genome.fa.s498.2.7.7.80.10.50.1000.12.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: Scaffold498
Parameters: 2 7 7 80 10 50 1000
Length:  1804022

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

This is table  12  of  17  ( 1953 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)
1152399--1152453	2	28.0	2	96	3	103	50	0	0	49	1.00
1152538--1152570	14	2.3	15	89	5	50	36	0	0	63	0.95
1153348--1153409	30	2.1	29	84	3	79	41	19	8	30	1.80
1153930--1153977	16	2.9	16	84	3	51	33	2	0	64	1.05
1153938--1153970	16	2.1	16	94	5	59	33	0	0	66	0.92
1155085--1155116	2	16.0	2	100	0	64	50	0	0	50	1.00
1155469--1155495	2	13.5	2	100	0	54	51	0	0	48	1.00
1155840--1155902	3	21.0	3	100	0	126	66	0	0	33	0.92
1156509--1156569	2	30.5	2	96	0	113	49	1	0	49	1.10
1157157--1157197	2	20.5	2	94	0	73	48	0	2	48	1.14
1157658--1157695	18	2.3	16	86	13	51	42	2	5	50	1.39
1157786--1157862	37	2.1	37	100	0	154	41	12	2	42	1.57
1158400--1158446	20	2.2	22	88	7	71	36	6	4	53	1.46
1158848--1158889	2	22.0	2	85	9	61	50	2	0	47	1.14
1160503--1160570	9	7.8	9	70	16	54	52	0	0	47	1.00
1160525--1160568	18	2.4	18	84	0	61	59	0	0	40	0.98
1160601--1160625	13	1.9	13	100	0	50	56	4	8	32	1.47
1165118--1165163	23	1.9	23	86	8	65	63	4	2	30	1.26
1166009--1166037	2	14.5	2	100	0	58	48	0	0	51	1.00
1166755--1166800	23	2.0	22	83	4	56	54	0	0	45	0.99
1166768--1166820	27	2.0	25	82	13	63	56	1	0	41	1.10
1167141--1167179	12	3.4	11	82	10	51	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)
1167129--1167179	23	2.2	24	85	3	68	37	0	1	60	1.08
1167158--1167207	20	2.7	18	87	12	66	46	2	0	52	1.12
1168187--1168216	2	15.0	2	100	0	60	0	50	0	50	1.00
1168216--1168242	2	13.5	2	100	0	54	48	0	0	51	1.00
1168792--1168898	43	2.4	45	81	9	128	34	9	2	53	1.48
1169264--1169381	43	2.7	42	76	17	100	34	9	2	53	1.47
1173599--1173690	46	2.1	43	84	15	118	48	1	0	50	1.08
1176660--1176711	21	2.4	21	81	12	61	61	0	0	38	0.96
1176660--1176714	22	2.6	21	78	18	60	61	0	0	38	0.96
1177340--1177408	6	12.5	6	76	11	51	50	1	1	46	1.19
1177340--1177415	27	2.8	27	84	4	100	51	1	1	46	1.17
1177376--1177415	12	3.1	12	80	19	53	55	0	0	45	0.99
1177376--1177431	27	2.1	27	83	6	69	57	0	3	39	1.16
1177662--1177692	2	15.5	2	100	0	62	51	0	0	48	1.00
1177692--1177720	2	14.5	2	100	0	58	51	0	48	0	1.00
1177828--1177933	34	3.2	32	80	15	117	56	0	0	43	0.99
1177806--1177927	19	6.8	19	67	21	68	55	0	0	44	0.99
1177841--1177933	33	2.8	32	85	12	116	55	0	0	44	0.99
1178860--1178957	45	2.2	46	79	5	110	29	14	36	19	1.91
1178967--1179062	45	2.1	45	82	3	113	28	13	37	20	1.91
1179058--1179695	45	14.2	46	73	8	481	27	16	35	21	1.94
1178790--1179131	105	3.3	105	93	0	551	28	14	37	19	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1179100--1179715	90	6.9	89	90	0	917	27	16	35	21	1.94
1179100--1179710	180	3.4	180	93	0	1017	27	16	35	21	1.94
1183010--1183086	16	4.8	16	73	10	68	49	0	0	50	1.00
1182996--1183067	33	2.2	32	82	9	83	43	2	0	54	1.15
1183010--1183086	33	2.4	33	86	6	104	49	0	0	50	1.00
1183417--1183442	2	13.0	2	100	0	52	50	0	0	50	1.00
1184559--1184600	22	2.0	21	90	9	68	59	0	2	38	1.10
1184552--1184600	11	5.0	10	83	16	59	61	0	2	36	1.08
1184698--1184734	19	1.9	20	88	5	58	51	0	0	48	1.00
1185153--1185181	2	14.5	2	100	0	58	0	48	0	51	1.00
1185383--1185424	15	2.8	16	82	10	52	28	4	0	66	1.12
1186104--1186144	12	3.6	12	74	12	50	73	0	0	26	0.84
1186368--1186407	18	2.2	18	90	0	62	57	0	2	40	1.12
1186796--1186852	23	2.6	21	78	13	60	33	0	1	64	1.04
1186827--1186873	24	2.0	22	84	8	58	34	0	0	65	0.93
1187759--1187889	66	2.0	64	94	2	226	42	9	6	41	1.61
1188448--1188486	19	2.0	19	85	5	51	46	7	2	43	1.46
1190321--1190386	22	2.8	24	74	19	59	69	0	1	28	0.97
1190335--1190399	9	6.4	10	74	15	53	70	0	1	27	0.96
1190322--1190390	30	2.3	29	85	9	86	69	0	1	28	0.97
1190670--1190713	23	1.9	22	86	9	61	47	0	0	52	1.00
1191255--1191295	18	2.3	18	86	0	55	53	0	7	39	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1192486--1192524	18	2.1	19	90	4	62	33	5	0	61	1.18
1193572--1193605	16	2.1	17	88	5	52	70	8	0	20	1.13
1201884--1201930	3	15.7	3	100	0	94	68	0	0	31	0.90
1204637--1204661	12	2.1	12	100	0	50	0	12	0	88	0.53
1205826--1205854	5	5.8	5	100	0	58	82	0	0	17	0.66
1205999--1206033	17	2.1	16	89	10	52	57	0	0	42	0.99
1206120--1206153	14	2.4	14	90	0	50	47	2	2	47	1.32
1206445--1206479	18	1.9	18	94	0	61	48	5	2	42	1.41
1206962--1206993	16	2.0	16	93	0	55	31	28	6	34	1.82
1211499--1211546	24	2.0	24	83	0	60	45	16	8	29	1.76
1214911--1214941	2	15.5	2	100	0	62	51	0	0	48	1.00
1214986--1215047	2	31.0	2	80	0	52	43	6	4	45	1.51
1215695--1215727	2	16.5	2	100	0	66	51	0	0	48	1.00
1216685--1216727	17	2.7	15	80	13	50	58	0	0	41	0.98
1216691--1216726	17	2.1	17	94	0	63	55	0	0	44	0.99
1216685--1216729	15	2.9	15	81	12	54	57	0	0	42	0.98
1216955--1216991	18	2.1	18	90	10	58	43	0	0	56	0.99
1216945--1217052	29	3.9	27	78	16	96	38	0	0	60	1.03
1220019--1220093	27	2.8	28	76	17	77	46	0	2	50	1.15
1220772--1220813	22	1.9	22	90	9	68	38	0	0	61	0.96
1225097--1225154	28	2.1	28	93	0	98	34	3	3	58	1.32
1233193--1233223	15	2.1	15	93	0	53	9	0	3	87	0.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1233385--1233424	21	1.9	21	84	0	53	55	2	5	37	1.35
1238265--1238318	20	2.7	20	88	8	74	29	16	12	40	1.86
1239147--1239171	13	1.9	13	100	0	50	32	16	16	36	1.90
1239199--1239273	20	3.8	19	85	3	78	36	16	14	33	1.89
1240137--1240211	33	2.3	33	95	0	132	32	18	26	22	1.97
1241556--1241597	18	2.3	19	87	8	68	52	0	19	28	1.46
1241689--1241728	13	3.1	13	85	0	53	37	12	12	37	1.81
1241716--1241767	20	2.6	20	93	0	86	42	11	15	30	1.82
1241776--1241815	20	2.0	21	90	5	64	32	12	12	42	1.80
1247999--1248051	20	2.7	20	88	8	74	43	16	15	24	1.87
1250172--1250402	51	4.5	51	80	3	232	44	11	13	30	1.79
1250582--1250669	44	2.0	44	95	0	158	43	18	19	19	1.89
1251416--1251450	13	2.6	13	90	4	52	34	0	5	60	1.21
1259567--1259617	18	2.8	19	88	8	72	50	3	0	45	1.20
1259568--1259622	17	3.1	18	87	7	69	47	5	0	47	1.25
1260036--1260074	20	2.0	20	90	10	62	38	0	0	61	0.96
1261732--1261758	2	13.5	2	100	0	54	51	0	0	48	1.00
1262185--1262272	13	7.2	12	74	14	56	69	0	0	30	0.89
1262174--1262253	35	2.3	35	86	6	108	68	1	1	28	1.05
1262187--1262256	13	5.6	13	85	11	94	71	0	0	28	0.86
1262225--1262287	19	3.3	19	84	4	74	65	3	0	31	1.09
1262254--1262368	52	2.4	48	81	11	130	57	3	0	39	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1262191--1262368	19	9.4	18	66	22	64	62	2	0	35	1.08
1262461--1262501	19	2.2	19	86	4	57	31	0	7	60	1.24
1262518--1262551	10	3.4	10	87	0	50	50	0	0	50	1.00
1262500--1262580	22	3.5	24	73	19	66	53	0	0	46	1.00
1263546--1263591	14	3.5	14	80	17	62	0	15	58	26	1.37
1269203--1269232	16	1.9	15	93	6	51	50	0	0	50	1.00
1269203--1269289	24	3.7	23	70	11	68	54	1	0	44	1.07
1269203--1269244	17	2.5	18	85	11	54	50	0	0	50	1.00
1269373--1269398	7	3.7	7	100	0	52	53	0	0	46	1.00
1270069--1270143	33	2.3	31	84	11	89	56	0	0	44	0.99

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