Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016711.1 Corchorus olitorius cultivar O-4 contig16744, 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: 10637
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:560 original size:26 final size:26
Alignment explanation
Indices: 531--581 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
521 GAAAGCCCAA
531 AGAAATGGACTTGAACAAAAGATAAG
1 AGAAATGGACTTGAACAAAAGATAAG
*
557 AGAAATGGACTTGACCAAAAGATAA
1 AGAAATGGACTTGAACAAAAGATAA
582 AATAGAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.53, C:0.10, G:0.22, T:0.16
Consensus pattern (26 bp):
AGAAATGGACTTGAACAAAAGATAAG
Found at i:941 original size:44 final size:44
Alignment explanation
Indices: 891--985 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 44
881 AAGAATGCCT
*
891 TGGATCAATCGAA-AAT-AA-ATTGAATAATTGAAGGAAGACCACCC
1 TGGATC-ATCGAACAATGAATATTG-A-AATTGAAGAAAGACCACCC
* *
935 TGGATCATTGAAGCATTGAATATTGAAATTGAAGAAAGACCACCC
1 TGGATCATCGAA-CAATGAATATTGAAATTGAAGAAAGACCACCC
980 TGGATC
1 TGGATC
986 GTTGAAGTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
43 5 0.11
44 6 0.14
45 26 0.59
46 3 0.07
47 4 0.09
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (44 bp):
TGGATCATCGAACAATGAATATTGAAATTGAAGAAAGACCACCC
Found at i:1030 original size:56 final size:56
Alignment explanation
Indices: 941--1236 Score: 468
Period size: 56 Copynumber: 5.3 Consensus size: 56
931 ACCCTGGATC
* *
941 ATTGAAGCATTGAA-TATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAA
1 ATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAA
* * * *
996 ATTGATGCATTGAAGAATTGAACTTGAAGCAAGACCACCCCGGATCGTTCAAGTAA
1 ATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAA
* * * *
1052 CTTGATGCATAGAAGAATTGAAATTGAAAAAATACCACCCTGGATCGTTGAAGTAA
1 ATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAA
*
1108 ATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCATTGAAGTAA
1 ATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAA
* *
1164 ATTAATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAATAA
1 ATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAA
1220 ATTGATGCATTGAAGAA
1 ATTGATGCATTGAAGAA
1237 AGACCACCCT
Statistics
Matches: 217, Mismatches: 23, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
55 13 0.06
56 204 0.94
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (56 bp):
ATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAA
Found at i:1153 original size:112 final size:112
Alignment explanation
Indices: 956--1457 Score: 746
Period size: 112 Copynumber: 4.6 Consensus size: 112
946 AGCATTGAAT
*
956 ATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAACTT
1 ATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATT
* * * * *
1021 GAAGCAAGACCACCCCGGATCGTTCAAGTAACTTGATGCATAGAAGA
66 GAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATAGAAGA
* *
1068 ATTGAAATTGAAAAAATACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATT
1 ATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATT
* *
1133 GAAGAAAGACCACCCTGGATCATTGAAGTAAATTAATGCATTGAAGA
66 GAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATAGAAGA
*
1180 ATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAATAAATTGATGC--------------ATT
1 ATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATT
*
1231 GAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTGAAGA
66 GAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATAGAAGA
* *
1278 ATTGAAATTGAAGAAAGACCACCCTGGATCATTGAAATAAATTGATGCATTGAAGAATTGAAATT
1 ATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATT
*
1343 GAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTA-AAGA
66 GAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCA-TAGAAGA
*
1390 ATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTAAAGAATTGAAATT
1 ATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATT
1455 GAA
66 GAA
1458 ACATTGAAGG
Statistics
Matches: 355, Mismatches: 20, Indels: 30
0.88 0.05 0.07
Matches are distributed among these distances:
98 96 0.27
112 258 0.73
113 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.25
Consensus pattern (112 bp):
ATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATT
GAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATAGAAGA
Found at i:1233 original size:42 final size:42
Alignment explanation
Indices: 1186--1278 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
1176 AAGAATTGAA
*
1186 ATTGAAGAAAGACCACCCTGGATCGTTGAAATAAATTGATGC
1 ATTGAAGAAAGACCACCCTGGATCATTGAAATAAATTGATGC
*
1228 ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGC
1 ATTGAAGAAAGACCACCCTGGATCATTGAAATAAATTGATGC
1270 ATTGAAGAA
1 ATTGAAGAA
1279 TTGAAATTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (42 bp):
ATTGAAGAAAGACCACCCTGGATCATTGAAATAAATTGATGC
Found at i:1243 original size:98 final size:98
Alignment explanation
Indices: 1130--1446 Score: 454
Period size: 98 Copynumber: 3.1 Consensus size: 98
1120 AAGAATTGAA
*
1130 ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTAATGCATTGAAGAATTGAAATTGAAGAA
1 ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGAA
1195 AGACCACCCTGGATCGTTGAAATAAATTGATGC
66 AGACCACCCTGGATCGTTGAAATAAATTGATGC
1228 ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGAA
1 ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGAA
*
1293 AGACCACCCTGGATCATTGAAATAAATTGATGC
66 AGACCACCCTGGATCGTTGAAATAAATTGATGC
* *
1326 ATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTAAAGAA
1 --------------ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTGAAGAA
*
1391 TTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGC
52 TTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAATAAATTGATGC
*
1438 ATTAAAGAA
1 ATTGAAGAA
1447 TTGAAATTGA
Statistics
Matches: 198, Mismatches: 7, Indels: 28
0.85 0.03 0.12
Matches are distributed among these distances:
98 104 0.53
112 94 0.47
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (98 bp):
ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGAA
AGACCACCCTGGATCGTTGAAATAAATTGATGC
Found at i:1243 original size:154 final size:155
Alignment explanation
Indices: 1073--1457 Score: 583
Period size: 154 Copynumber: 2.4 Consensus size: 155
1063 GAAGAATTGA
* *
1073 AATTGAAAAAATACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGA
1 AATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGA
*
1138 AAGACCACCCTGGATCATTGAAGTAAATTAATGCATTGAAGAATTGAAATTGAAGAAAGACCACC
66 AAGACCACCCTGGATCATTGAAATAAATTAATGCATTGAAGAATTGAAATTGAAGAAAGACCACC
1203 CTGGATCGTTGAAATAAATTGATGC
131 CTGGATCGTTGAAATAAATTGATGC
*
1228 -ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGA
1 AATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGA
*
1292 AAGACCACCCTGGATCATTGAAATAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACC
66 AAGACCACCCTGGATCATTGAAATAAATTAATGCATTGAAGAATTGAAATTGAAGAAAGACCACC
*
1357 CTGGATCGTTGAAGTAAATTGATGC
131 CTGGATCGTTGAAATAAATTGATGC
*
1382 ATTAAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTAAAGAA
1 -------------AATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAA
1447 TTGAAATTGAA
53 TTGAAATTGAA
1458 ACATTGAAGG
Statistics
Matches: 208, Mismatches: 8, Indels: 15
0.90 0.03 0.06
Matches are distributed among these distances:
154 148 0.71
168 60 0.29
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.25
Consensus pattern (155 bp):
AATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGA
AAGACCACCCTGGATCATTGAAATAAATTAATGCATTGAAGAATTGAAATTGAAGAAAGACCACC
CTGGATCGTTGAAATAAATTGATGC
Found at i:1281 original size:210 final size:210
Alignment explanation
Indices: 1019--1446 Score: 721
Period size: 210 Copynumber: 2.0 Consensus size: 210
1009 AGAATTGAAC
* * *
1019 TTGAAGCAAGACCACCCCGGATCGTTCAAGTAACTTGATGCATAGAAGAATTGAAATTGAAAAAA
1 TTGAAGAAAGACCACCCCGGATCATTCAAGTAAATTGATGCATAGAAGAATTGAAATTGAAAAAA
* * *
1084 TACCACCCTGGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCT
66 GACCACCCTGGATCATTGAAATAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCT
*
1149 GGATCATTGAAGTAAATTAATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTG
131 GGATCATTGAAGTAAATTAATGCATTAAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTG
1214 AAATAAATTGATGCA
196 AAATAAATTGATGCA
* * * *
1229 TTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGAAA
1 TTGAAGAAAGACCACCCCGGATCATTCAAGTAAATTGATGCATAGAAGAATTGAAATTGAAAAAA
1294 GACCACCCTGGATCATTGAAATAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCT
66 GACCACCCTGGATCATTGAAATAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCT
* *
1359 GGATCGTTGAAGTAAATTGATGCATTAAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTG
131 GGATCATTGAAGTAAATTAATGCATTAAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTG
*
1424 AAGTAAATTGATGCA
196 AAATAAATTGATGCA
*
1439 TTAAAGAA
1 TTGAAGAA
1447 TTGAAATTGA
Statistics
Matches: 203, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
210 203 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.25
Consensus pattern (210 bp):
TTGAAGAAAGACCACCCCGGATCATTCAAGTAAATTGATGCATAGAAGAATTGAAATTGAAAAAA
GACCACCCTGGATCATTGAAATAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCT
GGATCATTGAAGTAAATTAATGCATTAAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTG
AAATAAATTGATGCA
Found at i:1288 original size:56 final size:56
Alignment explanation
Indices: 1228--1457 Score: 415
Period size: 56 Copynumber: 4.1 Consensus size: 56
1218 AAATTGATGC
*
1228 ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTGAAGAATTGAA
1 ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTAAAGAATTGAA
* *
1284 ATTGAAGAAAGACCACCCTGGATCATTGAAATAAATTGATGCATTGAAGAATTGAA
1 ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTAAAGAATTGAA
*
1340 ATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTAAAGAATTGAA
1 ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTAAAGAATTGAA
*
1396 ATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATTAAAGAATTGAA
1 ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTAAAGAATTGAA
1452 ATTGAA
1 ATTGAA
1458 ACATTGAAGG
Statistics
Matches: 170, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 170 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (56 bp):
ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTAAAGAATTGAA
Found at i:1440 original size:266 final size:268
Alignment explanation
Indices: 916--1457 Score: 867
Period size: 266 Copynumber: 2.0 Consensus size: 268
906 TAAATTGAAT
*
916 AATTGAAGGAAGACCACCCTGGATCATTGAAGCATTGAATATTGAAATTGAAGAAAGACCACCCT
1 AATTGAAGAAAGACCACCCTGGATCATTGAA-CATTGAATATTGAAATTGAAGAAAGACCACCCT
* * * *
981 GGATCGTTGAAGTAAATTGATGCATTGAAGAATTGAACTTGAAGCAAGACCACCCCGGATCGTTC
65 GGATCATTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCCGGATCATTC
* * *
1046 AAGTAACTTGATGCATAGAAGAATTGAAATTGAAAAAATACCACCCTGGATCGTTGAAGTAAATT
130 AAATAAATTGATGCATAGAAGAATTGAAATTGAAAAAAGACCACCCTGGATCGTTGAAGTAAATT
* *
1111 GATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTAATGCATTG
195 GATGCATTAAAGAATTGAAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTAATGCATTA
1176 AAGAATTGA
260 AAGAATTGA
* *
1185 AATTGAAGAAAGACCACCCTGGATCGTTGAA-A-T-AA-ATTGATGCATTGAAGAAAGACCACCC
1 AATTGAAGAAAGACCACCCTGGATCATTGAACATTGAATATTGA--AATTGAAGAAAGACCACCC
*
1246 TGGATCATTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCATT
64 TGGATCATTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCCGGATCATT
* * *
1311 GAAATAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAAT
129 CAAATAAATTGATGCATAGAAGAATTGAAATTGAAAAAAGACCACCCTGGATCGTTGAAGTAAAT
* *
1376 TGATGCATTAAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAATTGATGCATT
194 TGATGCATTAAAGAATTGAAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTAATGCATT
1441 AAAGAATTGA
259 AAAGAATTGA
1451 AATTGAA
1 AATTGAA
1458 ACATTGAAGG
Statistics
Matches: 253, Mismatches: 18, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
264 5 0.02
265 2 0.01
266 216 0.85
267 1 0.00
269 29 0.11
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (268 bp):
AATTGAAGAAAGACCACCCTGGATCATTGAACATTGAATATTGAAATTGAAGAAAGACCACCCTG
GATCATTGAAGTAAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCCGGATCATTCA
AATAAATTGATGCATAGAAGAATTGAAATTGAAAAAAGACCACCCTGGATCGTTGAAGTAAATTG
ATGCATTAAAGAATTGAAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTAATGCATTAA
AGAATTGA
Found at i:1485 original size:22 final size:22
Alignment explanation
Indices: 1428--1487 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
1418 TCGTTGAAGT
** * *
1428 AAATTGATGCATTAAAGAATTG
1 AAATTGAAACATTGAAGGATTG
1450 AAATTGAAACATTGAAGGATTG
1 AAATTGAAACATTGAAGGATTG
*
1472 AATTTGAAGA-ATTGAA
1 AAATTGAA-ACATTGAA
1488 ATTGACCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (22 bp):
AAATTGAAACATTGAAGGATTG
Found at i:1979 original size:68 final size:68
Alignment explanation
Indices: 1811--2397 Score: 874
Period size: 68 Copynumber: 8.6 Consensus size: 68
1801 GTAAATGAAC
* * *** *
1811 TTGGCTTATGGAAAAGCCCCTGTTGCTTGGATGGAACCAAGGCTTAAACTAAATCATATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTGGCTCGTATGGAAAC
1876 GAGT
65 GAGT
* * * * *
1880 TTGGCTTGTGGAAAAGCCCTTACCGCCTGGATGGAACCAAGGCTTAACTGGCTCGTATAGAAACG
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
1945 AGT
66 AGT
*
1948 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTGGCTCGTATGGAAAC
*
2013 AAGT
65 GAGT
* *
2017 TTGGCTTGT-GAGAAAGCCCCTGCTGCTTGGATGGAACCAAGGTTTTACTGGCTCGTATGGAAAC
1 TTGGCTTGTGGA-AAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
2081 GAGT
65 GAGT
* *
2085 TTGGCTTGGGAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTGTGGAAAC
1 TTGGCTTGTG-GAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
2150 GAGT
65 GAGT
* *
2154 TTGGCTTGTTGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTTGTATGGAAACG
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
2219 AGT
66 AGT
* *
2222 TTGGCTTGTTGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTGGTATGGAAACG
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
2287 AGT
66 AGT
* * *
2290 TTGGCTTGTGCG-AAAGCCCCTACTGCTTGGATGGAACCAAAGCTTAATTGGCTCGTATGGAAAC
1 TTGGCTTGTG-GAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAAC
2354 GAGT
65 GAGT
*
2358 TTGGCTTGTGCG-AAAGCCCCTGTTGCTTGGATGGAACCAA
1 TTGGCTTGTG-GAAAAGCCCCTGCTGCTTGGATGGAACCAA
2398 AGCAAAATCT
Statistics
Matches: 475, Mismatches: 38, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
68 311 0.65
69 162 0.34
70 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (68 bp):
TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACG
AGT
Found at i:2057 original size:137 final size:136
Alignment explanation
Indices: 1811--2397 Score: 874
Period size: 137 Copynumber: 4.3 Consensus size: 136
1801 GTAAATGAAC
* * * * *
1811 TTGGCTTATGGAAAAGCCCCTGTTGCTTGGATGGAACCAAGGCTTAAACTAAATCATATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTGACTCGTATGGAAAC
* * * *
1876 GAGTTTGGCTTGTG-GAAAAGCCCTTACCGCCTGGATGGAACCAAGGCTTAACTGGCTCGTATAG
65 GAGTTTGGCTTGTGAG-AAAGCCCCTACTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGG
1940 AAACGAGT
129 AAACGAGT
1948 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTGACTCGTATGGAAAC
* * * *
2013 AAGTTTGGCTTGTGAGAAAGCCCCTGCTGCTTGGATGGAACCAAGGTTTTACTGGCTCGTATGGA
65 GAGTTTGGCTTGTGAGAAAGCCCCTACTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGA
2078 AACGAGT
130 AACGAGT
* * *
2085 TTGGCTTGGGAGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTGTGGAAAC
1 TTGGCTTGTG-GAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGACTCGTATGGAAAC
* *
2150 GAGTTTGGCTTGTTGA-AAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTTGTATGG
65 GAGTTTGGCTTG-TGAGAAAGCCCCTACTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGG
2214 AAACGAGT
129 AAACGAGT
* * *
2222 TTGGCTTGTTGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTGGTATGGAAACG
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGACTCGTATGGAAACG
* * *
2287 AGTTTGGCTTGTGCGAAAGCCCCTACTGCTTGGATGGAACCAAAGCTTAATTGGCTCGTATGGAA
66 AGTTTGGCTTGTGAGAAAGCCCCTACTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAA
2352 ACGAGT
131 ACGAGT
*
2358 TTGGCTTGTGCG-AAAGCCCCTGTTGCTTGGATGGAACCAA
1 TTGGCTTGTG-GAAAAGCCCCTGCTGCTTGGATGGAACCAA
2398 AGCAAAATCT
Statistics
Matches: 413, Mismatches: 32, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
135 2 0.00
136 152 0.37
137 220 0.53
138 39 0.09
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (136 bp):
TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAACTGACTCGTATGGAAACG
AGTTTGGCTTGTGAGAAAGCCCCTACTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAA
ACGAGT
Found at i:2658 original size:16 final size:19
Alignment explanation
Indices: 2637--2675 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2627 GACTGTTACT
2637 TTGAAT-CTT-TGCT-TTC
1 TTGAATCCTTCTGCTCTTC
2653 TTGAATCCTTCTGCTCTTC
1 TTGAATCCTTCTGCTCTTC
2672 TTGA
1 TTGA
2676 TTTGTCTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 3 0.15
18 4 0.20
19 7 0.35
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.51
Consensus pattern (19 bp):
TTGAATCCTTCTGCTCTTC
Found at i:3080 original size:50 final size:50
Alignment explanation
Indices: 3017--3125 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 50
3007 TAAAATGCCC
** * ** *
3017 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAACGCAATCTTAT
1 TTTGAAACTCGAATTTTGATATCAGACTCACAAATGGAACACAATCTTAT
*
3067 TTTGAAACTCGAATTTTGATATCAGACTCACAAATGGAATACAATCTTAT
1 TTTGAAACTCGAATTTTGATATCAGACTCACAAATGGAACACAATCTTAT
*
3117 TATGAAACT
1 TTTGAAACT
3126 TCTTGTTTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (50 bp):
TTTGAAACTCGAATTTTGATATCAGACTCACAAATGGAACACAATCTTAT
Found at i:3412 original size:6 final size:6
Alignment explanation
Indices: 3401--3440 Score: 53
Period size: 6 Copynumber: 6.2 Consensus size: 6
3391 TTTCTTCATT
3401 TTTTCA TTTTCA TTTTTTCA TTTTTCA TTTTCA TTTTCA T
1 TTTTCA TTTTCA --TTTTCA -TTTTCA TTTTCA TTTTCA T
3441 CATTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 19 0.59
7 7 0.22
8 6 0.19
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTCA
Found at i:3414 original size:14 final size:14
Alignment explanation
Indices: 3395--3440 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
3385 GCTTCTTTTC
3395 TTCATTTTTTCATT
1 TTCATTTTTTCATT
3409 TTCATTTTTTCATTT
1 TTCATTTTTTCA-TT
3424 TTCA--TTTTCATT
1 TTCATTTTTTCATT
3436 TTCAT
1 TTCAT
3441 CATTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.20
13 6 0.20
14 12 0.40
15 6 0.20
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCATTTTTTCATT
Found at i:3421 original size:22 final size:23
Alignment explanation
Indices: 3390--3448 Score: 95
Period size: 21 Copynumber: 2.7 Consensus size: 23
3380 CTAGAGCTTC
3390 TTTTCTTCATTTTTTCATTTTCA
1 TTTTCTTCATTTTTTCATTTTCA
3413 TTTT-TTCA-TTTTTCATTTTCA
1 TTTTCTTCATTTTTTCATTTTCA
*
3434 TTTTCATCATTTTTT
1 TTTTCTTCATTTTTT
3449 TTTGTATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 17 0.52
22 7 0.21
23 9 0.27
ACGTcount: A:0.14, C:0.15, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTCTTCATTTTTTCATTTTCA
Found at i:4759 original size:75 final size:76
Alignment explanation
Indices: 4608--4760 Score: 227
Period size: 75 Copynumber: 2.0 Consensus size: 76
4598 TGGATTCAGT
*
4608 CACCTCGAAATCATTGCTTTGACTAAAACTAATTTTTGAAACATCCTTTGATTAAAACTCATCAA
1 CACCTCGAAATCATTGCTTTGACTAAAACTAATTTTTGAAACATCCTTTAATTAAAACTCATCAA
*
4673 TCTTTTGCTCA
66 TCCTTTGCTCA
* * * * * *
4684 CACCTTGAAATCATTGCTTTGACTGAAACTGA-TTTTGAAACATCTTTTAATTAAAACTCATTAT
1 CACCTCGAAATCATTGCTTTGACTAAAACTAATTTTTGAAACATCCTTTAATTAAAACTCATCAA
4748 TCCTTTGCTCA
66 TCCTTTGCTCA
4759 CA
1 CA
4761 GTCCAGGTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
75 40 0.58
76 29 0.42
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (76 bp):
CACCTCGAAATCATTGCTTTGACTAAAACTAATTTTTGAAACATCCTTTAATTAAAACTCATCAA
TCCTTTGCTCA
Found at i:5530 original size:12 final size:13
Alignment explanation
Indices: 5513--5542 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
5503 CTTGACAAAT
5513 CATGAAAATGT-G
1 CATGAAAATGTAG
5525 CATGAAAATGTAG
1 CATGAAAATGTAG
5538 CATGA
1 CATGA
5543 CATGGCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.23
Consensus pattern (13 bp):
CATGAAAATGTAG
Found at i:7164 original size:52 final size:51
Alignment explanation
Indices: 7050--7226 Score: 273
Period size: 52 Copynumber: 3.4 Consensus size: 51
7040 TTCCCTAAGA
* * *
7050 GAAACCTGGTGGGAACTTTCCCAATTTGCAAAAGAGCTAGATTGAATACTTT
1 GAAAACTGATGGGAACTTTCCCAATTTG-AAAAGAGCTAAATTGAATACTTT
*
7102 GAAAACTGATGGGAACTTTCCCAAGTTGAAAAGAGCTAAATTGAATACTTT
1 GAAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTT
* * *
7153 AAAAAATTGATGGGAACTTTCCCAATTTAAAAAGAGCTAAATTGAATACTTT
1 -GAAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTT
7205 GAAAACTGATGGGAACTTTCCC
1 GAAAACTGATGGGAACTTTCCC
7227 GACTAGAAAA
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
51 42 0.37
52 72 0.63
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (51 bp):
GAAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTT
Done.