Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007314.1 Corchorus capsularis cultivar CVL-1 contig07335, 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: 12199
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:886 original size:14 final size:14
Alignment explanation
Indices: 869--902 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
859 GATTTGGAAT
869 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
*
883 TTGAAGTATTGAAA
1 TTGAAGAATTGAAA
897 TTGAAG
1 TTGAAG
903 CGTTAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (14 bp):
TTGAAGAATTGAAA
Found at i:944 original size:24 final size:24
Alignment explanation
Indices: 869--972 Score: 87
Period size: 24 Copynumber: 4.6 Consensus size: 24
859 GATTTGGAAT
869 TTGAAGAATTGAA--ATTGAAGT-A
1 TTGAAGAATTGAAGCATTGAA-TAA
* * * *
891 TTG-A-AATTGAAGCGTTAAAGAT
1 TTGAAGAATTGAAGCATTGAATAA
*
913 TTG-A-AATTGAGGCATTGAATAA
1 TTGAAGAATTGAAGCATTGAATAA
* *
935 TTGAGGAATTGAAGCATTGAATAC
1 TTGAAGAATTGAAGCATTGAATAA
959 TTGAAGAATTGAAG
1 TTGAAGAATTGAAG
973 AAAGATCACC
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
20 7 0.11
21 1 0.02
22 27 0.42
24 29 0.45
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (24 bp):
TTGAAGAATTGAAGCATTGAATAA
Found at i:974 original size:8 final size:8
Alignment explanation
Indices: 869--974 Score: 62
Period size: 8 Copynumber: 14.0 Consensus size: 8
859 GATTTGGAAT
869 TTGAAGAA
1 TTGAAGAA
877 TTG-A-AA
1 TTGAAGAA
*
883 TTGAAGTA
1 TTGAAGAA
891 TTG-A-AA
1 TTGAAGAA
**
897 TTGAAGCG
1 TTGAAGAA
* *
905 TTAAAGAT
1 TTGAAGAA
913 TTG-A-AA
1 TTGAAGAA
* *
919 TTGAGGCA
1 TTGAAGAA
*
927 TTGAATAA
1 TTGAAGAA
*
935 TTGAGGAA
1 TTGAAGAA
*
943 TTGAAGCA
1 TTGAAGAA
* *
951 TTGAATAC
1 TTGAAGAA
959 TTGAAGAA
1 TTGAAGAA
967 TTGAAGAA
1 TTGAAGAA
975 AGATCACCCT
Statistics
Matches: 69, Mismatches: 23, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
6 13 0.19
7 5 0.07
8 51 0.74
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.30
Consensus pattern (8 bp):
TTGAAGAA
Found at i:1009 original size:58 final size:57
Alignment explanation
Indices: 941--1085 Score: 220
Period size: 58 Copynumber: 2.5 Consensus size: 57
931 ATAATTGAGG
* **
941 AATTGAAGCATTGAATACTTGAAGAATTGAAGAAAGA-TCACCCTGGATCATTGAAGTA
1 AATTGAAGCATTGGATA-TTGAAGAATTGAAGAAAGACT-ACCCTAAATCATTGAAGTA
999 AATTGAAGCATTGGATGATTGAAGAATTGAAGAAAGACTACCCTAAATCATTGAAGTA
1 AATTGAAGCATTGGAT-ATTGAAGAATTGAAGAAAGACTACCCTAAATCATTGAAGTA
1057 AATTGAAGCATTGGATAATTGAAGAATTG
1 AATTGAAGCATTGGAT-ATTGAAGAATTG
1086 CAATTGCAGC
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
58 79 0.98
59 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (57 bp):
AATTGAAGCATTGGATATTGAAGAATTGAAGAAAGACTACCCTAAATCATTGAAGTA
Found at i:1122 original size:80 final size:81
Alignment explanation
Indices: 1016--1185 Score: 261
Period size: 80 Copynumber: 2.1 Consensus size: 81
1006 GCATTGGATG
* *
1016 ATTGAAGAATTGAAGAAAGACTACCCTAAATCATTGAAGTAAATTGAAGCATTGGATAA-TTGAA
1 ATTGAAGAATTGAAGAAAGACCACCCTAAATCATTGAAGTAAATTGAAGCATTGAATAATTTGAA
1080 GAATTGCAATTGCAGC
66 GAATTGCAATTGCAGC
* * *
1096 ATTGTAGAATTGAAGGAAGACCACCCTAGATCATTGAAGTAAATTGAAGCATTGAATAATTTGAA
1 ATTGAAGAATTGAAGAAAGACCACCCTAAATCATTGAAGTAAATTGAAGCATTGAATAATTTGAA
* * *
1161 GAATTGTAATTGAAGA
66 GAATTGCAATTGCAGC
1177 ATTGAAGAA
1 ATTGAAGAA
1186 AAAAAATTGA
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 54 0.68
81 26 0.32
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (81 bp):
ATTGAAGAATTGAAGAAAGACCACCCTAAATCATTGAAGTAAATTGAAGCATTGAATAATTTGAA
GAATTGCAATTGCAGC
Found at i:1181 original size:8 final size:8
Alignment explanation
Indices: 1137--1475 Score: 126
Period size: 8 Copynumber: 45.9 Consensus size: 8
1127 CATTGAAGTA
1137 AATTGAAG
1 AATTGAAG
* *
1145 CATTGAAT
1 AATTGAAG
1153 AATTTGAAG
1 AA-TTGAAG
*
1162 AATTG--T
1 AATTGAAG
1168 AATTGAAG
1 AATTGAAG
1176 AATTGAAG
1 AATTGAAG
* *
1184 AA--AAAA
1 AATTGAAG
1190 AATTG-A-
1 AATTGAAG
1196 AATTGAA-
1 AATTGAAG
1203 ACATTGAAG
1 A-ATTGAAG
*
1212 GATTG-AG
1 AATTGAAG
*
1219 -TTTGAAG
1 AATTGAAG
1226 AATTG--G
1 AATTGAAG
*
1232 ATTTGAAG
1 AATTGAAG
*
1240 GATTG-A-
1 AATTGAAG
*
1246 ATTTGAAAG
1 AATTG-AAG
*
1255 GATTG-A-
1 AATTGAAG
1261 AATTGAAG
1 AATTGAAG
*
1269 CATTG-A-
1 AATTGAAG
1275 AATTG-A-
1 AATTGAAG
1281 AATTGAAG
1 AATTGAAG
*
1289 CATTGAAG
1 AATTGAAG
1297 AATTG-A-
1 AATTGAAG
1303 AATTGAAG
1 AATTGAAG
*
1311 GATTGAAG
1 AATTGAAG
1319 AATTG-A-
1 AATTGAAG
1325 AATTG-A-
1 AATTGAAG
1331 AATTG-A-
1 AATTGAAG
1337 AATTGAAG
1 AATTGAAG
*
1345 GATTGAAG
1 AATTGAAG
1353 AATTG-AG
1 AATTGAAG
1360 -ATTGAAG
1 AATTGAAG
*
1367 CATTGAA-
1 AATTGAAG
1374 ATATTGAATTTG
1 A-ATTGAA---G
1386 AACTTGAAG
1 AA-TTGAAG
1395 AATTG--G
1 AATTGAAG
*
1401 AATAGAAG
1 AATTGAAG
*
1409 CATTGAAG
1 AATTGAAG
*
1417 GATTGAAG
1 AATTGAAG
1425 AATTG-A-
1 AATTGAAG
1431 AATTGAA-
1 AATTGAAG
1438 AGATTGAA-
1 A-ATTGAAG
1446 ATATTG-A-
1 A-ATTGAAG
1453 AATTGAA-
1 AATTGAAG
1460 ACATTGAAG
1 A-ATTGAAG
*
1469 ATTTGAA
1 AATTGAA
1476 ATTGACCAAC
Statistics
Matches: 257, Mismatches: 36, Indels: 76
0.70 0.10 0.21
Matches are distributed among these distances:
6 79 0.31
7 27 0.11
8 130 0.51
9 14 0.05
11 1 0.00
12 6 0.02
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (8 bp):
AATTGAAG
Found at i:1216 original size:22 final size:21
Alignment explanation
Indices: 1191--1480 Score: 126
Period size: 22 Copynumber: 13.5 Consensus size: 21
1181 AAGAAAAAAA
1191 ATTGAAATTGAAACATTGAAGG
1 ATTGAAATTGAAA-ATTGAAGG
**
1213 ATTGAGTTTGAAGAATT---GG
1 ATTGAAATTGAA-AATTGAAGG
*
1232 ATTTGAAGGATTG-AATTTGAAAGG
1 A-TTGAA--ATTGAAAATTG-AAGG
*
1256 ATTGAAATTGAAGCATTGAA--
1 ATTGAAATTGAA-AATTGAAGG
* *
1276 ATTGAAATTGAAGCATTGAAGA
1 ATTGAAATTGAA-AATTGAAGG
* *
1298 ATTGAAATTGAAGGATTGAAGA
1 ATTGAAATTGAA-AATTGAAGG
1320 ATTGAAATTG-AAATTGAA--
1 ATTGAAATTGAAAATTGAAGG
1338 ATTGAAGGATTGAAGAATTG-A-G
1 ATTGAA--ATTGAA-AATTGAAGG
1360 ATTGAAGCATTGAAATATTGAA--
1 ATTGAA--ATTGAAA-ATTGAAGG
* * *
1382 TTTGAACTTGAAGAATTG--GA
1 ATTGAAATTGAA-AATTGAAGG
* * *
1402 ATAGAAGCATTGAAGGATTGAAGA
1 ATTGAA--ATTGAA-AATTGAAGG
**
1426 ATTGAAATTGAAAGATTGAAAT
1 ATTGAAATTGAAA-ATTGAAGG
1448 ATTGAAATTGAAACATTGAA-G
1 ATTGAAATTGAAA-ATTGAAGG
1469 ATTTGAAATTGA
1 A-TTGAAATTGA
1481 CCAACTCTCA
Statistics
Matches: 218, Mismatches: 22, Indels: 56
0.74 0.07 0.19
Matches are distributed among these distances:
18 6 0.03
19 3 0.01
20 50 0.23
21 11 0.05
22 128 0.59
23 10 0.05
24 10 0.05
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.30
Consensus pattern (21 bp):
ATTGAAATTGAAAATTGAAGG
Found at i:1329 original size:14 final size:14
Alignment explanation
Indices: 1136--1480 Score: 179
Period size: 14 Copynumber: 24.5 Consensus size: 14
1126 TCATTGAAGT
*
1136 AAATTGAAGCATTG
1 AAATTGAAGAATTG
1150 AATAATTTGAAGAATTG
1 -A-AA-TTGAAGAATTG
*
1167 TAATTGAAGAATTG
1 AAATTGAAGAATTG
*
1181 -AA--GAA-AA--A
1 AAATTGAAGAATTG
1189 AAATTG-A-AATTG
1 AAATTGAAGAATTG
*
1201 AAACATTGAAGGATTG
1 -AA-ATTGAAGAATTG
**
1217 AGTTTGAAGAATTG
1 AAATTGAAGAATTG
* * *
1231 GATTTGAAGGATTG
1 AAATTGAAGAATTG
* *
1245 AATTTGAAAGGATTG
1 AAATTG-AAGAATTG
*
1260 AAATTGAAGCATTG
1 AAATTGAAGAATTG
1274 AAATTG-A-AATTG
1 AAATTGAAGAATTG
1286 AAGCATTGAAGAATTG
1 AA--ATTGAAGAATTG
*
1302 AAATTGAAGGATTG
1 AAATTGAAGAATTG
1316 AAGAATTG-A-AATTG
1 -A-AATTGAAGAATTG
1330 AAATTG-A-AATTG
1 AAATTGAAGAATTG
1342 AAGGATTGAAGAATTG
1 AA--ATTGAAGAATTG
* *
1358 AGATTGAAGCATTG
1 AAATTGAAGAATTG
*
1372 AAATATTG-A-ATTTG
1 -AA-ATTGAAGAATTG
*
1386 AACTTGAAGAATTG
1 AAATTGAAGAATTG
* * *
1400 GAATAGAAGCATTG
1 AAATTGAAGAATTG
1414 AAGGATTGAAGAATTG
1 AA--ATTGAAGAATTG
1430 AAATTGAA-AGATTG
1 AAATTGAAGA-ATTG
1444 AAATATTG-A-AATTG
1 -AA-ATTGAAGAATTG
*
1458 AAACATTGAAGATTTG
1 -AA-ATTGAAGAATTG
1474 AAATTGA
1 AAATTGA
1481 CCAACTCTCA
Statistics
Matches: 264, Mismatches: 33, Indels: 67
0.73 0.09 0.18
Matches are distributed among these distances:
9 2 0.01
10 5 0.02
11 4 0.02
12 22 0.08
13 10 0.04
14 132 0.50
15 31 0.12
16 48 0.18
17 10 0.04
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (14 bp):
AAATTGAAGAATTG
Found at i:2236 original size:49 final size:49
Alignment explanation
Indices: 2177--2585 Score: 489
Period size: 49 Copynumber: 8.3 Consensus size: 49
2167 AATCTTTATC
* * *
2177 TGCTTTTTCCCAAAGA-GCCCTTCCCAGACAGAAGCCATTTGTTTTTACT
1 TGCTATTTCCCAAA-ACGCCCTTCCCAGACGGAAGCCATTTATTTTTACT
* *
2226 TGCTATTTCCCAAAACACCCTTCCCAGACGGAAGCCATTTAATTTTACT
1 TGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACT
* *
2275 TGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTAATTTTACT
1 TGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACT
* * * * **
2324 TGTTATTTCCCAAAGCGCCCTTCCAGCGGATGGAAGCTGTTTATTTTTACT
1 TGCTATTTCCCAAAACGCCCTTCC--CAGACGGAAGCCATTTATTTTTACT
* **
2375 TGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTCGCT
1 TGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACT
* *
2424 TGCTATTTCCCAAAATGCCCTT-CCAGACGGAAGCCATTTATTTTTGCT
1 TGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACT
* * * * * *
2472 TGCTATCTCCCCAAAATGCCCTTTCCGGACGGAAGCCGTTTATCTTTACT
1 TGCTAT-TTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACT
* * ** * *
2522 TGCTATTTCCCAAAACTCCCTTCCCGGACGGAAGATATTTATTCTTACC
1 TGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACT
*
2571 TGCCATTTCCCAAAA
1 TGCTATTTCCCAAAA
2586 TGCCTTTTCC
Statistics
Matches: 316, Mismatches: 39, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
48 32 0.10
49 213 0.67
50 28 0.09
51 43 0.14
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (49 bp):
TGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACT
Found at i:2380 original size:149 final size:146
Alignment explanation
Indices: 2185--2585 Score: 500
Period size: 149 Copynumber: 2.7 Consensus size: 146
2175 TCTGCTTTTT
* * * *
2185 CCCAAAGA-GCCCTTCCCAGACAGAAGCCATTTGTTTTTACTTGCTATTTCCCAAAACACCCTTC
1 CCCAAA-ACGCCCTTCCCGGACGGAAGCCGTTTATTTTTACTTGCTATTTCCCAAAACACCCTTC
*
2249 CCAGACGGAAGCCATTTAATTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATT
65 CCAGACGGAAGCCATTT-ATTTTACTTGCTATTTCCCAAAACGCCCTT-CCAGACGGAAGCCATT
* *
2314 TAATTTTACTTGTTAT-TT
128 TAATTTTACTTGCTATCTC
* * * * *
2332 CCCAAAGCGCCCTTCCAGCGGATGGAAGCTGTTTATTTTTACTTGCTATTTCCCAAAGCGCCCTT
1 CCCAAAACGCCCTTCC--CGGACGGAAGCCGTTTATTTTTACTTGCTATTTCCCAAAACACCCTT
* *
2397 CCCAGACGGAAGCCATTTATTTTCGCTTGCTATTTCCCAAAATGCCCTTCCAGACGGAAGCCATT
64 CCCAGACGGAAGCCATTTATTTT-ACTTGCTATTTCCCAAAACGCCCTTCCAGACGGAAGCCATT
* *
2462 TATTTTTGCTTGCTATCTC
128 TAATTTTACTTGCTATCTC
* * * *
2481 CCCAAAATGCCCTTTCCGGACGGAAGCCGTTTATCTTTACTTGCTATTTCCCAAAACTCCCTTCC
1 CCCAAAACGCCCTTCCCGGACGGAAGCCGTTTATTTTTACTTGCTATTTCCCAAAACACCCTTCC
* ** * *
2546 CGGACGGAAGATATTTATTCTTACCTGCCATTTCCCAAAA
66 CAGACGGAAGCCATTTATT-TTACTTGCTATTTCCCAAAA
2586 TGCCTTTTCC
Statistics
Matches: 218, Mismatches: 30, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
147 89 0.41
148 36 0.17
149 93 0.43
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (146 bp):
CCCAAAACGCCCTTCCCGGACGGAAGCCGTTTATTTTTACTTGCTATTTCCCAAAACACCCTTCC
CAGACGGAAGCCATTTATTTTACTTGCTATTTCCCAAAACGCCCTTCCAGACGGAAGCCATTTAA
TTTTACTTGCTATCTC
Found at i:2522 original size:198 final size:196
Alignment explanation
Indices: 2176--2584 Score: 543
Period size: 198 Copynumber: 2.1 Consensus size: 196
2166 TAATCTTTAT
* * *
2176 CTGCTTTTTCCCAAAGAGCCCTTCCCAGACAGAAGCCATTTGTTTTTACTTGCTATTTCCCAAAA
1 CTGCTATTTCCCAAAGAGCCCTTCCCAGACAGAAGCCATTTATTTTCACTTGCTATTTCCCAAAA
* *
2241 CACCCTTCCCAGACGGAAGCCATTTAATTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGG
66 CACCCTTCCCAGACGGAAGCCATTTAATTTTACTTGCTATTCCCCAAAACGCCCTTCCCAGACGG
* * * * * *
2306 AAGCCATTTAATTTTACTTGTTATTTCCCAAAGCGCCCTTCCAGCGGATGGAAGCTGTTTATTTT
131 AAGCCATTTAATTTTACTTGCTATTTCCCAAAACGCCCTTCC--CGGACGGAAGATATTTATTCT
2371 TAC
194 TAC
* * * *
2374 TTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTTGCTATTTCCCAAAA
1 CTGCTATTTCCCAAAGAGCCCTTCCCAGACAGAAGCCATTTATTTTCACTTGCTATTTCCCAAAA
** * * * * *
2439 TGCCCTT-CCAGACGGAAGCCATTTATTTTTGCTTGCTATCTCCCCAAAATGCCCTTTCCGGACG
66 CACCCTTCCCAGACGGAAGCCATTTAATTTTACTTGCTAT-TCCCCAAAACGCCCTTCCCAGACG
* *
2503 GAAGCCGTTT-ATCTTTACTTGCTATTTCCCAAAACTCCCTTCCCGGACGGAAGATATTTATTCT
130 GAAGCCATTTAAT-TTTACTTGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGATATTTATTCT
2567 TAC
194 TAC
*
2570 CTGCCATTTCCCAAA
1 CTGCTATTTCCCAAA
2585 ATGCCTTTTC
Statistics
Matches: 183, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
196 33 0.18
197 32 0.17
198 118 0.64
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (196 bp):
CTGCTATTTCCCAAAGAGCCCTTCCCAGACAGAAGCCATTTATTTTCACTTGCTATTTCCCAAAA
CACCCTTCCCAGACGGAAGCCATTTAATTTTACTTGCTATTCCCCAAAACGCCCTTCCCAGACGG
AAGCCATTTAATTTTACTTGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGATATTTATTCTTA
C
Found at i:6057 original size:95 final size:96
Alignment explanation
Indices: 5879--6062 Score: 275
Period size: 95 Copynumber: 1.9 Consensus size: 96
5869 TTCCTAAAAC
* *
5879 AAAATTGTCTTTGCAAAAGAAAAGTGTTGTTTCTCGAAAAAGGTTTTTAGAGAAAATTGGTTTCA
1 AAAATAGTCTTTGCAAAAGAAAAGTGTTGTTTCTCGAAAAAGGTTTTTAGAGAAAACTGGTTTCA
5944 AAAGTTTTTCAAAGGCAAGCGCATAGTACAA
66 AAAGTTTTTCAAAGGCAAGCGCATAGTACAA
* * * *
5975 AAAATAGTTTTTGCAAAAGAAACGTGTTTTTTTTTC-AAAAAGG-TTTTAGAGAAAACTGGTTTC
1 AAAATAGTCTTTGCAAAAGAAAAGTG-TTGTTTCTCGAAAAAGGTTTTTAGAGAAAACTGGTTTC
6038 AAAAGTTTTTCGAAA-GCAAGCGCAT
65 AAAAGTTTTTC-AAAGGCAAGCGCAT
6063 GAAAAAGAGA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
95 40 0.50
96 33 0.41
97 7 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (96 bp):
AAAATAGTCTTTGCAAAAGAAAAGTGTTGTTTCTCGAAAAAGGTTTTTAGAGAAAACTGGTTTCA
AAAGTTTTTCAAAGGCAAGCGCATAGTACAA
Found at i:6078 original size:14 final size:15
Alignment explanation
Indices: 6061--6089 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6051 AAGCAAGCGC
6061 ATGAAAAAG-AGAAA
1 ATGAAAAAGAAGAAA
6075 ATGAAAAAGAAGAAA
1 ATGAAAAAGAAGAAA
6090 GAAGAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (15 bp):
ATGAAAAAGAAGAAA
Found at i:7315 original size:39 final size:39
Alignment explanation
Indices: 7162--7437 Score: 221
Period size: 39 Copynumber: 7.3 Consensus size: 39
7152 TTATCAGAGA
*
7162 TCATCTTTTCAATAAGTTATCAAAGTTGACTGGAAACAGG
1 TCATC-TTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
* ** * *
7202 TCATCTTTCAGCAA-TTATCTTA--CGAATGGAAACAGG
1 TCATCTTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
* * * * *
7238 TCGTCTTTCAGC-ACTTAT-TAGGTTTGACTGGAAACAGG
1 TCATCTTTCAACAAGTTATCAAAG-TTGACTGGAAACAGG
* *
7276 TCATCTTTTAATAAGTTATCAAAGTTGACTGGAAACAGG
1 TCATCTTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
* ** * * *
7315 TCATCTTTCAGCAA-TTATCTTA--CGACTCGACACAGG
1 TCATCTTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
* * * *
7351 TCGTCTTTCAAC-ACTTGTTC-AATTTGACTGGAAACAGG
1 TCATCTTTCAACAAGTT-ATCAAAGTTGACTGGAAACAGG
* * *
7389 TCATCTTTCAACAAGTTACCAAAATCGACTGGAAACAGG
1 TCATCTTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
7428 TCATCTTTCA
1 TCATCTTTCA
7438 GCAGTTTGCG
Statistics
Matches: 185, Mismatches: 39, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
35 3 0.02
36 51 0.28
37 2 0.01
38 55 0.30
39 67 0.36
40 7 0.04
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (39 bp):
TCATCTTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
Found at i:7377 original size:113 final size:113
Alignment explanation
Indices: 7162--7440 Score: 434
Period size: 113 Copynumber: 2.5 Consensus size: 113
7152 TTATCAGAGA
7162 TCATCTTTTCAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGA
1 TCATCTTTT-AATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGA
* * *
7227 ATGGAAACAGGTCGTCTTTCAGCACTTATTAGGTTTGACTGGAAACAGG
65 ATCGAAACAGGTCGTCTTTCAACACTTATTAGATTTGACTGGAAACAGG
*
7276 TCATCTTTTAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGAC
1 TCATCTTTTAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGAA
* *
7341 TCGACACAGGTCGTCTTTCAACACTTGTTCA-ATTTGACTGGAAACAGG
66 TCGAAACAGGTCGTCTTTCAACACTTATT-AGATTTGACTGGAAACAGG
* * * * *
7389 TCATCTTTCAACAAGTTACCAAAATCGACTGGAAACAGGTCATCTTTCAGCA
1 TCATCTTTTAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCA
7441 GTTTGCGGTT
Statistics
Matches: 153, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
113 143 0.93
114 10 0.07
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (113 bp):
TCATCTTTTAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGAA
TCGAAACAGGTCGTCTTTCAACACTTATTAGATTTGACTGGAAACAGG
Found at i:7514 original size:34 final size:33
Alignment explanation
Indices: 7466--7574 Score: 157
Period size: 34 Copynumber: 3.2 Consensus size: 33
7456 CAAGCGGAGG
* *
7466 ATTTGAACAACTTTTCAATTTTCAACTTTACAGC
1 ATTTCAACAACTTTTCAATTTACAACTTT-CAGC
7500 ATTTCAACAACTTTTCAATTTACAACTTTTCAGC
1 ATTTCAACAACTTTTCAATTTACAAC-TTTCAGC
7534 -TTTCAACAACTATTTCAATTTACAACTATTCAGC
1 ATTTCAACAACT-TTTCAATTTACAACT-TTCAGC
7568 ATTTCAA
1 ATTTCAA
7575 TTCACAACTT
Statistics
Matches: 69, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
33 12 0.17
34 48 0.70
35 9 0.13
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (33 bp):
ATTTCAACAACTTTTCAATTTACAACTTTCAGC
Found at i:7560 original size:16 final size:15
Alignment explanation
Indices: 7472--7565 Score: 80
Period size: 15 Copynumber: 5.7 Consensus size: 15
7462 GAGGATTTGA
7472 ACAACTTTTCAATTT
1 ACAACTTTTCAATTT
* *
7487 TCAACTTTACAGCATTT
1 ACAACTTTTCA--ATTT
7504 CAACAACTTTTCAATTT
1 --ACAACTTTTCAATTT
*
7521 ACAACTTTTCAGCTTT
1 ACAACTTTTCA-ATTT
7537 CAACAACTATTTCAATTT
1 --ACAACT-TTTCAATTT
*
7555 ACAACTATTCA
1 ACAACTTTTCA
7566 GCATTTCAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
15 24 0.38
16 9 0.14
17 8 0.12
18 9 0.14
19 14 0.22
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.40
Consensus pattern (15 bp):
ACAACTTTTCAATTT
Found at i:7575 original size:23 final size:23
Alignment explanation
Indices: 7545--7588 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
7535 TTCAACAACT
*
7545 ATTTCAATTTACAACTATTCAGC
1 ATTTCAATTCACAACTATTCAGC
*
7568 ATTTCAATTCACAACTTTTCA
1 ATTTCAATTCACAACTATTCA
7589 ATTGACGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (23 bp):
ATTTCAATTCACAACTATTCAGC
Found at i:7682 original size:48 final size:47
Alignment explanation
Indices: 7596--7743 Score: 217
Period size: 48 Copynumber: 3.1 Consensus size: 47
7586 TCAATTGACG
*
7596 ACTTCCATGTGAGTCAGCAATCTTCCGACCCAAGTTGGTCTTTCCTC
1 ACTTCCATGTGAGTCAGAAATCTTCCGACCCAAGTTGGTCTTTCCTC
7643 ACTTCCATGTGAGTCAGAAATCGTTCCGACCCAAGTTGGTCTTTCCTC
1 ACTTCCATGTGAGTCAGAAATC-TTCCGACCCAAGTTGGTCTTTCCTC
* * * *
7691 ACTTCCATGTGAATCAGAGATCCTT-CGACCAAAGTTGGTCTTTTTCTC
1 ACTTCCATGTGAGTCAGAAAT-CTTCCGACCCAAGTTGGTC-TTTCCTC
7739 ACTTC
1 ACTTC
7744 TACGCAAAGT
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
47 35 0.38
48 57 0.61
49 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (47 bp):
ACTTCCATGTGAGTCAGAAATCTTCCGACCCAAGTTGGTCTTTCCTC
Found at i:7886 original size:33 final size:31
Alignment explanation
Indices: 7857--7947 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 31
7847 TCTTCAAAGT
7857 TGACCTCAGACAGGTCTTTCCCAATTTCAATA
1 TGACCTCAGACAGGTCTTTCCCAATTTCAA-A
* *
7889 TCGACCACAGACTGGTCCTATT--CAATTTC--A
1 T-GACCTCAGACAGGT-CT-TTCCCAATTTCAAA
7919 -GACCTCAGACAGGTCTTTCCCAATTTCAA
1 TGACCTCAGACAGGTCTTTCCCAATTTCAA
7948 TATCAACCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
26 2 0.04
27 2 0.04
28 19 0.40
30 1 0.02
32 1 0.02
33 19 0.40
34 2 0.04
35 2 0.04
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (31 bp):
TGACCTCAGACAGGTCTTTCCCAATTTCAAA
Found at i:8143 original size:102 final size:103
Alignment explanation
Indices: 7976--8183 Score: 271
Period size: 102 Copynumber: 2.0 Consensus size: 103
7966 ACTAGTCTTA
* * * * *
7976 TTCAATTCCAGACCTCAAACGGGTCTCTCTCTCTCAATTTCATTTATCAAAGTTGACCTCGGACA
1 TTCAATTCCAGACCTCAAACAGG-CTCTCTCTCTAAATTTCAATTATCAAAATTGACCTCAGACA
* * *
8041 GGTCTTTCTTAGTTTTTCAATA-CGACCACAGACTGGTCCTC
65 GGTCTTTCTCA--ATTTCAAAAGCGACCACAGACTGGT-CTC
*
8082 TTCAATTCCAGACCTCATACAGG-TCT-T-TCTAAATTTCAATTATCAAAATTGACCTCAGACAG
1 TTCAATTCCAGACCTCAAACAGGCTCTCTCTCTAAATTTCAATTATCAAAATTGACCTCAGACAG
8144 GTCTTTCTCAATTTCAAAAGCGACCACAGACTGGTCTC
66 GTCTTTCTCAATTTCAAAAGCGACCACAGACTGGTCTC
8182 TT
1 TT
8184 TCTCAGATAT
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
100 12 0.13
101 15 0.16
102 40 0.43
103 1 0.01
104 3 0.03
106 21 0.23
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (103 bp):
TTCAATTCCAGACCTCAAACAGGCTCTCTCTCTAAATTTCAATTATCAAAATTGACCTCAGACAG
GTCTTTCTCAATTTCAAAAGCGACCACAGACTGGTCTC
Found at i:8162 original size:33 final size:33
Alignment explanation
Indices: 8117--8226 Score: 105
Period size: 33 Copynumber: 3.2 Consensus size: 33
8107 TTTCTAAATT
8117 TCAATTATCAAAATTGACCTCAGACAGGTCTTTC
1 TCAATT-TCAAAATTGACCTCAGACAGGTCTTTC
** * *
8151 TCAATTTCAAAAGCGACCACAGACTGGTCTCTTTC
1 TCAATTTCAAAATTGACCTCAGACAGG--TCTTTC
*
8186 TCAGATATTC-AATTTCAGACCTCAGACAGGTCTTTC
1 TCA-AT-TTCAAAATT--GACCTCAGACAGGTCTTTC
8222 TCAAT
1 TCAAT
8227 ATCGACCGCA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
33 17 0.28
34 6 0.10
35 11 0.18
36 13 0.21
37 3 0.05
38 11 0.18
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (33 bp):
TCAATTTCAAAATTGACCTCAGACAGGTCTTTC
Found at i:8328 original size:28 final size:28
Alignment explanation
Indices: 8191--8333 Score: 107
Period size: 28 Copynumber: 5.0 Consensus size: 28
8181 CTTTCTCAGA
*
8191 TATTCAATTTCAGACCTCAGACAGGT-C
1 TATTCAATTTCAGACCTCAGACTGGTCC
* * *
8218 TTTCTCAATATC-GACCGCAGACTGGTCC
1 TAT-TCAATTTCAGACCTCAGACTGGTCC
*
8246 TATTCAATTTCAGACCTCA-AATAGGT-C
1 TATTCAATTTCAGACCTCAGACT-GGTCC
*
8273 TTTCTCAATTTCAATATCGACCAT-AGACTGGTCC
1 TAT-TCAATTTC---A--GACC-TCAGACTGGTCC
*
8307 TATTCAATTTCAGACCTCAGACGGGTC
1 TATTCAATTTCAGACCTCAGACTGGTC
8334 TCTCTTAATT
Statistics
Matches: 90, Mismatches: 12, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
27 27 0.30
28 39 0.43
30 1 0.01
31 1 0.01
33 16 0.18
34 6 0.07
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (28 bp):
TATTCAATTTCAGACCTCAGACTGGTCC
Found at i:8344 original size:61 final size:60
Alignment explanation
Indices: 8191--8344 Score: 192
Period size: 61 Copynumber: 2.6 Consensus size: 60
8181 CTTTCTCAGA
* *
8191 TATTCAATTTCAGACCTCAGACAGG---TCTT--TCTCAATATCGACCGCAGACTGGTCC
1 TATTCAATTTCAGACCTCAGACAGGTCTTCTTAATTTCAATATCGACCACAGACTGGTCC
* * * *
8246 TATTCAATTTCAGACCTCAAATAGGTCTTTCTCAATTTCAATATCGACCATAGACTGGTCC
1 TATTCAATTTCAGACCTCAGACAGGTC-TTCTTAATTTCAATATCGACCACAGACTGGTCC
*
8307 TATTCAATTTCAGACCTCAGACGGGTCTCTCTTAATTT
1 TATTCAATTTCAGACCTCAGACAGGTCT-TCTTAATTT
8345 TTAAAAGGGG
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
55 23 0.28
59 3 0.04
60 1 0.01
61 55 0.67
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (60 bp):
TATTCAATTTCAGACCTCAGACAGGTCTTCTTAATTTCAATATCGACCACAGACTGGTCC
Found at i:8650 original size:27 final size:27
Alignment explanation
Indices: 8618--8689 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
8608 TAAGTCGTAT
8618 AGGGGCATTTTGGTCATTTTTGCACCCA
1 AGGGGCATTTTGGTCATTTTTGCA-CCA
* *
8646 A-GGGCATTTTGGTCA-TTTTGTACTA
1 AGGGGCATTTTGGTCATTTTTGCACCA
8671 AGGGGGCATTTTGGTCATT
1 A-GGGGCATTTTGGTCATT
8690 CTTAATTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 3 0.08
26 6 0.15
27 28 0.72
28 2 0.05
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.39
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTTGCACCA
Found at i:11804 original size:49 final size:48
Alignment explanation
Indices: 11741--12191 Score: 647
Period size: 49 Copynumber: 9.3 Consensus size: 48
11731 CTCCCAAACA
* * *
11741 GAAGCCATTTGTTTTTACTTACTATTTCCCAAAGCGCCCTTCCCAGACA
1 GAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTT-CCAGACG
* * * * *
11790 AAAGCCATTTGTTTTTACTTGCTATTTCCCAAAACACCATTTCCAGACG
1 GAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCC-CTTCCAGACG
* *
11839 GAAGCCATTTAATTTTACTTGATATTTCCCAAAGCGCCCTTCCAGACG
1 GAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCAGACG
* ** ***
11887 GAAGTCATTTATTTTCGCTTGCTATTTCCCAAAATACCCTTCCAGACG
1 GAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCAGACG
*
11935 GAAGCCATTTATTTTTGCTTGCTATTTTCCCAAAGCGCCCTTCCAGACG
1 GAAGCCATTTATTTTTACTTGCTA-TTTCCCAAAGCGCCCTTCCAGACG
*
11984 GAAGCCATTTATTTTCACTTGCTATTTCCCAAAGCGCCCTTCCCAGACG
1 GAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTT-CCAGACG
12033 GAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCAGACG
1 GAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCAGACG
12081 GAAGCCA-TTATTTTCGT-CTTGC-ATTTCCCAAAGCGCCCTTCCCAGACG
1 GAAGCCATTTATTTT--TACTTGCTATTTCCCAAAGCGCCCTT-CCAGACG
12129 GAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCAGACG
1 GAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCAGACG
*
12177 GAAGTCATTTATTTT
1 GAAGCCATTTATTTT
12192 CGCTTGCT
Statistics
Matches: 363, Mismatches: 30, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
47 26 0.07
48 147 0.40
49 188 0.52
50 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (48 bp):
GAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCAGACG
Found at i:12070 original size:194 final size:193
Alignment explanation
Indices: 11732--12199 Score: 697
Period size: 194 Copynumber: 2.4 Consensus size: 193
11722 ACCTGCTTTC
* * * * **
11732 TCCCAAACAGAAGCCATTTGTTTTTACTTACTATTTCCCAAAGCGCCCTTCCCAGACAAAAGCCA
1 TCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTT-CCAGACGGAAGCCA
* * *
11797 TTTGTTTTTACTTGCTATTTCCCAAAACACCATTTCCAGACGGAAGCCATTTAATTTTACTTGAT
65 TTTATTTTCACTTGCTATTTCCCAAAACACCATTCCCAGACGGAAGCCATTTAATTTTACTTGAT
* *
11862 ATTTCCCAAAGCGCCCTTCCAGACGGAAGTCATTTATTTTCG-CTTGCTATTTCCCAAAATACCC
130 ATTTCCCAAAGCGCCCTTCCAGACGGAAGCCA-TTATTTTCGTCTTGC-ATTTCCCAAAACACCC
11926 T
193 T
*
11927 T-CCAGACGGAAGCCATTTATTTTTGCTTGCTATTTTCCCAAAGCGCCCTTCCAGACGGAAGCCA
1 TCCCAGACGGAAGCCATTTATTTTTACTTGCTA-TTTCCCAAAGCGCCCTTCCAGACGGAAGCCA
* * * * *
11991 TTTATTTTCACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCT
65 TTTATTTTCACTTGCTATTTCCCAAAACACCATTCCCAGACGGAAGCCATTTAATTTTACTTGAT
* *
12056 ATTTCCCAAAGCGCCCTTCCAGACGGAAGCCATTATTTTCGTCTTGCATTTCCCAAAGCGCCCT
130 ATTTCCCAAAGCGCCCTTCCAGACGGAAGCCATTATTTTCGTCTTGCATTTCCCAAAACACCCT
*
12120 TCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCAGACGGAAGTCAT
1 TCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCAGACGGAAGCCAT
*
12185 TTATTTTCGCTTGCT
66 TTATTTTCACTTGCT
Statistics
Matches: 248, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
193 69 0.28
194 161 0.65
195 18 0.07
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (193 bp):
TCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCAGACGGAAGCCAT
TTATTTTCACTTGCTATTTCCCAAAACACCATTCCCAGACGGAAGCCATTTAATTTTACTTGATA
TTTCCCAAAGCGCCCTTCCAGACGGAAGCCATTATTTTCGTCTTGCATTTCCCAAAACACCCT
Done.