genome.fa.s4.2.7.7.80.10.50.1000.3.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: CP032248.1 Gossypioides kirkii chromosome KI_06
Parameters: 2 7 7 80 10 50 1000
Length:  60359545

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   

This is table  3  of  193  ( 23090 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)
944692--944761	23	3.0	23	80	2	77	27	12	17	42	1.85
950187--950255	26	2.6	26	81	9	68	62	5	2	28	1.33
951480--951523	22	2.0	22	95	0	79	36	9	15	38	1.80
955803--956402	301	2.0	296	87	5	850	37	15	17	30	1.91
960891--960959	32	2.2	31	84	5	95	50	10	7	31	1.63
969490--969515	3	8.7	3	100	0	52	34	0	0	65	0.93
984172--984203	4	8.0	4	100	0	64	50	25	0	25	1.50
983910--984204	132	2.2	130	78	11	330	40	19	12	27	1.88
984183--984466	134	2.1	134	84	2	374	42	16	10	30	1.82
984317--984696	154	2.5	154	80	8	437	41	17	10	31	1.83
992946--993167	91	2.5	90	88	0	318	30	9	16	44	1.79
1011009--1011074	32	2.1	31	82	2	78	46	19	7	25	1.76
1015346--1015551	83	2.5	84	83	2	236	33	10	19	36	1.85
1054479--1054820	181	1.9	180	86	1	488	39	20	14	25	1.91
1064373--1064406	13	2.6	13	100	0	68	38	14	5	41	1.70
1067600--1067666	31	2.3	27	74	18	64	41	7	8	41	1.64
1067904--1067939	16	2.2	17	90	5	56	55	2	0	41	1.14
1077662--1077692	14	2.1	15	94	5	55	70	0	0	29	0.87
1090221--1090299	39	2.0	39	85	4	106	53	6	12	27	1.63
1103419--1103470	23	2.2	24	80	13	63	34	15	21	28	1.94
1103921--1103961	21	2.0	20	86	13	57	41	12	7	39	1.70
1105875--1105933	18	3.3	18	75	13	59	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)
1116838--1116880	11	4.0	11	81	3	52	41	0	4	53	1.21
1116838--1116880	22	2.0	22	86	4	61	41	0	4	53	1.21
1118503--1118565	33	2.0	32	84	12	85	19	14	6	60	1.55
1118834--1119239	58	7.0	59	83	6	467	33	29	2	34	1.72
1118843--1119062	29	7.5	29	66	19	84	33	26	3	36	1.73
1118830--1119239	117	3.5	114	84	8	474	33	29	2	34	1.72
1121778--1121806	8	3.6	8	100	0	58	37	0	10	51	1.36
1125894--1125939	25	1.9	25	86	8	69	32	4	6	56	1.45
1127009--1127059	19	2.5	22	79	17	58	23	3	1	70	1.14
1127043--1127080	16	2.4	16	86	4	51	10	10	2	76	1.12
1133707--1133994	30	9.8	29	76	9	221	40	2	22	34	1.69
1133688--1133997	59	5.3	59	76	10	244	39	2	23	34	1.70
1135901--1136266	173	2.1	174	84	2	477	24	23	15	37	1.93
1136073--1136690	209	2.9	206	85	3	806	23	21	16	37	1.94
1136619--1136739	48	2.5	48	82	7	156	26	23	12	37	1.91
1136493--1136859	171	2.1	172	88	1	540	24	22	15	37	1.92
1136285--1137068	380	2.1	381	87	2	1119	24	21	16	38	1.93
1136782--1136946	85	1.9	85	85	0	222	24	24	15	35	1.94
1135901--1137275	589	2.3	593	87	3	1940	23	21	16	37	1.93
1136663--1137577	208	4.4	208	87	2	1282	24	20	17	37	1.93
1149398--1149669	30	9.2	30	81	9	292	43	1	20	34	1.61
1149378--1149669	59	5.0	60	82	9	320	43	1	20	34	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1149398--1149669	89	3.1	90	81	8	321	43	1	20	34	1.61
1151181--1151213	6	5.7	6	85	7	50	51	0	0	48	1.00
1152984--1153025	11	3.6	11	81	12	57	59	2	0	38	1.10
1152987--1153053	24	2.8	24	80	10	75	55	1	1	41	1.18
1166311--1166671	179	2.0	179	99	0	713	28	14	18	38	1.90
1179385--1179504	58	2.1	58	90	3	188	35	0	16	48	1.47
1179642--1179680	9	4.3	9	86	0	51	35	10	7	46	1.67
1179735--1179764	14	2.1	14	100	0	60	40	6	6	46	1.56
1191507--1191636	42	3.1	42	78	13	133	30	18	0	51	1.46
1197938--1198294	59	6.1	59	85	1	450	33	3	30	31	1.75
1198062--1198164	30	3.5	31	69	23	94	36	4	26	32	1.78
1200090--1200140	17	3.1	17	80	2	59	54	0	1	43	1.11
1200101--1200162	6	11.2	6	73	16	53	54	0	1	43	1.09
1200101--1200162	27	2.2	28	80	13	83	54	0	1	43	1.09
1211640--1211997	73	4.9	73	94	3	637	35	9	14	41	1.77
1216963--1217137	84	2.1	84	88	2	253	44	6	17	30	1.75
1220812--1220993	96	1.9	96	83	6	235	39	14	17	29	1.89
1221225--1221360	59	2.3	59	79	3	150	34	5	25	34	1.78
1221259--1221392	58	2.3	59	82	5	157	38	5	23	32	1.79
1221363--1221572	29	7.2	30	77	10	141	34	4	26	34	1.77
1221259--1221402	59	2.5	59	78	10	152	36	6	25	31	1.81
1221352--1221613	30	8.9	29	78	9	167	35	4	26	33	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1221352--1221624	59	4.7	58	73	13	168	34	4	26	35	1.75
1221581--1221638	29	2.0	29	83	6	73	37	5	24	32	1.77
1222853--1222882	2	15.0	2	100	0	60	50	0	0	50	1.00
1223428--1223541	52	2.2	52	90	1	174	43	7	15	32	1.76
1226139--1226240	52	2.0	52	100	0	204	34	7	11	46	1.70
1228249--1228311	24	2.6	24	89	0	99	50	11	14	23	1.74
1230233--1230295	24	2.6	24	87	0	90	50	9	14	25	1.72
1230525--1230562	20	1.9	20	94	0	67	26	2	0	71	1.00
1245159--1245187	15	1.9	15	100	0	58	41	6	31	20	1.79
1246006--1246074	17	4.1	17	86	3	86	36	1	4	57	1.27
1246001--1246082	6	13.8	6	75	13	55	39	1	3	56	1.25
1246081--1246116	15	2.5	15	90	4	56	55	16	5	22	1.62
1246380--1246448	17	4.1	17	86	3	86	36	2	4	56	1.34
1246375--1246456	6	13.8	6	75	13	55	39	2	3	54	1.31
1246375--1246456	23	3.5	23	77	11	62	39	2	3	54	1.31
1246455--1246491	15	2.5	15	91	4	58	56	16	5	21	1.59
1247061--1247088	10	2.8	10	100	0	56	71	0	0	28	0.86
1248256--1248575	29	10.9	29	77	8	256	33	28	3	34	1.74
1248256--1248575	59	5.5	59	76	13	268	33	28	3	34	1.74
1248295--1248523	30	7.8	28	79	10	167	33	28	3	34	1.73
1248277--1248597	88	3.6	87	81	5	265	33	28	3	33	1.75
1248295--1248575	117	2.4	116	81	7	320	33	28	3	34	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1250310--1250356	23	2.0	23	100	0	94	57	0	29	12	1.36
1251746--1251804	29	2.0	30	90	3	93	30	3	15	50	1.60
1255466--1255536	31	2.4	29	79	9	72	25	8	9	56	1.60
1256030--1256061	16	2.0	16	100	0	64	37	31	6	25	1.81
1262391--1262423	2	16.5	2	100	0	66	51	0	0	48	1.00
1265066--1265104	21	1.9	21	85	15	55	53	5	5	35	1.45
1281891--1281932	16	2.6	16	84	0	57	57	19	0	23	1.41
1282006--1282041	18	1.9	18	88	5	54	5	5	0	88	0.61
1293210--1293247	17	2.3	17	90	4	60	21	0	2	76	0.91
1293206--1293254	25	2.0	25	87	0	71	24	0	4	71	1.03
1309624--1309648	6	4.2	6	100	0	50	16	0	0	84	0.63
1313626--1313704	40	2.0	41	90	7	126	65	11	1	21	1.31
1320440--1320620	83	2.1	86	87	5	269	32	5	20	41	1.75
1326284--1326319	16	2.2	16	90	0	54	61	22	0	16	1.35
1326292--1326357	32	2.1	31	86	8	89	59	15	1	24	1.45
1327246--1327297	9	5.7	9	77	4	50	34	0	0	65	0.93
1339846--1339913	31	2.2	31	89	0	100	36	17	10	35	1.84
1341990--1342061	20	3.3	23	70	21	64	33	0	4	62	1.14
1350756--1350785	2	15.0	2	92	0	51	46	0	3	50	1.18
1357952--1357984	16	2.0	17	88	5	50	36	6	9	48	1.60
1364840--1364886	12	3.9	12	100	0	94	25	34	6	34	1.81
1366215--1366258	15	2.9	15	82	3	52	40	4	2	52	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1367595--1367635	21	2.0	21	85	0	55	43	7	4	43	1.53
1372575--1372646	25	2.8	26	78	4	83	45	6	0	47	1.29
1375707--1375744	10	3.8	10	86	10	51	86	10	0	2	0.66
1378469--1378530	23	2.7	23	87	2	79	43	8	11	37	1.70
1380309--1380553	105	2.3	105	81	4	278	39	27	11	21	1.88
1382507--1382537	6	5.2	6	100	0	62	16	32	16	35	1.91
1392069--1392120	25	2.1	25	100	0	104	32	7	19	40	1.80
1395867--1396053	66	2.8	66	94	0	329	35	16	26	22	1.94
1411754--1411809	10	5.4	10	76	16	51	5	7	16	71	1.27
1411754--1411842	20	4.2	22	74	11	87	7	8	15	67	1.40

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193