Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015757.1 Corchorus olitorius cultivar O-4 contig15790, 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: 25808
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1105 original size:35 final size:35
Alignment explanation
Indices: 882--1718 Score: 530
Period size: 35 Copynumber: 23.7 Consensus size: 35
872 TAGTTTCATA
*
882 TTGACCTAGGGCGGTCTTTCTTCAGTTGT-TTTCAAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTT-TATTTC-AG
* * * *
918 TTGATCCAGGGCGATCCTTCTTAAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
953 TTGACCTAGGGTGGTATCTCTTTCAGTTAATCAGTTTATTTCAAG
1 TTGACCCAGGGCGG----TCTTTC---T--TCAGTTTATTTC-AG
* * * * * *
998 TTGACCCAAGGTGGTCGTTCTTCAGTTCAGTTCGG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *** * * * * *
1033 AATGATTGAGAGTGGCCGTTCTTCATTTTATTTCAG
1 -TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
1069 TTGACCCGGGGCGGTCTTTTTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * *
1104 TTGACCTAGGGTGGTCTTTCTTTAGTTGT-TTTCAAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTT-TATTTC-AG
* ** * * *
1140 TTAATTCAGGTCAGTCATTCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
1175 TTGACCCATGGCAGTCTTTCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * * *
1210 TTGACCTAGGGTGGTCTTTACTTCAGTTTATGTCCG
1 TTGACCCAGGGCGGTCTTT-CTTCAGTTTATTTCAG
* * * * *
1246 AATGATCAAGGGTGGTCGTTCTTCAGTTTATTTCAG
1 -TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
*
1282 TTGACCCAGGGCGGTCTTTCTTCAATTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
1317 TTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAG
1 TTGACCCAGGGCGGTC-TTTCTTCAGTTTATTTCAG
* * * * * *
1353 AATGATCGAGGGTGGTCGTTCTTCAGTTTATTTTAG
1 -TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
1389 TTGACCCAGGGCGGTCTTTCTTCAG------T---
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
*
1415 TT-ACCCAGGGCGGTCTTTCTTCAGTTTATGTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * * * * * *
1449 AATGATCGAGGGTGGCCGTTCTTCAGTTTATTTTAG
1 -TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * * *
1485 TTGACCTAGGGCGGTCTTTCTTCAATTTACTTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * * *
1520 TTGATCCAGGGCGATCTTTCTTCA-ATTAGTTTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTA-TTTCAG
* * * * * *
1555 TTGATCCAGGGCGATCATTCTTCAGTTTACTCCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * * * *
1590 TTGATCCAGGGCGATCATTCTTCAGTTTACTTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * ** * *
1625 TTGATCTAGGGCAATCTTTCTTCAGTTAATTTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * * * * * *
1660 TCGATCCAGGGCGATCATTCTTCAGTTCACTTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * *
1695 TTGATCCATGGCGATCTTTCTTCA
1 TTGACCCAGGGCGGTCTTTCTTCA
1719 AGTTAACCTA
Statistics
Matches: 636, Mismatches: 133, Indels: 65
0.76 0.16 0.08
Matches are distributed among these distances:
25 22 0.03
26 2 0.00
29 1 0.00
31 1 0.00
34 3 0.00
35 368 0.58
36 174 0.27
37 28 0.04
38 1 0.00
39 5 0.01
41 5 0.01
42 1 0.00
44 11 0.02
45 14 0.02
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (35 bp):
TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
Found at i:1302 original size:107 final size:106
Alignment explanation
Indices: 983--1718 Score: 634
Period size: 107 Copynumber: 7.0 Consensus size: 106
973 TTTCAGTTAA
* * * * * * *
983 TCAGTTTATTTCAAGTTGACCCAAGGTGGTCGTTCTTCAGTTCA-GTTCGGAATGATTGAGAGTG
1 TCAGTTTATTTC-AGTTGACCTAGGGTGGTCTTTCTTCAGTTTATG-TCCGAATGATCGAGGGTG
* * * *
1047 GCCGTTCTTCATTTTATTTCAGTTGACCCGGGGCGGTCTTTTT
64 GTCGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCT
* * *
1090 TCAGTTTATTTCAGTTGACCTAGGGTGGTCTTTCTTTAGTTGT-T-TTC-AAGTTAATTC-A-GG
1 TCAGTTTATTTCAGTTGACCTAGGGTGGTCTTTCTTCAGTT-TATGTCCGAA--TGA-TCGAGGG
* * * *
1150 TCAGTCATTCTTCAGTTTATTTCAGTTGACCCATGGCAGTCTTTCT
62 T-GGTCGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCT
*
1196 TCAGTTTATTTCAGTTGACCTAGGGTGGTCTTTACTTCAGTTTATGTCCGAATGATCAAGGGTGG
1 TCAGTTTATTTCAGTTGACCTAGGGTGGTCTTT-CTTCAGTTTATGTCCGAATGATCGAGGGTGG
1261 TCGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCT
65 TCGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCT
* * *
1303 TCAATTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGG
1 TCAGTTTATTTCAGTTGACCTAGGGTGGTC-TTTCTTCAGTTTATGTCCGAATGATCGAGGGTGG
*
1368 TCGTTCTTCAGTTTATTTTAGTTGACCCAGGGCGGTCTTTCT
65 TCGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCT
* * *
1410 TCAGTTTA---C------CC-AGGGCGGTCTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGC
1 TCAGTTTATTTCAGTTGACCTAGGGTGGTCTTTCTTCAGTTTATGTCCGAATGATCGAGGGTGGT
* *
1465 CGTTCTTCAGTTTATTTTAGTTGACCTAGGGCGGTCTTTCT
66 CGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCT
* * * * * * * * *
1506 TCAATTTACTTCAATTGATCC-AGGGCGATCTTTCTTCA-ATTA-GTTTC-AATTGATCCAGGGC
1 TCAGTTTATTTCAGTTGA-CCTAGGGTGGTCTTTCTTCAGTTTATG-TCCGAA-TGATCGAGGGT
* * * * * * * *
1567 GATCATTCTTCAGTTTACTCCAATTGATCCAGGGCGATCATTCT
63 GGTCGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCT
* * * *** * * * * *
1611 TCAGTTTACTTCAATTGATCTAGGGCAATCTTTCTTCAGTTAAT-TTC-AATCGATCCAGGGCGA
1 TCAGTTTATTTCAGTTGACCTAGGGTGGTCTTTCTTCAGTTTATGTCCGAAT-GATCGAGGGTGG
* * * * * * *
1674 TCATTCTTCAGTTCACTTCAATTGATCCATGGCGATCTTTCT
65 TCGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCT
1716 TCA
1 TCA
1719 AGTTAACCTA
Statistics
Matches: 539, Mismatches: 61, Indels: 60
0.82 0.09 0.09
Matches are distributed among these distances:
96 81 0.15
97 8 0.01
98 2 0.00
99 1 0.00
104 8 0.01
105 140 0.26
106 120 0.22
107 169 0.31
108 8 0.01
109 2 0.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (106 bp):
TCAGTTTATTTCAGTTGACCTAGGGTGGTCTTTCTTCAGTTTATGTCCGAATGATCGAGGGTGGT
CGTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCT
Found at i:1421 original size:25 final size:25
Alignment explanation
Indices: 1387--1442 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
1377 AGTTTATTTT
*
1387 AGTTGACCCAGGGCGGTCTTTCTTC
1 AGTTTACCCAGGGCGGTCTTTCTTC
1412 AGTTTACCCAGGGCGGTCTTTCTTC
1 AGTTTACCCAGGGCGGTCTTTCTTC
1437 AGTTTA
1 AGTTTA
1443 TGTCAGAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (25 bp):
AGTTTACCCAGGGCGGTCTTTCTTC
Found at i:1458 original size:96 final size:97
Alignment explanation
Indices: 1312--1514 Score: 354
Period size: 96 Copynumber: 2.1 Consensus size: 97
1302 TTCAATTTAT
* * *
1312 TTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTCTTC
1 TTCAGTTTACCCAGGGCGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGCCGTTCTTC
1377 AGTTTATTTTAGTTGACCCAGGGCGGTCTTTC
66 AGTTTATTTTAGTTGACCCAGGGCGGTCTTTC
1409 TTCAGTTTACCCAGGGCGGTC-TTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGCCGTTCTTC
1 TTCAGTTTACCCAGGGCGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGCCGTTCTTC
*
1473 AGTTTATTTTAGTTGACCTAGGGCGGTCTTTC
66 AGTTTATTTTAGTTGACCCAGGGCGGTCTTTC
*
1505 TTCAATTTAC
1 TTCAGTTTAC
1515 TTCAATTGAT
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 82 0.81
97 19 0.19
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.39
Consensus pattern (97 bp):
TTCAGTTTACCCAGGGCGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGCCGTTCTTC
AGTTTATTTTAGTTGACCCAGGGCGGTCTTTC
Found at i:1474 original size:132 final size:131
Alignment explanation
Indices: 1277--1543 Score: 320
Period size: 132 Copynumber: 2.0 Consensus size: 131
1267 TTCAGTTTAT
* * **
1277 TTCAGTTGACCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCA
1 TTCAGTTGACCCAGGGCGGTCTTTCTTCAATTTATGTCAGATGACCCAGGGTGGTCCGTTCTTCA
* * * * * * *
1342 GTTTATGTCAGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTTAGTTGACCCAGGGCGGTCTT
66 GTTTATGTCAG-ATGACCGAGGGCGGTCGTTCTTCAATTTACTTCAATTGACCCAGGGCGATCTT
1407 TC
130 TC
* * * *
1409 TTCAGTTTACCCAGGGCGGTCTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGG-CCGTTCTTC
1 TTCAGTTGACCCAGGGCGGTCTTTCTTCAATTTATGTCAG-ATGACCCAGGGTGGTCCGTTCTTC
* * * * * *
1473 AGTTTATTTTAGTTGACCTAGGGCGGTCTTTCTTCAATTTACTTCAATTGATCCAGGGCGATCTT
65 AGTTTATGTCAGATGACCGAGGGCGGTCGTTCTTCAATTTACTTCAATTGACCCAGGGCGATCTT
1538 TC
130 TC
1540 TTCA
1 TTCA
1544 ATTAGTTTCA
Statistics
Matches: 113, Mismatches: 21, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
131 48 0.42
132 54 0.48
133 11 0.10
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (131 bp):
TTCAGTTGACCCAGGGCGGTCTTTCTTCAATTTATGTCAGATGACCCAGGGTGGTCCGTTCTTCA
GTTTATGTCAGATGACCGAGGGCGGTCGTTCTTCAATTTACTTCAATTGACCCAGGGCGATCTTT
C
Found at i:1812 original size:16 final size:16
Alignment explanation
Indices: 1781--1831 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1771 TCAATGCTCC
* *
1781 ATTCTTCAATTATTCA
1 ATTCTCCAATTCTTCA
1797 ATGT-TCCAATTCTTCA
1 AT-TCTCCAATTCTTCA
*
1813 ATTCTCCAATGCTTCA
1 ATTCTCCAATTCTTCA
1829 ATT
1 ATT
1832 TACTTCAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (16 bp):
ATTCTCCAATTCTTCA
Found at i:1814 original size:8 final size:8
Alignment explanation
Indices: 1781--1831 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
1771 TCAATGCTCC
1781 ATTCTTCA
1 ATTCTTCA
*
1789 ATTATTCA
1 ATTCTTCA
*
1797 ATGT-TCCA
1 AT-TCTTCA
1805 ATTCTTCA
1 ATTCTTCA
*
1813 ATTCTCCA
1 ATTCTTCA
*
1821 ATGCTTCA
1 ATTCTTCA
1829 ATT
1 ATT
1832 TACTTCAAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
7 1 0.03
8 32 0.94
9 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (8 bp):
ATTCTTCA
Found at i:1822 original size:24 final size:24
Alignment explanation
Indices: 1772--1831 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1762 TGGGGGTATT
* *
1772 CAATGCTCC-ATTCTTCAATTATT
1 CAATGTTCCAATTCTTCAATTATC
*
1795 CAATGTTCCAATTCTTCAATTCTC
1 CAATGTTCCAATTCTTCAATTATC
1819 CAATGCTT-CAATT
1 CAATG-TTCCAATT
1832 TACTTCAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.25
24 22 0.69
25 2 0.06
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.42
Consensus pattern (24 bp):
CAATGTTCCAATTCTTCAATTATC
Found at i:2007 original size:51 final size:51
Alignment explanation
Indices: 1878--2107 Score: 344
Period size: 51 Copynumber: 4.6 Consensus size: 51
1868 TTTCGGTGGT
*
1878 TTCAAA-TGATCCAGTGCGATCAATCAAGTTTACAGTGATTTAAGTTTTTC
1 TTCAAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTC
*
1928 TTC-AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTATAAGTTTTTC
1 TTCAAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTC
* * *
1978 TTCAAAGTGATCCAGTACGATCAGTCAAGTTTACAGTGGTTTTAGTTTTTC
1 TTCAAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTC
2029 TTCAAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAG--TTTC
1 TTCAAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTC
* *
2078 CTAAAAGTGATCCAAGTGCTG-TCAATCAAG
1 TTCAAAGTGATCC-AGTGC-GATCAATCAAG
2108 AAAGTTTCCT
Statistics
Matches: 165, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
49 17 0.10
50 62 0.38
51 86 0.52
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (51 bp):
TTCAAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTC
Found at i:2075 original size:102 final size:100
Alignment explanation
Indices: 1878--2076 Score: 335
Period size: 101 Copynumber: 2.0 Consensus size: 100
1868 TTTCGGTGGT
*
1878 TTCAAATGATCCAGTGCGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAGTGATCCAGT
1 TTCAAATGATCCAGTACGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAGTGATCCAGT
1943 GCGATCAATCAAGTTTACAGTGGTATAAGTTTTTC
66 GCGATCAATCAAGTTTACAGTGGTATAAGTTTTTC
* * *
1978 TTCAAAGTGATCCAGTACGATCAGTCAAGTTTACAGTGGTTTTAGTTTTTCTTCAAAGTGATCCA
1 TTCAAA-TGATCCAGTACGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTC-AAGTGATCCA
*
2043 GTGCGATCAATCAAGTTTACAGTGGTTTAAGTTT
64 GTGCGATCAATCAAGTTTACAGTGGTATAAGTTT
2077 CCTAAAAGTG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
100 6 0.07
101 43 0.47
102 43 0.47
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (100 bp):
TTCAAATGATCCAGTACGATCAATCAAGTTTACAGTGATTTAAGTTTTTCTTCAAGTGATCCAGT
GCGATCAATCAAGTTTACAGTGGTATAAGTTTTTC
Found at i:2113 original size:38 final size:37
Alignment explanation
Indices: 2071--2147 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 37
2061 ACAGTGGTTT
2071 AAGTTTCCTAAAAGTGATCCAAGTGCT-GTCAATCAAGA
1 AAGTTTCCTAAAAGTGATCC-AGTG-TGGTCAATCAAGA
*
2109 AAGTTTCCTAAAGGTGATCCAGTGTGGTCAATCAAGA
1 AAGTTTCCTAAAAGTGATCCAGTGTGGTCAATCAAGA
2146 AA
1 AA
2148 ATTTATAGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 1 0.03
37 17 0.46
38 19 0.51
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (37 bp):
AAGTTTCCTAAAAGTGATCCAGTGTGGTCAATCAAGA
Found at i:2192 original size:54 final size:54
Alignment explanation
Indices: 2122--2234 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
2112 TTTCCTAAAG
** * *
2122 GTGATCCAGTGTGGTCAATCAAGAAAATTTAT-AGTGGTTTTA-GTTTATCTTCAA
1 GTGATCCAGTACGGTCAATCAAGAAAATTT-TCAGT-GATTTAGGCTTATCTTCAA
* * *
2176 GTGATCCAGTACGGTCAGTCAAGGAAGTTTTCAGTGATTTAGGCTTATCTTCAA
1 GTGATCCAGTACGGTCAATCAAGAAAATTTTCAGTGATTTAGGCTTATCTTCAA
2230 GTGAT
1 GTGAT
2235 TCGGTGAATC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 6 0.12
54 44 0.88
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (54 bp):
GTGATCCAGTACGGTCAATCAAGAAAATTTTCAGTGATTTAGGCTTATCTTCAA
Found at i:2331 original size:42 final size:42
Alignment explanation
Indices: 2232--2436 Score: 306
Period size: 42 Copynumber: 4.9 Consensus size: 42
2222 ATCTTCAAGT
*
2232 GATTCGGTGAATCAGATGACTCGGGGTAGCATCATCAAGC--
1 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
*
2272 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTTAAGCGG
1 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
*
2314 GATTCAGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
1 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
* * ** *
2356 GATTCGGTGAATTAGATGACTCAGTATAGCATCTTCAAGTGG
1 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
* *
2398 GATTCGGTGAATCAGATTACTCGGTGTAGCATCTTCAAG
1 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAG
2437 ATTGGAATTC
Statistics
Matches: 149, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
40 38 0.26
42 111 0.74
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (42 bp):
GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
Found at i:2582 original size:89 final size:90
Alignment explanation
Indices: 2429--2630 Score: 241
Period size: 89 Copynumber: 2.3 Consensus size: 90
2419 CGGTGTAGCA
* * * **
2429 TCTTC-AAGATTGGAATTCGGTGAGCTCGGTGCAACACATTTTCAGATAGATCAGGGTGACTCGG
1 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAACACATTTTCAAACAGATAAGGACGACTCGG
2493 TGAATCAAGTTAATGCGGTGC-ATT
66 TGAATCAAGTTAATGCGGTGCAATT
* * * *
2517 TCTTCAAAGATTGGAATTCGGTGAGCTTGGTGCAGCACATTTTCAAACAGTTAAGGACGATTCGG
1 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAACACATTTTCAAACAGATAAGGACGACTCGG
* * *
2582 TGAATTAAGTTACTGCTGTGCAGTATT
66 TGAATCAAGTTAATGCGGTGCA--ATT
*
2609 TCTTCAAAG-TTTG-ATTCGGTGA
1 TCTTCAAAGATTGGAATTCGGTGA
2631 ATCAAGGTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
88 5 0.05
89 68 0.70
90 9 0.09
91 3 0.03
92 12 0.12
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (90 bp):
TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAACACATTTTCAAACAGATAAGGACGACTCGG
TGAATCAAGTTAATGCGGTGCAATT
Found at i:9230 original size:20 final size:20
Alignment explanation
Indices: 9205--9245 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
9195 GAATTTCCAA
9205 TGACTTTCATCAATAAATTG
1 TGACTTTCATCAATAAATTG
9225 TGACTTTCATCAATAAATTG
1 TGACTTTCATCAATAAATTG
9245 T
1 T
9246 TCTACACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
TGACTTTCATCAATAAATTG
Found at i:13505 original size:39 final size:39
Alignment explanation
Indices: 13442--13522 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
13432 TTTGTAAATA
* *
13442 GGGAAGCAAATGTACTTGCTCATTCTCTAGCTAAAGACT
1 GGGAAGCAAATGTACTTGCACATTCTCTAGCTAAAAACT
*
13481 GGGAAGCCAATGTA-TTCGCACATTCTCTAGCTAAAAACT
1 GGGAAGCAAATGTACTT-GCACATTCTCTAGCTAAAAACT
13520 GGG
1 GGG
13523 CTGGATAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.05
39 36 0.95
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (39 bp):
GGGAAGCAAATGTACTTGCACATTCTCTAGCTAAAAACT
Found at i:19664 original size:123 final size:125
Alignment explanation
Indices: 19512--19736 Score: 328
Period size: 123 Copynumber: 1.8 Consensus size: 125
19502 TAACAACGGT
* * * *
19512 GGTAATGGTAATGATTTTACTTTTGAGGTTCCTCAAGTCTCTGAAGATGATGGTATTTCATTGAT
1 GGTAACGGTAATGATTTTACATTAGAGGTTCCTCAAGTCTCTGAAGATGATGATATTTCATTGAT
19577 G-GAAAT-CTGCACAGAAGATGATGCAGAATTCATTACTTATATCGATGGTCAAATGACA
66 GTGAAATCCTGCACAGAAGATGATGCAGAATTCATTACTTATATCGATGGTCAAATGACA
* *
19635 GGTAACGGTAATGATTTTACATTAGAGGTTCCTCCAGTTTCTGAAGATGATGATATTTCATTGAT
1 GGTAACGGTAATGATTTTACATTAGAGGTTCCTCAAGTCTCTGAAGATGATGATATTTCATTGAT
** * * *
19700 GTTGGCATCCTTCATAGAAGATGATGCAGCATTCATT
66 G-TGAAATCCTGCACAGAAGATGATGCAGAATTCATT
19737 GAGGTTCCTC
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
123 60 0.68
125 3 0.03
126 25 0.28
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (125 bp):
GGTAACGGTAATGATTTTACATTAGAGGTTCCTCAAGTCTCTGAAGATGATGATATTTCATTGAT
GTGAAATCCTGCACAGAAGATGATGCAGAATTCATTACTTATATCGATGGTCAAATGACA
Found at i:19771 original size:78 final size:78
Alignment explanation
Indices: 19654--19876 Score: 358
Period size: 78 Copynumber: 2.8 Consensus size: 78
19644 AATGATTTTA
*
19654 CATTAGAGGTTCCTCCAGTTTCTGAAGATGATGATATTTCATTGATGTTGGCATCCTTCATAGAA
1 CATT-GAGGTTCCTCAAGTTTCTGAAGATGATGATATTTCATTGATGTTGGCATCCTTCATAGAA
*
19719 GATGATGCAGCATT
65 GATAATGCAGCATT
* *
19733 CATTGAGGTTCCTCAAGTTTCTGAAGATGATGATATTTCATTGATGTTGGCATCCTTCGTAGGAG
1 CATTGAGGTTCCTCAAGTTTCTGAAGATGATGATATTTCATTGATGTTGGCATCCTTCATAGAAG
19798 ATAATGCAGCATT
66 ATAATGCAGCATT
* * *
19811 CATTGAGGTTCCTCAAGATTCTGGAGATGATGATA-TTCAATTGATGTTGGCATCGTTCATAGAA
1 CATTGAGGTTCCTCAAGTTTCTGAAGATGATGATATTTC-ATTGATGTTGGCATCCTTCATAGAA
19875 GA
65 GA
19877 GGAAGATTGG
Statistics
Matches: 134, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
77 3 0.02
78 127 0.95
79 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (78 bp):
CATTGAGGTTCCTCAAGTTTCTGAAGATGATGATATTTCATTGATGTTGGCATCCTTCATAGAAG
ATAATGCAGCATT
Found at i:22985 original size:70 final size:70
Alignment explanation
Indices: 22898--23041 Score: 288
Period size: 70 Copynumber: 2.1 Consensus size: 70
22888 CAAATCATTT
22898 TAACTCTTGAATTACCGACGCAATTATGCCAGAGGCCACACACATTAGGGTTACTAATCTTCTAG
1 TAACTCTTGAATTACCGACGCAATTATGCCAGAGGCCACACACATTAGGGTTACTAATCTTCTAG
22963 CATAG
66 CATAG
22968 TAACTCTTGAATTACCGACGCAATTATGCCAGAGGCCACACACATTAGGGTTACTAATCTTCTAG
1 TAACTCTTGAATTACCGACGCAATTATGCCAGAGGCCACACACATTAGGGTTACTAATCTTCTAG
23033 CATAG
66 CATAG
23038 TAAC
1 TAAC
23042 GGAGGGTCCT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (70 bp):
TAACTCTTGAATTACCGACGCAATTATGCCAGAGGCCACACACATTAGGGTTACTAATCTTCTAG
CATAG
Found at i:25786 original size:12 final size:12
Alignment explanation
Indices: 25743--25788 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
25733 AAAAGCCCGC
*
25743 TTTAGTTTTTTT
1 TTTATTTTTTTT
25755 TTT-TTTTTTTT
1 TTTATTTTTTTT
*
25766 TTTNTTTTTTTT
1 TTTATTTTTTTT
25778 TTTAATTTTTT
1 TTT-ATTTTTT
25789 AACTACTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 10 0.33
12 14 0.47
13 6 0.20
ACGTcount: A:0.07, C:0.00, G:0.02, T:0.89
Consensus pattern (12 bp):
TTTATTTTTTTT
Found at i:25788 original size:1 final size:1
Alignment explanation
Indices: 25748--25780 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
25738 CCCGCTTTAG
*
25748 TTTTTTTTTTTTTTTTTTTTTNTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
25781 AATTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Done.