genome.fa.s65.2.7.7.80.10.50.1000.5.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: Scaffold65
Parameters: 2 7 7 80 10 50 1000
Length:  3097370

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

This is table  5  of  17  ( 1956 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)
1105519--1105547	11	2.5	12	94	5	51	41	0	0	58	0.98
1105526--1105609	17	4.8	18	69	20	63	44	0	0	55	0.99
1105531--1105638	18	6.3	18	67	26	58	45	0	0	54	0.99
1105558--1105610	16	3.2	16	75	19	56	45	0	0	54	0.99
1105557--1105638	33	2.4	36	82	12	100	45	0	0	54	0.99
1107294--1107382	44	2.0	44	100	0	178	37	13	22	26	1.91
1107696--1107824	21	6.1	21	79	12	122	46	14	28	10	1.77
1107695--1107819	42	3.0	42	81	6	146	47	15	28	9	1.76
1107695--1107817	63	2.0	63	83	6	160	46	15	28	9	1.77
1133659--1133708	25	2.0	25	100	0	100	32	4	16	48	1.64
1134718--1134753	18	2.0	17	89	10	54	77	0	2	19	0.88
1140107--1140132	11	2.4	11	100	0	52	84	0	15	0	0.62
1141160--1141191	16	2.0	16	93	0	55	59	0	25	15	1.36
1159001--1159209	105	2.0	104	91	0	337	45	15	18	21	1.85
1160432--1160458	4	6.8	4	100	0	54	22	0	0	77	0.76
1160600--1160670	26	2.6	28	74	14	76	39	0	0	60	0.97
1160599--1160660	13	4.3	15	72	17	60	37	0	0	62	0.95
1160747--1160780	17	1.9	17	88	5	50	41	0	0	58	0.98
1161156--1161216	17	3.6	18	73	20	51	45	1	0	52	1.10
1161155--1161216	16	3.7	17	74	20	51	45	1	0	53	1.10
1163485--1163514	8	3.8	8	90	0	51	33	10	13	43	1.77
1163485--1163517	16	2.1	16	100	0	66	30	12	12	45	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1168840--1168878	2	19.5	2	100	0	78	48	0	0	51	1.00
1170831--1170856	2	13.0	2	100	0	52	50	0	0	50	1.00
1172188--1172234	24	2.0	24	84	8	62	63	0	0	36	0.94
1172356--1172407	17	3.1	17	74	20	63	50	0	1	48	1.12
1172361--1172416	16	3.3	17	69	16	53	46	0	1	51	1.11
1174176--1174242	26	2.9	21	69	26	55	29	4	4	61	1.36
1176168--1176200	2	16.5	2	100	0	66	0	48	0	51	1.00
1177530--1177617	43	2.0	43	100	0	176	39	11	17	31	1.85
1186856--1186904	3	16.3	3	100	0	98	34	0	0	65	0.93
1187130--1187154	2	12.5	2	100	0	50	52	0	0	48	1.00
1187336--1187415	19	4.4	18	73	17	67	57	2	2	37	1.26
1187422--1187457	17	2.1	17	89	0	54	30	2	0	66	1.06
1188472--1188519	22	2.3	21	85	7	62	35	0	4	60	1.16
1189196--1189239	23	1.9	23	81	9	54	36	11	22	29	1.89
1189264--1189297	2	17.0	2	100	0	68	50	0	0	50	1.00
1190563--1190684	61	2.0	60	91	1	199	29	19	14	36	1.92
1196523--1196560	13	2.7	15	84	16	62	26	23	13	36	1.91
1201883--1201918	2	18.0	2	94	0	63	50	2	0	47	1.15
1202135--1202165	9	3.4	9	95	0	53	61	3	25	9	1.42
1202429--1202463	2	17.5	2	93	0	61	48	2	0	48	1.16
1205450--1205474	2	12.5	2	100	0	50	52	0	0	48	1.00
1208088--1208121	11	2.9	11	87	12	50	23	2	0	73	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1208090--1208123	18	1.9	17	88	5	50	23	2	0	73	0.97
1209164--1209188	13	1.9	13	100	0	50	32	0	0	68	0.90
1209467--1209512	17	2.8	17	77	12	51	56	0	0	43	0.99
1209505--1209530	13	2.0	13	100	0	52	30	0	0	69	0.89
1210044--1210105	18	3.3	20	70	22	62	37	3	4	54	1.38
1210631--1210671	17	2.5	17	84	7	59	43	0	0	56	0.99
1211050--1211074	11	2.3	11	100	0	50	8	20	0	72	1.10
1211547--1211604	23	2.5	23	82	2	71	67	5	0	27	1.12
1211566--1211669	31	3.5	30	74	12	90	62	2	0	34	1.10
1211689--1211755	26	2.5	26	81	9	82	67	2	0	29	1.06
1212187--1212240	24	2.2	24	74	9	56	53	1	0	44	1.11
1212219--1212255	18	2.0	20	89	10	60	40	5	0	54	1.24
1212297--1212360	33	1.9	33	87	6	94	45	3	0	51	1.17
1212358--1212401	13	3.4	13	75	12	54	38	0	0	61	0.96
1212334--1212423	26	3.2	29	81	16	109	36	3	0	60	1.14
1212416--1212634	114	1.9	114	97	1	413	45	10	7	35	1.68
1213108--1213141	14	2.4	15	85	14	54	73	0	2	23	0.97
1214677--1214730	12	4.8	12	73	17	53	27	0	3	68	1.06
1214680--1214728	14	3.1	14	75	25	53	24	0	4	71	1.03
1215138--1215212	28	2.7	28	81	8	73	42	6	0	50	1.28
1215096--1215214	59	2.0	58	81	12	136	41	5	2	50	1.40
1216074--1216098	2	12.5	2	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1216765--1216790	2	13.0	2	100	0	52	50	0	0	50	1.00
1217975--1218004	2	15.0	2	92	0	51	50	3	0	46	1.18
1219317--1219425	48	2.3	48	83	0	137	33	10	24	31	1.89
1219333--1219447	48	2.4	48	82	0	122	33	12	20	33	1.90
1220732--1220794	31	2.0	31	85	11	85	31	0	1	66	1.01
1220732--1220788	12	5.5	11	73	24	52	33	0	1	64	1.04
1223117--1223181	28	2.4	28	82	12	82	50	0	1	47	1.10
1223439--1223487	20	2.4	21	76	10	57	38	2	0	59	1.09
1223761--1223813	22	2.4	22	78	6	63	43	0	0	56	0.99
1223772--1223811	21	1.9	21	85	10	55	37	0	0	62	0.95
1223990--1224021	2	16.0	2	93	0	55	50	3	0	46	1.17
1224588--1224618	2	15.5	2	100	0	62	51	0	0	48	1.00
1227191--1227285	44	2.1	44	96	1	172	28	16	9	45	1.79
1227531--1227635	33	3.1	34	78	12	92	41	0	0	57	1.05
1240321--1240353	14	2.4	14	90	5	50	54	0	0	45	0.99
1240711--1240765	12	4.6	12	77	8	58	32	0	0	67	0.91
1240658--1240762	31	3.3	31	81	11	115	39	0	0	60	1.04
1240740--1240781	15	2.5	17	77	18	52	23	2	2	71	1.10
1240882--1240950	28	2.5	26	77	11	66	40	1	2	55	1.24
1240915--1240954	20	2.0	20	85	9	55	50	0	0	50	1.00
1241001--1241046	12	4.2	11	78	18	51	28	2	0	69	1.00
1241001--1241057	23	2.3	24	85	8	71	28	1	0	70	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1242994--1243049	29	2.0	28	89	3	85	41	0	3	55	1.17
1243740--1243790	21	2.4	21	78	9	59	50	0	0	49	1.00
1245021--1245046	2	13.0	2	100	0	52	50	0	0	50	1.00
1245097--1245138	2	21.0	2	100	0	84	0	0	50	50	1.00
1247379--1247410	2	16.0	2	100	0	64	0	0	50	50	1.00
1247660--1247699	20	2.0	20	85	0	53	42	0	0	57	0.98
1247716--1247759	15	3.0	15	80	6	54	47	0	0	52	1.00
1251498--1251525	3	9.3	3	100	0	56	67	0	0	32	0.91
1255308--1255341	16	2.1	16	100	0	68	67	5	5	20	1.33
1256430--1256462	2	16.5	2	100	0	66	51	0	0	48	1.00
1264116--1264177	29	2.1	29	100	0	124	35	9	20	33	1.86
1266879--1267022	45	3.0	45	84	13	216	25	10	25	38	1.87
1266901--1267010	52	2.1	52	98	0	211	27	9	23	40	1.85
1267461--1267507	13	3.5	14	77	16	55	36	0	2	61	1.08
1267706--1267748	2	21.5	2	100	0	86	48	0	0	51	1.00
1269970--1270018	24	2.0	24	96	0	89	2	40	6	51	1.38
1270330--1270434	53	2.0	53	98	0	201	47	18	20	13	1.82
1274288--1274334	19	2.5	19	89	6	60	53	0	0	46	1.00
1274291--1274334	20	2.2	21	92	8	74	50	0	0	50	1.00
1277238--1277272	2	17.5	2	100	0	70	48	0	0	51	1.00
1277481--1277534	24	2.3	25	81	9	60	33	1	0	64	1.04
1277539--1277598	21	2.8	20	73	9	57	65	0	0	35	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1277625--1277689	16	4.1	15	71	13	51	53	1	0	44	1.09
1278243--1278321	39	1.9	39	82	12	97	45	0	0	54	0.99
1279285--1279319	17	2.0	18	88	5	54	45	0	0	54	0.99
1279342--1279391	17	3.1	17	82	5	68	54	0	0	46	1.00
1279905--1279934	13	2.3	13	94	0	51	50	0	6	43	1.28
1280145--1280172	5	5.6	5	100	0	56	78	0	0	21	0.75
1280143--1280201	18	3.5	17	75	13	59	62	0	0	37	0.95
1286643--1286762	38	3.2	38	72	22	103	60	0	0	39	0.97
1287176--1287212	14	2.6	14	86	0	56	62	0	0	37	0.96
1287164--1287202	19	2.0	20	90	5	62	58	0	2	38	1.12

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