genome.fa.s2549.2.7.7.80.10.50.1000.4.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: scaffold197
Parameters: 2 7 7 80 10 50 1000
Length:  1875808

Tables:   1   2   3   4   5   6   

This is table  4  of  6  ( 609 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)
1021819--1021954	31	4.4	31	71	8	107	24	16	13	44	1.84
1024573--1024606	15	2.3	14	90	10	50	67	5	5	20	1.33
1024700--1024729	2	15.0	2	92	0	51	50	0	3	46	1.18
1025467--1025500	15	2.3	14	90	10	50	67	5	5	20	1.33
1025594--1025623	2	15.0	2	92	0	51	50	0	3	46	1.18
1028103--1028380	88	3.2	88	89	2	418	24	25	22	26	2.00
1028218--1028356	44	3.2	44	68	15	142	23	23	25	26	2.00
1030955--1031064	42	2.6	41	80	8	116	10	11	5	71	1.28
1038870--1038919	21	2.5	20	75	18	50	28	8	4	60	1.43
1043827--1043871	22	2.0	22	87	8	65	40	26	2	31	1.68
1045881--1045909	9	3.2	9	100	0	58	24	44	10	20	1.82
1054571--1054708	72	2.0	71	87	8	203	40	2	6	50	1.40
1057404--1057487	28	3.0	29	82	3	100	25	22	15	36	1.93
1058615--1058689	35	2.1	35	95	0	132	36	33	2	28	1.71
1077048--1077722	51	13.3	50	79	4	699	28	14	25	30	1.95
1077048--1077689	102	6.3	102	98	0	1230	28	14	26	30	1.95
1077746--1077875	51	2.6	50	83	4	163	22	17	26	33	1.96
1078004--1078076	37	1.9	37	84	13	96	42	1	23	32	1.63
1083596--1083667	19	3.9	19	70	12	60	26	5	1	66	1.21
1087455--1087522	27	2.5	27	92	0	118	20	33	27	17	1.95
1094227--1094289	18	3.6	18	70	14	60	1	28	0	69	0.97
1094226--1094357	34	3.7	34	79	10	149	2	28	0	68	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1094245--1094361	24	5.0	24	69	22	70	2	30	0	66	1.05
1094259--1094360	4	25.0	4	71	21	54	1	29	0	68	1.00
1094413--1094481	27	2.6	27	88	0	102	17	30	34	17	1.93
1094619--1094728	27	4.1	27	100	0	220	36	19	18	26	1.94
1094932--1094969	18	2.1	18	85	14	51	71	5	2	21	1.19
1095556--1095605	13	3.8	13	78	21	50	64	0	0	36	0.94
1095555--1095595	18	2.1	18	86	13	55	63	0	0	36	0.95
1095555--1095605	20	2.6	19	81	15	59	64	0	0	35	0.94
1101770--1101800	16	1.9	16	93	0	53	51	22	19	6	1.69
1102557--1102603	4	11.8	4	100	0	94	23	0	25	51	1.49
1103234--1103340	53	2.0	53	100	0	214	33	13	16	36	1.88
1106488--1106519	12	2.6	13	85	14	50	37	0	6	56	1.25
1107974--1108020	19	2.3	21	85	7	62	44	0	12	42	1.42
1107980--1108028	21	2.3	23	80	16	61	46	0	12	40	1.41
1108264--1108380	46	2.6	46	87	2	166	35	13	23	28	1.93
1108316--1108435	51	2.3	51	87	4	170	32	15	25	26	1.96
1118006--1118043	20	1.9	20	88	0	58	52	5	5	36	1.47
1118994--1119029	19	1.9	19	88	5	56	50	2	2	44	1.31
1119131--1119181	24	2.1	25	85	10	70	25	1	0	72	0.95
1120317--1120428	56	2.0	57	87	1	163	28	12	15	43	1.83
1125145--1125191	19	2.5	18	83	10	58	78	12	8	0	0.95
1125236--1125266	5	6.2	5	92	0	53	58	0	3	38	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1125280--1125751	234	2.0	235	99	0	937	45	27	8	19	1.79
1135559--1135604	22	2.0	23	84	12	60	10	4	19	65	1.41
1137804--1137838	18	1.9	18	94	0	61	20	14	34	31	1.92
1146921--1146974	24	2.3	23	80	3	63	74	1	3	20	1.07
1147439--1147465	8	3.4	8	100	0	54	77	0	0	22	0.76
1147820--1147860	17	2.5	16	84	4	55	4	19	0	75	0.98
1149564--1149590	2	13.5	2	100	0	54	51	0	0	48	1.00
1155348--1155373	2	13.0	2	100	0	52	50	0	0	50	1.00
1161520--1161571	4	13.0	4	95	0	95	50	23	0	26	1.50
1175703--1175747	17	2.7	16	86	13	56	33	0	0	66	0.92
1177507--1177556	22	2.2	21	82	10	55	50	4	2	44	1.32
1190545--1190603	25	2.4	25	88	0	91	33	16	23	25	1.96
1190615--1190675	26	2.3	26	85	0	86	40	16	18	24	1.90
1194434--1194486	25	2.1	26	85	3	72	37	13	9	39	1.77
1194595--1194712	62	1.9	61	82	3	148	49	2	6	41	1.43
1197427--1197778	178	2.0	178	94	2	618	26	23	11	38	1.89
1200103--1200142	9	4.4	9	87	0	53	27	7	25	40	1.82
1200159--1200231	29	2.5	29	97	0	137	34	8	13	43	1.74
1218941--1218973	14	2.4	14	94	0	57	15	60	9	15	1.58
1219239--1219282	14	3.1	14	90	0	70	20	54	9	15	1.68
1219554--1219659	44	2.4	44	93	1	176	20	6	29	43	1.77
1220898--1220960	22	3.2	22	64	36	61	39	4	14	41	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1220896--1220967	37	1.9	37	100	0	144	38	5	15	40	1.70
1221256--1221332	14	5.0	15	71	20	52	44	14	6	35	1.71
1221272--1221311	20	2.0	20	90	0	62	50	12	10	27	1.72
1222084--1222123	11	3.6	11	93	6	64	22	35	0	42	1.54
1222192--1222235	12	3.8	12	81	3	54	40	0	0	59	0.98
1223113--1223137	7	3.6	7	100	0	50	28	0	12	60	1.32
1223788--1223827	18	2.2	18	90	0	62	20	30	7	42	1.79
1227961--1228003	21	2.0	21	95	0	77	18	16	16	48	1.81
1228211--1228577	124	3.0	120	84	7	460	33	22	14	29	1.94
1235524--1235563	18	2.2	18	95	0	71	50	17	2	30	1.59
1237481--1237576	21	4.6	21	77	0	111	16	21	16	44	1.86
1237481--1237589	21	5.3	21	76	3	98	15	22	16	45	1.84
1237762--1237810	21	2.4	20	86	6	71	40	8	28	22	1.82
1238360--1238469	55	2.0	55	98	0	211	23	13	31	30	1.93
1242511--1242547	13	2.7	14	83	8	58	70	2	0	27	1.01
1247125--1247165	20	2.0	20	100	0	82	43	9	0	46	1.36
1249079--1249198	44	2.8	43	78	16	131	24	20	27	28	1.99
1253638--1253668	15	2.1	15	93	0	53	41	0	9	48	1.36
1262161--1262224	3	21.3	3	93	0	110	67	0	1	31	1.00
1262416--1262445	15	2.0	15	100	0	60	26	6	13	53	1.64
1266034--1266102	21	3.2	21	84	11	61	59	2	2	34	1.27
1266065--1266104	21	1.9	21	100	0	80	57	2	0	40	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1266183--1266324	39	3.7	38	78	7	133	33	4	15	46	1.65
1266337--1266453	39	3.0	39	91	2	189	32	5	23	39	1.76
1278941--1278980	20	2.0	20	90	5	62	35	2	0	62	1.09
1282492--1282559	21	3.3	19	78	15	64	45	2	1	50	1.26
1285244--1285364	20	6.3	19	68	18	65	62	2	3	31	1.24
1285244--1285403	19	8.3	18	69	19	58	62	1	3	31	1.23
1285243--1285290	19	2.5	20	82	6	62	62	2	2	33	1.18
1285283--1285394	10	11.6	10	67	18	51	65	1	4	28	1.22
1285407--1285461	19	2.8	21	75	13	62	63	1	9	25	1.34
1286351--1286391	19	2.2	18	91	4	64	29	0	4	65	1.13
1286852--1286899	18	2.5	19	77	19	55	45	0	0	54	0.99
1286851--1286899	20	2.5	19	81	12	55	46	0	0	53	1.00
1288621--1288661	18	2.2	19	86	4	57	29	0	14	56	1.39
1299154--1299240	38	2.3	38	93	0	147	9	24	33	33	1.87
1299252--1299331	41	2.0	41	82	0	97	16	12	30	41	1.85
1302755--1302786	16	2.0	16	93	0	55	28	6	3	62	1.34
1306326--1306401	38	2.0	38	100	0	152	44	18	18	18	1.87
1317072--1317540	44	10.7	44	78	7	436	28	15	24	31	1.95
1317075--1317540	132	3.5	132	92	2	747	27	15	24	31	1.96
1317565--1317680	43	2.7	44	84	1	135	31	17	19	31	1.95
1318971--1319002	16	2.0	16	93	0	55	28	6	3	62	1.34
1318990--1319045	28	1.9	30	86	13	82	41	8	1	48	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1329074--1329144	25	2.8	25	84	0	88	35	12	15	36	1.86
1335734--1335857	60	2.0	61	98	1	241	45	18	3	33	1.66
1335744--1335836	30	3.1	29	65	15	73	47	16	3	33	1.62
1341777--1341805	2	14.5	2	100	0	58	51	0	48	0	1.00
1344696--1344751	26	2.2	25	84	9	69	37	7	1	53	1.39
1346653--1346713	30	2.0	30	96	0	113	27	3	24	44	1.69
1349798--1349908	51	2.2	51	91	0	177	35	15	21	27	1.94
1352436--1352663	68	3.5	68	73	12	258	39	3	6	50	1.46
1352421--1352760	129	2.6	129	95	2	596	40	3	6	50	1.45
1357190--1357222	12	2.8	12	95	0	57	33	12	33	21	1.90

Tables:   1   2   3   4   5   6