genome.fa.s39.2.7.7.80.10.50.1000.5.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: scaffold165.1
Parameters: 2 7 7 80 10 50 1000
Length:  1724686

Tables:   1   2   3   4   5   6   7   8   

This is table  5  of  8  ( 876 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)
1050805--1050956	9	18.0	9	74	13	135	30	1	23	45	1.61
1051006--1051150	12	13.2	12	66	26	81	35	2	14	47	1.59
1051035--1051157	54	2.3	54	97	2	230	34	3	17	44	1.65
1051098--1051161	33	1.9	33	93	0	110	35	3	15	45	1.62
1051310--1051454	60	2.4	60	95	1	254	48	6	3	40	1.47
1051331--1051423	16	6.1	16	68	18	72	47	7	2	43	1.43
1051328--1051424	30	3.2	30	69	11	90	49	7	2	41	1.42
1051420--1051447	13	2.2	13	100	0	56	46	7	7	39	1.59
1051356--1051469	30	3.8	30	75	9	124	50	7	5	37	1.52
1051495--1051537	19	2.3	19	95	0	77	48	6	4	39	1.51
1053300--1053345	23	2.0	23	87	8	67	28	13	6	52	1.65
1055067--1055471	41	9.9	41	85	3	510	30	29	19	20	1.97
1055067--1055471	123	3.3	123	88	2	571	30	29	19	20	1.97
1055518--1055635	40	3.0	38	78	8	137	25	16	17	40	1.90
1056849--1056892	18	2.5	19	82	10	58	72	0	15	11	1.11
1056880--1056920	11	3.7	11	83	0	55	78	0	19	2	0.87
1056880--1056922	17	2.6	17	77	3	52	76	0	20	2	0.89
1057015--1057117	42	2.5	42	91	0	161	28	14	33	24	1.94
1058412--1058866	132	3.5	130	85	3	608	30	17	24	27	1.97
1058901--1059068	51	3.3	50	82	3	194	30	13	25	30	1.94
1058867--1059074	102	2.0	102	84	0	272	30	15	25	29	1.96
1059052--1059095	21	2.1	21	86	0	61	38	2	34	25	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1059239--1059374	72	1.9	72	93	0	236	34	12	29	23	1.92
1058996--1059349	194	1.8	193	88	1	548	32	13	26	26	1.94
1059001--1059394	194	2.0	194	83	2	497	32	14	26	25	1.95
1060246--1060272	10	2.7	10	100	0	54	18	18	51	11	1.74
1061548--1061582	17	2.1	17	94	0	61	51	0	5	42	1.25
1061750--1061782	16	2.0	17	94	5	59	63	0	0	36	0.95
1070832--1070861	15	2.1	14	93	6	51	66	6	20	6	1.38
1075376--1075648	41	6.7	41	79	7	259	26	21	21	30	1.98
1075404--1075635	81	2.9	78	80	7	243	25	21	20	32	1.98
1075745--1075795	26	2.0	26	84	0	66	58	5	11	23	1.55
1076035--1076067	14	2.3	15	94	5	59	30	0	33	36	1.58
1076160--1076304	63	2.3	63	87	1	209	29	0	23	46	1.52
1076223--1076387	88	1.9	89	94	1	296	28	1	24	45	1.61
1077313--1077362	20	2.4	21	74	12	50	44	8	0	48	1.32
1078599--1079825	613	2.0	613	99	0	2436	32	12	18	37	1.88
1080614--1080671	22	2.6	23	81	8	75	39	1	1	56	1.19
1080642--1080682	19	2.2	19	86	8	57	46	0	2	51	1.14
1080744--1080831	12	8.1	11	79	15	85	47	13	0	38	1.43
1080742--1080800	21	2.6	24	79	12	72	49	15	0	35	1.45
1080762--1080865	32	3.0	36	87	8	128	49	11	0	39	1.39
1080688--1080932	128	1.9	128	92	1	411	48	14	0	36	1.44
1080774--1080932	32	5.0	32	71	17	141	48	13	0	37	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1080908--1080952	23	1.9	24	90	4	74	42	17	0	40	1.50
1080967--1081033	16	4.6	16	68	24	58	49	22	0	28	1.50
1080941--1081040	41	2.4	40	83	6	112	46	24	2	28	1.64
1080932--1081012	25	3.2	25	78	1	99	46	20	2	29	1.64
1080939--1081234	9	34.9	9	65	21	115	45	19	2	32	1.62
1081082--1081106	13	1.9	13	100	0	50	48	16	0	36	1.46
1081007--1081127	61	2.0	62	80	11	142	47	18	0	33	1.54
1081080--1081123	22	2.0	21	91	4	70	47	15	0	36	1.46
1081092--1081171	30	2.5	33	78	8	94	46	16	2	35	1.60
1081137--1081221	25	3.4	25	85	0	116	47	18	0	34	1.49
1083271--1083327	29	2.0	29	92	0	96	28	8	26	36	1.86
1083960--1084049	46	2.0	46	95	0	162	34	15	16	33	1.91
1088776--1088941	43	4.0	42	73	12	137	33	25	14	27	1.94
1092664--1092693	14	2.1	14	100	0	60	46	0	0	53	1.00
1094527--1094579	24	2.2	24	96	0	97	56	7	0	35	1.28
1096920--1096945	7	3.7	7	100	0	52	26	0	15	57	1.38
1097873--1098055	93	2.0	92	96	1	339	36	3	3	55	1.36
1097995--1098113	54	2.2	54	83	4	141	42	0	5	52	1.29
1098080--1098110	9	3.6	9	91	8	55	35	0	0	64	0.94
1101093--1101362	126	2.1	126	88	6	395	30	15	15	37	1.89
1101411--1101523	34	3.4	33	79	11	115	48	12	0	38	1.41
1122325--1122397	36	2.1	34	82	5	83	53	8	10	27	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1122733--1122782	18	2.8	18	82	8	57	12	8	4	76	1.15
1122750--1122793	18	2.4	19	80	3	54	15	9	2	72	1.19
1122748--1122790	19	2.3	19	84	8	52	16	9	2	72	1.21
1122796--1122838	13	3.2	13	86	3	50	18	0	4	76	0.95
1122796--1122840	23	2.0	23	86	4	65	20	0	4	75	0.97
1122792--1122825	9	3.8	9	85	14	52	17	0	2	79	0.86
1122903--1122944	21	2.0	20	90	4	66	38	0	0	61	0.96
1122884--1123003	36	3.5	32	80	10	132	39	2	1	56	1.23
1123007--1123035	14	2.1	14	100	0	58	51	0	0	48	1.00
1123055--1123125	26	2.6	28	81	16	87	47	1	0	50	1.09
1123055--1123131	29	2.8	29	79	13	74	48	1	0	50	1.09
1123110--1123150	14	3.0	14	79	13	50	51	0	0	48	1.00
1123468--1123510	20	2.2	20	83	8	52	37	2	2	58	1.24
1123443--1123543	33	3.0	32	85	8	121	39	0	1	57	1.17
1123508--1123569	21	3.0	21	77	13	65	48	0	1	50	1.10
1123503--1123560	20	2.8	20	78	17	66	44	0	1	53	1.10
1123614--1123692	34	2.4	34	79	8	92	36	0	3	59	1.16
1123624--1123708	24	3.6	24	77	19	81	35	0	4	60	1.18
1123614--1123692	10	7.2	10	72	20	52	36	0	3	59	1.16
1123658--1123703	13	3.7	13	75	21	53	39	0	4	56	1.19
1123648--1123727	24	3.3	24	87	5	99	40	0	2	57	1.12
1123762--1123798	10	3.5	11	82	17	51	35	0	0	64	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1123763--1123790	12	2.3	12	100	0	56	28	0	0	71	0.86
1123749--1123817	22	3.0	22	78	18	70	37	0	1	60	1.06
1123793--1123842	12	3.7	13	76	23	50	48	0	0	52	1.00
1126946--1126986	16	2.3	18	80	12	50	51	12	2	34	1.52
1127170--1127302	30	4.4	30	89	0	176	28	18	24	28	1.98
1129629--1129711	41	2.0	42	92	2	141	54	3	7	34	1.46
1129640--1129705	20	3.2	20	66	19	55	51	3	7	37	1.46
1130769--1130811	9	4.8	9	83	11	52	74	4	0	20	1.00
1130783--1130858	9	8.2	9	71	10	55	78	2	2	15	0.97
1136944--1136974	12	2.6	12	94	0	53	83	6	3	6	0.88
1148437--1148464	12	2.3	12	100	0	56	28	14	14	42	1.84
1150649--1150686	5	7.6	5	100	0	76	78	0	0	21	0.74
1152459--1152501	7	6.1	7	91	0	68	16	2	37	44	1.60
1152925--1153078	70	2.2	70	97	2	290	28	14	7	48	1.72
1159081--1159135	25	2.2	25	83	0	65	36	18	25	20	1.94
1161905--1161987	41	2.0	41	92	0	139	22	8	24	44	1.80
1163393--1163796	43	9.4	43	88	1	519	33	32	18	16	1.93
1163393--1163881	129	3.8	130	82	5	514	31	31	18	17	1.95
1163436--1163881	43	10.3	42	79	7	240	31	32	18	18	1.95
1164125--1164163	9	4.3	9	86	0	51	2	23	43	30	1.67
1168466--1168507	22	1.9	22	85	0	57	33	7	14	45	1.72
1168488--1168582	16	5.3	18	71	15	72	33	2	18	45	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1168535--1168605	22	3.5	20	78	21	78	36	1	16	45	1.57
1168516--1168610	38	2.4	38	89	3	136	33	2	18	45	1.62
1168488--1168582	9	10.6	9	71	17	72	33	2	18	45	1.62
1168560--1168614	22	2.5	22	81	3	74	34	0	14	50	1.43
1168644--1168771	21	5.8	21	66	18	64	48	3	5	42	1.42
1168748--1168797	26	1.9	26	84	8	66	46	4	0	50	1.20
1168607--1168800	69	2.8	69	91	3	304	46	4	5	44	1.44
1169485--1169515	16	1.9	16	100	0	62	51	6	3	38	1.44
1169981--1170038	26	2.2	26	93	0	98	39	3	17	39	1.66
1171120--1171165	24	2.0	22	91	8	74	23	0	41	34	1.55

Tables:   1   2   3   4   5   6   7   8