genome.fa.s1129.2.7.7.80.10.50.1000.6.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: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  21326069

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   

This is table  6  of  89  ( 10573 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)
1075257--1075289	16	2.1	16	88	11	50	39	0	0	60	0.97
1075474--1075509	18	1.9	18	88	5	54	44	2	0	52	1.15
1075472--1075523	19	2.6	20	76	17	54	44	1	0	53	1.11
1076333--1076390	24	2.4	24	80	8	64	53	5	1	39	1.33
1077022--1077199	68	2.6	68	86	3	245	39	10	17	32	1.83
1078275--1078392	37	3.2	37	80	10	123	44	8	0	46	1.33
1078515--1078549	14	2.5	14	95	0	61	48	5	5	40	1.51
1078815--1078940	35	3.8	32	70	20	91	46	1	1	50	1.20
1079081--1079137	22	2.8	19	78	17	60	54	0	1	43	1.10
1079080--1079131	22	2.3	22	83	9	61	53	0	1	44	1.11
1080574--1080605	15	2.1	15	100	0	64	65	0	0	34	0.93
1085689--1085726	18	2.1	18	100	0	76	23	23	31	21	1.98
1086685--1086725	18	2.3	19	79	12	50	26	0	2	70	0.99
1096502--1096540	2	20.0	2	94	5	71	48	0	0	51	1.00
1098869--1098927	30	2.0	30	96	0	109	61	13	8	16	1.56
1101939--1101963	13	1.9	13	100	0	50	40	16	8	36	1.77
1107557--1107627	20	3.5	20	94	3	108	26	15	23	33	1.95
1107647--1107725	19	4.1	19	76	12	88	32	12	20	34	1.90
1108257--1108305	27	1.9	24	88	12	71	63	0	26	10	1.26
1112161--1112185	12	2.1	12	100	0	50	8	8	16	68	1.38
1115535--1115576	17	2.5	17	92	0	66	35	26	0	38	1.57
1117889--1117919	13	2.4	13	94	0	53	16	19	48	16	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1117932--1117995	9	6.6	10	87	8	80	34	28	21	15	1.94
1125095--1125135	18	2.3	18	100	0	82	9	21	51	17	1.74
1125089--1125118	13	2.3	13	100	0	60	13	23	46	16	1.82
1125113--1125145	13	2.5	13	95	0	57	15	21	48	15	1.81
1125086--1125156	31	2.3	31	85	0	106	18	23	42	15	1.88
1132950--1133008	28	2.1	27	81	12	66	47	10	16	25	1.78
1134017--1134091	31	2.4	30	78	8	87	46	0	13	40	1.43
1147294--1147466	52	3.3	52	95	0	319	43	16	16	23	1.87
1148250--1148294	14	3.3	14	90	9	67	46	28	2	22	1.63
1148835--1148994	67	2.4	66	84	6	196	25	20	11	42	1.86
1149020--1149121	43	2.5	41	82	4	116	23	33	19	23	1.97
1149002--1149617	131	4.6	132	80	7	613	26	30	17	25	1.97
1149000--1149608	265	2.3	264	83	3	747	26	30	17	25	1.97
1149814--1149873	12	5.2	12	73	20	56	43	0	0	56	0.99
1153137--1153195	29	2.0	29	100	0	118	49	13	13	23	1.78
1157723--1157781	29	2.0	29	100	0	118	49	13	13	23	1.78
1164758--1164782	10	2.5	10	100	0	50	20	20	8	52	1.71
1164802--1164860	13	4.7	13	77	14	52	62	15	8	13	1.53
1169261--1169324	20	3.1	21	85	12	73	0	26	1	71	0.94
1169279--1169330	19	2.7	18	80	11	59	0	26	3	69	1.06
1173593--1174070	105	4.6	105	89	6	722	21	22	19	36	1.95
1174980--1175031	17	2.9	17	81	16	61	7	11	0	80	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1174994--1175031	9	4.4	9	93	6	62	7	10	0	81	0.87
1174981--1175032	9	5.6	9	78	17	52	5	11	0	82	0.82
1192156--1192211	25	2.3	26	78	12	64	60	3	8	26	1.43
1193585--1194287	48	14.6	48	76	5	567	29	23	14	32	1.94
1193652--1194154	193	2.6	193	87	0	704	29	22	14	33	1.93
1201199--1201249	21	2.4	21	86	0	66	64	3	3	27	1.28
1202002--1202096	27	3.6	27	95	2	167	41	15	11	31	1.83
1204163--1204210	22	2.2	22	96	0	87	31	10	10	47	1.71
1206387--1206426	21	1.9	21	94	0	71	47	12	5	35	1.63
1206874--1206911	17	2.2	17	90	0	58	50	0	0	50	1.00
1208869--1208918	3	18.0	3	84	15	63	30	0	2	68	1.01
1208866--1208918	16	3.0	19	81	13	69	30	0	1	67	1.01
1213793--1213836	22	2.0	22	86	8	63	47	15	18	18	1.83
1213793--1213837	12	4.0	11	81	16	56	46	17	17	17	1.84
1216227--1216271	2	22.5	2	100	0	90	48	0	0	51	1.00
1216446--1216504	30	2.1	28	87	9	84	20	11	11	55	1.67
1221734--1221771	20	1.9	20	100	0	76	34	15	0	50	1.45
1225215--1225258	20	2.2	20	95	0	79	25	15	11	47	1.79
1226328--1226420	38	2.5	37	89	5	143	38	39	10	10	1.75
1229133--1229163	13	2.3	14	94	5	55	48	45	0	6	1.28
1234702--1234896	41	4.7	41	73	10	132	32	16	18	32	1.93
1234684--1234908	83	2.8	81	79	6	231	32	15	18	34	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1234741--1235045	122	2.5	121	78	7	272	32	16	17	34	1.92
1239179--1239496	42	7.4	42	80	6	325	26	22	17	33	1.96
1240116--1240288	45	3.8	44	78	9	168	42	6	20	30	1.78
1240643--1240694	13	4.1	12	78	11	50	21	25	15	38	1.92
1241074--1241250	45	4.0	44	88	5	266	29	24	7	38	1.82
1241362--1241511	40	3.8	40	92	0	246	34	26	15	24	1.95
1241827--1241875	24	2.0	24	100	0	98	42	12	12	32	1.79
1242528--1242596	31	2.3	31	82	7	79	34	21	7	36	1.81
1243066--1243104	14	2.8	14	84	0	51	35	28	12	23	1.91
1246199--1246246	2	24.5	2	95	4	89	47	0	0	52	1.00
1255616--1255647	15	2.1	15	94	0	55	9	34	0	56	1.32
1255605--1255656	21	2.5	21	90	0	86	11	32	0	55	1.36
1257128--1257162	7	5.0	7	89	0	52	65	0	0	34	0.93
1261775--1261862	23	3.9	23	77	7	83	19	20	23	36	1.95
1261797--1261866	22	3.1	22	78	10	79	20	18	24	37	1.94
1267597--1267626	14	2.1	15	93	6	53	36	0	13	50	1.42
1267772--1267875	31	3.3	31	91	2	163	27	19	17	35	1.94
1267772--1267890	31	3.8	30	84	6	121	28	18	17	35	1.94
1267772--1267890	63	1.9	63	85	3	168	28	18	17	35	1.94
1271919--1271976	2	30.0	2	89	6	93	50	1	0	48	1.11
1272139--1272185	18	2.5	19	79	10	51	25	0	23	51	1.49
1272177--1272206	14	2.1	15	93	6	53	36	0	13	50	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1272353--1272473	31	3.8	32	82	4	149	26	18	20	34	1.95
1274523--1274561	20	2.0	20	89	0	60	33	10	23	33	1.88
1277286--1277344	5	11.0	5	80	10	55	72	3	3	20	1.13
1277296--1277350	28	2.0	28	82	7	67	69	1	5	23	1.19
1278038--1278062	11	2.3	11	100	0	50	76	0	8	16	1.02
1282349--1282405	25	2.3	25	85	11	73	0	12	10	77	1.00
1283804--1283874	24	3.1	24	64	15	69	26	16	22	33	1.96
1283753--1283877	44	2.8	44	86	0	169	28	17	23	30	1.97
1285067--1285121	19	2.8	21	83	10	71	1	20	0	78	0.85
1285069--1285124	14	4.1	14	81	6	62	1	21	0	76	0.87
1285068--1285122	20	2.8	20	89	8	78	1	20	0	78	0.85
1294801--1294834	15	2.3	15	89	0	50	20	0	17	61	1.34
1294810--1294840	15	2.1	15	93	0	53	12	3	16	67	1.35
1298612--1298815	101	2.0	102	89	2	313	27	18	25	28	1.98
1300930--1300999	33	2.2	33	84	7	90	64	14	1	20	1.36
1300948--1300999	16	3.2	16	76	13	52	63	15	0	21	1.31
1303992--1304044	23	2.3	23	96	0	97	50	0	20	28	1.48
1305572--1305691	60	2.0	61	81	4	145	21	10	15	52	1.72
1310926--1310955	12	2.5	12	94	0	51	16	13	10	60	1.59
1313866--1313921	22	2.5	22	100	0	112	37	0	35	26	1.57
1316729--1316753	13	1.9	13	100	0	50	36	0	0	64	0.94
1317366--1317420	25	2.0	26	83	13	67	63	0	0	36	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1317320--1317414	36	2.6	35	74	9	84	56	0	2	41	1.11
1320807--1320854	20	2.4	20	100	0	96	43	8	10	37	1.69
1321145--1321194	17	2.8	18	80	19	61	40	0	4	56	1.18
1321146--1321195	16	2.9	17	82	8	57	40	0	4	56	1.18
1326050--1326157	20	5.4	20	94	2	173	43	5	21	29	1.75
1326044--1326167	20	6.3	19	91	6	169	42	6	23	27	1.78
1328217--1328297	30	2.7	30	73	14	78	20	12	11	55	1.67
1330127--1330188	32	1.9	32	90	0	97	17	16	8	58	1.62
1336464--1336522	21	2.8	21	97	0	109	20	44	30	5	1.73
1337467--1337525	18	3.2	18	69	21	59	32	5	8	54	1.53

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