genome.fa.s112.2.7.7.80.10.50.1000.8.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: Scaffold112
Parameters: 2 7 7 80 10 50 1000
Length:  1714866

Tables:   1   2   3   4   5   6   7   8   9   10   11   

This is table  8  of  11  ( 1240 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)
1033932--1033957	1	26.0	1	100	0	52	0	0	100	0	0.00
1034229--1034254	6	4.3	6	100	0	52	30	0	19	50	1.48
1039363--1039425	22	2.8	22	79	13	67	41	3	3	52	1.33
1040456--1040516	2	32.0	2	74	21	51	49	1	1	47	1.21
1041056--1041109	22	2.5	22	87	0	72	55	12	1	29	1.48
1041039--1041087	16	3.1	15	77	11	53	53	14	2	30	1.52
1041078--1041151	16	4.6	16	75	9	69	62	8	0	29	1.24
1041051--1041125	38	2.0	38	83	0	96	57	12	1	29	1.43
1049718--1049831	33	3.0	38	73	21	98	58	0	0	40	1.04
1049710--1049831	11	11.2	11	71	15	76	58	0	0	40	1.04
1049864--1050058	105	1.9	105	81	6	243	40	22	8	29	1.84
1050466--1050499	16	2.1	17	88	5	52	2	23	2	70	1.15
1053716--1053758	15	2.9	15	80	13	52	74	2	23	0	0.93
1054112--1054303	96	2.0	96	96	0	357	31	11	18	38	1.87
1055635--1055672	18	2.1	18	90	5	58	47	0	2	50	1.15
1060624--1060654	13	2.4	13	94	0	53	54	0	3	41	1.16
1060615--1060652	7	5.4	7	84	9	51	57	0	2	39	1.12
1063631--1063739	27	3.6	31	77	15	88	55	0	0	44	1.06
1063665--1063750	15	6.0	15	65	24	60	58	1	0	40	1.06
1063661--1063748	18	4.7	19	72	20	69	57	1	0	40	1.06
1065234--1065274	2	20.5	2	92	0	64	43	0	2	53	1.13
1065242--1065280	12	3.2	12	92	0	60	38	0	5	56	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1065722--1065837	30	3.9	30	90	0	178	28	33	16	21	1.95
1068493--1068520	2	14.0	2	100	0	56	50	0	0	50	1.00
1069050--1069098	22	2.2	22	92	0	80	57	6	18	18	1.61
1069498--1069537	9	4.6	9	81	6	55	40	0	0	60	0.97
1069477--1069541	26	2.3	29	76	20	82	41	1	0	56	1.08
1069486--1069539	26	2.1	26	92	0	90	37	1	0	61	1.07
1071632--1071689	26	2.4	25	85	8	75	63	0	0	36	0.94
1072000--1072040	20	2.0	21	85	4	57	56	0	0	43	0.99
1079525--1079549	2	12.5	2	100	0	50	48	0	0	52	1.00
1082565--1083331	274	2.9	269	83	6	889	43	18	11	25	1.85
1086782--1086826	22	2.0	22	91	0	72	35	26	13	24	1.92
1090222--1090263	6	7.0	6	94	0	75	35	0	64	0	0.94
1090345--1090395	26	2.0	26	88	7	77	50	0	0	49	1.00
1090649--1090848	71	2.8	71	85	8	257	45	5	6	44	1.50
1091271--1091309	17	2.2	17	86	4	51	87	7	2	2	0.73
1091270--1091309	18	2.2	18	86	0	53	87	7	2	2	0.71
1091361--1091387	2	13.5	2	100	0	54	51	0	48	0	1.00
1091397--1091431	18	1.9	18	88	11	54	51	25	22	0	1.48
1097155--1097220	29	2.3	30	79	12	75	40	0	0	59	0.98
1098756--1098939	2	91.0	2	78	2	188	44	6	3	45	1.47
1100976--1101050	28	2.6	29	76	21	86	42	0	0	57	0.98
1101008--1101085	22	3.4	22	70	16	59	35	1	1	61	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1100980--1101036	27	2.1	29	84	15	77	38	0	0	61	0.96
1101707--1101759	19	2.8	19	88	5	65	60	1	0	37	1.08
1111288--1111362	20	3.8	20	80	3	80	40	12	13	34	1.81
1111285--1111362	40	2.0	39	87	2	111	39	12	12	34	1.82
1111873--1113408	28	55.3	28	91	6	2238	20	17	33	28	1.95
1111873--1113409	56	27.7	56	93	4	2559	20	17	33	28	1.95
1111873--1113409	83	18.5	84	92	4	2539	20	17	33	28	1.95
1114629--1114671	1	43.0	1	80	0	50	0	2	6	90	0.52
1114614--1114671	10	5.8	10	86	6	55	3	5	6	84	0.86
1114631--1114671	15	2.7	15	88	3	64	0	2	7	90	0.54
1114619--1114666	10	4.5	11	87	10	57	2	4	8	85	0.80
1124399--1124425	4	6.8	4	100	0	54	77	0	0	22	0.76
1127750--1127801	22	2.3	23	96	3	97	59	9	11	19	1.59
1128712--1128786	20	3.8	20	80	3	80	40	12	13	34	1.81
1128709--1128786	40	2.0	39	87	2	111	39	12	12	34	1.82
1129175--1129214	12	3.3	12	83	13	55	37	7	10	45	1.66
1129460--1129519	23	2.6	23	79	7	68	26	1	5	66	1.21
1136879--1136913	18	1.9	18	94	0	61	74	0	0	25	0.82
1136881--1136930	21	2.4	21	83	3	57	74	0	4	22	0.99
1136949--1136978	2	15.0	2	92	0	51	46	0	3	50	1.18
1137359--1137419	24	2.5	24	72	15	63	36	3	1	59	1.24
1137412--1137442	16	2.0	15	93	6	53	35	0	0	64	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1142652--1142699	20	2.3	20	75	3	51	64	4	8	22	1.38
1143293--1143346	24	2.2	24	83	6	65	50	1	1	46	1.23
1148606--1148645	19	2.1	19	85	0	53	70	0	5	25	1.08
1148671--1148700	2	15.0	2	100	0	60	50	0	0	50	1.00
1152562--1152610	11	4.2	12	74	25	52	34	0	0	65	0.93
1154283--1154325	3	14.3	3	100	0	86	34	0	0	65	0.93
1156536--1156576	19	2.2	18	91	4	64	63	0	2	34	1.08
1157202--1157336	73	1.9	72	90	1	198	36	5	1	56	1.33
1157489--1157565	29	2.8	28	83	13	88	61	1	0	37	1.05
1159591--1159664	37	1.9	39	81	10	91	48	0	1	50	1.09
1159613--1159693	17	4.8	17	69	13	60	50	0	2	46	1.14
1159855--1159924	20	3.4	20	76	4	59	51	0	0	48	1.00
1161389--1161427	15	2.5	16	87	4	62	53	0	0	46	1.00
1161379--1161426	16	3.1	16	81	6	62	47	2	2	47	1.25
1161719--1161744	6	4.3	6	100	0	52	34	0	15	50	1.45
1162467--1162504	17	2.2	17	100	0	76	55	10	5	28	1.56
1167040--1167103	3	22.7	3	76	23	68	64	0	0	35	0.94
1167054--1167143	25	3.8	25	79	16	95	63	0	0	36	0.95
1167041--1167176	44	3.0	45	79	16	122	61	0	0	38	0.96
1167121--1167239	32	3.5	33	77	11	107	54	1	0	43	1.10
1167121--1167203	33	2.5	32	88	3	121	55	1	0	43	1.07
1167063--1167221	14	11.5	14	70	28	55	56	0	0	42	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1167155--1167210	18	3.4	17	74	20	55	51	1	0	46	1.11
1168812--1169012	106	1.9	106	84	0	267	51	3	7	37	1.49
1169367--1169407	22	1.9	22	85	14	59	39	2	0	58	1.11
1169918--1169965	21	2.3	21	77	0	51	2	33	29	35	1.69
1169935--1170021	30	2.9	30	96	0	156	0	35	27	36	1.57
1170798--1171002	34	6.2	34	72	14	124	43	22	5	28	1.76
1170848--1170939	29	3.0	29	82	9	103	39	22	7	30	1.82
1170848--1170973	63	2.0	63	81	3	146	42	22	5	29	1.76
1172037--1172066	15	2.1	15	93	6	53	43	0	0	56	0.99
1173944--1173994	22	2.4	22	87	9	70	43	0	0	56	0.99
1175254--1175290	19	2.0	18	89	5	56	56	5	0	37	1.22
1175283--1175341	30	1.9	31	89	3	93	50	1	0	47	1.11
1176801--1176839	20	2.0	19	85	5	51	51	0	0	48	1.00
1177121--1177223	38	2.7	38	87	0	143	51	11	0	36	1.39
1177119--1177223	4	26.2	4	89	0	93	51	11	0	37	1.38
1177523--1177572	23	2.2	22	80	19	59	32	12	2	54	1.49
1178015--1178039	12	2.1	12	100	0	50	44	8	0	48	1.32
1178079--1178111	2	16.5	2	100	0	66	51	0	0	48	1.00
1178226--1178260	3	11.7	3	100	0	70	31	0	0	68	0.90
1180527--1180580	19	2.8	18	83	10	63	62	0	0	37	0.95
1180549--1180578	13	2.2	14	94	5	53	63	0	0	36	0.95
1180512--1180577	32	2.1	32	85	5	89	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1180939--1180973	2	18.0	2	88	5	54	48	0	2	48	1.16
1182945--1183030	41	2.1	40	91	6	136	44	16	0	39	1.48
1184698--1184741	12	3.6	12	87	6	70	70	0	4	25	1.06
1191193--1191217	12	2.1	12	100	0	50	16	0	32	52	1.44
1198203--1198230	2	14.0	2	100	0	56	50	0	0	50	1.00
1199248--1199285	16	2.4	16	90	0	58	50	7	2	39	1.46
1199290--1199330	22	2.0	21	85	9	57	58	2	0	39	1.11
1200438--1200482	22	2.0	24	86	8	67	66	0	0	33	0.92
1202385--1202449	32	2.0	32	96	0	121	30	23	6	40	1.79
1205979--1206015	2	18.5	2	100	0	74	51	0	0	48	1.00

Tables:   1   2   3   4   5   6   7   8   9   10   11