genome.fa.s41.2.7.7.80.10.50.1000.12.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  12  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)
1225274--1225341	15	4.6	15	68	17	52	48	0	0	51	1.00
1225609--1225650	17	2.4	18	80	11	52	23	0	2	73	0.94
1225618--1225656	20	2.0	20	85	10	53	28	0	0	71	0.86
1225968--1226032	30	2.2	31	83	8	82	44	1	7	46	1.41
1230723--1230769	21	2.2	21	84	0	58	40	17	2	40	1.61
1231420--1231580	53	3.0	53	98	0	304	25	18	12	43	1.85
1234541--1234575	2	17.5	2	100	0	70	48	0	0	51	1.00
1234867--1234955	27	3.2	28	74	7	74	55	0	1	43	1.07
1234881--1234919	11	3.5	11	89	0	60	64	0	2	33	1.08
1240938--1240962	6	4.2	6	100	0	50	52	0	0	48	1.00
1245732--1245760	2	14.5	2	100	0	58	48	0	0	51	1.00
1248648--1248687	20	2.0	21	85	9	57	35	0	5	60	1.19
1249023--1249131	44	2.4	45	74	14	118	55	0	2	41	1.14
1249110--1249135	7	3.7	7	100	0	52	69	0	0	30	0.89
1249108--1249147	14	2.7	15	84	7	55	65	0	0	35	0.93
1252407--1252440	12	2.8	12	90	0	50	52	14	2	29	1.56
1253857--1253925	28	2.5	28	85	2	86	28	2	1	66	1.14
1254265--1254326	19	3.2	20	82	11	67	41	0	0	58	0.98
1254314--1254375	17	3.6	17	73	18	56	61	1	0	37	1.06
1254324--1254392	34	2.1	32	86	5	93	63	1	0	34	1.03
1254718--1254751	15	2.3	15	90	10	52	41	0	0	58	0.98
1259686--1259737	22	2.3	23	87	12	81	46	0	1	51	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1260092--1260126	13	2.8	12	83	8	52	45	0	0	54	0.99
1260097--1260146	16	3.3	16	81	13	54	40	0	0	60	0.97
1260056--1260142	42	2.1	42	82	8	106	39	2	1	57	1.19
1260129--1260172	23	1.9	23	85	0	61	43	0	2	54	1.12
1260153--1260195	22	2.0	21	86	9	59	55	0	2	41	1.12
1262374--1262419	24	1.9	24	90	0	74	21	6	28	43	1.77
1263269--1263325	21	2.8	21	81	2	71	36	12	19	31	1.89
1263371--1263396	13	2.0	13	100	0	52	38	15	15	30	1.88
1263352--1263416	32	2.0	33	87	3	96	41	16	13	27	1.87
1267461--1267491	15	2.1	15	93	0	53	48	16	22	12	1.80
1269506--1269583	20	3.6	21	74	15	70	28	15	16	39	1.89
1270025--1270067	20	2.1	20	82	4	50	20	44	25	9	1.81
1272138--1272163	13	2.0	13	100	0	52	38	15	15	30	1.88
1272119--1272183	32	2.0	33	87	3	96	41	16	13	27	1.87
1276802--1276887	28	3.4	24	82	6	82	23	5	22	48	1.71
1276852--1276897	24	1.9	24	86	0	65	23	6	23	45	1.76
1279316--1279368	15	3.4	14	73	26	52	71	11	0	16	1.13
1279325--1279376	19	2.8	19	85	8	63	71	9	0	19	1.13
1280384--1280725	114	3.0	113	82	6	339	43	6	5	43	1.55
1295992--1296022	14	2.2	14	100	0	62	45	0	25	29	1.54
1297006--1297038	10	3.3	10	95	0	57	33	12	15	39	1.84
1298950--1299041	46	2.0	47	85	6	125	45	21	10	21	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1303448--1303472	12	2.1	12	100	0	50	52	0	0	48	1.00
1319218--1319264	16	3.1	16	79	17	55	70	10	14	4	1.31
1319209--1319286	37	2.1	36	81	11	88	70	10	14	5	1.31
1323220--1323340	52	2.3	52	95	0	215	30	18	16	34	1.93
1323220--1323360	52	2.7	52	89	4	196	32	17	16	33	1.92
1323346--1323373	13	2.2	13	100	0	56	39	17	14	28	1.89
1323416--1323469	20	2.7	20	85	0	72	42	14	11	31	1.81
1324135--1325193	82	12.8	82	90	2	1540	23	33	14	29	1.94
1324135--1325193	27	38.5	27	90	3	1528	23	33	14	29	1.94
1325164--1325485	58	5.6	58	80	8	225	30	30	15	23	1.96
1325216--1325453	28	8.4	28	87	2	251	31	29	15	23	1.95
1325326--1325736	32	13.2	32	83	6	377	31	31	16	21	1.95
1325440--1325736	97	3.1	97	86	4	397	30	31	17	21	1.96
1325222--1325736	129	4.2	122	82	8	482	30	30	16	22	1.96
1326974--1327022	14	3.4	15	78	21	52	75	0	22	2	0.90
1326974--1327024	20	2.9	17	86	13	61	76	0	21	1	0.88
1333418--1333461	23	1.9	23	95	0	79	56	4	9	29	1.50
1335097--1335203	55	1.9	56	83	5	137	39	14	15	30	1.87
1335156--1335367	111	1.9	112	80	6	252	39	16	17	26	1.90
1335459--1335740	111	2.5	112	77	8	272	37	15	19	26	1.92
1335532--1335663	55	2.4	55	82	10	162	37	12	21	28	1.91
1335079--1335739	56	11.9	56	72	9	298	38	15	18	27	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1336962--1337006	23	2.0	22	87	12	65	80	2	15	2	0.92
1337956--1338134	76	2.3	75	78	6	180	32	14	17	35	1.90
1339647--1339671	13	1.9	13	100	0	50	32	16	16	36	1.90
1339680--1339800	52	2.3	52	97	0	224	34	18	18	28	1.94
1348057--1348199	31	4.6	30	83	9	164	25	29	19	25	1.99
1348057--1348201	62	2.3	61	85	9	188	25	29	19	25	1.98
1348186--1349025	34	25.8	32	77	14	557	20	35	12	31	1.90
1348298--1348462	87	1.9	88	93	1	287	20	33	13	32	1.92
1348243--1348698	158	2.8	158	84	9	554	20	35	12	31	1.90
1348407--1349060	63	10.0	64	82	11	637	21	35	13	29	1.91
1348401--1349037	288	2.2	291	90	5	998	21	35	12	30	1.91
1348407--1349037	34	19.3	34	80	14	640	21	35	12	29	1.91
1349023--1349163	65	2.2	64	91	6	232	29	36	16	17	1.91
1349023--1349163	33	4.4	32	87	8	200	29	36	16	17	1.91
1348401--1349135	288	2.5	281	84	8	816	22	35	13	28	1.92
1349248--1349442	43	4.2	43	75	17	192	26	27	17	29	1.97
1349161--1349485	49	6.7	49	84	6	419	26	26	17	29	1.98
1349382--1349600	115	1.9	116	84	0	296	25	26	17	31	1.97
1349498--1349740	48	5.1	48	86	7	343	25	26	18	30	1.98
1349556--1349748	43	4.2	43	79	14	197	26	25	17	30	1.97
1349650--1349788	52	2.6	52	82	4	161	26	23	15	34	1.94
1349556--1349748	95	2.1	91	91	3	305	26	25	17	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1349650--1349804	56	2.9	54	82	3	179	26	23	14	35	1.94
1350678--1350702	13	1.9	13	100	0	50	36	16	16	32	1.90
1350658--1350727	33	2.1	33	89	0	104	34	11	14	40	1.82
1350768--1350792	13	1.9	13	100	0	50	32	16	16	36	1.90
1350801--1350921	52	2.3	52	97	0	224	34	18	18	28	1.94
1356204--1356236	17	1.9	17	93	0	57	57	0	30	12	1.35
1357813--1358248	57	7.7	57	79	3	405	33	14	19	32	1.92
1357824--1358253	169	2.5	171	81	5	505	33	14	20	32	1.93
1357812--1358233	226	1.9	227	83	3	564	32	14	20	32	1.93
1362901--1362975	10	6.9	10	72	14	51	16	4	2	77	1.03
1368829--1368873	21	2.1	22	87	4	65	0	44	0	55	0.99
1369115--1369165	6	8.5	6	95	0	75	17	29	15	37	1.91
1377427--1377547	52	2.3	52	95	0	215	30	18	16	34	1.93
1377427--1377567	52	2.7	52	89	4	196	32	17	16	33	1.92
1377553--1377580	13	2.2	13	100	0	56	39	17	14	28	1.89
1377622--1377675	20	2.7	20	85	0	72	42	14	11	31	1.81
1378341--1379399	82	12.8	82	90	2	1540	23	33	14	29	1.94
1378341--1379399	27	38.5	27	90	3	1528	23	33	14	29	1.94
1379422--1379691	28	9.4	28	84	4	234	31	29	15	22	1.95
1379407--1379852	86	4.9	84	78	9	309	30	30	16	22	1.96
1379532--1379942	32	13.2	32	82	6	359	30	30	16	21	1.95
1379646--1379942	97	3.1	97	85	4	379	29	30	17	21	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1379428--1379942	64	8.4	63	80	8	392	30	30	16	22	1.96
1381180--1381228	14	3.4	15	78	21	52	75	0	22	2	0.90
1381180--1381230	20	2.9	17	86	13	61	76	0	21	1	0.88
1387625--1387668	23	1.9	23	95	0	79	56	4	9	29	1.50
1389291--1389397	55	1.9	56	83	5	137	39	14	15	30	1.87
1389350--1389561	111	1.9	112	80	6	252	39	16	17	26	1.90
1389653--1389934	111	2.5	112	78	8	281	37	15	20	26	1.92
1389273--1389933	56	11.9	56	72	9	307	37	15	18	27	1.91
1392152--1392330	76	2.3	75	78	6	180	32	14	17	35	1.90
1393765--1393789	13	1.9	13	100	0	50	36	16	16	32	1.90

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