Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015426.1 Corchorus olitorius cultivar O-4 contig15459, 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: 63047
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:954 original size:333 final size:333
Alignment explanation
Indices: 26--1951 Score: 3106
Period size: 333 Copynumber: 5.8 Consensus size: 333
16 GAAATTAGGG
* *
26 TTTTGTTATGAGTGTTGTGGCCAAAAATTGAGGAAAATAATTTTCGGGGCAGTTTTTGCAAAATT
1 TTTT-TTATGAGTGTTGTGGCCAAAAATTGAGGAAAA-ATTTTTCGGGACAGTTTTTGCAAAATT
*
91 TTGTTCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAACGCATTCCTGGGCACCGACAC
64 TTGTTCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGACAC
156 AGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAG
129 AGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAG
* * *
221 CCACAATGGATTTATAGATAAGGCTTTACGACCATCTGAATTATAATTCCATTTAATTATAAATT
194 CCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATT
* * *
286 AATTCAGGAAAAATTAGGAAAAACGATAGTTGAAGCGTCTAAAGCCCTTCAATCTTCTTGGACTT
259 AATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTT
351 GAATTATATA
324 GAATTATATA
* *
361 TTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGTACAGTTTATGCAAAATTTT
1 TTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTT
* *
426 GTTCGAAATCGTGTACTTACAATCACAGTTTTTGGCTAAAAACGCGTTCCTCGGCACCGACACAG
66 GTTCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGACACAG
* *
491 -TTTCGGTGATTTTTGGCAGCAAAACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGCC
131 TTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGCC
* * *
555 ACAATGGATTTATAGATAAGGCTATACGACCATCTGAATTATAATTCGATTTAATTAGATATTAA
196 ACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTAA
* * * *
620 TTCGGGAAAAATTAGGAAAAATGATAATTGATGCGTCTAAAGCCCATCAATCTTCTTGGACTTGA
261 TTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGA
685 ATTATATATA
326 A-T-TATATA
* * * *
695 TTTTTTATGAATGTTGTGGCCAAAAATTGTGGAAAAATCTTTCGGTACAGTTTTTGCAAAATTTT
1 TTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTT
* *
760 GTTCGAAATCGTGTAC-TA-CATCACAGTTTTTGGCTAAAAACGTGTTCCTGGGCACAGACACAG
66 GTTCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGACACAG
* *
823 TTTTGGGTGATTTTTTGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGAC
131 TTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGCC
* * *
888 ACAATGGATTTATGGATAAGGCTTTATGACCATCTGAATCATAATTCGATTTAATCAGAAATTAA
196 ACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTAA
* *
953 TTCGGGAAAAATCAGGAAAAACGATAATTGAACCGTCTAAAGCCCTTCAATCTTTTTGGACTTGA
261 TTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGA
1018 ATTATATA
326 ATTATATA
* *
1026 TTTTTTATGAATGTTCTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTT
1 TTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTT
* * * * * *
1091 GTTCGAAATTGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCGTTTCTGGGCACCGTCCCAG
66 GTTCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGACACAG
*
1156 TTCTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGCC
131 TTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGCC
* * * *
1221 ACAATGGATTTTTTGATAAGGCTTTAAGACCATCTGAAATATAATTCGATTTAATTAGAAATTAA
196 ACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTAA
*
1286 TTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACATGA
261 TTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGA
1351 ATTATATA
326 ATTATATA
* *
1359 TTTTCTATGAGTGTTGTGGCCAAAAATTGAGGAACAATTTTTCGGTG-CAGTTTTTGCAAAATTT
1 TTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGG-GACAGTTTTTGCAAAATTT
* * *
1423 TGTTCGAAATCATGTACTTACCACCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGACGCA
65 TGTTCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGACACA
* *
1488 GTTTTGGGTGATTTTTGGCAACAAGACTCCTTAAAATATGTAACTTCATCTGACCAAATCTCAGC
130 GTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGC
* *
1553 CACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATCATAATTCGATTTAATCAGAAATTA
195 CACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTA
* *
1618 ATTCGAGAAAAATTAGGAAAAACGATAATTGAAGCGTATAAAGCCCTTCAATCTTTTTGGACTTG
260 ATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTG
1683 AATTATATA
325 AATTATATA
*
1692 TTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTT
1 TTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTT
* * * **
1757 -TGGCCAATATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCAATCCTGGGCACCGACAC
66 GT-TCGAA-ATCGTGTACTTACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGACAC
* * *
1821 AGTTTTGGGTGAGTTTTGGCAGCAAGACTCCTTAAAATATGTAAATTAATCTAACCAAATCTCAG
129 AGTTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAG
* * *
1886 CCACAATGGATTTATGGATAAGGCTTTACGACCATATGAATTTTATTTCGATTTAATTAGAAATT
194 CCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATT
1951 A
259 A
1952 GGGTTTTGTT
Statistics
Matches: 1471, Mismatches: 111, Indels: 19
0.92 0.07 0.01
Matches are distributed among these distances:
331 82 0.06
332 229 0.16
333 869 0.59
334 287 0.20
335 4 0.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (333 bp):
TTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTT
GTTCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGACACAG
TTTTGGGTGATTTTTGGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGCC
ACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTAA
TTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGA
ATTATATA
Found at i:3097 original size:333 final size:333
Alignment explanation
Indices: 1963--4118 Score: 2610
Period size: 333 Copynumber: 6.5 Consensus size: 333
1953 GGTTTTGTTT
**
1963 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTG-AAAATTTTGGCCGAA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTTGTTCGAA
* * * * *
2027 ATCGTGTACGT-----T-ATAGTTTTTGACTAAAAACGCGTTCTTGGGCCCCGGCAAAGTTTTGC
66 ATCGTGTAC-TAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCCCCGGCACAGTTTTGG
* * ** * * * * * * ** * *
2086 ATTATTTTTGGC-GCCAGTGTCATTTAAATATCTATATTCATTTAAGCAGTTCTTAGCCACATTG
130 ATGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTAACCAAATCTCAGCCACAATG
* * ** ** * * * * *
2150 GATTGATGGTTTTGTTTTTACGAGCATTTGAATCA-AGTTTCAATTTAATTAGAAATTAATTCGG
195 GATTTATGGATAAGGCTTTACGACCATCTGAATTATA-ATTCGATTTAATTAGAAATTAATTCGG
*
2214 GAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCATTTTGGACTTGAATTAT
259 GAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATTAT
*
2279 ATCTTTTTTA
324 ATATTTTTTA
* *
2289 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGAGACAGTTTTCGCAAAATTTTGTTCGAA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTTGTTCGAA
* * *
2354 ATCGTG----AA--ATCACAGTTTTCGGCTAAAAA-GCCGTTCCTGGGCCCCGGTACAGTTTTGC
66 ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACG-CGTTCCTGGGCCCCGGCACAGTTTTGG
* * * ** * * ** * * * *
2412 ATGACTTTTGG-TACCAGTGTCATTGAAATACCTATATTCATCTAACCAATTCTTAGCCACATTG
130 ATGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTAACCAAATCTCAGCCACAATG
* * ** ** * * ** * **
2476 GATTGATGGTTTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTATAAATTAATTCAAG
195 GATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTAATTCGGG
* * *
2541 AAAAATTAGGAAAAATGATAATTGAAGTGTCTATAGCCCTTCAATCTTTTTGGACTTGAATTATA
260 AAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATTATA
2606 TA-TTTTTA
325 TATTTTTTA
*
2614 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGAGACAGTTTTTGCAAAATTTTGTTCGAA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTTGTTCGAA
* * ** *
2679 ATCGTGTACTAACCATCATAGTTTTTGCCTAAAAACGCGTTCCTGGGCATCGGCACAGTTTTGGG
66 ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCCCCGGCACAGTTTTGGA
* * * *
2744 TGATTTTTAGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTAAGCCACAATGG
131 TGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTAACCAAATCTCAGCCACAATGG
*
2809 ATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTTGATTTAATTAGAAATTAATTCGGGA
196 ATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTAATTCGGGA
* *
2874 AAAATTAGGAAAAACGTTAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATAATAT
261 AAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATTATAT
2939 ATTTTTTA
326 ATTTTTTA
* *
2947 TGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAATTTTTGCAAAATTTTGTTCGAA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTTGTTCGAA
* * * * * *
3012 ATCGTGTACTAACTATCACAGTTTTTTGCTAAAAACGCGTTCCGGGGCACCGACACAGTTTTGGG
66 ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCCCCGGCACAGTTTTGGA
* **
3077 TGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGTTACAATGG
131 TGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTAACCAAATCTCAGCCACAATGG
** * **
3142 ATTTATAAATAAGGCTTTACGACCATCTGACTTATAATTCGATTTAATGGGAAATTAATTCGGGA
196 ATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTAATTCGGGA
* *
3207 AAAATTAGGAAAAACTATAATTGAAGCGTCTAATGCCCTTCAATCTTTTTGGACTTGAATTATAT
261 AAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATTATAT
3272 A-TTTTTA
326 ATTTTTTA
* * * *
3279 TGAGTGTTGTGGCCAAAAATTGTGGAAAAATTTTTCGGAACAGTTTTTGCAAAATTTTGTCCGAA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTTGTTCGAA
* * * *
3344 ATCGTATACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGACACAGTTTTGGG
66 ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCCCCGGCACAGTTTTGGA
* **
3409 TGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGTTACAATGG
131 TGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTAACCAAATCTCAGCCACAATGG
* **
3474 ATTTATGGATAAGGCTTTACGACCATCTGACTTATAATTCGATTTAATGGGAAATTAATTCGGGA
196 ATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTAATTCGGGA
* * *
3539 AAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATATTTTTGGACATGAATTATGT
261 AAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATTATAT
3604 ATTTTTTA
326 ATTTTTTA
3612 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTTG-TCTGA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTTGTTC-GA
*
3676 AATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCATTCCTGGGCCCCGGCACAGTTTTGG
65 AATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCCCCGGCACAGTTTTGG
* * * * * *
3741 ATGATTTGTGGCAGCAAGACTCCTTAAAATATATAAATACATCTAACCAAATTTCAGCTACAATG
130 ATGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTAACCAAATCTCAGCCACAATG
* ** * * * * * **
3806 GATTTAAGGATAAGATTTTACGACCATTTGATTTAAAATTCGATTTTATTAAAAATTAATT-TAG
195 GATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTAATTCGGG
* * * * * *
3870 AAAAA-TAGAAAAAACGAT-ATTAGAA--GTCTAAAATGCCATTAAAAT-TTATAGG-CGTTGAG
260 AAAAATTAGGAAAAACGATAATT-GAAGCGTCT-AAA-GCCCTT-CAATCTTTTTGGAC-TTGAA
3929 TTATATATTTTTTA
320 TTATATATTTTTTA
** * * * * *
3943 TGAGTACTGTGGCTAAAAA-TAAGGAAAAAATTTTTGGGACAGTTTTTGCAAAATTTTG-GCCAA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTTGTTCGAA
* * *
4006 ATCATGTACTAACCATCACAGTTTTCGGCTAAAAACGCGTTCCTGGGCCCCGGCACAGTTTTGCA
66 ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCCCCGGCACAGTTTTGGA
* * * * * *
4071 TTATTTTTGGC-GTC-AGTCTCATTGAAATATCTATATTCATCTAACCAA
131 TGATTTTTGGCTG-CAAGACTCCTTAAAATATGTAAATTCATCTAACCAA
4119 TTTTTAGCCA
Statistics
Matches: 1637, Mismatches: 168, Indels: 48
0.88 0.09 0.03
Matches are distributed among these distances:
325 78 0.05
326 261 0.16
327 19 0.01
328 29 0.02
329 79 0.05
330 45 0.03
331 106 0.06
332 480 0.29
333 540 0.33
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (333 bp):
TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTTGTTCGAA
ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCCCCGGCACAGTTTTGGA
TGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTAACCAAATCTCAGCCACAATGG
ATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTTAATTAGAAATTAATTCGGGA
AAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATTATAT
ATTTTTTA
Found at i:3403 original size:665 final size:662
Alignment explanation
Indices: 1963--4118 Score: 2633
Period size: 665 Copynumber: 3.3 Consensus size: 662
1953 GGTTTTGTTT
*
1963 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTG-AAAATTTTGGCCGAA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGAACAGTTTTTGCAAAATTTTGGCCGAA
* * * * * *
2027 ATCGTGTACGT-----T-ATAGTTTTTGACTAAAAACGCGTTCTTGGGCCCCGGCAAAGTTTTGC
66 ATCGTGTAC-TAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGGCACAGTTTTGG
* * * ** * * * * * * * ** * *
2086 ATTATTTTTGGCGCCAGTGTCATTTAAATATCTATATTCATTTAAGCAGTTCTTAGCCACATTGG
130 GTGATTTTTGGCGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTAAGCCACAATGG
* * ** ** * * * * *
2151 ATTGATGGTTTTGTTTTTACGAGCATTTGAATCA-AGTTTCAATTTAATTAGAAATTAATTCGGG
195 ATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTT-GATTTAATTAGAAATTAATTCGGG
*
2215 AAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCATTTTGGACTTGAATTATA
259 AAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATTATA
* * *
2280 TCTTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGAGACAGTTTTCGCAAAATT
324 TATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATT
* *
2345 TTGTTCGAAATCGTG----AA-ATCACAGTTTTCGGCTAAAAA-GCCGTTCCTGGGCCCCGGTAC
389 TTGTTCGAAATCGTGTACTAACATCACAGTTTTTGGCTAAAAACG-CGTTCCTGGGCCCCGGCAC
* * * * ** * * ** * * *
2404 AGTTTTGCATGACTTTTGG-TACCAGTGTCATTGAAATACCTATATTCATCTAACCAATTCTTAG
453 AGTTTTGGATGATTTTTGGCTGCAAGACTCCTTAAAATATATAAATTCATCTAACCAAATCTCAG
* * * * * ** * * * ** *
2468 CCACATTGGATTGATGGTTTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTATAAATT
518 CTACAATGGATTTATAGATAAGATTTTACGACCATCTGAATTATAATTCGATTTAATTAAAAATT
2533 AATTCAAGAAAAATTAGGAAAAA-TGATAATTGAAGTGTCT-ATAGCCCTTCAATCTTTTTGGAC
583 AATTCAAGAAAAATTAGGAAAAACT-ATAATTGAAG-GTCTAAT-GCCCTTCAATCTTTTTGGAC
2596 TTGAATTATATATTTTTA
645 TTGAATTATATATTTTTA
**
2614 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTC-GAGACAGTTTTTGCAAAATTTTGTTCGA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGA-ACAGTTTTTGCAAAATTTTGGCCGA
* * *
2678 AATCGTGTACTAACCATCATAGTTTTTGCCTAAAAACGCGTTCCTGGGCATCGGCACAGTTTTGG
65 AATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGGCACAGTTTTGG
*
2743 GTGATTTTTAGCAGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTAAGCCACAATG
130 GTGATTTTTGGC-GCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTAAGCCACAATG
2808 GATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTTGATTTAATTAGAAATTAATTCGGG
194 GATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTTGATTTAATTAGAAATTAATTCGGG
* *
2873 AAAAATTAGGAAAAACGTTAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATAATA
259 AAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATTATA
* *
2938 TATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAATTTTTGCAAAATT
324 TATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATT
* * * *
3003 TTGTTCGAAATCGTGTACTAACTATCACAGTTTTTTGCTAAAAACGCGTTCCGGGGCACCGACAC
389 TTGTTCGAAATCGTGTACTAAC-ATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCCCCGGCAC
* * *
3068 AGTTTTGGGTGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAG
453 AGTTTTGGATGATTTTTGGCTGCAAGACTCCTTAAAATATATAAATTCATCTAACCAAATCTCAG
* * ** * ***
3133 TTACAATGGATTTATAAATAAGGCTTTACGACCATCTGACTTATAATTCGATTTAATGGGAAATT
518 CTACAATGGATTTATAGATAAGATTTTACGACCATCTGAATTATAATTCGATTTAATTAAAAATT
**
3198 AATTCGGGAAAAATTAGGAAAAACTATAATTGAAGCGTCTAATGCCCTTCAATCTTTTTGGACTT
583 AATTCAAGAAAAATTAGGAAAAACTATAATTGAAG-GTCTAATGCCCTTCAATCTTTTTGGACTT
3263 GAATTATATATTTTTA
647 GAATTATATATTTTTA
* * *
3279 TGAGTGTTGTGGCCAAAAATTGTGGAAAAATTTTTCGGAACAGTTTTTGCAAAATTTTGTCCGAA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGAACAGTTTTTGCAAAATTTTGGCCGAA
* *
3344 ATCGTATACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGACACAGTTTTGGG
66 ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGGCACAGTTTTGGG
* **
3409 TGATTTTTGGCTGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTCAGTTACAATGG
131 TGATTTTTGGC-GCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTAAGCCACAATGG
* * **
3474 ATTTATGGATAAGGCTTTACGACCATCTGACTTATAATTCGATTTAATGGGAAATTAATTCGGGA
195 ATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTTGATTTAATTAGAAATTAATTCGGGA
* * *
3539 AAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATATTTTTGGACATGAATTATGT
260 AAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATTATAT
3604 ATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTT
325 ATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTT
*
3669 TG-TCTGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCATTCCTGGGCCCCGGCAC
390 TGTTC-GAAATCGTGTACTAA-CATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCCCCGGCAC
* * * *
3733 AGTTTTGGATGATTTGTGGCAGCAAGACTCCTTAAAATATATAAATACATCTAACCAAATTTCAG
453 AGTTTTGGATGATTTTTGGCTGCAAGACTCCTTAAAATATATAAATTCATCTAACCAAATCTCAG
* * * *
3798 CTACAATGGATTTA-AGGATAAGATTTTACGACCATTTGATTTAAAATTCGATTTTATTAAAAAT
518 CTACAATGGATTTATA-GATAAGATTTTACGACCATCTGAATTATAATTCGATTTAATTAAAAAT
* * * * * * *
3862 TAATT-TAGAAAAA-TAGAAAAAACGAT-ATTAGAA-GTCTAAAATGCCATTAAAAT-TTATAGG
582 TAATTCAAGAAAAATTAGGAAAAACTATAATT-GAAGGTCT--AATGCCCTT-CAATCTTTTTGG
*
3922 -CGTTGAGTTATATATTTTTTA
643 AC-TTGAATTATATA-TTTTTA
** * * * *
3943 TGAGTACTGTGGCTAAAAA-TAAGGAAAAAATTTTTGGGACAGTTTTTGCAAAATTTTGGCC-AA
1 TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGAACAGTTTTTGCAAAATTTTGGCCGAA
* * * **
4006 ATCATGTACTAACCATCACAGTTTTCGGCTAAAAACGCGTTCCTGGGCCCCGGCACAGTTTTGCA
66 ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGGCACAGTTTTGGG
* * * * * * *
4071 TTATTTTTGGCGTC-AGTCTCATTGAAATATCTATATTCATCTAACCAA
131 TGATTTTTGGCG-CAAGACTCCTTAAAATATGTAAATTCATCTGACCAA
4119 TTTTTAGCCA
Statistics
Matches: 1307, Mismatches: 167, Indels: 52
0.86 0.11 0.03
Matches are distributed among these distances:
650 1 0.00
651 47 0.04
652 22 0.02
656 1 0.00
657 50 0.04
658 224 0.17
659 4 0.00
661 33 0.03
662 77 0.06
663 74 0.06
664 84 0.06
665 684 0.52
666 6 0.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (662 bp):
TGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGAACAGTTTTTGCAAAATTTTGGCCGAA
ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCACCGGCACAGTTTTGGG
TGATTTTTGGCGCAAGACTCCTTAAAATATGTAAATTCATCTGACCAAATCTAAGCCACAATGGA
TTTATGGATAAGGCTTTACGACCATCTGAATTATAATTTGATTTAATTAGAAATTAATTCGGGAA
AAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCTTTTTGGACTTGAATTATATA
TTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGGGACAGTTTTTGCAAAATTTT
GTTCGAAATCGTGTACTAACATCACAGTTTTTGGCTAAAAACGCGTTCCTGGGCCCCGGCACAGT
TTTGGATGATTTTTGGCTGCAAGACTCCTTAAAATATATAAATTCATCTAACCAAATCTCAGCTA
CAATGGATTTATAGATAAGATTTTACGACCATCTGAATTATAATTCGATTTAATTAAAAATTAAT
TCAAGAAAAATTAGGAAAAACTATAATTGAAGGTCTAATGCCCTTCAATCTTTTTGGACTTGAAT
TATATATTTTTA
Found at i:5658 original size:331 final size:333
Alignment explanation
Indices: 4142--5871 Score: 2274
Period size: 333 Copynumber: 5.2 Consensus size: 333
4132 TTCAGTCTCA
*
4142 TTGAATTATATATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGACAGTTT
1 TTGAATTATATATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTT
* * * *
4207 TTGCAAAATTTTAGGCCGATATTGTGTACTAA-CATCACAGTTTTTGGCTAAAAAGGCGTTCCTG
66 TTGCAAAATTTT-GTCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTG
* * * **
4271 GGCACCGGCACAATTTTAGGTGATTTTTGGCAGCCAGACTCCTTAAAATATATAAATTCATCTTC
130 GGCACCGGCACAGTTTTGGGTGATTTTTGGCAGCCAAACTCCTTAAAATATATAAATTCATCTAA
* * * * **** * * *
4336 CCAATTCTTAGCCACATTGGATTGATGGTTTTCTTTTTACGAGCATCTGAATCATGTTTCGATTT
195 CCAATTCTCAGCCACAATGGATTTATGGATAAGGTTTTACGACCATCTGAATTATATTTCGATTT
** * * *
4401 AAAAAGTAATTAATTCGGGAAAAATTAGGAAAAATGATAATCGAAGCGTCTAAAGCCCTTCAATC
260 AATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATC
4466 TTTTTGGAC
325 TTTTTGGAC
* * *
4475 TTGAATTATATATTTTTTATGAGTGCTGTGGCCAAAAATTGAGGAAAAAATTTTCGAGACAGTTT
1 TTGAATTATATATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTT
* * * *
4540 TTGCAAAATTTTGTTCGAAATCGTGTACTAACCATCATAGATTTTGCCTAAAAACGCGTTCCTGG
66 TTGCAAAATTTTGTCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGG
* * * *
4605 GCATCGGCACAGTTTTGGGTGATTTTTGGCAG-CAAGACTCCTTAAAATATGTAAATTCTTCTGA
131 GCACCGGCACAGTTTTGGGTGATTTTTGGCAGCCAA-ACTCCTTAAAATATATAAATTCATCTAA
* * *
4669 CCAAATCTAAGCCACAATGGATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTT-GATT
195 CCAATTCTCAGCCACAATGGATTTATGGATAAGGTTTTACGACCATCTGAATTAT-ATTTCGATT
4733 TAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAAT
259 TAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAAT
4798 CTTTTTGGAC
324 CTTTTTGGAC
** * *
4808 ACGAATTATATATTTTTTATGAGTGTTGTGGCAAAAAAATTGAGGAAAAATTTTTCGGGATAGTT
1 TTGAATTATATATTTTTTATGAGTGTTGTGGC-CAAAAATTGAGGAAAAATTTTTCGGGACAGTT
*
4873 TTTACAAAATTTTGTCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTG
65 TTTGCAAAATTTTGTCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTG
* * * * *
4938 AGC-CCAGCACAGTTTTAGATGATTTTTGGCTG-CAAGACTCCTTAAAATATATAAATTCATCTA
130 GGCACCGGCACAGTTTTGGGTGATTTTTGGCAGCCAA-ACTCCTTAAAATATATAAATTCATCTA
* * *
5001 ACCAAATT-TCAGCCACAATGGATTTAAGGATAAGGTTTTACGACCATCTGAATTAAAATTCGAT
194 ACC-AATTCTCAGCCACAATGGATTTATGGATAAGGTTTTACGACCATCTGAATTATATTTCGAT
* ** * **
5065 TTAATTAAAAATTAATT-TAGAAAAA-TAGAAAAAACGAT-ATTAGAA--GTCTAAAATGCGATT
258 TTAATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATT-GAAGCGTCT-AAA-GCCCTT
* *
5125 AAAT-TTTATAGG-C
320 CAATCTTT-TTGGAC
* ** * * *
5138 GTTGAGTTATATATTTTTTATGAGTACTGTGGCTAAAAATTAAGGAAAAATTTTTTGGGACAGTT
1 -TTGAATTATATATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTT
* **
5203 TTTGCAAAATTTTGGCC-AAATTATGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTG
65 TTTGCAAAATTTTGTCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTG
* ** * ** * * * *
5267 GGCCCCGGCACAGTTTTGCATTATTTTTGGC-GCCAATGTCATTGAAATATCTATATTCATCTAA
130 GGCACCGGCACAGTTTTGGGTGATTTTTGGCAGCCAAACTCCTTAAAATATATAAATTCATCTAA
* * * * ** * * * *
5331 CCAATTCTTAGCCACATTGGATTGATGGTTTTGTTTTTACGAGCATCTGAATCATGTTTCGATTT
195 CCAATTCTCAGCCACAATGGATTTATGGATAAGGTTTTACGACCATCTGAATTATATTTCGATTT
*
5396 AATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGTGTCTAAAGCCCTTCAATC
260 AATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATC
*
5461 TTTTAGGAC
325 TTTTTGGAC
* * *
5470 TTGAATTATATATTTCTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAAATTTTCGAGACAGTTT
1 TTGAATTATATATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTT
* *
5535 TTGCAAAATTTTGTTCGAAATCGTGTACTAA-CAGTCACAGTTTTTGGCTAAATACGCGTTCCTG
66 TTGCAAAATTTTGTCCGAAATCGTGTACTAACCA-TCACAGTTTTTGGCTAAAAACGCGTTCCTG
* *
5599 GGCACCGGCACAATTTTGGGTGATTTTTGGCAGCCAAACTCCTT-AAA-ATATAAATTCATCTGA
130 GGCACCGGCACAGTTTTGGGTGATTTTTGGCAGCCAAACTCCTTAAAATATATAAATTCATCTAA
* * * *
5662 CCAAATCTCAGCCACAATCGATTTATGGATAAGGCTTTACGACCATCTGAATTATAATTCGATTT
195 CCAATTCTCAGCCACAATGGATTTATGGATAAGGTTTTACGACCATCTGAATTATATTTCGATTT
5727 AATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAA-CCGCTTCAAT
260 AATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCC-CTTCAAT
5791 CTTTTTGGAC
324 CTTTTTGGAC
*
5801 TTGAATTATATATTTTTTATGAGTGTTGTGGCCAAAAATTGAAGAAAAATTTTTCGGGACAGTTT
1 TTGAATTATATATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTT
5866 TTGCAA
66 TTGCAA
5872 TTTGCTAAAC
Statistics
Matches: 1210, Mismatches: 162, Indels: 52
0.85 0.11 0.04
Matches are distributed among these distances:
328 4 0.00
329 135 0.11
330 87 0.07
331 350 0.29
332 106 0.09
333 432 0.36
334 96 0.08
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (333 bp):
TTGAATTATATATTTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTT
TTGCAAAATTTTGTCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGG
GCACCGGCACAGTTTTGGGTGATTTTTGGCAGCCAAACTCCTTAAAATATATAAATTCATCTAAC
CAATTCTCAGCCACAATGGATTTATGGATAAGGTTTTACGACCATCTGAATTATATTTCGATTTA
ATTAGAAATTAATTCGGGAAAAATTAGGAAAAACGATAATTGAAGCGTCTAAAGCCCTTCAATCT
TTTTGGAC
Found at i:6076 original size:58 final size:57
Alignment explanation
Indices: 6006--6120 Score: 221
Period size: 58 Copynumber: 2.0 Consensus size: 57
5996 ACGACCATCT
6006 GAATTAAAATTCGATTTAATTAAAAATTAATTAAGAAAAATAGAAAAAAACGATATTA
1 GAATTAAAATTCGATTTAATTAAAAATTAATTAAGAAAAATAG-AAAAAACGATATTA
6064 GAATTAAAATTCGATTTAATTAAAAATTAATTAAGAAAAATAGAAAAAACGATATTA
1 GAATTAAAATTCGATTTAATTAAAAATTAATTAAGAAAAATAGAAAAAACGATATTA
6121 AAAGTCTAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 14 0.25
58 43 0.75
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (57 bp):
GAATTAAAATTCGATTTAATTAAAAATTAATTAAGAAAAATAGAAAAAACGATATTA
Found at i:7016 original size:14 final size:14
Alignment explanation
Indices: 6997--7028 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
6987 AAGGTAGAAG
6997 TAGAAGAGTCTCAT
1 TAGAAGAGTCTCAT
7011 TAGAAGAGTCTCAT
1 TAGAAGAGTCTCAT
7025 TAGA
1 TAGA
7029 CTCTTATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (14 bp):
TAGAAGAGTCTCAT
Found at i:7806 original size:62 final size:62
Alignment explanation
Indices: 7722--8176 Score: 838
Period size: 62 Copynumber: 7.3 Consensus size: 62
7712 ACGAAGACAT
7722 GAGAAGACAGAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
1 GAGAAGACAGAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
*
7784 GAGAAGACAGAGGAAGAAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
1 GAGAAGACAGAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
* *
7846 GAGAAGACAGTGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACAAAGGTACAC
1 GAGAAGACAGAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
* *
7908 GAGTAGACAGAGGAAGAAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
1 GAGAAGACAGAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
*
7970 GAGAAGACAGTGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
1 GAGAAGACAGAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
*
8032 GAGTAGACAGAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
1 GAGAAGACAGAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
*
8094 GAGAAGACACAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
1 GAGAAGACAGAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
8156 GAGAAGACAGAGGAAGACAGA
1 GAGAAGACAGAGGAAGACAGA
8177 CACGAAGGTA
Statistics
Matches: 377, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 377 1.00
ACGTcount: A:0.35, C:0.23, G:0.38, T:0.04
Consensus pattern (62 bp):
GAGAAGACAGAGGAAGACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACAC
Found at i:8186 original size:34 final size:34
Alignment explanation
Indices: 8143--8259 Score: 153
Period size: 34 Copynumber: 3.2 Consensus size: 34
8133 GGCCAGCAGG
8143 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
*
8177 CACGAAGGTAAACGAGAAGACAGAGGAAGACAGACACGAAGA
1 CACGAAGGTACACGAGAAGACAGA-G--GA-AG--AC--AGA
8219 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
8253 CACGAAG
1 CACGAAG
8260 ACACCAAGGT
Statistics
Matches: 73, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
34 33 0.45
35 1 0.01
36 2 0.03
37 2 0.03
38 4 0.05
39 2 0.03
40 2 0.03
41 1 0.01
42 26 0.36
ACGTcount: A:0.48, C:0.18, G:0.32, T:0.03
Consensus pattern (34 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
Found at i:8217 original size:22 final size:22
Alignment explanation
Indices: 8192--8262 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
8182 AGGTAAACGA
8192 GAAGACAGAGGAAGACAGACAC
1 GAAGACAGAGGAAGACAGACAC
* *
8214 GAAGACACGAAGGTACAC-G--A-
1 GAAGACA-G-AGGAAGACAGACAC
8234 GAAGACAGAGGAAGACAGACAC
1 GAAGACAGAGGAAGACAGACAC
8256 GAAGACA
1 GAAGACA
8263 CCAAGGTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
18 6 0.15
19 2 0.05
20 7 0.18
21 2 0.05
22 14 0.36
23 2 0.05
24 6 0.15
ACGTcount: A:0.49, C:0.18, G:0.31, T:0.01
Consensus pattern (22 bp):
GAAGACAGAGGAAGACAGACAC
Found at i:8224 original size:42 final size:42
Alignment explanation
Indices: 8174--8294 Score: 224
Period size: 42 Copynumber: 2.9 Consensus size: 42
8164 AGAGGAAGAC
8174 AGACACGAAGGTAAACGAGAAGACAGAGGAAGACAGACACGA
1 AGACACGAAGGTAAACGAGAAGACAGAGGAAGACAGACACGA
*
8216 AGACACGAAGGTACACGAGAAGACAGAGGAAGACAGACACGA
1 AGACACGAAGGTAAACGAGAAGACAGAGGAAGACAGACACGA
*
8258 AGACACCAAGGTAAACGAGAAGACAGAGGAAGACAGA
1 AGACACGAAGGTAAACGAGAAGACAGAGGAAGACAGA
8295 GGCCTCCGCA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.50, C:0.17, G:0.31, T:0.02
Consensus pattern (42 bp):
AGACACGAAGGTAAACGAGAAGACAGAGGAAGACAGACACGA
Found at i:8454 original size:2 final size:2
Alignment explanation
Indices: 8449--8506 Score: 66
Period size: 2 Copynumber: 30.0 Consensus size: 2
8439 AGAAACACAC
* * * *
8449 AG AG AG AG AG GG AG AG AG AG AG AG GG AG AG CG AG -G AG -G GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8489 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
8507 TGTGACAAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.41, C:0.02, G:0.57, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8468 original size:14 final size:14
Alignment explanation
Indices: 8449--8506 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
8439 AGAAACACAC
8449 AGAGAGAGAGGGAG
1 AGAGAGAGAGGGAG
8463 AGAGAGAGAGGGAG
1 AGAGAGAGAGGGAG
*
8477 AGCGAG-GAGGG-G
1 AGAGAGAGAGGGAG
*
8489 AGAGAGAGAGAGAG
1 AGAGAGAGAGGGAG
8503 AGAG
1 AGAG
8507 TGTGACAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
12 6 0.15
13 9 0.23
14 24 0.62
ACGTcount: A:0.41, C:0.02, G:0.57, T:0.00
Consensus pattern (14 bp):
AGAGAGAGAGGGAG
Found at i:21593 original size:51 final size:51
Alignment explanation
Indices: 21517--21613 Score: 185
Period size: 51 Copynumber: 1.9 Consensus size: 51
21507 AAATTGCAAT
*
21517 ACTTCTAGTGGTGATATGAAGTCTAATTATCTATCTATGTATTTATTATAA
1 ACTTCTAGTGGTGATATGAAGTCTAATTATCTATCTATATATTTATTATAA
21568 ACTTCTAGTGGTGATATGAAGTCTAATTATCTATCTATATATTTAT
1 ACTTCTAGTGGTGATATGAAGTCTAATTATCTATCTATATATTTAT
21614 ATTATAACAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (51 bp):
ACTTCTAGTGGTGATATGAAGTCTAATTATCTATCTATATATTTATTATAA
Found at i:26276 original size:2 final size:2
Alignment explanation
Indices: 26262--26301 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
26252 TTGCTACTAG
26262 TA TA TA GTA -A TA TA TA TA -A TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26302 ATCTATACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.09
2 29 0.85
3 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:26289 original size:22 final size:22
Alignment explanation
Indices: 26262--26303 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
26252 TTGCTACTAG
26262 TATATAGTA-ATATATATAATAA
1 TATATA-TATATATATATAATAA
26284 TATATATATATATATATAAT
1 TATATATATATATATATAAT
26304 CTATACTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATATATATATATATATAATAA
Found at i:28725 original size:21 final size:21
Alignment explanation
Indices: 28699--28740 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28689 ATCTTTCTGT
*
28699 AATCCTTATGCCCTGTAGACC
1 AATCCTTATCCCCTGTAGACC
28720 AATCCTTATCCCCTGTAGACC
1 AATCCTTATCCCCTGTAGACC
28741 TCTTAGGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.36, G:0.12, T:0.29
Consensus pattern (21 bp):
AATCCTTATCCCCTGTAGACC
Found at i:31704 original size:3 final size:3
Alignment explanation
Indices: 31696--31723 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31686 ATAGTTTTGA
31696 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
31724 TTAAAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:43951 original size:6 final size:6
Alignment explanation
Indices: 43940--43975 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
43930 ACAGTGTGGC
* *
43940 CTGCCT CTGCCT CTGCCT CTGCCA CTGCCA CTGCCT
1 CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT
43976 GGTGGCCTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.06, C:0.50, G:0.17, T:0.28
Consensus pattern (6 bp):
CTGCCT
Found at i:59051 original size:7 final size:7
Alignment explanation
Indices: 59030--59059 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
59020 TTTCAGGTTG
59030 TATCATA
1 TATCATA
59037 TCATCATA
1 T-ATCATA
59045 TATCATA
1 TATCATA
59052 TATCATA
1 TATCATA
59059 T
1 T
59060 CATATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (7 bp):
TATCATA
Done.