Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016475.1 Corchorus capsularis cultivar CVL-1 contig16496, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7998
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:842 original size:14 final size:14
Alignment explanation
Indices: 825--872 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
815 GAAACATTGA
*
825 AATTGAACTCGAAG
1 AATTGAAATCGAAG
*
839 AATTGAAATGGAAG
1 AATTGAAATCGAAG
*
853 AATTGAAATTGAAG
1 AATTGAAATCGAAG
*
867 CATTGA
1 AATTGA
873 CATGTTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (14 bp):
AATTGAAATCGAAG
Found at i:883 original size:22 final size:21
Alignment explanation
Indices: 855--938 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 21
845 AATGGAAGAA
855 TTGAAATTGAAGCATTGACAT
1 TTGAAATTGAAGCATTGACAT
* *
876 GTTGAAATTGAAACATTGGCAT
1 -TTGAAATTGAAGCATTGACAT
* * *
898 TTGGAATTTGAAGAATTGAAAT
1 TT-GAAATTGAAGCATTGACAT
*
920 TT-AAGCATTGAAGAATTGA
1 TTGAA--ATTGAAGCATTGA
939 GATCGAAGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.04
21 2 0.04
22 47 0.92
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (21 bp):
TTGAAATTGAAGCATTGACAT
Found at i:931 original size:14 final size:15
Alignment explanation
Indices: 835--931 Score: 55
Period size: 14 Copynumber: 6.7 Consensus size: 15
825 AATTGAACTC
*
835 GAAGAATTGAAA-TG
1 GAAGAATTGAAATTT
849 GAAGAATTGAAA-TT
1 GAAGAATTGAAATTT
* *
863 GAAGCATTGACATGTT
1 GAAGAATTGAAAT-TT
*
879 G-A-AATTGAAACATT
1 GAAGAATTGAAA-TTT
* *
893 G--GCATTTGGAATTT
1 GAAG-AATTGAAATTT
907 GAAGAATTGAAATTT
1 GAAGAATTGAAATTT
*
922 -AAGCATTGAA
1 GAAGAATTGAA
932 GAATTGAGAT
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
14 44 0.69
15 16 0.25
16 4 0.06
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (15 bp):
GAAGAATTGAAATTT
Found at i:996 original size:16 final size:16
Alignment explanation
Indices: 961--1010 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
951 AAAGATTTGA
* *
961 AATTGAGGTATTGAGG
1 AATTGAAGTATTGAAG
*
977 AATTGAAGTATTGAAT
1 AATTGAAGTATTGAAG
*
993 AATTGAAGGATTGAAG
1 AATTGAAGTATTGAAG
1009 AA
1 AA
1011 AGATCACCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (16 bp):
AATTGAAGTATTGAAG
Found at i:1070 original size:22 final size:22
Alignment explanation
Indices: 1034--1294 Score: 148
Period size: 22 Copynumber: 11.8 Consensus size: 22
1024 TCATTAAAGT
* * *
1034 AAATGGAAGCATTGAATAATTG
1 AAATTGAAACATTGAAGAATTG
*
1056 AAATTGAAATC-TTGAAGAGTTG
1 AAATTGAAA-CATTGAAGAATTG
* * * *
1078 AGACTGAAGCATTGAA-ACGTTG
1 AAATTGAAACATTGAAGA-ATTG
* *
1100 AAATTGAAACATTGAAGGATCG
1 AAATTGAAACATTGAAGAATTG
*
1122 -AATTGGAAGA-ACTGGAAGAATTG
1 AAATT-GAA-ACA-TTGAAGAATTG
*
1145 AAATTGAAACATTG-AGATAGTG
1 AAATTGAAACATTGAAGA-ATTG
1167 AAATTGAAACATTGAAGAATTG
1 AAATTGAAACATTGAAGAATTG
* *
1189 AAATTGAAACATTGATGGATTG
1 AAATTGAAACATTGAAGAATTG
*
1211 AATTTGAAGA-ATTG-A-AATTG
1 AAATTGAA-ACATTGAAGAATTG
* * *
1231 AGGCACTG-AA-ATTGAA-ACATCG
1 A--AATTGAAACATTGAAGA-ATTG
* *
1253 AAGAATTGAAGCATTTGAAGGATTG
1 -A-AATTGAAACA-TTGAAGAATTG
1278 AAATTGAAACATTGAAG
1 AAATTGAAACATTGAAG
1295 GTTTGAACTT
Statistics
Matches: 184, Mismatches: 34, Indels: 42
0.71 0.13 0.16
Matches are distributed among these distances:
20 10 0.05
21 12 0.07
22 119 0.65
23 29 0.16
24 6 0.03
25 8 0.04
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (22 bp):
AAATTGAAACATTGAAGAATTG
Found at i:1151 original size:89 final size:89
Alignment explanation
Indices: 1051--1221 Score: 222
Period size: 89 Copynumber: 1.9 Consensus size: 89
1041 AGCATTGAAT
* * *
1051 AATTGAAATTGAAATC-TTGA-AGAGTTGAGACTGAAGCATTGAA-ACGTTGAAATTGAAACATT
1 AATTGAAATTGAAA-CATTGAGAGAG-TGAAACTGAAACATTGAAGA-ATTGAAATTGAAACATT
1113 GAAGGATCGAATTGGAAGAACTGGAAG
63 GAAGGATCGAATTGGAAGAACTGGAAG
* * *
1140 AATTGAAATTGAAACATTGAGATAGTGAAATTGAAACATTGAAGAATTGAAATTGAAACATTGAT
1 AATTGAAATTGAAACATTGAGAGAGTGAAACTGAAACATTGAAGAATTGAAATTGAAACATTGAA
* *
1205 GGATTGAATTTGAAGAA
66 GGATCGAATTGGAAGAA
1222 TTGAAATTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
88 1 0.01
89 66 0.93
90 4 0.06
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (89 bp):
AATTGAAATTGAAACATTGAGAGAGTGAAACTGAAACATTGAAGAATTGAAATTGAAACATTGAA
GGATCGAATTGGAAGAACTGGAAG
Found at i:1195 original size:36 final size:36
Alignment explanation
Indices: 1146--1388 Score: 176
Period size: 36 Copynumber: 6.6 Consensus size: 36
1136 GAAGAATTGA
* *
1146 AATTGAAACATTGAGATAGTGAAATTGAAACATTGAAG
1 AATTG-AA-ATTGAGACATTGAAATTGAAACATTGAAG
* * *
1184 AATTGAAATTGAAACATTGATGGATTG-AA-TTTGAAG
1 AATTGAAATTGAGACATTGA--AATTGAAACATTGAAG
* * *
1220 AATTGAAATTGAGGCACTGAAATTGAAACATCGAAG
1 AATTGAAATTGAGACATTGAAATTGAAACATTGAAG
*
1256 AATTGAAGCATTTGA-AGGATTGAAATTGAAACATTGAAG
1 AATTGAA--A-TTGAGA-CATTGAAATTGAAACATTGAAG
** * *
1295 GTTTGAACTTGAAGA-ATTGAAATTGAAGCATTGAAG
1 AATTGAAATTG-AGACATTGAAATTGAAACATTGAAG
* * * *
1331 AATTGGAATTGAAACATTGGAGCATTG-AA-TTTGAAG
1 AATTGAAATTGAGACATT-GA-AATTGAAACATTGAAG
1367 AATTGAAATTG-GAGCATTGAAA
1 AATTGAAATTGAGA-CATTGAAA
1389 ATTTGGAATT
Statistics
Matches: 161, Mismatches: 30, Indels: 32
0.72 0.13 0.14
Matches are distributed among these distances:
34 5 0.03
35 7 0.04
36 98 0.61
37 8 0.05
38 15 0.09
39 28 0.17
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.28
Consensus pattern (36 bp):
AATTGAAATTGAGACATTGAAATTGAAACATTGAAG
Found at i:1241 original size:50 final size:52
Alignment explanation
Indices: 1187--1284 Score: 137
Period size: 50 Copynumber: 1.9 Consensus size: 52
1177 ATTGAAGAAT
* * *
1187 TGAAATTGAAACATTGATGGATTG-A-ATTTGAAGAATTGAAATTGAGGCAC
1 TGAAATTGAAACATCGAAGAATTGAACATTTGAAGAATTGAAATTGAGGCAC
*
1237 TGAAATTGAAACATCGAAGAATTGAAGCATTTGAAGGATTGAAATTGA
1 TGAAATTGAAACATCGAAGAATTGAA-CATTTGAAGAATTGAAATTGA
1285 AACATTGAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
50 21 0.51
51 1 0.02
53 19 0.46
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (52 bp):
TGAAATTGAAACATCGAAGAATTGAACATTTGAAGAATTGAAATTGAGGCAC
Found at i:1328 original size:22 final size:22
Alignment explanation
Indices: 1214--1373 Score: 91
Period size: 22 Copynumber: 7.2 Consensus size: 22
1204 TGGATTGAAT
*
1214 TTGAAGAATTGAAATTGAGGCA
1 TTGAAGAATTGAAATTGAAGCA
* * *
1236 CTG-A-AATTGAAACATCGAAGAA
1 TTGAAGAATTG-AA-ATTGAAGCA
*
1258 TTGAAGCATTTGAAGGATTGAA--A
1 TTGAAG-AATTGAA--ATTGAAGCA
*
1281 TTGAA-ACATTGAAGGTTTGAA-C-
1 TTGAAGA-ATTGAA--ATTGAAGCA
1303 TTGAAGAATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
* *
1325 TTGAAGAATTGGAATTGAAACA
1 TTGAAGAATTGAAATTGAAGCA
* * * *
1347 TTGGAGCATTGAATTTGAAGAA
1 TTGAAGAATTGAAATTGAAGCA
1369 TTGAA
1 TTGAA
1374 ATTGGAGCAT
Statistics
Matches: 107, Mismatches: 20, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
20 10 0.09
21 5 0.05
22 73 0.68
23 8 0.07
24 2 0.02
25 9 0.08
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.28
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAGCA
Found at i:1345 original size:58 final size:58
Alignment explanation
Indices: 1256--1400 Score: 202
Period size: 58 Copynumber: 2.5 Consensus size: 58
1246 AACATCGAAG
* * **
1256 AATTGAAGCATTTGAAGGATTGAAATTGAAACATTGAAGGTTTGAACTTGAAGAATTGA
1 AATTGAAGCA-TTGAAGAATTGGAATTGAAACATTGAAGCATTGAACTTGAAGAATTGA
* *
1315 AATTGAAGCATTGAAGAATTGGAATTGAAACATTGGAGCATTGAATTTGAAGAATTGA
1 AATTGAAGCATTGAAGAATTGGAATTGAAACATTGAAGCATTGAACTTGAAGAATTGA
*
1373 AATTGGAGCATTGAA-AATTTGGAATTGA
1 AATTGAAGCATTGAAGAA-TTGGAATTGA
1401 GGCATTAAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
57 2 0.03
58 66 0.85
59 10 0.13
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.30
Consensus pattern (58 bp):
AATTGAAGCATTGAAGAATTGGAATTGAAACATTGAAGCATTGAACTTGAAGAATTGA
Found at i:1356 original size:89 final size:89
Alignment explanation
Indices: 1168--1329 Score: 254
Period size: 89 Copynumber: 1.8 Consensus size: 89
1158 GAGATAGTGA
* * *
1168 AATTGAAACA-TTGAAGAATTGAAATTGAAACATTGATGGATTGAATTTGAAGAATTGAAATTGA
1 AATTGAAGCATTTGAAGAATTGAAATTGAAACATTGAAGGATTGAACTTGAAGAATTGAAATTGA
*
1232 GGCACTGAAATTGAAACATCGAAG
66 AGCACTGAAATTGAAACATCGAAG
* *
1256 AATTGAAGCATTTGAAGGATTGAAATTGAAACATTGAAGGTTTGAACTTGAAGAATTGAAATTGA
1 AATTGAAGCATTTGAAGAATTGAAATTGAAACATTGAAGGATTGAACTTGAAGAATTGAAATTGA
*
1321 AGCATTGAA
66 AGCACTGAA
1330 GAATTGGAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
88 9 0.14
89 57 0.86
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.28
Consensus pattern (89 bp):
AATTGAAGCATTTGAAGAATTGAAATTGAAACATTGAAGGATTGAACTTGAAGAATTGAAATTGA
AGCACTGAAATTGAAACATCGAAG
Found at i:1373 original size:14 final size:14
Alignment explanation
Indices: 1136--1388 Score: 95
Period size: 14 Copynumber: 17.9 Consensus size: 14
1126 GGAAGAACTG
1136 GAAGAATTGAAATT
1 GAAGAATTGAAATT
*
1150 GAA-ACATTGAGATAGT
1 GAAGA-ATTGA-A-ATT
1166 G-A-AATTGAAACATT
1 GAAGAATTG-AA-ATT
1180 GAAGAATTGAAATT
1 GAAGAATTGAAATT
1194 GAA-ACATTG--A-T
1 GAAGA-ATTGAAATT
*
1205 G--G-ATTGAATTT
1 GAAGAATTGAAATT
1216 GAAGAATTGAAATT
1 GAAGAATTGAAATT
* * *
1230 GAGGCACTGAAATT
1 GAAGAATTGAAATT
*
1244 GAA-ACATCGAAGAATT
1 GAAGA-ATTG-A-AATT
*
1260 GAAGCATTTGAAGGATT
1 GAAG-AATTGAA--ATT
1277 G-A-AATTGAAACATT
1 GAAGAATTG-AA-ATT
** *
1291 GAAGGTTTGAACTT
1 GAAGAATTGAAATT
1305 GAAGAATTGAAATT
1 GAAGAATTGAAATT
*
1319 GAAGCATTGAAGAATT
1 GAAGAATTG-A-AATT
1335 G--GAATTGAAACATT
1 GAAGAATTG-AA-ATT
* * *
1349 GGAGCATTGAATTT
1 GAAGAATTGAAATT
1363 GAAGAATTGAAATT
1 GAAGAATTGAAATT
* *
1377 GGAGCATTGAAA
1 GAAGAATTGAAA
1389 ATTTGGAATT
Statistics
Matches: 179, Mismatches: 31, Indels: 58
0.67 0.12 0.22
Matches are distributed among these distances:
8 4 0.02
11 4 0.02
12 1 0.01
13 4 0.02
14 112 0.63
15 17 0.09
16 30 0.17
17 6 0.03
18 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.28
Consensus pattern (14 bp):
GAAGAATTGAAATT
Found at i:1399 original size:14 final size:13
Alignment explanation
Indices: 1324--1400 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 13
1314 AAATTGAAGC
1324 ATTGAAGAATTGGA
1 ATTGAA-AATTGGA
1338 ATTGAAACATTGGA
1 ATTGAAA-ATTGGA
*
1352 GCATTG-AATTTGAAGA
1 --ATTGAAAATTG--GA
1368 ATTG-AAATTGGA
1 ATTGAAAATTGGA
1380 GCATTGAAAATTTGGA
1 --ATTGAAAA-TTGGA
1396 ATTGA
1 ATTGA
1401 GGCATTAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
12 2 0.04
13 1 0.02
14 33 0.63
15 5 0.10
16 11 0.21
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (13 bp):
ATTGAAAATTGGA
Found at i:1551 original size:24 final size:24
Alignment explanation
Indices: 1478--1552 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
1468 TGGGTCATTG
* *
1478 AAGTGAATTGAAGAATTGAAGTATT
1 AAGTG-ATTGAAGAATTGAAGCAAT
* * * *
1503 TAGTAATTGAAGAGTTTAAGCAAT
1 AAGTGATTGAAGAATTGAAGCAAT
* *
1527 AAGTGATCGAAGAATTGAAGGAAT
1 AAGTGATTGAAGAATTGAAGCAAT
1551 AA
1 AA
1553 ATTGAAGTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
24 35 0.92
25 3 0.08
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.28
Consensus pattern (24 bp):
AAGTGATTGAAGAATTGAAGCAAT
Found at i:1601 original size:8 final size:8
Alignment explanation
Indices: 1598--1654 Score: 78
Period size: 8 Copynumber: 7.1 Consensus size: 8
1588 AAATTGAATC
1598 ATTGAAGA
1 ATTGAAGA
1606 ATTGAAGA
1 ATTGAAGA
*
1614 ATTGAATA
1 ATTGAAGA
*
1622 ATGGAAGA
1 ATTGAAGA
*
1630 ATTGAAGC
1 ATTGAAGA
*
1638 ATTGAATA
1 ATTGAAGA
1646 ATTGAAGA
1 ATTGAAGA
1654 A
1 A
1655 AGAGATCATT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.23, T:0.26
Consensus pattern (8 bp):
ATTGAAGA
Found at i:1617 original size:24 final size:24
Alignment explanation
Indices: 1589--1654 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
1579 CGAAGAGATA
*
1589 AATTGAATCATTGAAGAATTGAAG
1 AATTGAATAATTGAAGAATTGAAG
*
1613 AATTGAATAATGGAAGAATTGAAG
1 AATTGAATAATTGAAGAATTGAAG
*
1637 CATTGAATAATTGAAGAA
1 AATTGAATAATTGAAGAA
1655 AGAGATCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.27
Consensus pattern (24 bp):
AATTGAATAATTGAAGAATTGAAG
Found at i:1714 original size:10 final size:9
Alignment explanation
Indices: 1589--1713 Score: 58
Period size: 8 Copynumber: 14.8 Consensus size: 9
1579 CGAAGAGATA
1589 AATTGAAT-
1 AATTGAATG
*
1597 CATTGAA-G
1 AATTGAATG
1605 AATTGAA-G
1 AATTGAATG
1613 AATTGAAT-
1 AATTGAATG
*
1621 AATGGAA-G
1 AATTGAATG
1629 AATTGAA-G
1 AATTGAATG
*
1637 CATTGAAT-
1 AATTGAATG
1645 AATTGAA-G
1 AATTGAATG
* *
1653 AA-AGAGATC
1 AATTGA-ATG
* *
1662 ATTTTGAGATA
1 A-ATTGA-ATG
1673 AATTGAA-G
1 AATTGAATG
*
1681 CATTGAATG
1 AATTGAATG
1690 -ATTGAAT-
1 AATTGAATG
1697 AATTGAACTG
1 AATTGAA-TG
1707 AATTGAA
1 AATTGAA
1714 CAAGATTAGC
Statistics
Matches: 90, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
7 2 0.02
8 67 0.74
9 4 0.04
10 11 0.12
11 6 0.07
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.30
Consensus pattern (9 bp):
AATTGAATG
Found at i:2706 original size:7 final size:8
Alignment explanation
Indices: 2672--2727 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
2662 CTCTTTTCCA
*
2672 TTCATTTC
1 TTCATTTT
2680 TTCATTTT
1 TTCATTTT
*
2688 CTCATTTTT
1 TTCA-TTTT
*
2697 TTTATTTT
1 TTCATTTT
2705 TTCATTTTT
1 TTCA-TTTT
*
2714 TTTATTTT
1 TTCATTTT
2722 TTCATT
1 TTCATT
2728 GCACTTGGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 26 0.67
9 13 0.33
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (8 bp):
TTCATTTT
Found at i:2709 original size:17 final size:17
Alignment explanation
Indices: 2683--2727 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
2673 TCATTTCTTC
*
2683 ATTTTCTCATTTTTTTT
1 ATTTTTTCATTTTTTTT
2700 ATTTTTTCATTTTTTTT
1 ATTTTTTCATTTTTTTT
2717 ATTTTTTCATT
1 ATTTTTTCATT
2728 GCACTTGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (17 bp):
ATTTTTTCATTTTTTTT
Done.