	1.9	115	97	0	419	26	16	14	42	1.86
1033849--1033881	2	16.5	2	100	0	66	51	0	0	48	1.00
1034487--1034516	2	15.0	2	100	0	60	50	0	0	50	1.00
1036078--1036148	23	3.0	25	70	21	71	39	0	0	60	0.97
1036024--1036137	23	5.3	20	72	19	79	36	0	1	61	1.07
1036198--1036299	47	2.1	48	94	1	179	22	15	5	55	1.61
1037434--1037506	34	2.1	34	94	0	128	57	4	0	38	1.18
1037631--1037664	2	17.0	2	100	0	68	50	0	0	50	1.00
1038968--1039013	2	23.0	2	86	8	67	50	0	4	45	1.21
1041090--1041121	17	1.9	17	93	6	57	71	0	0	28	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1041136--1041177	2	20.5	2	90	4	57	47	0	7	45	1.30
1045092--1045153	30	2.1	30	96	0	115	17	24	25	32	1.97
1045125--1045269	49	3.0	49	95	0	263	29	17	20	33	1.95
1046925--1046949	2	12.5	2	100	0	50	48	0	0	52	1.00
1049199--1049229	2	15.5	2	100	0	62	48	0	0	51	1.00
1049624--1049679	26	2.2	26	84	12	73	55	0	0	44	0.99
1049635--1049697	17	3.8	17	75	8	58	58	0	0	41	0.98
1049688--1049730	17	2.7	15	76	13	50	44	0	0	55	0.99
1049693--1049743	17	2.8	19	73	11	52	43	0	0	56	0.99
1051518--1051559	17	2.5	17	85	11	52	59	0	2	38	1.10
1052525--1052560	2	18.0	2	94	0	63	47	0	0	52	1.00
1053834--1053869	14	2.4	15	90	9	56	2	30	0	66	1.06
1054389--1054446	24	2.4	25	83	11	68	36	1	0	62	1.06
1055506--1055551	17	2.5	20	73	23	55	52	0	6	41	1.27
1055889--1055935	13	3.4	14	81	18	55	51	8	0	40	1.33
1055893--1055946	16	3.5	15	82	14	58	53	9	0	37	1.33
1056825--1056867	4	10.5	4	85	5	59	23	2	2	72	1.08
1060673--1060707	17	2.0	18	88	5	54	40	0	0	60	0.97
1068307--1068387	27	3.0	27	78	5	83	54	1	1	43	1.16
1070922--1070997	27	2.9	27	76	5	75	38	0	0	61	0.96
1081588--1081627	2	20.0	2	100	0	80	50	0	0	50	1.00
1082200--1082230	16	1.9	16	93	0	53	61	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1082594--1082624	2	15.5	2	100	0	62	51	0	0	48	1.00
1082624--1082651	12	2.3	12	100	0	56	67	7	17	7	1.37
1086241--1086322	41	2.0	41	92	0	137	17	13	15	53	1.73
1089979--1090017	20	2.0	21	90	10	64	51	0	0	48	1.00
1089979--1090038	22	3.0	20	80	15	63	46	0	0	53	1.00
1089993--1090042	23	2.2	23	82	7	57	44	0	0	56	0.99
1090031--1090066	16	2.2	17	90	5	56	66	0	0	33	0.92
1090404--1090440	18	2.1	18	90	5	58	35	0	2	62	1.10
1090898--1090923	7	3.7	7	100	0	52	26	30	30	11	1.92
1091387--1091435	24	2.0	24	84	7	64	12	16	0	71	1.14
1091932--1091971	18	2.2	18	90	0	62	65	0	0	35	0.93
1095539--1095574	3	12.0	3	100	0	72	66	0	0	33	0.92
1095649--1095686	19	2.0	19	85	10	51	52	5	5	36	1.47
1095829--1095883	16	3.4	17	73	16	62	41	0	1	56	1.10
1095831--1095875	17	2.7	18	76	13	51	40	0	2	57	1.11
1096139--1096180	2	21.0	2	95	0	75	47	0	2	50	1.14
1106893--1106924	2	16.5	2	93	6	57	50	0	0	50	1.00
1107087--1107116	13	2.3	13	94	0	51	36	6	36	20	1.79
1107196--1107282	28	3.3	26	75	12	72	48	21	6	22	1.74
1112676--1112710	17	2.1	16	89	5	52	48	0	0	51	1.00
1112676--1112710	8	4.2	8	85	7	52	48	0	0	51	1.00
1120714--1120754	21	2.0	20	85	4	55	43	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1120714--1120759	23	2.2	20	88	11	65	43	0	0	56	0.99
1127013--1127105	22	3.9	22	71	21	71	40	1	0	58	1.05
1127024--1127150	52	2.4	52	96	2	229	42	1	0	55	1.09
1127063--1127105	20	2.0	22	86	8	63	37	0	0	62	0.95
1127026--1127095	29	2.3	32	76	9	76	40	1	0	58	1.07
1127038--1127118	23	3.3	23	70	19	65	43	2	0	54	1.13
1127048--1127142	19	5.3	19	67	19	60	42	2	0	55	1.11
1131547--1131811	137	2.0	134	85	6	365	38	3	15	42	1.64
1138285--1138309	13	1.9	13	100	0	50	8	4	16	72	1.24
1141106--1141131	2	13.0	2	100	0	52	0	50	0	50	1.00
1142116--1142148	15	2.2	15	89	10	50	51	0	3	45	1.16
1142738--1142785	16	3.1	16	78	3	53	39	0	0	60	0.97
1142737--1142774	14	2.9	14	88	7	53	36	0	0	63	0.95
1145846--1145916	6	11.7	6	75	11	56	46	0	4	49	1.21
1145944--1146010	22	2.8	22	71	22	55	49	1	0	49	1.10
1145947--1145995	24	2.0	25	88	4	73	46	0	0	53	1.00
1147262--1147294	2	17.0	2	93	6	59	48	0	0	51	1.00
1154976--1155030	13	4.1	14	80	20	55	67	0	3	29	1.08
1154987--1155041	13	4.5	12	74	17	51	69	0	1	29	0.99
1156033--1156105	31	2.3	31	83	9	94	45	0	0	54	0.99
1156034--1156102	33	2.2	33	84	10	90	47	0	0	52	1.00
1160554--1160623	11	6.1	11	76	14	61	52	0	2	44	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1160554--1160638	33	2.6	33	81	10	86	56	0	2	41	1.12
1168619--1168647	3	9.7	3	100	0	58	31	0	0	68	0.89
1184087--1184223	33	3.9	34	72	17	102	56	0	0	42	1.04
1184095--1184173	33	2.4	32	87	4	104	54	0	1	44	1.08
1184095--1184182	32	2.7	32	84	5	106	53	0	1	45	1.07
1184161--1184226	6	11.5	6	71	12	50	60	0	0	39	0.97
1184087--1184188	17	6.1	17	72	15	79	55	0	0	43	1.06
1184121--1184215	49	2.0	44	82	13	111	54	0	0	45	0.99
1184161--1184222	22	2.8	22	80	14	74	59	0	0	40	0.97
1188718--1188751	2	17.0	2	100	0	68	50	0	0	50	1.00
1190681--1190726	20	2.3	20	84	0	56	36	4	45	13	1.63
1195249--1195294	20	2.3	20	84	0	56	36	4	45	13	1.63
1197914--1197960	23	2.0	23	100	0	94	31	8	29	29	1.87
1202962--1203004	11	4.0	11	81	6	52	27	6	0	65	1.18
1202955--1202998	21	2.1	21	95	0	79	22	11	0	65	1.24
1210561--1210593	16	2.1	16	88	11	50	51	0	0	48	1.00
1217285--1217315	16	1.9	16	100	0	62	19	6	12	61	1.53
1217400--1217447	22	2.0	22	84	11	60	43	16	6	33	1.73
1217980--1218011	2	16.0	2	100	0	64	50	0	0	50	1.00
1220485--1220583	30	3.3	30	100	0	198	13	28	16	42	1.85
1222250--1222292	17	2.4	17	84	7	50	48	0	0	51	1.00
1231244--1231275	3	10.7	3	100	0	64	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1232494--1232520	7	3.9	7	100	0	54	85	0	0	14	0.61
1235701--1235746	3	15.3	3	78	17	51	58	0	2	39	1.10
1238466--1238535	25	2.7	26	80	10	81	48	0	0	51	1.00
1238475--1238552	25	3.2	26	80	12	76	43	1	0	55	1.08
1240257--1240288	16	2.0	16	93	0	55	34	6	21	37	1.79
1245208--1245253	24	1.9	24	81	0	56	41	4	4	50	1.42
1245244--1245289	6	8.3	6	83	13	55	30	0	0	69	0.89
1245244--1245284	16	2.6	16	92	0	64	31	0	0	68	0.90
1245700--1245779	39	2.1	37	81	9	90	43	1	0	55	1.08
1250250--1250276	2	13.5	2	100	0	54	0	51	0	48	1.00

Tables:   1   2   3   4   5   6   7   8