Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017550.1 Corchorus olitorius cultivar O-4 contig17583, 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: 28519
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6317 original size:80 final size:80
Alignment explanation
Indices: 6135--6300 Score: 278
Period size: 81 Copynumber: 2.1 Consensus size: 80
6125 ACTGAATAAT
* * *
6135 TGAGAAGTCAGATTCTGTTAAGAATGAGCACTGCTTAACCATCTTGGTGATTCTCAACAACTAAA
1 TGAGAAGTCAGATACAGTTAAGAATGAGCACTGCTTAACCATCTGGGTGATTCTCAACAACTAAA
6200 AACATTGAATTTTGA
66 AACATTGAATTTTGA
* *
6215 TGAGAAGTCAGATTCTGTTAAGAATGAGCACTGCTTAACCAATCTGGGTGATTCTCAACAACTAA
1 TGAGAAGTCAGATACAGTTAAGAATGAGCACTGCTTAACC-ATCTGGGTGATTCTCAACAACTAA
6280 AAACATTGAATTTTGA
65 AAACATTGAATTTTGA
6296 TGAGA
1 TGAGA
6301 TATAATCACA
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
80 40 0.48
81 44 0.52
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (80 bp):
TGAGAAGTCAGATACAGTTAAGAATGAGCACTGCTTAACCATCTGGGTGATTCTCAACAACTAAA
AACATTGAATTTTGA
Found at i:8188 original size:2 final size:2
Alignment explanation
Indices: 8181--8206 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8171 TTTTACTGTA
8181 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8207 TGTATCTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17998 original size:30 final size:30
Alignment explanation
Indices: 17958--18017 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
17948 CAAGAACAAG
* *
17958 AAGAAAAGGAAACCCAAAGTGGGTTTGAGC
1 AAGAAAAGGAAAACCAAAGTGGGTTCGAGC
*
17988 AAGAAGAGGAAAACCAAAGTGGGTTCGAGC
1 AAGAAAAGGAAAACCAAAGTGGGTTCGAGC
18018 CAAGCCTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.13, G:0.32, T:0.12
Consensus pattern (30 bp):
AAGAAAAGGAAAACCAAAGTGGGTTCGAGC
Found at i:20851 original size:1 final size:1
Alignment explanation
Indices: 20847--20883 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
20837 TTGGTTACCC
20847 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20884 CTTGTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25091 original size:666 final size:665
Alignment explanation
Indices: 23766--25437 Score: 2505
Period size: 666 Copynumber: 2.5 Consensus size: 665
23756 AATTGTGGCC
* * * * *
23766 ATACTAACCATCATGATTTTTGGCTGAAAACGGGTTCCGGGGCCCAGTTTAGTTTTACATGATTT
1 ATAC-AACCATCACGATTTTTGGCTGAAAACGCGTTCCGGGGCCCGGCTTAGTTTTGCATGATTT
* * *
23831 TTGGCGCAAAGACTCATTGAGTTATCCTTATTCATCATTCCAAGTCTCAGCCACGTTGGATTTAA
65 TTGGCGCAAAGACTCATTGAATTATCCTTATTCATCATTCGAAATCTCAGCCACGTTGGATTTAA
*
23896 GGATTTGATTTTGCGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAAA-T
130 GGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAAATT
* * *
23960 TAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCATTGAATTGTATATTTTT
195 TAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTT
* *
24025 TACGAGTATTGCGGTTATAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAGTTTTTGCCG
260 TACGTGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAGTTTTTGCCG
*
24090 AAATCGTGTACTAA-CCATCACGATTCTTGGCTGAAAACGCGTTCCGGGTCCCGGCTCAGTTTTG
325 AAATCGTGTACTAACCCATCACGATTCTTGGCTGAAAACGCGTTCCGGGTCCCGACTCAGTTTTG
* *
24154 CATGATTTTTGGCGCCAAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGTT
390 CATGATTTCTGGCGCCAACACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGTT
* *
24219 GGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTAGG
455 GGATGTAAGGATTTGATTTTACGAGCATTCGAATCATGTTTCGATTTAATCGGAAATTAATTAGG
* *
24284 AAAAAATTAAAATAAAATGATATTAGAAGCGTCGAAAGCCGTTCAATCTTTCTGGCGTTGAATTA
520 AAAAAATTAAAATAAAAAGATATTAGAAGCGTCGAAAGCCCTTCAATCTTTCTGGCGTTGAATTA
*
24349 TATAATTTTTACGAGTATTGCGGTTAACAATAGAGGAAAAATCTCTCGGGTCAATTTTTGCAAAA
585 TATAATTTTTACGAGTATTGCGGTTAAAAATAGAGGAAAAATCTCTCGGGTCAATTTTTGCAAAA
24414 TTTTTGCCGAAATCGT
650 TTTTTGCCGAAATCGT
* *
24430 ATA-AA-CATCACGATTTTTGGCTGAAAACGCGTTTCGAGGGCCTCGGCTCAGTTTTGCATGATT
1 ATACAACCATCACGATTTTTGGCTGAAAACGCGTTCCG-GGGCC-CGGCTTAGTTTTGCATGATT
* * * *
24493 TTTGGCGCAAAGACTCATTGAATTATCCTTATTCATCATTCGAAATCTTAGCCATGGTAGATTTA
64 TTTGGCGCAAAGACTCATTGAATTATCCTTATTCATCATTCGAAATCTCAGCCACGTTGGATTTA
* * *
24558 TGGATTTGATTTTACGAGCATTCGAATCATGTCTCGATTTAATCGGAAATTAATTCGGAAAAAAT
129 AGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAAAT
* * *
24623 TTAAAAAAATGATATTAGAAGCGTGGAAAGCCTTTTATTATTTTTGGCGTTGAATTATATATTTT
194 TTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTT
* * *
24688 TTACGTGTATTGCGGTTAAAAATTGAGGAAAAATCTATCGGGTCAATTTTTGCAAAATTTTTACC
259 TTACGTGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAGTTTTTGCC
* * *
24753 GAAATCGTGTTCTAACCCATCACGATTCTTGGCTGAAAACGCTTTCCGGGGTCCCGACTTAGTTT
324 GAAATCGTGTACTAACCCATCACGATTCTTGGCTGAAAACGCGTTCC-GGGTCCCGACTCAGTTT
*
24818 TGCATGATTTCTGGCGTCAACACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACG
388 TGCATGATTTCTGGCGCCAACACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACG
* * *
24883 TTGGATGTAAGGATTTGATTTTACGAGCATTCGAATTATGTTTCGATTTAATCGGAAATTTATTC
453 TTGGATGTAAGGATTTGATTTTACGAGCATTCGAATCATGTTTCGATTTAATCGGAAATTAATTA
* *
24948 GGAAAAAAATTAAAA-AAAAAGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAA
518 GG-AAAAAATTAAAATAAAAAGATATTAGAAGCGTCGAAAGCCCTTCAATCTTTCTGGCGTTGAA
* * * *
25012 TTATATATTTTTTACGAGTATTGTGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCA
582 TTATATAATTTTTACGAGTATTGCGGTTAAAAATAGAGGAAAAATCTCTCGGGTCAATTTTTGCA
25077 AAATTTTTGCCGAAATCGT
647 AAATTTTTGCCGAAATCGT
* * * *
25096 ATACTAACCATCACGATTCTTGGCTGATAACGCGTTCCGCGGCCCCGACTTAGTTTTGCATGATT
1 ATAC-AACCATCACGATTTTTGGCTGAAAACGCGTTCCG-GGGCCCGGCTTAGTTTTGCATGATT
* * * * * * *
25161 TTTGGCGCCAAGACTCATTGTATTAT-CTATAGTCATCATCCTG-AATCACAACCACCTTGGATT
64 TTTGGCGCAAAGACTCATTGAATTATCCT-TATTCATCATTC-GAAATCTCAGCCACGTTGGATT
* * ***
25224 TAAGGATTTGATTTTACAAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCTGATTTT
127 TAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGA-AAA
** ** *
25289 TTTTTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATACATTTGGCGTTGAATGATATAT
191 AATTTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATATTTTTGGCGTTGAATTATATAT
* * * *
25354 TTTTTACTTGTATTGCGGTTAAAATTTGTGG-AAAATCCTTTCGGGTCAGTTTTTGCAAAGTTTT
256 TTTTTACGTGTATTGCGGTTAAAAATTGAGGAAAAAT-CTTTCGGGTCAATTTTTGCAAAGTTTT
*
25418 TGCCGAAATCGCGTACTAAC
320 TGCCGAAATCGTGTACTAAC
25438 GGCAAGTATT
Statistics
Matches: 902, Mismatches: 93, Indels: 21
0.89 0.09 0.02
Matches are distributed among these distances:
661 28 0.03
662 7 0.01
663 134 0.15
664 136 0.15
665 30 0.03
666 266 0.29
667 14 0.02
668 128 0.14
669 159 0.18
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (665 bp):
ATACAACCATCACGATTTTTGGCTGAAAACGCGTTCCGGGGCCCGGCTTAGTTTTGCATGATTTT
TGGCGCAAAGACTCATTGAATTATCCTTATTCATCATTCGAAATCTCAGCCACGTTGGATTTAAG
GATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAAATTT
AAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTT
ACGTGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAGTTTTTGCCGA
AATCGTGTACTAACCCATCACGATTCTTGGCTGAAAACGCGTTCCGGGTCCCGACTCAGTTTTGC
ATGATTTCTGGCGCCAACACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGTTG
GATGTAAGGATTTGATTTTACGAGCATTCGAATCATGTTTCGATTTAATCGGAAATTAATTAGGA
AAAAATTAAAATAAAAAGATATTAGAAGCGTCGAAAGCCCTTCAATCTTTCTGGCGTTGAATTAT
ATAATTTTTACGAGTATTGCGGTTAAAAATAGAGGAAAAATCTCTCGGGTCAATTTTTGCAAAAT
TTTTGCCGAAATCGT
Found at i:25109 original size:334 final size:331
Alignment explanation
Indices: 23766--25437 Score: 2390
Period size: 334 Copynumber: 5.0 Consensus size: 331
23756 AATTGTGGCC
* * * * *
23766 ATACTAACCATCATGATTTTTGGCTGAAAACGGGTTCCGGGGCCC-AGTTTAGTTTTACATGATT
1 ATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCGA-CTTAGTTTTGCATGATT
* *
23830 TTTGGCGCAAAGACTCATTGAGTTATCCTTATTCATCATTCCAAGTCTCAGCCACGTTGGATTTA
65 TTTGGCGC-AAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGTTGGATTTA
*
23895 AGGATTTGATTTTGCGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAAAT
129 AGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAAAT
* *
23960 T-AAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCATTGAATTGTATATTTT
194 TAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTT
* *
24024 TTACGAGTATTGCGGTTATAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAGTTTTTGCC
259 TTACGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCC
24089 GAAATCGT
324 GAAATCGT
* * * *
24097 GTACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCGGGTCCCGGCTCAGTTTTGCATGATTT
1 ATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCGACTTAGTTTTGCATGATTT
24162 TTGGCGCCAAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGTTGGATTTAA
66 TTGGCG-CAAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGTTGGATTTAA
*
24227 GGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTAGGAAAAAATT
130 GGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAAATT
* * * *
24292 AAAATAAAATGATATTAGAAGCGTCGAAAGCCGTTCAATCTTTCTGGCGTTGAATTATATAATTT
195 AAAA-AAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTT
* * *
24357 TTACGAGTATTGCGGTTAACAATAGAGGAAAAATCTCTCGGGTCAATTTTTGCAAAATTTTTGCC
259 TTACGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCC
24422 GAAATCGT
324 GAAATCGT
* * * *
24430 ATA--AA-CATCACGATTTTTGGCTGAAAACGCGTTTCGAGGGCCTCGGCTCAGTTTTGCATGAT
1 ATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCG-GGGCC-CGACTTAGTTTTGCATGAT
* * * * *
24492 TTTTGGCGCAAAGACTCATTGAATTATCCTTATTCATCATTCGAAATCTTAGCCATGGTAGATTT
64 TTTTGGCGC-AAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGTTGGATTT
* * *
24557 ATGGATTTGATTTTACGAGCATTCGAATCATGTCTCGATTTAATCGGAAATTAATTCGGAAAAAA
128 AAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAAA
* * * * *
24622 TTTAAAAAAATGATATTAGAAGCGTGGAAAGCCTTTTATTATTTTTGGCGTTGAATTATATATTT
193 TTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTT
* * *
24687 TTTACGTGTATTGCGGTTAAAAATTGAGGAAAAATCTATCGGGTCAATTTTTGCAAAATTTTTAC
258 TTTACGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGC
24752 CGAAATCGT
323 CGAAATCGT
* * *
24761 GTTCTAACCCATCACGATTCTTGGCTGAAAACGCTTTCCGGGGTCCCGACTTAGTTTTGCATGAT
1 ATACTAA-CCATCACGATTCTTGGCTGAAAACGCGTTCCGGGG-CCCGACTTAGTTTTGCATGAT
* * *
24826 TTCTGGCGTCAACACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGTTGGATGT
64 TTTTGGCG-CAAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGTTGGATTT
* * *
24891 AAGGATTTGATTTTACGAGCATTCGAATTATGTTTCGATTTAATCGGAAATTTATTCGGAAAAAA
128 AAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGG-AAAAA
*
24956 ATTAAAAAAAAAGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATT
192 ATTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATT
*
25021 TTTTACGAGTATTGTGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTG
257 TTTTACGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTG
25086 CCGAAATCGT
322 CCGAAATCGT
* *
25096 ATACTAACCATCACGATTCTTGGCTGATAACGCGTTCCGCGGCCCCGACTTAGTTTTGCATGATT
1 ATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCG-GGGCCCGACTTAGTTTTGCATGATT
* * * * * *
25161 TTTGGCGCCAAGACTCATTGTATTAT-CTATAGTCATCA-TCCTGAATCACAACCACCTTGGATT
65 TTTGGCG-CAAGACTCATTGAATTATCCT-TATTCATCATTCC-AAATCTCAGCCACGTTGGATT
* * ***
25224 TAAGGATTTGATTTTACAAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCTGATTTT
127 TAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGA-AAA
** * * *
25289 TTTTTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATAC-ATTTGGCGTTGAATGATATA
191 AATTAAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAAT-CTTTTTGGCGTTGAATTATATA
** * * * *
25353 TTTTTTACTTGTATTGCGGTTAAAATTTGTGG-AAAATCCTTTCGGGTCAGTTTTTGCAAAGTTT
255 TTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAAAAT-CTTTCGGGTCAATTTTTGCAAAATTT
*
25417 TTGCCGAAATCGC
319 TTGCCGAAATCGT
*
25430 GTACTAAC
1 ATACTAAC
25438 GGCAAGTATT
Statistics
Matches: 1204, Mismatches: 117, Indels: 37
0.89 0.09 0.03
Matches are distributed among these distances:
330 29 0.02
331 308 0.26
332 147 0.12
333 137 0.11
334 409 0.34
335 174 0.14
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (331 bp):
ATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCGACTTAGTTTTGCATGATTT
TTGGCGCAAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGTTGGATTTAAG
GATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATTCGGAAAAAATTA
AAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTT
ACGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGA
AATCGT
Found at i:26135 original size:175 final size:175
Alignment explanation
Indices: 25844--26166 Score: 556
Period size: 175 Copynumber: 1.8 Consensus size: 175
25834 AATGGATCGT
* **
25844 TAACCATCACGATTCTTGGCTGAAAACGCGTTCCAGGGCCCCAGCTCAGTTTTGCATGATTTTTT
1 TAACCATCACGATTCTTGCCTGAAAACGCGTTCCAAAGCCCCAGCTCAGTTTTGCATGATTTTTT
* *
25909 GCACCACGACTCATTGAAATATCTATATTCATCAGCCCAAATCTCAGCCACATTGGATTTAAGAA
66 CCACCAAGACTCATTGAAATATCTATATTCATCAGCCCAAATCTCAGCCACATTGGATTTAAGAA
25974 TTTGATTTTACGAGCATTTGCAAAATTTTTGCCGAAATCGTATAC
131 TTTGATTTTACGAGCATTTGCAAAATTTTTGCCGAAATCGTATAC
*
26019 TAACCATCACGATTCTTGCCTGAAAACGCGTTCCAAAGCCCCGGCTCAGTTTTGCATGATTTTTT
1 TAACCATCACGATTCTTGCCTGAAAACGCGTTCCAAAGCCCCAGCTCAGTTTTGCATGATTTTTT
* ** *
26084 CCGCCAAGACTCATTGAAATATCTATATTCATCATTCCAAATCTCAGCCACATTGGATTTAAGTA
66 CCACCAAGACTCATTGAAATATCTATATTCATCAGCCCAAATCTCAGCCACATTGGATTTAAGAA
26149 TTTGATTTTACGAGCATT
131 TTTGATTTTACGAGCATT
26167 CGAATCATGT
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
175 138 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (175 bp):
TAACCATCACGATTCTTGCCTGAAAACGCGTTCCAAAGCCCCAGCTCAGTTTTGCATGATTTTTT
CCACCAAGACTCATTGAAATATCTATATTCATCAGCCCAAATCTCAGCCACATTGGATTTAAGAA
TTTGATTTTACGAGCATTTGCAAAATTTTTGCCGAAATCGTATAC
Found at i:27033 original size:333 final size:332
Alignment explanation
Indices: 25990--27656 Score: 2267
Period size: 333 Copynumber: 5.0 Consensus size: 332
25980 TTTACGAGCA
* *
25990 TTTGCAAAATTTTTGCCGAAATCGTATACTAACCATCACGATTCTTGCCTGAAAACGCGTTCCAA
1 TTTGCAAAATTTTTGCCGAAATCGTATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCGA
* * * * *
26055 AGCCCCGGCTCAGTTTTGCATGATTTTTTCCGCCAAGACTCATTGAAATATCTATATTCATCATT
66 GGACCCGGCTTAGTTTTGCATGATTTTTGCC-CCAAGACTCATTGAATTATCTATATTCATCATT
*
26120 CCAAATCTCAGCCACATTGGATTTAAGTATTTGATTTTACGAGCATTCGAATCATGTTTCGATTT
130 CCAAATCTCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTCGAATCATGTTTCGATTT
* *
26185 AATCGGAAATTAATTCGGAAAAAATTTAAAAAAATGATATTAGAAGCGTGGAAATCCGTTCAATC
195 AATCGGAAATTAATTCGGAAAAAATTTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATC
* * * *
26250 TTTATGGCGTTGAATTATATATTTTTTACAAGTATTGCGGTTGAAAATTGAGGAAAAATCTCTCT
260 TTTTTGGCGTTGAATTATATATTTTTTACAAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCG
26315 GGTCAATT
325 GGTCAATT
* * * *
26323 TTTGCAAAATTTTTGCCGAAATCGTATACAAACCAACACGATTTTTGGCTGAAAACGCGTTCCGG
1 TTTGCAAAATTTTTGCCGAAATCGTATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCGA
* ** *
26388 GGCCCCGGCTTTCTTTTGCATGATTTCTTGCGCCAAGACTCATTGAATTATCCT-TATTCATCAT
66 GGACCCGGCTTAGTTTTGCATGATTT-TTGCCCCAAGACTCATTGAATTAT-CTATATTCATCAT
* * * * *
26452 TCCAAATCTCAGCCACGTTGGATGTAAGGATTTGATTTTGCGAGCATTTGGATCATGTTTCGATT
129 TCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTCGAATCATGTTTCGATT
** ***
26517 TAATTAGAAATTAATTC-GAAATTTTTTTTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCA
194 TAATCGGAAATTAATTCGGAAA--AAATTTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCA
* * * * *
26581 ATCTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGTGGTTAAAAATTGGGGGAAAATTTT
257 ATCTTTTTGGCGTTGAATTATATATTTTTTACAAGTATTGCGGTTAAAAATTGAGGAAAAATCTT
*
26646 TCAGGTCAATT
322 TCGGGTCAATT
* * *
26657 TTTGCAAAATTTTTGCCGAAATCGTGTACTAATCATCACGATTCTTGGCTGAAAACGCGTTCCGC
1 TTTGCAAAATTTTTGCCGAAATCGTATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCGA
*
26722 GGACCCGGCTTAGTTTTGCATGATTTTTGGCCCCAAGACTCATTGAATTATCTATAGTCATCA-T
66 GGACCCGGCTTAGTTTTGCATGATTTTT-GCCCCAAGACTCATTGAATTATCTATATTCATCATT
* * * **
26786 CCTGAATCTCAGCCACCTTGGATTTAAGGATTTGATTTTACGAACATTTAAATCATGTTTCGATT
130 CC-AAATCTCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTCGAATCATGTTTCGATT
26851 TAATCGGAAATTAATTCGGAAAAAATTTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAAT
194 TAATCGGAAATTAATTCGGAAAAAATTTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAAT
* ** * *
26916 TTTTTTGGCGTTGAATTATATATTTTTTACTTGTATTGTGGTTAAAAATTGAGTAAAAATCTTTC
259 CTTTTTGGCGTTGAATTATATATTTTTTACAAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTC
**
26981 GGGTCAGGT
324 GGGTCAATT
* * *
26990 TTTGCAAAGTTTTTGCCGAAATCGTGTACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCAA
1 TTTGCAAAATTTTTGCCGAAATCGTATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCGA
* * * *
27055 AG-CCCTGACTTAGTTTTGCAT-ATTTTTTCCGCCAAGACTCATTGAAATATCTATATTCATCAT
66 GGACCC-GGCTTAGTTTTGCATGATTTTTGCC-CCAAGACTCATTGAATTATCTATATTCATCAT
* * *
27118 CCCAAATCTCAGCCACATTGGATTTAAGTATTTGATTTAACGAGCATTCGAATCA----T-G-TT
129 TCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTCGAATCATGTTTCGATT
* * * * *
27177 T--T--G-ATTTAA-TCGGAAAAAATTT-TAAAAATGATATTAGAAGAGTGGAAATCCGTTCAAT
194 TAATCGGAAATTAATTCGGAAAAAATTTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAAT
* * *
27235 CTTTATGGCGTTGAATTATATATTTTTTACAAGTATTGCGGTTGAAAATTGAGGAAAAATCTCTC
259 CTTTTTGGCGTTGAATTATATATTTTTTACAAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTC
*
27300 TGGTCAATT
324 GGGTCAATT
* *
27309 TTTGCAAAATTTTTACCGAAATCGTATACTAACCATCACGATTTTTGGCTGAAAACGCGTTCCG-
1 TTTGCAAAATTTTTGCCGAAATCGTATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCGA
**
27373 GGATCCCGGCTTAGTTTTGCATGATTTTTGGCATCAAGACTCATTGAATTATCCT-TATTCATCA
66 GGA-CCCGGCTTAGTTTTGCATGATTTTT-GCCCCAAGACTCATTGAATTAT-CTATATTCATCA
* ** *
27437 TTCCAAATCTCAACCATGTTGGATTTAAGGATTTGATTTTACGAGCATTCGAATTATGTTTCGAT
128 TTCCAAATCTCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTCGAATCATGTTTCGAT
*
27502 TTAATCGGAAATTTATTCGGAAAAAATTTTAAAAAAGATGATATTAGAAGCGTGGAAAGCCCTTC
193 TTAATCGGAAATTAATTCGGAAAAAA-TTTAAAAAA-ATGATATTAGAAGCGTGGAAAGCCCTTC
* * * * * *
27567 AACCTTTTTCGCATTGAATTATATATTTTTTACGATTATTGCGGTTAAAAATTAAGGAAAAATCT
256 AATCTTTTTGGCGTTGAATTATATATTTTTTACAAGTATTGCGGTTAAAAATTGAGGAAAAATCT
27632 TTCGGGTCAATT
321 TTCGGGTCAATT
*
27644 TTTGCAAAGTTTT
1 TTTGCAAAATTTT
27657 AGCCACAATT
Statistics
Matches: 1167, Mismatches: 136, Indels: 60
0.86 0.10 0.04
Matches are distributed among these distances:
318 1 0.00
319 168 0.14
320 97 0.08
321 8 0.01
322 1 0.00
324 2 0.00
325 1 0.00
326 6 0.01
327 1 0.00
328 2 0.00
330 1 0.00
331 6 0.01
332 97 0.08
333 375 0.32
334 293 0.25
335 108 0.09
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (332 bp):
TTTGCAAAATTTTTGCCGAAATCGTATACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCGA
GGACCCGGCTTAGTTTTGCATGATTTTTGCCCCAAGACTCATTGAATTATCTATATTCATCATTC
CAAATCTCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTCGAATCATGTTTCGATTTA
ATCGGAAATTAATTCGGAAAAAATTTAAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCT
TTTTGGCGTTGAATTATATATTTTTTACAAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGG
GTCAATT
Found at i:28275 original size:18 final size:19
Alignment explanation
Indices: 28240--28277 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28230 GGCCCCGGAA
28240 TGTGTTTTCAGCCAAAAAT
1 TGTGTTTTCAGCCAAAAAT
*
28259 TGTGTTTTC-GGCAAAAAT
1 TGTGTTTTCAGCCAAAAAT
28277 T
1 T
28278 TTGCAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (19 bp):
TGTGTTTTCAGCCAAAAAT
Done.