genome.fa.s41.2.7.7.80.10.50.1000.11.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: Scaffold41
Parameters: 2 7 7 80 10 50 1000
Length:  2798036

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   

This is table  11  of  21  ( 2447 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)
1124874--1124927	3	18.0	3	100	0	108	66	0	0	33	0.92
1124928--1124952	3	8.3	3	100	0	50	32	0	0	68	0.90
1125817--1125845	15	1.9	15	100	0	58	31	0	0	68	0.89
1126233--1126466	70	3.2	68	77	14	193	33	1	8	56	1.38
1126278--1126453	75	2.4	69	80	10	199	34	0	8	56	1.34
1127536--1127590	21	2.6	21	83	11	67	61	3	0	34	1.13
1128206--1128254	21	2.3	21	86	6	64	57	0	0	42	0.99
1131179--1131298	59	2.0	59	98	0	231	44	10	15	30	1.80
1132375--1132431	28	2.0	28	100	0	114	43	17	7	31	1.76
1133157--1133247	20	4.8	19	72	20	68	20	27	8	42	1.82
1133188--1133247	17	3.4	17	78	13	75	20	26	6	46	1.75
1133144--1133247	37	2.8	37	89	2	145	22	27	7	42	1.80
1134274--1134313	21	1.9	21	90	10	64	40	0	0	60	0.97
1134451--1134496	22	2.0	24	87	8	69	39	0	0	60	0.97
1134413--1134490	29	2.7	27	73	24	63	38	1	0	60	1.05
1138609--1138642	16	2.2	16	89	5	52	52	0	0	47	1.00
1139759--1139798	13	3.2	12	82	10	53	35	2	0	62	1.09
1139759--1139809	26	2.0	25	85	11	68	37	1	0	60	1.08
1146165--1146209	15	3.0	15	80	0	54	24	40	4	31	1.75
1147320--1147351	17	1.9	16	93	6	55	71	0	0	28	0.86
1147345--1147387	19	2.2	20	92	8	72	60	0	0	39	0.97
1150048--1150086	20	2.0	20	85	10	53	64	0	0	35	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1150911--1150946	15	2.4	15	95	0	63	50	0	11	38	1.38
1152949--1153004	24	2.4	23	82	8	69	50	1	0	48	1.11
1152949--1153006	23	2.5	24	86	5	75	50	1	0	48	1.11
1152964--1153006	22	1.9	22	90	4	68	48	0	0	51	1.00
1153507--1153597	41	2.2	40	84	5	112	48	0	2	49	1.13
1153566--1153626	16	3.4	16	74	22	59	52	0	3	44	1.17
1154784--1154808	9	2.8	9	100	0	50	68	0	0	32	0.90
1159230--1159298	33	2.1	33	83	5	86	33	4	7	55	1.47
1159554--1159682	22	5.5	23	72	13	95	65	0	1	31	1.07
1159554--1159649	11	8.5	11	77	7	95	67	1	2	29	1.08
1159568--1159651	27	3.1	27	70	14	73	67	1	1	29	1.05
1159563--1159625	13	4.8	12	77	14	63	69	0	1	28	0.97
1159602--1159699	17	5.4	18	70	21	62	62	1	1	35	1.09
1159844--1159888	21	2.1	21	84	8	56	64	0	2	33	1.06
1159854--1159930	17	4.9	16	79	16	74	68	0	2	28	1.02
1159900--1159924	7	3.6	7	100	0	50	72	0	0	28	0.86
1159867--1159933	16	4.2	16	71	22	61	70	0	1	28	0.96
1160335--1160414	32	2.5	32	86	6	101	35	1	6	57	1.32
1160335--1160401	16	4.2	16	84	0	89	34	0	5	59	1.22
1160433--1160493	26	2.2	29	85	8	83	40	0	0	59	0.98
1160448--1160557	14	7.4	16	66	25	64	43	0	0	55	1.06
1161600--1161635	16	2.1	16	90	10	54	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1161610--1161669	17	3.3	18	80	15	63	33	5	0	61	1.17
1161617--1161675	31	1.9	31	82	6	75	28	6	0	64	1.19
1161601--1161656	18	3.2	17	80	9	60	33	1	0	64	1.04
1164144--1164217	21	3.7	20	79	16	73	52	0	0	47	1.00
1164125--1164198	21	3.8	19	73	18	71	55	1	0	43	1.08
1164157--1164211	20	2.7	22	83	13	73	56	0	0	43	0.99
1164469--1164514	11	4.3	11	81	13	51	56	0	0	43	0.99
1164789--1164837	22	2.2	22	85	7	64	34	0	2	63	1.06
1164820--1164874	19	3.1	18	73	17	51	43	0	0	56	0.99
1173398--1173466	33	2.1	33	97	0	129	42	5	20	31	1.76
1174641--1174681	21	2.0	21	100	0	82	17	24	24	34	1.96
1175967--1175992	2	13.0	2	100	0	52	50	0	0	50	1.00
1177003--1177039	19	2.1	18	90	10	58	56	2	0	40	1.13
1176998--1177062	31	2.2	30	79	17	73	50	3	0	46	1.17
1176998--1177053	29	1.9	30	88	3	87	51	3	0	44	1.18
1177161--1177185	2	12.5	2	100	0	50	52	0	0	48	1.00
1177502--1177543	22	1.9	22	85	9	59	45	2	0	52	1.13
1178227--1178264	20	1.9	20	89	10	60	52	2	2	42	1.29
1178292--1178316	13	1.9	13	100	0	50	72	0	8	20	1.10
1178236--1178538	127	2.4	122	82	11	339	53	2	3	40	1.31
1178461--1178508	22	2.1	24	84	7	64	60	0	0	39	0.97
1178815--1179126	103	2.9	104	82	13	384	43	2	2	51	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1178816--1179131	112	2.9	108	83	12	393	43	2	2	51	1.28
1179093--1179151	31	1.9	30	86	3	82	50	1	0	47	1.11
1179600--1179757	2	85.0	2	68	22	78	47	1	5	45	1.34
1179592--1179651	14	4.4	14	74	16	63	36	1	5	56	1.31
1179688--1179768	7	11.0	7	77	12	74	51	1	3	43	1.27
1179684--1179766	22	3.8	22	78	9	82	51	1	3	43	1.26
1183249--1183735	89	5.5	89	89	1	685	27	16	15	40	1.88
1183759--1183812	22	2.5	22	77	14	67	70	1	0	27	0.98
1183807--1183927	7	18.6	7	78	13	109	41	0	2	55	1.19
1183818--1183928	2	62.0	2	72	21	86	42	0	1	54	1.17
1184878--1184929	19	2.8	18	80	5	68	73	1	0	25	0.94
1185003--1185136	2	73.0	2	72	21	107	49	2	1	47	1.23
1185002--1185087	7	12.1	7	77	14	79	48	0	1	50	1.08
1185026--1185130	31	3.6	28	68	25	51	51	2	0	44	1.22
1185003--1185137	15	8.4	16	78	14	127	49	2	1	46	1.23
1185216--1185785	89	6.4	89	85	4	722	40	14	16	28	1.88
1188911--1189010	33	3.0	33	91	0	155	34	12	12	42	1.79
1188964--1188988	13	1.9	13	100	0	50	36	16	16	32	1.90
1188944--1189012	20	3.8	19	71	26	69	30	11	10	47	1.73
1189051--1189075	13	1.9	13	100	0	50	32	16	16	36	1.90
1189084--1189203	52	2.3	52	92	0	195	35	16	17	30	1.92
1192847--1192895	22	2.2	22	78	7	55	69	6	0	24	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1192904--1193027	2	67.0	2	73	20	92	44	2	1	51	1.24
1192893--1192957	18	3.8	18	84	9	66	38	1	3	56	1.24
1192893--1193027	7	19.4	7	72	15	68	43	2	2	51	1.26
1192893--1193021	29	4.3	29	75	10	107	42	2	2	52	1.26
1192892--1193021	45	2.8	46	76	14	99	43	2	2	52	1.26
1193087--1193137	20	2.5	21	81	12	61	15	39	17	27	1.90
1193784--1193817	16	2.1	16	88	0	50	20	23	11	44	1.84
1193999--1194037	20	2.0	19	90	5	60	41	0	0	58	0.98
1197376--1197413	19	2.0	19	94	0	67	18	0	15	65	1.27
1197402--1197483	32	2.6	31	77	12	85	34	0	8	57	1.29
1197444--1197483	16	2.5	15	80	11	53	32	0	5	62	1.17
1197453--1197503	23	2.3	23	86	3	77	39	0	5	54	1.24
1201607--1201676	33	2.1	33	89	0	104	34	11	14	40	1.82
1201627--1201651	13	1.9	13	100	0	50	36	16	16	32	1.90
1201716--1201740	13	1.9	13	100	0	50	32	16	16	36	1.90
1201749--1201873	52	2.4	52	95	0	223	36	18	17	28	1.94
1205618--1206115	247	2.0	247	98	0	969	37	19	23	19	1.94
1209552--1209674	55	2.2	53	80	10	149	35	28	13	22	1.92
1209611--1209766	55	2.8	55	76	9	147	29	31	16	22	1.96
1210020--1210067	15	3.2	16	85	11	66	50	8	16	25	1.73
1213926--1213966	21	2.0	21	85	9	57	68	2	14	14	1.32
1214422--1214559	69	2.0	69	100	0	276	31	10	23	34	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1216493--1216532	16	2.5	16	88	8	55	50	0	2	47	1.14
1220879--1220972	46	2.0	46	100	0	188	42	10	17	29	1.82
1221080--1221113	11	3.1	11	82	0	50	70	0	0	29	0.87
1221151--1221195	24	1.9	24	86	4	65	46	0	2	51	1.13
1222907--1223031	19	7.1	19	71	17	56	42	0	0	56	1.04
1222918--1222964	14	3.4	14	82	5	51	38	0	0	61	0.96
1222939--1223031	33	2.9	31	79	17	77	45	0	0	54	0.99
1224504--1224611	19	5.7	19	66	25	52	37	0	1	59	1.15
1224846--1224875	16	1.9	15	93	6	51	33	0	0	66	0.92
1225270--1225338	16	4.6	16	68	14	56	49	0	0	50	1.00

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21