Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009628.1 Corchorus olitorius cultivar O-4 contig09660, 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: 5617
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Found at i:467 original size:102 final size:101
Alignment explanation
Indices: 252--516 Score: 339
Period size: 102 Copynumber: 2.6 Consensus size: 101
242 CTCTTTTTTT
* *
252 ATTATTATTATAGAGTTTTAGAAAT-TAAT-AAAACTAATTTCACTAAGTTTAGCCCCAAAATT-
1 ATTATTATTATAGGGTTTTAGAAATAAAATAAAAACTAATTTCACTAAGTTTAGCCCC-AAATTA
314 -TTATTTTTATTTTAAGGGTAAATTTCAAAATTAATA
65 ATTATTTTTATTTTAAGGGTAAATTTCAAAATTAATA
* *
350 ATTTATTATTATAGGGTTTTAGAAATAAAATACAAAATTAATTTCACTAAGTTCAGCCCCAAATT
1 A-TTATTATTATAGGGTTTTAGAAATAAAATA-AAAACTAATTTCACTAAGTTTAGCCCCAAATT
*
415 AATT-TTTTTAAATTTTAAGGGTAAATTTCATAATTAATA
64 AATTATTTTT--ATTTTAAGGGTAAATTTCAAAATTAATA
* * * *
454 A-TATTGTTGTAGGGTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTA-ACCCAAATTA
1 ATTATTATTATAGGGTTTTAGAAATAAAATA-AAAACTAATTTCACTAAGTTTAGCCCCAAATTA
516 A
65 A
517 AATTAAATTT
Statistics
Matches: 147, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
98 1 0.01
99 23 0.16
100 13 0.09
101 17 0.12
102 63 0.43
103 2 0.01
104 28 0.19
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.41
Consensus pattern (101 bp):
ATTATTATTATAGGGTTTTAGAAATAAAATAAAAACTAATTTCACTAAGTTTAGCCCCAAATTAA
TTATTTTTATTTTAAGGGTAAATTTCAAAATTAATA
Found at i:1095 original size:90 final size:90
Alignment explanation
Indices: 872--1148 Score: 405
Period size: 90 Copynumber: 3.1 Consensus size: 90
862 AAATTTTAAT
* *
872 AGTCAAACCCC--AAACATCATTGCACATGCATGGTAAAACCCCAAAGTTCGATTGTCAAACCAC
1 AGTCAAACCCCAAAAACATCATTGCACATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCAC
*
935 AAAAAATATTTTCATTGTATATGCAC
66 AAAAAACA-TTTCATTGTATATGCAC
* * * *
961 GGTCAAACCCTAAAAAACATCATTGTACATGCATGGTCAAACCCCAAAGTTCAATAGTCAAACCA
1 AGTCAAACCC-CAAAAACATCATTGCACATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCA
* * *
1026 CAAAAAACATTTCTTTGTAAATGCAT
65 CAAAAAACATTTCATTGTATATGCAC
* *
1052 AGTCAAACCCCAAAAACATCATTACGCATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCAC
1 AGTCAAACCCCAAAAACATCATTGCACATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCAC
*
1117 AAAAAACCTTTCATTGTATATGCAC
66 AAAAAACATTTCATTGTATATGCAC
1142 AGTCAAA
1 AGTCAAA
1149 TACCAAATTT
Statistics
Matches: 165, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
89 9 0.05
90 78 0.47
91 23 0.14
92 55 0.33
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (90 bp):
AGTCAAACCCCAAAAACATCATTGCACATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCAC
AAAAAACATTTCATTGTATATGCAC
Found at i:1120 original size:54 final size:53
Alignment explanation
Indices: 1050--1232 Score: 172
Period size: 54 Copynumber: 3.3 Consensus size: 53
1040 TTGTAAATGC
*
1050 ATAGTCAAACCCCAAAAACATCATTACGCATGCATGGTCAAACCCCAAAGTTCG
1 ATAGTCAAACCACAAAAACATCATTACG-ATGCATGGTCAAACCCCAAAGTTCG
* * ** ** * **
1104 ATAGTCAAACCACAAAAAACCTTTCATTGTA-TATGCACAGTCAAATACCAAATTTTA
1 ATAGTCAAACCAC-AAAAA-C-ATCA-T-TACGATGCATGGTCAAACCCCAAAGTTCG
* *
1161 ATAGTCAAGCCCCAAAAACATCATTGTACG-TGCATGGTCAAACCCCAAAGTTCG
1 ATAGTCAAACCACAAAAACATCA-T-TACGATGCATGGTCAAACCCCAAAGTTCG
1215 ATAGTCAAACCACAAAAA
1 ATAGTCAAACCACAAAAA
1233 ACATTTCATC
Statistics
Matches: 100, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
54 53 0.53
55 6 0.06
56 6 0.06
57 32 0.32
58 1 0.01
59 2 0.02
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (53 bp):
ATAGTCAAACCACAAAAACATCATTACGATGCATGGTCAAACCCCAAAGTTCG
Found at i:1197 original size:111 final size:115
Alignment explanation
Indices: 1049--1374 Score: 385
Period size: 111 Copynumber: 2.8 Consensus size: 115
1039 TTTGTAAATG
1049 CATAGTCAAACCCCAAAAACATCAT-TACGCATGCATGGTCAAACCCCAAAGTTCGATAGTCAAA
1 CATAGTCAAACCCCAAAAACATCATGTACG--TGCATGGTCAAACCCCAAAGTTCGATAGTCAAA
* ** *
1113 CCACAAAAAACCTTTCATTGTATATGCACAGTCAAA-T-ACCAA-AT-TTTA
64 CCACAAAAAACATTTCATTGTATATGCACAGTCAAACTCAAAAACATCTGTA
*
1161 -ATAGTCAAGCCCCAAAAACATCATTGTACGTGCATGGTCAAACCCCAAAGTTCGATAGTCAAAC
1 CATAGTCAAACCCCAAAAACATCA-TGTACGTGCATGGTCAAACCCCAAAGTTCGATAGTCAAAC
* **
1225 CACAAAAAACATTTCATCGTATATGCATGGTCAAACCTCAAAAACATCACTGTA
65 CACAAAAAACATTTCATTGTATATGCACAGTCAAA-CTCAAAAACAT--CTGTA
* *
1279 CATGCATGGTCAAACCTCAAAAACATCACTGTACATGCATGGTCAAACCCCAAAGTTCGATAGTC
1 CAT--A--GTCAAACCCCAAAAACATCA-TGTACGTGCATGGTCAAACCCCAAAGTTCGATAGTC
* * * *
1344 AAGCCACATAAAGCATTCCATTGTATATGCA
61 AAACCACAAAAAACATTTCATTGTATATGCA
1375 TGATCAAACC
Statistics
Matches: 183, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
111 87 0.48
112 1 0.01
113 5 0.03
114 3 0.02
115 2 0.01
118 3 0.02
119 2 0.01
121 1 0.01
123 79 0.43
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.23
Consensus pattern (115 bp):
CATAGTCAAACCCCAAAAACATCATGTACGTGCATGGTCAAACCCCAAAGTTCGATAGTCAAACC
ACAAAAAACATTTCATTGTATATGCACAGTCAAACTCAAAAACATCTGTA
Found at i:1261 original size:57 final size:57
Alignment explanation
Indices: 1079--1389 Score: 256
Period size: 57 Copynumber: 5.4 Consensus size: 57
1069 ATCATTACGC
*
1079 ATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACCTTTCATTGTAT
1 ATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTCATTGTAT
** ** * ** * * *
1136 ATGCACAGTCAAATACCAAATTTTAATAGTCAAGCC-CCAAAAACA--TCATTGTAC
1 ATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTCATTGTAT
* *
1190 GTGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTCATCGTAT
1 ATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTCATTGTAT
* * * * *
1247 ATGCATGGTCAAACCTCAAAAACATCACTGTACATGCATGGTCAAACCTC-AAAAACA--TCACT
1 ATGCATGGTCAAACC-C-----CA--A-AGTTC--G-ATAGTCAAACCACAAAAAACATTTCATT
*
1309 GTAC
54 GTAT
* * * *
1313 ATGCATGGTCAAACCCCAAAGTTCGATAGTCAAGCCACATAAAGCATTCCATTGTAT
1 ATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTCATTGTAT
*
1370 ATGCATGATCAAACCCCAAA
1 ATGCATGGTCAAACCCCAAA
1390 TATCAGTTAA
Statistics
Matches: 194, Mismatches: 42, Indels: 36
0.71 0.15 0.13
Matches are distributed among these distances:
54 45 0.23
55 14 0.07
56 7 0.04
57 77 0.40
58 2 0.01
60 2 0.01
63 2 0.01
65 2 0.01
66 24 0.12
68 8 0.04
69 11 0.06
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (57 bp):
ATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTCATTGTAT
Found at i:1289 original size:33 final size:33
Alignment explanation
Indices: 1247--1332 Score: 163
Period size: 33 Copynumber: 2.6 Consensus size: 33
1237 TTCATCGTAT
1247 ATGCATGGTCAAACCTCAAAAACATCACTGTAC
1 ATGCATGGTCAAACCTCAAAAACATCACTGTAC
1280 ATGCATGGTCAAACCTCAAAAACATCACTGTAC
1 ATGCATGGTCAAACCTCAAAAACATCACTGTAC
*
1313 ATGCATGGTCAAACCCCAAA
1 ATGCATGGTCAAACCTCAAA
1333 GTTCGATAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.20
Consensus pattern (33 bp):
ATGCATGGTCAAACCTCAAAAACATCACTGTAC
Found at i:1383 original size:123 final size:122
Alignment explanation
Indices: 1164--1553 Score: 451
Period size: 123 Copynumber: 3.1 Consensus size: 122
1154 AATTTTAATA
* *
1164 GTCAAGCCCCAAAAACATCATTGTACGTGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACA
1 GTCAAACCCCAAAAACATCATTGTACATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACA
* * * *
1229 AAAAACATTTCATCGTATATGCATGGTCAAACCTCAAAAACATCACTGTACATGCATG
66 AAAAGCA-TTCATTGTATATGCATGGTCAAACCACAAAAACATCACTGAACATGCATG
* * *
1287 GTCAAACCTCAAAAACATCACTGTACATGCATGGTCAAACCCCAAAGTTCGATAGTCAAGCCACA
1 GTCAAACCCCAAAAACATCATTGTACATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACA
* * * * * ** *
1352 TAAAGCATTCCATTGTATATGCATGATCAAACCCCAAATATCAGTTAAATCCCAAAGGATG-ATG
66 AAAAGCATT-CATTGTATATGCATGGTCAAACCACAAA-AACA--T-CA--CTGAA-CATGCATG
* * *
1416 GTCAAACCACAAAAAAAATCATTGTACATGCATGGTCAAACCCCAAAGTTCAATAGTCAAACCAC
1 GTCAAACC-CCAAAAACATCATTGTACATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCAC
* * *
1481 AGAAAGCATTTATTTGTATATGCATGGTCAAACCACAAAAACATCA-TCGCACATGCATG
65 AAAAAGCATTCA-TTGTATATGCATGGTCAAACCACAAAAACATCACT-GAACATGCATG
1540 GTCAAACCCCAAAA
1 GTCAAACCCCAAAA
1554 TTCGATAGTC
Statistics
Matches: 222, Mismatches: 33, Indels: 24
0.80 0.12 0.09
Matches are distributed among these distances:
122 2 0.01
123 98 0.44
124 15 0.07
126 2 0.01
127 2 0.01
129 17 0.08
130 86 0.39
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (122 bp):
GTCAAACCCCAAAAACATCATTGTACATGCATGGTCAAACCCCAAAGTTCGATAGTCAAACCACA
AAAAGCATTCATTGTATATGCATGGTCAAACCACAAAAACATCACTGAACATGCATG
Found at i:1538 original size:90 final size:91
Alignment explanation
Indices: 1413--1603 Score: 287
Period size: 90 Copynumber: 2.1 Consensus size: 91
1403 CCAAAGGATG
* * *
1413 ATGGTCAAACCACAAAAAAAATCATTGTACATGCATGGTCAAACCCCAAAGTTCAATAGTCAAAC
1 ATGGTCAAACCACAAAAAAAATCATCGCACATGCATGGTCAAACCCCAAAATTCAATAGTCAAAC
*
1478 CACAGAAAGCATTT-ATTTGTATATGC
66 CACAAAAAGCATTTCA-TTGTATATGC
* * *
1504 ATGGTCAAACCAC-AAAAACATCATCGCACATGCATGGTCAAACCCCAAAATTCGATAGTCAGAC
1 ATGGTCAAACCACAAAAAAAATCATCGCACATGCATGGTCAAACCCCAAAATTCAATAGTCAAAC
*
1568 CATAAAAAGCATTTCATTGTATATGC
66 CACAAAAAGCATTTCATTGTATATGC
1594 ATGGTCAAAC
1 ATGGTCAAAC
1604 TCCAAATTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 77 0.85
91 14 0.15
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (91 bp):
ATGGTCAAACCACAAAAAAAATCATCGCACATGCATGGTCAAACCCCAAAATTCAATAGTCAAAC
CACAAAAAGCATTTCATTGTATATGC
Found at i:1602 original size:57 final size:57
Alignment explanation
Indices: 1507--1723 Score: 262
Period size: 57 Copynumber: 3.9 Consensus size: 57
1497 TATATGCATG
* * * *
1507 GTCAAACCACAAAAA-CA--TCATCGCACATGCATGGTCAAACCCCAAAATTCGATA
1 GTCAAACCACAAAAAGCATTTCATTGTATATGCATGGTCAAACCCCAAAATTCAATA
* * * * *
1561 GTCAGACCATAAAAAGCATTTCATTGTATATGCATGGTCAAACTCCAAATTTTAATA
1 GTCAAACCACAAAAAGCATTTCATTGTATATGCATGGTCAAACCCCAAAATTCAATA
* * * * * *
1618 GTCAAACCCCAAAAA-AATATCATTGTACATGTATGGTCAAACCCTAAAATTCAATA
1 GTCAAACCACAAAAAGCATTTCATTGTATATGCATGGTCAAACCCCAAAATTCAATA
*
1674 GTCAAACCACAAAAAGCATTTCTTTGTATATGCATGGTCAAACCCCAAAA
1 GTCAAACCACAAAAAGCATTTCATTGTATATGCATGGTCAAACCCCAAAA
1724 ACATCATTGC
Statistics
Matches: 132, Mismatches: 27, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
54 13 0.10
55 2 0.02
56 47 0.36
57 70 0.53
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.24
Consensus pattern (57 bp):
GTCAAACCACAAAAAGCATTTCATTGTATATGCATGGTCAAACCCCAAAATTCAATA
Found at i:1715 original size:113 final size:113
Alignment explanation
Indices: 1517--1722 Score: 322
Period size: 113 Copynumber: 1.8 Consensus size: 113
1507 GTCAAACCAC
* * *
1517 AAAAACATCATCGCACATGCATGGTCAAACCCCAAAATTCGATAGTCAGACCATAAAAAGCATTT
1 AAAAACATCATCGCACATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAAGCATTT
*
1582 CATTGTATATGCATGGTCAAACTCCAAATTTTAATAGTCAAACCCCAA
66 CATTGTATATGCATGGTCAAACCCCAAATTTTAATAGTCAAACCCCAA
* * * * *
1630 AAAAATATCATTGTACATGTATGGTCAAACCCTAAAATTCAATAGTCAAACCACAAAAAGCATTT
1 AAAAACATCATCGCACATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAAGCATTT
*
1695 CTTTGTATATGCATGGTCAAACCCCAAA
66 CATTGTATATGCATGGTCAAACCCCAAA
1723 AACATCATTG
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
113 83 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.25
Consensus pattern (113 bp):
AAAAACATCATCGCACATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAAGCATTT
CATTGTATATGCATGGTCAAACCCCAAATTTTAATAGTCAAACCCCAA
Found at i:1747 original size:90 final size:92
Alignment explanation
Indices: 1618--1810 Score: 273
Period size: 90 Copynumber: 2.1 Consensus size: 92
1608 AATTTTAATA
* * * *
1618 GTCAAACCCCAAAAAAATATCATTGTACATGTATGGTCAAACCCTAAAATTCAATAGTCAAACCA
1 GTCAAACCCC-AAAAAACATCATTGCACATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCA
* * *
1683 CAAAAAGCA-TTTCTTTGTATATGCATG
65 CAAAAAACATTTTCATTGTATATGCACG
* * *
1710 GTCAAACCCC-AAAAACATCATTGCACATGCATTGTCAAACCCCAAAGTTCGATAGTCAAACCAC
1 GTCAAACCCCAAAAAACATCATTGCACATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCAC
1774 AAAAAACATTTTCATTGTATATGCACG
66 AAAAAACATTTTCATTGTATATGCACG
1801 GTCAAACCCC
1 GTCAAACCCC
1811 CAAATTTTAA
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
90 54 0.60
91 26 0.29
92 10 0.11
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (92 bp):
GTCAAACCCCAAAAAACATCATTGCACATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCAC
AAAAAACATTTTCATTGTATATGCACG
Found at i:1805 original size:58 final size:57
Alignment explanation
Indices: 1743--1871 Score: 177
Period size: 58 Copynumber: 2.2 Consensus size: 57
1733 CACATGCATT
* *
1743 GTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTTCATTGTATATGCACG
1 GTCAAACCCCAAAGTTCAATAGTCAAACCACAAAAAACA-TTTCATCGTATATGCACG
* * * * *
1801 GTCAAACCCCCAAATTTTAATAGTCAAATCACAAAAAGCATTTCATCGTATATGCATG
1 GTCAAA-CCCCAAAGTTCAATAGTCAAACCACAAAAAACATTTCATCGTATATGCACG
1859 GTCAAACCCCAAA
1 GTCAAACCCCAAA
1872 AACATCATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
57 7 0.11
58 28 0.44
59 28 0.44
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (57 bp):
GTCAAACCCCAAAGTTCAATAGTCAAACCACAAAAAACATTTCATCGTATATGCACG
Found at i:1859 original size:149 final size:146
Alignment explanation
Indices: 1581--1900 Score: 424
Period size: 149 Copynumber: 2.2 Consensus size: 146
1571 AAAAAGCATT
* * * * *
1581 TCATTGTATATGCATGGTCAAACTCCAAATTTTAATAGTCAAACCCCAAAAAAATATCATTGTAC
1 TCATTGTACATGCATGGTCAAACCCCAAAGTTCAATAGTCAAACCACAAAAAAATATCATTGTAC
* * * * *
1646 ATGTATGGTCAAACCCTAAAATTCAATAGTCAAACCACAAAAAGCATTTCTTTGTATATGCATGG
66 ATGCACGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAAGCATTTCATCGTATATGCATGG
1711 TCAAACCCCAAAAACA
131 TCAAACCCCAAAAACA
* * * *
1727 TCATTGCACATGCATTGTCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTTCATTGT
1 TCATTGTACATGCATGGTCAAACCCCAAAGTTCAATAGTCAAACCACAAAAAA-A-TATCATTGT
* * * *
1792 ATATGCACGGTCAAACCCCCAAATTTTAATAGTCAAATCACAAAAAGCATTTCATCGTATATGCA
64 ACATGCACGGTCAAA-CCCCAAAATTCAATAGTCAAACCACAAAAAGCATTTCATCGTATATGCA
1857 TGGTCAAACCCCAAAAACA
128 TGGTCAAACCCCAAAAACA
* **
1876 TCATTATACATGCATGACCAAACCC
1 TCATTGTACATGCATGGTCAAACCC
1901 TAAATGATGA
Statistics
Matches: 148, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
146 45 0.30
147 1 0.01
148 20 0.14
149 82 0.55
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (146 bp):
TCATTGTACATGCATGGTCAAACCCCAAAGTTCAATAGTCAAACCACAAAAAAATATCATTGTAC
ATGCACGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAAAGCATTTCATCGTATATGCATGG
TCAAACCCCAAAAACA
Found at i:1926 original size:203 final size:203
Alignment explanation
Indices: 1416--1872 Score: 549
Period size: 203 Copynumber: 2.2 Consensus size: 203
1406 AAGGATGATG
* * *
1416 GTCAAACCACAAAAAAA-ATCATTGTACATGCATGGTCAAACCCCAAAGTTCAATAGTCAAACCA
1 GTCAAACCACAAAAAAATATCATCGTACATGCATGGTCAAACCCCAAAATACAATAGTCAAACCA
* * * ** ** *
1480 CAGAAAGCATTTA-TTTGTATATGCATGGTCAAACCACAAAAACATCATCGCACATGCATGGTCA
66 CAAAAACCA-TAACCCTAAATATGCATGGTCAAACCCCAAAAACATCATCGCACATGCATGGTCA
* * * * *
1544 AACCCCAAAATTCGATAGTCAGACCATAAAAAGCATTTCATTGTATATGCATGGTCAAACTCCAA
130 AACCCCAAAATTCGATAGTCAAACCACAAAAAACATTTCATTGTATATGCACGGTCAAACCCCAA
1609 ATTTTAATA
195 ATTTTAATA
* * * * *
1618 GTCAAACCCCAAAAAAATATCATTGTACATGTATGGTCAAACCCTAAAATTCAATAGTCAAACCA
1 GTCAAACCACAAAAAAATATCATCGTACATGCATGGTCAAACCCCAAAATACAATAGTCAAACCA
* ** ** ** * *
1683 CAAAAAGCATTTCTTTGTATATGCATGGTCAAACCCCAAAAACATCATTGCACATGCATTGTCAA
66 CAAAAACCATAACCCTAAATATGCATGGTCAAACCCCAAAAACATCATCGCACATGCATGGTCAA
*
1748 ACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTTCATTGTATATGCACGGTCAAACCCCCA
131 ACCCCAAAATTCGATAGTCAAACCACAAAAAACA-TTTCATTGTATATGCACGGTCAAA-CCCCA
1813 AATTTTAATA
194 AATTTTAATA
* * * *
1823 GTCAAATCACAAAAAGCATTTCATCGTATATGCATGGTCAAACCCCAAAA
1 GTCAAACCACAAAAA-AATATCATCGTACATGCATGGTCAAACCCCAAAA
1873 ACATCATTAT
Statistics
Matches: 227, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
202 18 0.08
203 131 0.58
204 23 0.10
205 27 0.12
206 28 0.12
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (203 bp):
GTCAAACCACAAAAAAATATCATCGTACATGCATGGTCAAACCCCAAAATACAATAGTCAAACCA
CAAAAACCATAACCCTAAATATGCATGGTCAAACCCCAAAAACATCATCGCACATGCATGGTCAA
ACCCCAAAATTCGATAGTCAAACCACAAAAAACATTTCATTGTATATGCACGGTCAAACCCCAAA
TTTTAATA
Found at i:2129 original size:21 final size:21
Alignment explanation
Indices: 2106--2150 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2096 ATGCATGGTC
*
2106 AAACAACAAATTTTGATAGTCA
1 AAAC-ACAAAGTTTGATAGTCA
*
2128 AAACCCAAAGTTTGATAGTCA
1 AAACACAAAGTTTGATAGTCA
2149 AA
1 AA
2151 TCATGTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (21 bp):
AAACACAAAGTTTGATAGTCA
Found at i:3167 original size:22 final size:23
Alignment explanation
Indices: 3115--3170 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
3105 ATCAAAGAGG
* *
3115 CGGGTCGCGACCTGGTCACGGTT
1 CGGGTCGCGACCTGGCCACGGCT
* *
3138 TGGGTCGCGACCT-GCCATGGCT
1 CGGGTCGCGACCTGGCCACGGCT
3160 CGGGTCGCGAC
1 CGGGTCGCGAC
3171 GCGATCGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.09, C:0.32, G:0.39, T:0.20
Consensus pattern (23 bp):
CGGGTCGCGACCTGGCCACGGCT
Found at i:3317 original size:3 final size:3
Alignment explanation
Indices: 3309--3337 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3299 TTTCATGTTT
3309 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3338 TAAAGGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3583 original size:14 final size:15
Alignment explanation
Indices: 3566--3594 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3556 TTGTTTTACT
3566 TGAATGA-TTTTGAA
1 TGAATGAGTTTTGAA
3580 TGAATGAGTTTTGAA
1 TGAATGAGTTTTGAA
3595 AGTTTGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (15 bp):
TGAATGAGTTTTGAA
Found at i:5442 original size:33 final size:33
Alignment explanation
Indices: 5359--5443 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
5349 AATGGTCGGT
* * *
5359 GCCGCCCTGCTAGGGCGGCATGGACTTGGCCAT
1 GCCGCCCTGCTAGGGCGGCATGGACATAGCCAC
* * *
5392 GGCGCCCTCGGT-GGGCGGCATGGTCATAGCCAC
1 GCCGCCCT-GCTAGGGCGGCATGGACATAGCCAC
*
5425 GCCGCCCTGCTAAGGCGGC
1 GCCGCCCTGCTAGGGCGGC
5444 GCCCACCAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
32 2 0.05
33 37 0.90
34 2 0.05
ACGTcount: A:0.12, C:0.35, G:0.38, T:0.15
Consensus pattern (33 bp):
GCCGCCCTGCTAGGGCGGCATGGACATAGCCAC
Done.