genome.fa.s54.2.7.7.80.10.50.1000.7.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: Scaffold54
Parameters: 2 7 7 80 10 50 1000
Length:  3629595

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   

This is table  7  of  20  ( 2342 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)
988171--988216	22	2.0	23	83	4	58	60	0	0	39	0.97
989575--989632	26	2.1	28	79	20	70	55	0	0	44	0.99
989664--989690	2	13.5	2	100	0	54	51	0	0	48	1.00
990407--990438	2	16.0	2	100	0	64	0	50	0	50	1.00
1006027--1006061	13	2.6	14	95	4	63	62	5	0	31	1.18
1016030--1016085	18	3.2	17	74	16	53	53	0	0	46	1.00
1016078--1016133	28	2.0	28	86	10	78	57	0	1	41	1.09
1021704--1021741	2	19.0	2	100	0	76	50	0	0	50	1.00
1021741--1021765	2	12.5	2	100	0	50	52	0	48	0	1.00
1026169--1026378	103	2.0	103	99	0	413	38	10	4	46	1.59
1028705--1028739	2	17.5	2	93	0	61	51	0	0	48	1.00
1030434--1030505	34	2.1	34	89	0	108	48	9	6	34	1.63
1030451--1030504	17	3.2	17	70	0	54	50	11	7	31	1.66
1031101--1031142	2	21.0	2	100	0	84	50	0	0	50	1.00
1045824--1045869	20	2.3	20	88	0	65	50	0	0	50	1.00
1048198--1048227	15	2.1	15	93	6	53	63	0	0	36	0.95
1048961--1049000	18	2.2	18	86	0	53	52	2	2	42	1.28
1048961--1048987	6	4.5	6	100	0	54	55	0	0	44	0.99
1048989--1049017	14	2.0	15	93	6	51	55	0	10	34	1.34
1057660--1057685	11	2.4	11	100	0	52	34	0	0	65	0.93
1057677--1057770	24	3.7	25	78	12	93	44	1	1	53	1.14
1058809--1058850	21	2.0	21	86	9	59	52	2	0	45	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1060475--1060535	28	2.2	28	82	11	72	40	3	0	55	1.16
1064249--1064285	16	2.3	15	86	13	56	51	0	0	48	1.00
1065182--1065229	21	2.3	20	85	3	60	41	2	2	54	1.24
1065236--1065269	15	2.1	17	89	10	54	41	0	8	50	1.34
1065290--1065328	20	1.9	21	89	5	62	51	2	0	46	1.14
1065932--1066031	12	9.4	11	81	10	88	41	0	9	50	1.34
1065943--1066031	10	9.5	10	81	14	118	40	0	8	50	1.34
1065943--1066037	4	23.8	4	82	0	109	40	0	9	50	1.35
1065945--1066029	6	14.8	6	83	9	88	40	0	9	50	1.35
1066667--1066727	22	2.7	23	77	12	63	45	0	0	54	1.00
1066723--1066795	24	3.0	25	78	13	62	56	2	0	41	1.14
1071397--1071471	21	3.4	23	72	20	63	56	1	0	42	1.08
1071397--1071440	23	1.9	22	86	9	61	59	0	0	40	0.98
1071396--1071455	28	2.1	28	84	9	77	60	0	0	40	0.97
1072710--1072759	23	2.3	23	83	10	70	52	0	0	48	1.00
1072845--1072879	2	17.5	2	100	0	70	48	0	0	51	1.00
1076436--1076479	23	1.9	24	86	9	65	50	0	0	50	1.00
1076506--1076550	20	2.1	22	84	15	60	42	0	0	57	0.98
1077849--1077904	12	4.4	12	73	20	51	42	0	0	57	0.99
1077861--1077919	19	3.1	19	78	14	50	44	0	0	55	0.99
1079422--1079463	14	2.7	15	82	14	50	61	4	0	33	1.17
1080201--1080242	2	21.0	2	90	0	66	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1081598--1081625	2	14.0	2	100	0	56	50	0	0	50	1.00
1086631--1086727	49	2.0	49	85	0	131	53	16	0	29	1.43
1086725--1086755	15	2.1	15	93	0	53	35	16	3	45	1.63
1095915--1095978	20	3.3	20	68	12	53	20	14	10	54	1.69
1097497--1097529	12	2.7	12	95	4	57	51	0	0	48	1.00
1097603--1097635	15	2.4	14	90	10	50	63	0	0	36	0.95
1098146--1098200	22	2.5	24	85	11	73	49	0	1	49	1.11
1100957--1100988	17	1.9	16	93	6	55	81	0	0	18	0.70
1101276--1101306	3	10.3	3	100	0	62	67	0	32	0	0.91
1103014--1103063	23	2.2	23	89	3	75	34	0	4	62	1.14
1103589--1103641	24	2.2	23	80	12	54	47	9	5	37	1.60
1103823--1103914	25	3.4	25	72	22	62	45	1	0	53	1.07
1104750--1104863	52	2.2	52	93	3	194	56	7	21	15	1.63
1105073--1105107	18	1.9	18	88	0	52	28	2	0	68	1.04
1105120--1105157	18	2.1	19	85	5	51	36	5	2	55	1.37
1107184--1107245	25	2.6	23	77	10	61	46	4	1	46	1.33
1109068--1109117	22	2.1	25	82	10	61	44	2	14	40	1.56
1114881--1114913	12	2.8	12	95	0	57	42	0	6	51	1.26
1123544--1123598	25	2.3	24	78	15	60	49	1	1	47	1.23
1123900--1123940	16	2.7	16	85	7	50	41	0	0	58	0.98
1124302--1124337	18	1.9	19	94	5	65	69	0	0	30	0.89
1124299--1124343	17	2.6	16	80	13	54	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)
1129085--1129145	31	2.0	31	96	0	113	45	14	13	26	1.81
1129660--1129692	17	1.9	17	100	0	66	12	18	33	36	1.88
1131784--1131827	20	2.0	23	87	12	67	40	0	2	56	1.11
1132076--1132127	24	2.3	22	80	6	59	48	0	0	51	1.00
1133398--1133464	29	2.3	29	85	12	93	37	0	1	61	1.05
1137943--1137986	6	6.8	6	80	14	52	18	2	63	15	1.41
1138015--1138061	21	2.2	21	84	0	58	25	4	55	14	1.58
1138087--1138141	21	2.6	21	85	0	74	14	5	60	20	1.54
1138284--1138333	24	2.1	24	84	0	64	14	2	68	16	1.31
1138284--1138325	15	2.8	15	85	0	57	14	0	66	19	1.25
1138345--1138384	21	1.9	21	84	0	53	17	5	67	10	1.37
1138285--1138427	66	2.2	66	83	5	173	17	3	62	16	1.47
1140609--1140665	21	2.9	20	76	7	55	47	0	1	50	1.11
1141503--1141535	2	16.5	2	100	0	66	48	0	0	51	1.00
1142308--1142388	30	2.7	30	77	11	85	46	3	2	46	1.33
1143053--1143115	25	2.6	23	85	9	81	63	3	4	28	1.30
1143116--1143198	20	4.7	18	71	23	52	54	1	0	44	1.08
1143170--1143221	22	2.4	22	77	6	61	65	0	0	34	0.93
1143164--1143216	26	2.0	24	86	13	70	64	0	0	35	0.94
1143489--1143523	7	5.3	7	86	13	56	28	17	0	54	1.43
1143489--1143523	13	2.6	14	86	13	56	28	17	0	54	1.43
1145547--1145584	20	1.9	19	94	5	67	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1145583--1145652	32	2.2	33	84	5	90	37	0	2	60	1.12
1148242--1148275	2	17.5	2	93	6	61	47	0	0	52	1.00
1156064--1156099	2	18.5	2	94	5	65	50	0	0	50	1.00
1161085--1161216	17	7.5	17	66	19	74	54	2	3	40	1.28
1161147--1161216	16	4.3	17	78	8	74	61	0	0	38	0.96
1161151--1161217	32	2.1	32	91	5	109	61	0	0	38	0.96
1162435--1162482	17	3.0	16	81	6	53	52	2	0	45	1.12
1162458--1162498	17	2.3	18	80	16	50	48	7	0	43	1.30
1163081--1163158	12	6.5	12	75	18	65	35	0	0	64	0.94
1163104--1163152	20	2.5	19	90	3	71	38	0	0	61	0.96
1163546--1163593	19	2.6	18	83	9	60	62	2	0	35	1.07
1165561--1165602	21	2.0	21	86	9	59	61	0	0	38	0.96
1166478--1166525	15	3.1	15	81	3	51	62	0	2	35	1.07
1166498--1166538	20	2.0	20	86	9	57	73	0	0	26	0.84
1168473--1168507	2	17.5	2	100	0	70	48	0	0	51	1.00
1168506--1168532	3	9.0	3	100	0	54	33	33	0	33	1.58
1170485--1170509	2	12.5	2	100	0	50	52	0	0	48	1.00
1182068--1182096	2	14.5	2	100	0	58	51	0	0	48	1.00
1182141--1182181	22	1.9	21	85	5	55	46	4	12	36	1.63
1183115--1183179	24	2.6	25	73	11	62	52	0	1	46	1.10
1186726--1186776	20	2.5	20	72	12	50	41	1	5	50	1.37
1187921--1187959	19	2.1	19	85	0	51	69	2	2	25	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1191199--1191223	5	5.0	5	100	0	50	80	0	0	20	0.72
1199681--1199719	18	2.2	18	85	0	51	35	2	2	58	1.25
1200521--1200548	2	14.0	2	100	0	56	50	0	0	50	1.00
1200885--1200910	2	13.0	2	100	0	52	50	0	0	50	1.00
1201518--1201579	25	2.4	27	79	17	78	46	1	0	51	1.10
1201581--1201619	13	3.1	13	85	7	53	48	5	0	46	1.24
1204794--1204829	18	2.0	18	100	0	72	11	16	11	61	1.57
1207977--1208016	19	2.2	19	90	4	64	62	0	0	37	0.95
1223018--1223081	28	2.3	28	78	8	67	39	1	0	59	1.07
1224134--1224175	18	2.4	18	80	11	52	38	4	0	57	1.20

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20