Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009519.1 Corchorus capsularis cultivar CVL-1 contig09540, 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: 95856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:615 original size:334 final size:334
Alignment explanation
Indices: 1--762 Score: 1276
Period size: 334 Copynumber: 2.3 Consensus size: 334
1 AGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGC
1 AGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGC
66 AAAAGACTAATAAAAAATATATAATTCAACGCAAAAAGATTGAATGTTTTTTCACGTTTCTAATA
66 AAAAGACTAATAAAAAATATATAATTCAACGCAAAAAGATTGAATGTTTTTTCACGTTTCTAATA
*
131 TAGTTTTTCCTATTTCTTTATAATTAATTTATAATTAAATCGAAACAATATTCAGATGCCCGTAA
131 TAGTTATTCCTATTTCTTTATAATTAATTTATAATTAAATCGAAACAATATTCAGATGCCCGTAA
* * * * * *
196 AAACGAATCCTTAAATCCAAAATAGGCTGGGATTTGGTTAGATGATTAATAGATACTTCAAGGAG
196 AAACGAATCCCTAAATCCAAAATAGACTGAGATTTGGTTAGATAAATAATAGATAATTCAAGGAG
* *
261 TCTCGGCGCCAAAAATCACGCAAAATTGAGTCGGGGCCTC-GGAGTGGGTATTTAGCCAAAACCC
261 TCTCGGCGCCAAAAATCACGCAAAATTGAGTCGGGGCCCCAGGAGCGGGTATTTAGCCAAAACCC
325 ATGATGGTT
326 ATGATGGTT
* * *
334 AGTACCCGATTTCTGCTAAAATTCCGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGC
1 AGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGC
399 AAAAGACTAAT-AAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAA
66 AAAAGACTAATAAAAAATATATAATTCAACG-CAAAAAGATTGAA-TGTTTTTTCACGTTTCTAA
* * * *
463 TATTGTTATTCCTATTTCTTTATAATTAATTTCTAATTCAATCGAAACAATTTTCAGATGCCCGT
129 TATAGTTATTCCTATTTCTTTATAATTAATTTATAATTAAATCGAAACAATATTCAGATGCCCGT
* *
528 AAAAATGAATCCCTAAATCCAAAATAGACTGAGATTTGGTTAGATAAATAATAGATAATTCGAGG
194 AAAAACGAATCCCTAAATCCAAAATAGACTGAGATTTGGTTAGATAAATAATAGATAATTCAAGG
** * * *
593 AGTCTTTGCGCCAAACATCACGCAAAATTGAGTCGGGTCCCCAGGAGCGGGTATTTAGCCAAAAT
259 AGTCTCGGCGCCAAAAATCACGCAAAATTGAGTCGGGGCCCCAGGAGCGGGTATTTAGCCAAAAC
*
658 CCGTGATGGTT
324 CCATGATGGTT
669 AGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGC
1 AGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGC
734 AAAAGACTAATAAAAAATATATAATTCAA
66 AAAAGACTAATAAAAAATATATAATTCAA
763 TCTTTATAAT
Statistics
Matches: 398, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
332 19 0.05
333 86 0.22
334 173 0.43
335 103 0.26
336 17 0.04
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (334 bp):
AGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGC
AAAAGACTAATAAAAAATATATAATTCAACGCAAAAAGATTGAATGTTTTTTCACGTTTCTAATA
TAGTTATTCCTATTTCTTTATAATTAATTTATAATTAAATCGAAACAATATTCAGATGCCCGTAA
AAACGAATCCCTAAATCCAAAATAGACTGAGATTTGGTTAGATAAATAATAGATAATTCAAGGAG
TCTCGGCGCCAAAAATCACGCAAAATTGAGTCGGGGCCCCAGGAGCGGGTATTTAGCCAAAACCC
ATGATGGTT
Found at i:2271 original size:334 final size:333
Alignment explanation
Indices: 763--3809 Score: 4345
Period size: 334 Copynumber: 9.1 Consensus size: 333
753 TATAATTCAA
* *
763 TCTTTATAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCCCGTAAAAACGAATCCCTGA
1 TCTTT-TAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCGTAAAAACGAAT-CCTAA
* * * *
828 ATCCAAAATAGACTGAGATTT-GATAGATAAATAATAGATACTTCGAGGAGTCTTGACGCCAAAA
64 ATCCAAAATAGGCTGAGATTTGGTTAGATAAATAATAGATACTTCAAGGAGTCTTGGCGCCAAAA
* * *
892 ATCACGCAAAATTGATTCGGGGCCCCAGAGC-GGTATTTAGCCAAAAACCGTGATTGTTAGTACA
129 ATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACA
* **
956 CGATTTCGGCTAAAACTT-TCCAAAAATTGACCCGAAATAAATTTTTTTCAATTTTTA-GCAAAA
194 CGATTTCGGCTAAAA-TTCTGCAAAAATTGACTTGAAAT-AATTTTTTTCAATTTTTAGGC-AAA
* *
1019 AGACAAATAAAATATATATAATTCAACGCCAAAAAGATTGAAG-GTTTTTTCACGTTTCTAATAT
256 AGACTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAATAT
* *
1083 CGTTTTTCCTATT
321 TGTTATTCCTATT
* * * * * *
1096 T-TTTTAATCAATTTCTAATTAAATAGAAACAAGATTCAGATGTCTGTAAAAACGAATCCTTATT
1 TCTTTTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCGTAAAAACGAATCCTAAAT
* * * * *
1160 CCAAAATAGGCAGGGATTTGGTTAGATGAATAATAGATACTTCAAGGAGTCTCGGCGCCAAAAAC
66 CCAAAATAGGCTGAGATTTGGTTAGATAAATAATAGATACTTCAAGGAGTCTTGGCGCCAAAAAT
* * * * *
1225 CACACAAAATTGAGTCGAGGCCCCGGAGCGGGTATTTAGCCAAAACCCATGATTGTTAGTACACG
131 CACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACACG
* *
1290 ATTTCTAG-TAAAATTCTACAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGCAAAAGAC
196 ATTTC-GGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGCAAAAGAC
*
1354 TAATAAAAAATATATAATTCAACGCCAAAAAGATTGAA-TG-TTTTTCACGTTTCTAATATCGTT
260 TAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAATATTGTT
1417 ATTCCTATT
325 ATTCCTATT
* *
1426 TCTTTATAATTAATTTCTAGATTAAAATCGAAACAATATTCAGATGCCCGTAAAAATGAATCCCT
1 TCTTT-TAATTAATTTCTA-ATT-AAATCGAAACAAGATTCAGATGCCCGTAAAAACGAAT-CCT
* * ** *
1491 AAATCCAAAATAGACTGAGATTTGGTTAGATAAATAATAGATAATTTGAGGAGTCTTGGCGTCAA
62 AAATCCAAAATAGGCTGAGATTTGGTTAGATAAATAATAGATACTTCAAGGAGTCTTGGCGCCAA
* *
1556 AAATCACGCAAAATTGAGTCGGGTCCCCGGAGCGGGTATTTAGCCAAAAATCGTGATGGTTAGTA
127 AAATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTA
1621 CACGATTTCGGCTAAAATTCTAGCAAAAATTGACTTAGAAATAA-TTTTTTCAATTTTTAGGC-A
192 CACGATTTCGGCTAAAATTCT-GCAAAAATTGACTT-GAAATAATTTTTTTCAATTTTTAGGCAA
*
1684 AAGACTAATAAAAATTATATAATTTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAAT
255 AAGACTAATAAAAAATATATAA-TTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAAT
1749 ATTGTTATTCCT-TT
319 ATTGTTATTCCTATT
* * * * * * * *
1763 TTTTTTAATCAATTTTTAATTAAATGGAAATAAGATTCAGATGCCTGTAAAAACGAATCCTTATT
1 TCTTTTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCGTAAAAACGAATCCTAAAT
* *
1828 CCAAAATAGGCTGAGATTTGGTTAGATGAATAATAGATTCTTCAAGGAGTCTTGGCGCCAAAAAT
66 CCAAAATAGGCTGAGATTTGGTTAGATAAATAATAGATACTTCAAGGAGTCTTGGCGCCAAAAAT
1893 CACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACACG
131 CACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACACG
1958 ATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGCAAAAGACT
196 ATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGCAAAAGACT
*
2023 AAT-AAAAATATATAATTTAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAATATTGTTA
261 AATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAATATTGTTA
*
2087 TTCCTTTT
326 TTCCTATT
* *
2095 TCTTTATAATTAATTTCTAATTAAATCTAAACAATATTCAGATGCCCGTAAAAACGAATCACTAA
1 TCTTT-TAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCGTAAAAACGAATC-CTAA
* * * * *
2160 ATCCAAAATAGACCGAGATTTGCTGAGATAAATAATAGATACTTCGAGGAGTCTTGGCGCCAAAA
64 ATCCAAAATAGGCTGAGATTTGGTTAGATAAATAATAGATACTTCAAGGAGTCTTGGCGCCAAAA
* *
2225 ATCACGCAAAATTGATTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGACGGTTAGTACA
129 ATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACA
*** * ***
2290 CGATTTCGGCTAAAATTCTGCAAAAATTGACCCCAAATAAATTTTTTTCAATTCTTATTAAAAAG
194 CGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAAT-AATTTTTTTCAATTTTTAGGCAAAAG
* * * * *
2355 ACAAATAAAAAATATATAATGCAATGCCAAAAAGTTTGAAG-GTTTTTTTCACGTTTCTAATATC
258 ACTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTG-TTTTTTCACGTTTCTAATATT
* * *
2419 CTTTTTCATATT
322 GTTATTCCTATT
* * * *
2431 TTTTTTAATCAATTTCTAATTAAATGGAAACAAGATTCAGATGCCTGTAAAAACGAATCCTTAAA
1 TCTTTTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCGTAAAAACGAATCC-TAAA
* * * * *
2496 TCCAAAATAGGCTGGGATTTGGTTAGATGAATAATAGATACTTCAAGGAGTCTCGGTGCCAAAAT
65 TCCAAAATAGGCTGAGATTTGGTTAGATAAATAATAGATACTTCAAGGAGTCTTGGCGCCAAAAA
*
2561 TCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAA-CATGATGGTTAGTACAC
130 TCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACAC
2625 GATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAAATAATTTTTTTCAA-TTTTAGGCAAAAGA
195 GATTTCGGCTAAAATTCTGCAAAAATTGACTTG-AAATAATTTTTTTCAATTTTTAGGCAAAAGA
* *
2689 CTAATAAAAAATATATAATTCAACGCCAAAGAGATTGAACTGTTTTTTCACGTTTCTAATATTGT
259 CTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAATATTGT
2754 TATTCCTATT
324 TATTCCTATT
* *
2764 TCTTTATAATTAATTTCTAATTAAATCGAAACAATATTCAGATGTCCGTAAAAACGAATCCCTAA
1 TCTTT-TAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCGTAAAAACGAAT-CCTAA
* * *
2829 ATCCAAACTAGACTGAGATTTGGTTAGATAAATAATAGATACTTCGAGGAGTCTTGGCGCCAAAA
64 ATCCAAAATAGGCTGAGATTTGGTTAGATAAATAATAGATACTTCAAGGAGTCTTGGCGCCAAAA
* * *
2894 ATCACGCAAAATTGATTCGGGGCCTCGGAGC-GGTATTTAGCCAAAAACCGTGATTGTTAGTACA
129 ATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACA
* * ** **
2958 TGATTTCGGCTAAAATTCTGCAAATATTGACCCGAAATAATTATTTTTCAATTTTTAGTAAAAAG
194 CGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATT-TTTTTCAATTTTTAGGCAAAAG
* * *
3023 ACAAATAAAATATATATAATTCAACGCCAAAAAGATTGAAG-GTTTTTTCACGTTTCTAATATCG
258 ACTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAATATTG
*
3087 TTTTTCCTATT
323 TTATTCCTATT
* * * * * *
3098 ACTTTTAATCAATTTCTAATTAAATGGAAACAAGATTCAGATGCCTGTAAAAACTAATCCTTAAT
1 TCTTTTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCGTAAAAACGAATCC-TAAA
* * *
3163 TCCAAAATAGGCTGGGATTTTGTTAGATGAATAATAGATACTTCAAGGAGTCTTGGCGCCAAAAA
65 TCCAAAATAGGCTGAGATTTGGTTAGATAAATAATAGATACTTCAAGGAGTCTTGGCGCCAAAAA
* * * * * *
3228 TCACGCAAAATTAAGTCGGAGCCCCAGAGCGGATATTTTGCCAAAAACCGTGATGGTTAATACAC
130 TCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACAC
*
3293 GATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAAGTTTTTTCAATTTTTAGGCAAAAGAC
195 GATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGCAAAAGAC
* * * *
3358 TTATAAAAAATATATAATTTAACGCCAAAAAGATTTAAGTGTTTTTTCACGTTTCTAATATTTTT
260 TAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAATATTGTT
3423 ATTCCTATT
325 ATTCCTATT
* * *
3432 TCTTTTTAATTAATTTCTAATTAAATCGAAACAATATTCAGATGTCCGTAAAAACGAATCCTTGA
1 TC-TTTTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCGTAAAAACGAATCC-TAA
* * *
3497 ATCCAAAATAGGCTGAGATTTGATTAGATAAATAATAGATACTTCAAGGAGTCTTGCCGTCAAAA
64 ATCCAAAATAGGCTGAGATTTGGTTAGATAAATAATAGATACTTCAAGGAGTCTTGGCGCCAAAA
* * * *
3562 ATCACGCAAAATTGATTC-GGGACCCAGAGCGGGTATTTAGCCAAAAACCGTGATAGTTAGTACA
129 ATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACA
* *** **
3626 CGATTTCGGCTAAAATTATGCAAAAATTGACCCAAAATAAATTTTTTTTCAATTTTTAGTAAAAA
194 CGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAAT-AA-TTTTTTTCAATTTTTAGGCAAAA
*
3691 GACAAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAG-GTTTTTTCACGTTTCTAATATT
257 GACTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAATATT
*
3755 GTTTTTCCT-TT
322 GTTATTCCTATT
* *
3766 TTTTTTAATTAATTTCTAATTAAATGGAAACAAGATTCAGATGC
1 TCTTTTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
3810 AAGTAAGCAT
Statistics
Matches: 2416, Mismatches: 259, Indels: 78
0.88 0.09 0.03
Matches are distributed among these distances:
330 53 0.02
331 239 0.10
332 128 0.05
333 535 0.22
334 682 0.28
335 553 0.23
336 183 0.08
337 15 0.01
338 28 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (333 bp):
TCTTTTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCGTAAAAACGAATCCTAAAT
CCAAAATAGGCTGAGATTTGGTTAGATAAATAATAGATACTTCAAGGAGTCTTGGCGCCAAAAAT
CACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACACG
ATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAGGCAAAAGACT
AATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAATATTGTTA
TTCCTATT
Found at i:2364 original size:668 final size:668
Alignment explanation
Indices: 763--3809 Score: 4908
Period size: 668 Copynumber: 4.6 Consensus size: 668
753 TATAATTCAA
*
763 TCTTTATAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCCCGTAAAAACGAATCCCTGA
1 TCTTTATAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCCCGTAAAAACGAATCCCTAA
*
828 ATCCAAAATAGACTGAGATTTGA-TAGATAAATAATAGATACTTCGAGGAGTCTTGACGCCAAAA
66 ATCCAAAATAGACTGAGATTTGATTAGATAAATAATAGATACTTCGAGGAGTCTTGGCGCCAAAA
* *
892 ATCACGCAAAATTGATTCGGGGCCCCAGAGC-GGTATTTAGCCAAAAACCGTGATTGTTAGTACA
131 ATCACGCAAAATTGATTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACA
* *
956 CGATTTCGGCTAAAACTT-TCCAAAAATTGACCCGAAATAAATTTTTTTCAATTTTTAGCAAAAA
196 CGATTTCGGCTAAAA-TTCTGCAAAAATTGACCCGAAATAAATTTTTTTCAATTTTTAGTAAAAA
1020 GACAAAT-AAAATATATATAATTCAACGCCAAAAAGATTGAAGGTTTTTTCACGTTTCTAATATC
260 GACAAATAAAAAT-TATATAATTCAACGCCAAAAAGATTGAAGGTTTTTTCACGTTTCTAATATC
* * *
1084 GTTTTTCCTATTTTTTTAATCAATTTCTAATTAAATAGAAACAAGATTCAGATGTCTGTAAAAAC
324 GTTTTTCCTTTTTTTTTAATCAATTTCTAATTAAATGGAAACAAGATTCAGATGCCTGTAAAAAC
*
1149 GAATCCTT-ATTCCAAAATAGGCAGGGATTTGGTTAGATGAATAATAGATACTTCAAGGAGTCTC
389 GAATCCTTAATTCCAAAATAGGCTGGGATTTGGTTAGATGAATAATAGATACTTCAAGGAGTCTC
* * * *
1213 GGCGCCAAAAACCACACAAAATTGAGTCGAGGCCCCGGAGCGGGTATTTAGCCAAAACCCATGAT
454 GGCGCCAAAAATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCATGAT
* * *
1278 TGTTAGTACACGATTTCTAG-TAAAATTCTACAAAAATTGACTTGAAATAATTTTTTTCAATTTT
519 GGTTAGTACACGATTTC-GGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTT
1342 TAGGCAAAAGACTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAA-TG-TTTTTCACGTT
583 TAGGCAAAAGACTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTT
*
1405 TCTAATATCGTTATTCCTATT
648 TCTAATATTGTTATTCCTATT
*
1426 TCTTTATAATTAATTTCTAGATTAAAATCGAAACAATATTCAGATGCCCGTAAAAATGAATCCCT
1 TCTTTATAATTAATTTCTA-ATT-AAATCGAAACAATATTCAGATGCCCGTAAAAACGAATCCCT
* * * *
1491 AAATCCAAAATAGACTGAGATTTGGTTAGATAAATAATAGATAATTTGAGGAGTCTTGGCGTCAA
64 AAATCCAAAATAGACTGAGATTTGATTAGATAAATAATAGATACTTCGAGGAGTCTTGGCGCCAA
* * *
1556 AAATCACGCAAAATTGAGTCGGGTCCCCGGAGCGGGTATTTAGCCAAAAATCGTGATGGTTAGTA
129 AAATCACGCAAAATTGATTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTA
** **
1621 CACGATTTCGGCTAAAATTCTAGCAAAAATTGACTTAGAAAT-AA-TTTTTTCAATTTTTAG-GC
194 CACGATTTCGGCTAAAATTCT-GCAAAAATTGAC-CCGAAATAAATTTTTTTCAATTTTTAGTAA
*
1683 AAAGACTAATAAAAATTATATAATTTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCTAA
257 AAAGACAAATAAAAATTATATAA-TTCAACGCCAAAAAGATTGAAG-GTTTTTTCACGTTTCTAA
* * * *
1748 TATTGTTATTCCTTTTTTTTTAATCAATTTTTAATTAAATGGAAATAAGATTCAGATGCCTGTAA
320 TATCGTTTTTCCTTTTTTTTTAATCAATTTCTAATTAAATGGAAACAAGATTCAGATGCCTGTAA
* *
1813 AAACGAATCCTT-ATTCCAAAATAGGCTGAGATTTGGTTAGATGAATAATAGATTCTTCAAGGAG
385 AAACGAATCCTTAATTCCAAAATAGGCTGGGATTTGGTTAGATGAATAATAGATACTTCAAGGAG
* *
1877 TCTTGGCGCCAAAAATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCG
450 TCTCGGCGCCAAAAATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCA
1942 TGATGGTTAGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAAT
515 TGATGGTTAGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAAT
*
2007 TTTTAGGCAAAAGACTAAT-AAAAATATATAATTTAACGCCAAAAAGATTGAAGTGTTTTTTCAC
580 TTTTAGGCAAAAGACTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCAC
*
2071 GTTTCTAATATTGTTATTCCTTTT
645 GTTTCTAATATTGTTATTCCTATT
* *
2095 TCTTTATAATTAATTTCTAATTAAATCTAAACAATATTCAGATGCCCGTAAAAACGAATCACTAA
1 TCTTTATAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCCCGTAAAAACGAATCCCTAA
* * *
2160 ATCCAAAATAGACCGAGATTTGCTGAGATAAATAATAGATACTTCGAGGAGTCTTGGCGCCAAAA
66 ATCCAAAATAGACTGAGATTTGATTAGATAAATAATAGATACTTCGAGGAGTCTTGGCGCCAAAA
*
2225 ATCACGCAAAATTGATTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGACGGTTAGTACA
131 ATCACGCAAAATTGATTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACA
* * *
2290 CGATTTCGGCTAAAATTCTGCAAAAATTGACCCCAAATAAATTTTTTTCAATTCTTATTAAAAAG
196 CGATTTCGGCTAAAATTCTGCAAAAATTGACCCGAAATAAATTTTTTTCAATTTTTAGTAAAAAG
* * * * *
2355 ACAAATAAAAAATATATAATGCAATGCCAAAAAGTTTGAAGGTTTTTTTCACGTTTCTAATATCC
261 ACAAATAAAAATTATATAATTCAACGCCAAAAAGATTGAAGG-TTTTTTCACGTTTCTAATATCG
*
2420 TTTTTCATATTTTTTTTAATCAATTTCTAATTAAATGGAAACAAGATTCAGATGCCTGTAAAAAC
325 TTTTTCCT-TTTTTTTTAATCAATTTCTAATTAAATGGAAACAAGATTCAGATGCCTGTAAAAAC
*
2485 GAATCCTTAAATCCAAAATAGGCTGGGATTTGGTTAGATGAATAATAGATACTTCAAGGAGTCTC
389 GAATCCTTAATTCCAAAATAGGCTGGGATTTGGTTAGATGAATAATAGATACTTCAAGGAGTCTC
* *
2550 GGTGCCAAAATTCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAA-CATGAT
454 GGCGCCAAAAATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCATGAT
2614 GGTTAGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAAATAATTTTTTTCAA-TTT
519 GGTTAGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTG-AAATAATTTTTTTCAATTTT
* *
2678 TAGGCAAAAGACTAATAAAAAATATATAATTCAACGCCAAAGAGATTGAACTGTTTTTTCACGTT
583 TAGGCAAAAGACTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTT
2743 TCTAATATTGTTATTCCTATT
648 TCTAATATTGTTATTCCTATT
*
2764 TCTTTATAATTAATTTCTAATTAAATCGAAACAATATTCAGATGTCCGTAAAAACGAATCCCTAA
1 TCTTTATAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCCCGTAAAAACGAATCCCTAA
* *
2829 ATCCAAACTAGACTGAGATTTGGTTAGATAAATAATAGATACTTCGAGGAGTCTTGGCGCCAAAA
66 ATCCAAAATAGACTGAGATTTGATTAGATAAATAATAGATACTTCGAGGAGTCTTGGCGCCAAAA
* *
2894 ATCACGCAAAATTGATTCGGGGCCTCGGAGC-GGTATTTAGCCAAAAACCGTGATTGTTAGTACA
131 ATCACGCAAAATTGATTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACA
* *
2958 TGATTTCGGCTAAAATTCTGCAAATATTGACCCGAAAT-AATTATTTTTCAATTTTTAGTAAAAA
196 CGATTTCGGCTAAAATTCTGCAAAAATTGACCCGAAATAAATT-TTTTTCAATTTTTAGTAAAAA
3022 GACAAAT-AAAATATATATAATTCAACGCCAAAAAGATTGAAGGTTTTTTCACGTTTCTAATATC
260 GACAAATAAAAAT-TATATAATTCAACGCCAAAAAGATTGAAGGTTTTTTCACGTTTCTAATATC
**
3086 GTTTTTCCTATTACTTTTAATCAATTTCTAATTAAATGGAAACAAGATTCAGATGCCTGTAAAAA
324 GTTTTTCCT-TTTTTTTTAATCAATTTCTAATTAAATGGAAACAAGATTCAGATGCCTGTAAAAA
* *
3151 CTAATCCTTAATTCCAAAATAGGCTGGGATTTTGTTAGATGAATAATAGATACTTCAAGGAGTCT
388 CGAATCCTTAATTCCAAAATAGGCTGGGATTTGGTTAGATGAATAATAGATACTTCAAGGAGTCT
* * * * * * *
3216 TGGCGCCAAAAATCACGCAAAATTAAGTCGGAGCCCCAGAGCGGATATTTTGCCAAAAACCGTGA
453 CGGCGCCAAAAATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCATGA
* *
3281 TGGTTAATACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAAGTTTTTTCAATTTT
518 TGGTTAGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTT
* * *
3346 TAGGCAAAAGACTTATAAAAAATATATAATTTAACGCCAAAAAGATTTAAGTGTTTTTTCACGTT
583 TAGGCAAAAGACTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTT
*
3411 TCTAATATTTTTATTCCTATT
648 TCTAATATTGTTATTCCTATT
* * * *
3432 TCTTTTTAATTAATTTCTAATTAAATCGAAACAATATTCAGATGTCCGTAAAAACGAATCCTTGA
1 TCTTTATAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCCCGTAAAAACGAATCCCTAA
* * * *
3497 ATCCAAAATAGGCTGAGATTTGATTAGATAAATAATAGATACTTCAAGGAGTCTTGCCGTCAAAA
66 ATCCAAAATAGACTGAGATTTGATTAGATAAATAATAGATACTTCGAGGAGTCTTGGCGCCAAAA
* * *
3562 ATCACGCAAAATTGATTC-GGGACCCAGAGCGGGTATTTAGCCAAAAACCGTGATAGTTAGTACA
131 ATCACGCAAAATTGATTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACA
* *
3626 CGATTTCGGCTAAAATTATGCAAAAATTGACCCAAAATAAATTTTTTTTCAATTTTTAGTAAAAA
196 CGATTTCGGCTAAAATTCTGCAAAAATTGACCCGAAATAAA-TTTTTTTCAATTTTTAGTAAAAA
* *
3691 GACAAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGTTTTTTCACGTTTCTAATATTG
260 GACAAATAAAAATTATATAATTCAACGCCAAAAAGATTGAAGGTTTTTTCACGTTTCTAATATCG
*
3756 TTTTTCCTTTTTTTTTAATTAATTTCTAATTAAATGGAAACAAGATTCAGATGC
325 TTTTTCCTTTTTTTTTAATCAATTTCTAATTAAATGGAAACAAGATTCAGATGC
3810 AAGTAAGCAT
Statistics
Matches: 2208, Mismatches: 147, Indels: 53
0.92 0.06 0.02
Matches are distributed among these distances:
663 19 0.01
664 3 0.00
665 67 0.03
666 98 0.04
667 588 0.27
668 942 0.43
669 485 0.22
670 6 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (668 bp):
TCTTTATAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCCCGTAAAAACGAATCCCTAA
ATCCAAAATAGACTGAGATTTGATTAGATAAATAATAGATACTTCGAGGAGTCTTGGCGCCAAAA
ATCACGCAAAATTGATTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCGTGATGGTTAGTACA
CGATTTCGGCTAAAATTCTGCAAAAATTGACCCGAAATAAATTTTTTTCAATTTTTAGTAAAAAG
ACAAATAAAAATTATATAATTCAACGCCAAAAAGATTGAAGGTTTTTTCACGTTTCTAATATCGT
TTTTCCTTTTTTTTTAATCAATTTCTAATTAAATGGAAACAAGATTCAGATGCCTGTAAAAACGA
ATCCTTAATTCCAAAATAGGCTGGGATTTGGTTAGATGAATAATAGATACTTCAAGGAGTCTCGG
CGCCAAAAATCACGCAAAATTGAGTCGGGGCCCCGGAGCGGGTATTTAGCCAAAAACCATGATGG
TTAGTACACGATTTCGGCTAAAATTCTGCAAAAATTGACTTGAAATAATTTTTTTCAATTTTTAG
GCAAAAGACTAATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGTGTTTTTTCACGTTTCT
AATATTGTTATTCCTATT
Found at i:26718 original size:27 final size:27
Alignment explanation
Indices: 26681--26741 Score: 113
Period size: 27 Copynumber: 2.2 Consensus size: 27
26671 TATATATTAC
26681 TCCCTCTGTTCCTTTTTAATTGTCCCTT
1 TCCCT-TGTTCCTTTTTAATTGTCCCTT
26709 TCCCTTGTTCCTTTTTAATTGTCCCTT
1 TCCCTTGTTCCTTTTTAATTGTCCCTT
26736 TCCCTT
1 TCCCTT
26742 ATTTTCCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.07, C:0.33, G:0.07, T:0.54
Consensus pattern (27 bp):
TCCCTTGTTCCTTTTTAATTGTCCCTT
Found at i:39363 original size:213 final size:213
Alignment explanation
Indices: 38989--39839 Score: 1414
Period size: 213 Copynumber: 4.0 Consensus size: 213
38979 AACTTAAAAC
* *
38989 TACTAGAGTTCGTCGGTCTTCAATTACGGAAGAAAGTGAAGCAGTACCCGATGCAGTTATGAGGT
1 TACTAGAGTTCGTCGGTCTTCAAATAAGGAAGAAAGTGAAGCAGTACCCGATGCAGTTATGAGGT
*
39054 CTTCCCCCGGTAGCACTACCCCTAGTGCCTCCAAACAGCCTGATCAACTGCAGTCTACTCCTGAA
66 CTTCCCCCAGTAGCACTACCCCTAGTGCCTCCAAACAGCCTGATCAACTGCAGTCTACTCCTGAA
* *
39119 AGAAGTGTTGGCATTGATGATTTTAAGAGCAAAGAACGGATAGCAGCACCAAATAACATGCTCTC
131 AGAAGTCTTGGCATTGATAATTTTAAGAGCAAAGAACGGATAGCAGCACCAAATAACATGCTCTC
39184 TTCACGGGACAAGCTGAG
196 TTCACGGGACAAGCTGAG
* *
39202 TACTAGGGTTCGTCGGTCTTCAATTAAGGAAGAAAGTGAAGCAGTACCCGATGCAGTTATGAGGT
1 TACTAGAGTTCGTCGGTCTTCAAATAAGGAAGAAAGTGAAGCAGTACCCGATGCAGTTATGAGGT
*
39267 CTTCCCCCGGTAGCACTACCCCTAGTGCCTCCAAACAGCCTGATCAACTGCAGTCTACTCCTGAA
66 CTTCCCCCAGTAGCACTACCCCTAGTGCCTCCAAACAGCCTGATCAACTGCAGTCTACTCCTGAA
* *
39332 AGAAGTGTTGGCATTGATGATTTTAAGAGCAAAGAACGGATAGCAGCACCAAATAACATGCTCTC
131 AGAAGTCTTGGCATTGATAATTTTAAGAGCAAAGAACGGATAGCAGCACCAAATAACATGCTCTC
*
39397 TTCATGGGACAAGCTGAG
196 TTCACGGGACAAGCTGAG
* * * * *
39415 TACTAGGGTTTGTCGGTCTTCAAATAAGCAAGAAAGTGAAGCAGTACCCGATACAGTGATGAGGT
1 TACTAGAGTTCGTCGGTCTTCAAATAAGGAAGAAAGTGAAGCAGTACCCGATGCAGTTATGAGGT
* * * * *
39480 CTTCCCCCAATAACTCTATCCCTAGTGCCTCCAAACAGCCTGGTCAACTGCAGTCTACTCCTGAA
66 CTTCCCCCAGTAGCACTACCCCTAGTGCCTCCAAACAGCCTGATCAACTGCAGTCTACTCCTGAA
* *
39545 AGAAGTCTTAGCATTGATAATTTTAAGAGCAAAGAACGGATAGCAGCACCAAATAACATGCTTTC
131 AGAAGTCTTGGCATTGATAATTTTAAGAGCAAAGAACGGATAGCAGCACCAAATAACATGCTCTC
*
39610 TTCACGGGACAAGCTGAC
196 TTCACGGGACAAGCTGAG
* * *
39628 TACTAGAGTTCGTCGGTCTTCAAATAAGAAAGAAAGTGAAGCAGTAACCGATGCAGTAATGAGGT
1 TACTAGAGTTCGTCGGTCTTCAAATAAGGAAGAAAGTGAAGCAGTACCCGATGCAGTTATGAGGT
* * *
39693 GTTCCCCCAGTAGCTCTATCCCTAGTGCCTCCAAACAGCCTGATCAACTGCAGTCTACTCCTGAA
66 CTTCCCCCAGTAGCACTACCCCTAGTGCCTCCAAACAGCCTGATCAACTGCAGTCTACTCCTGAA
*
39758 AGAAGTCTTGGCATTGATAATTTTAAGAGCAAAGAACGGATAGCAGCACCAAATAACATGCTTTC
131 AGAAGTCTTGGCATTGATAATTTTAAGAGCAAAGAACGGATAGCAGCACCAAATAACATGCTCTC
*
39823 TTCACGTGACAAGCTGA
196 TTCACGGGACAAGCTGA
39840 CTGCGAATGG
Statistics
Matches: 606, Mismatches: 32, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
213 606 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (213 bp):
TACTAGAGTTCGTCGGTCTTCAAATAAGGAAGAAAGTGAAGCAGTACCCGATGCAGTTATGAGGT
CTTCCCCCAGTAGCACTACCCCTAGTGCCTCCAAACAGCCTGATCAACTGCAGTCTACTCCTGAA
AGAAGTCTTGGCATTGATAATTTTAAGAGCAAAGAACGGATAGCAGCACCAAATAACATGCTCTC
TTCACGGGACAAGCTGAG
Found at i:50372 original size:9 final size:10
Alignment explanation
Indices: 50349--50374 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
50339 TAAAGATTAA
50349 AAAAAATAAT
1 AAAAAATAAT
50359 AAAAAATAAT
1 AAAAAATAAT
50369 AAAAAA
1 AAAAAA
50375 AAACCTCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:58492 original size:31 final size:31
Alignment explanation
Indices: 58368--58510 Score: 128
Period size: 31 Copynumber: 4.5 Consensus size: 31
58358 GACAAAAATG
* * * **
58368 ACACGTGGCATGCCACATGCCATTTTTTGAA
1 ACACGTGGCGTGCCACATGTCACTTTTTGGT
* * * *
58399 ACATGTGGCATGCCACGTGTCACGTTTTGGT
1 ACACGTGGCGTGCCACATGTCACTTTTTGGT
*
58430 ACACGTGTCGTG--ACATGTGACACGACTTTTTGGT
1 ACACGTGGCGTGCCACATGT----C-ACTTTTTGGT
*
58464 ACATGTGGCGTGCCACATGTCACTTTTTGGT
1 ACACGTGGCGTGCCACATGTCACTTTTTGGT
58495 ACACGTGGCGTGCCAC
1 ACACGTGGCGTGCCAC
58511 GTCGGACACC
Statistics
Matches: 90, Mismatches: 15, Indels: 14
0.76 0.13 0.12
Matches are distributed among these distances:
29 5 0.06
31 58 0.64
32 1 0.01
33 1 0.01
34 19 0.21
36 6 0.07
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (31 bp):
ACACGTGGCGTGCCACATGTCACTTTTTGGT
Found at i:60754 original size:3 final size:3
Alignment explanation
Indices: 60739--60802 Score: 112
Period size: 3 Copynumber: 21.3 Consensus size: 3
60729 TCTTATATAT
60739 ATA ATA TATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
60784 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
60803 CAACAACAAC
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:70176 original size:823 final size:830
Alignment explanation
Indices: 68623--70189 Score: 2576
Period size: 827 Copynumber: 1.9 Consensus size: 830
68613 AACTGATTGA
*
68623 AATTATATAAGGGCCAAGAACATTTTTTTGTTATAGAGTGGTCCTTGATTGATTAATTGATTGAA
1 AATTATATAAGGGCCAAGAACATTTTTTGGTTATAGAGTGGTCCTTGATTGATTAATTGATTGAA
*
68688 TTATATAAGGTTGCAGTAAAAATGCAATTTAAATGGATTAGTTTTAATGTTGTCTCTTGATATTG
66 TTATATAAGGTTGCAGTAAAAATGCAATTTAAATGGATTAGTTCTAATGTTGTCTC------TTG
*
68753 GCATAAATCTTTGTAAGCCAACTTTTTAGACATGCAAAATTAATAAGGTCAAAGAACATGTTTTT
125 GCATAAATCTTTGTAAGCCAACTTTTTAGACATGCAAAATTAAGAAGGTCAAAGAACATGTTTTT
*
68818 ATTTGTAAGTAATAGGATGTGCAAAGAGGTAATAAAATATGTTGTTAATTGGATAATAATACTCA
190 ATTTGTAAGTAATAGGAAGTGCAAAGAGGTAATAAAATATGTTGTTAATTGGATAATAATACTCA
* * * * *
68883 CATTGAACGAAGGGTGGTTTTAATTTAGAAGGTGAAAAATATTGAACGGTCTATATTTAAGGGAT
255 CATTGAACAAAGGGTGGTTTTAATTCAGAAGGGGAAAAATATTGAACGGTCCATATTGAAGGGAT
* * * *
68948 TGAGACGGAAAAGAAAGAAGAAAGTGATACGAAGGTGAAAAAAGAGGGTAGTGATGCAAATGTTC
320 GGAGACGGAAAAGAAAGAAGAAAGAGATACGAAGGTGAAAAAAGAGGGGAGTGATGAAAATGTTC
*
69013 GATTTTTGGCAAACATGAAGATTGATCAGCACCGAGGAGTTGAAAGAACGCAGCAACTGAGTTGG
385 GATTTTTGGCAAACATGAAGATTCATCAGCACCGAGGAGTTGAAAGAACGCAGCAACTGAGTTGG
* *
69078 TGAGTGGACAAAAGAAAACAGCGAGAGAAACATTTATTAAAAGTAACTAAGGGTTTAGGGTTTAG
450 TGAGAGGACAAAAGAAAACAGCGAGAGAAACATTAATTAAAAGTAACTAAGGGTTTAGGGTTTAG
* * * *
69143 AAGTAATTAATTAAAAGTCTTAAACATTAATTAAAAATAATTAAGGAAGGGAAATGTGTAATTAC
515 AAGCAATTAATTAAAAGGCTTAAACATTAATTAAAAACAATTAAGGAAGGGAAACGTGTAATTAC
*
69208 AAAAAAAGGGTAGAAGGAAAAGGAATGGGGAAAACTCATAGAGGGGCTTTTTAGTCATCCGAAAA
580 AAAAAAAGGGTAGAAGGAAAAGGAATGGAGAAAACTCATAGAGGGGCTTTTTAGTCATCCGAAAA
**
69273 ATGAGAAAAGACCAAAAATGGCCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTA
645 ATGAGAAAAGACCAAAAATAACCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTA
69338 ATTTCCATAGTAGTTAAAAATAATATATACAAGTTATATTAGCCCGTGCTGGCGCTACGGGCGTT
710 ATTTCCATAGTAGTTAAAAATAATATATACAAGTTATATTAGCCCGTGCTGGCGCTACGGGCGTT
69403 TTTTTATTTTAGAATGATGTTTGATTATCTGATTGAATAAGGATATTAATATAACC
775 TTTTTATTTTAGAATGATGTTTGATTATCTGATTGAATAAGGATATTAATATAACC
* * *
69459 AATTATATAAGGGTCAAGAACA-TTTTTGGTTCTAGAGTGGTGCTTGATTGATTAATTGATTGAA
1 AATTATATAAGGGCCAAGAACATTTTTTGGTTATAGAGTGGTCCTTGATTGATTAATTGATTGAA
69523 TTATATAAGGTTGCAGTAAAAATGCAATTTAAATGGATTAGTTCTAAT-TATGTCTC-TGGCATA
66 TTATATAAGGTTGCAGTAAAAATGCAATTTAAATGGATTAGTTCTAATGT-TGTCTCTTGGCATA
* *
69586 AATCTTTGTAAGCTAACTTTTTAGACATGCAAAATTAAGAAGGT-TAAGAACATGTTTTTATTTG
130 AATCTTTGTAAGCCAACTTTTTAGACATGCAAAATTAAGAAGGTCAAAGAACATGTTTTTATTTG
69650 TAAGTAATAGGAAGTGCAAAGAGGTAATAAAATATGTTGTTAATTGGATAATAATACTCACATTG
195 TAAGTAATAGGAAGTGCAAAGAGGTAATAAAATATGTTGTTAATTGGATAATAATACTCACATTG
* * *
69715 AACAAATGGTGGTTTTAATTCAGAAGGGGAAAAATATTGAATGGTCCATGTTGAAGGGATGGAGA
260 AACAAAGGGTGGTTTTAATTCAGAAGGGGAAAAATATTGAACGGTCCATATTGAAGGGATGGAGA
* * * * *
69780 CGGAGAA-AAAGAGGAAAGAGATATGAAGGTGAAAACAGAGGGGAGTGATGAAAATGTTTGATTT
325 CGGAAAAGAAAGAAGAAAGAGATACGAAGGTGAAAAAAGAGGGGAGTGATGAAAATGTTCGATTT
* * *
69844 TTGGCAAACCTGAAGATTCATTAGCACTGAGGAGTTGAAAAGAA-GCAGCAACTGAGTTGGTGAG
390 TTGGCAAACATGAAGATTCATCAGCACCGAGGAGTTG-AAAGAACGCAGCAACTGAGTTGGTGAG
* *
69908 AGGA-AAAA-AAATCAGCGAGAGAAACATTAATTAAAAGTAATTAAGGGTTTAGGGTTTAGAAGC
454 AGGACAAAAGAAAACAGCGAGAGAAACATTAATTAAAAGTAACTAAGGGTTTAGGGTTTAGAAGC
*
69971 AATTAATTAAAAGGCTTAAACATTGATTAAAAACAATTAAGGAAGGGAAACGTGTAATTAC-AAA
519 AATTAATTAAAAGGCTTAAACATTAATTAAAAACAATTAAGGAAGGGAAACGTGTAATTACAAAA
* * * *
70035 AAAGGGTAGAAGGAAAAGGAATGGAGAAAATTCGTAGAGGGGCTTTTTAGTCATCCGAAAAGTGT
584 AAAGGGTAGAAGGAAAAGGAATGGAGAAAACTCATAGAGGGGCTTTTTAGTCATCCGAAAAATGA
70100 GAAAAGACCAAAAATAACCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTT
649 GAAAAGACCAAAAATAACCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTT
*
70165 CCATTGTAGTTAAAAATAATATATA
714 CCATAGTAGTTAAAAATAATATATA
70190 GTATATATAC
Statistics
Matches: 682, Mismatches: 47, Indels: 17
0.91 0.06 0.02
Matches are distributed among these distances:
823 150 0.22
824 108 0.16
825 4 0.01
826 106 0.16
827 151 0.22
828 49 0.07
834 1 0.00
835 92 0.13
836 21 0.03
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.29
Consensus pattern (830 bp):
AATTATATAAGGGCCAAGAACATTTTTTGGTTATAGAGTGGTCCTTGATTGATTAATTGATTGAA
TTATATAAGGTTGCAGTAAAAATGCAATTTAAATGGATTAGTTCTAATGTTGTCTCTTGGCATAA
ATCTTTGTAAGCCAACTTTTTAGACATGCAAAATTAAGAAGGTCAAAGAACATGTTTTTATTTGT
AAGTAATAGGAAGTGCAAAGAGGTAATAAAATATGTTGTTAATTGGATAATAATACTCACATTGA
ACAAAGGGTGGTTTTAATTCAGAAGGGGAAAAATATTGAACGGTCCATATTGAAGGGATGGAGAC
GGAAAAGAAAGAAGAAAGAGATACGAAGGTGAAAAAAGAGGGGAGTGATGAAAATGTTCGATTTT
TGGCAAACATGAAGATTCATCAGCACCGAGGAGTTGAAAGAACGCAGCAACTGAGTTGGTGAGAG
GACAAAAGAAAACAGCGAGAGAAACATTAATTAAAAGTAACTAAGGGTTTAGGGTTTAGAAGCAA
TTAATTAAAAGGCTTAAACATTAATTAAAAACAATTAAGGAAGGGAAACGTGTAATTACAAAAAA
AGGGTAGAAGGAAAAGGAATGGAGAAAACTCATAGAGGGGCTTTTTAGTCATCCGAAAAATGAGA
AAAGACCAAAAATAACCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTTCC
ATAGTAGTTAAAAATAATATATACAAGTTATATTAGCCCGTGCTGGCGCTACGGGCGTTTTTTTA
TTTTAGAATGATGTTTGATTATCTGATTGAATAAGGATATTAATATAACC
Found at i:76998 original size:2 final size:2
Alignment explanation
Indices: 76991--77029 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
76981 ATTCTTGCAG
76991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77030 GGACGAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:78965 original size:14 final size:13
Alignment explanation
Indices: 78941--78995 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
78931 GGGATTCTTG
78941 TTTTTTT-T-TTT
1 TTTTTTTCTGTTT
*
78952 CTTTTTTCTGTTT
1 TTTTTTTCTGTTT
**
78965 TTTGGATTCTGTTT
1 TTT-TTTTCTGTTT
78979 TTTTTATTCTGTTT
1 TTTTT-TTCTGTTT
78993 TTT
1 TTT
78996 GGATTCTGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
11 6 0.18
12 1 0.03
13 5 0.15
14 22 0.65
ACGTcount: A:0.04, C:0.07, G:0.09, T:0.80
Consensus pattern (13 bp):
TTTTTTTCTGTTT
Found at i:78972 original size:36 final size:37
Alignment explanation
Indices: 78925--78994 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 37
78915 TTTGTGATGT
*
78925 TTTTTTGGGATTCTTGTTTTTTTTTTTCT-TTTTTCTG
1 TTTTTTGGGATTC-TGTTTTTTTTATTCTGTTTTTCTG
78962 TTTTTT-GGATTCTGTTTTTTTTATTCTGTTTTT
1 TTTTTTGGGATTCTGTTTTTTTTATTCTGTTTTT
78995 TGGATTCTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 14 0.45
36 11 0.35
37 6 0.19
ACGTcount: A:0.04, C:0.07, G:0.13, T:0.76
Consensus pattern (37 bp):
TTTTTTGGGATTCTGTTTTTTTTATTCTGTTTTTCTG
Found at i:78979 original size:28 final size:29
Alignment explanation
Indices: 78948--79009 Score: 110
Period size: 28 Copynumber: 2.2 Consensus size: 29
78938 TTGTTTTTTT
78948 TTTTCTTTT-TTCTGTTTTTTGGATTCTG
1 TTTTCTTTTATTCTGTTTTTTGGATTCTG
78976 TTTT-TTTTATTCTGTTTTTTGGATTCTG
1 TTTTCTTTTATTCTGTTTTTTGGATTCTG
79004 TTTTCT
1 TTTTCT
79010 GCATATTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 4 0.12
28 27 0.84
29 1 0.03
ACGTcount: A:0.05, C:0.10, G:0.13, T:0.73
Consensus pattern (29 bp):
TTTTCTTTTATTCTGTTTTTTGGATTCTG
Found at i:79001 original size:14 final size:14
Alignment explanation
Indices: 78957--79007 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
78947 TTTTTCTTTT
78957 TTCTGTTTTTTGGA
1 TTCTGTTTTTTGGA
**
78971 TTCTGTTTTTTTTA
1 TTCTGTTTTTTGGA
78985 TTCTGTTTTTTGGA
1 TTCTGTTTTTTGGA
78999 TTCTGTTTT
1 TTCTGTTTT
79008 CTGCATATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.06, C:0.08, G:0.16, T:0.71
Consensus pattern (14 bp):
TTCTGTTTTTTGGA
Found at i:85989 original size:54 final size:54
Alignment explanation
Indices: 85907--86015 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
85897 CTCTTGAGGC
*
85907 AGTTTCTGAGGAAGCTGATAATGAGGCCATAGTCGGTGAAGAGCCCAAAGAAAT
1 AGTTTCTGAGGAAGCTGATAATGAGGCCACAGTCGGTGAAGAGCCCAAAGAAAT
* * * *
85961 AGTTTGTGAGGAAGTTGATAGTGAGGCCACAGTCGGTGAAGAGCCCGAAGAAAT
1 AGTTTCTGAGGAAGCTGATAATGAGGCCACAGTCGGTGAAGAGCCCAAAGAAAT
86015 A
1 A
86016 TCGGATGCCT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (54 bp):
AGTTTCTGAGGAAGCTGATAATGAGGCCACAGTCGGTGAAGAGCCCAAAGAAAT
Found at i:86560 original size:22 final size:22
Alignment explanation
Indices: 86532--86578 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
86522 TATTAAGTGC
86532 AAATCGTTGCTCAAGTTCAAGA
1 AAATCGTTGCTCAAGTTCAAGA
*
86554 AAATCGTTGCTCATGTTCAAGA
1 AAATCGTTGCTCAAGTTCAAGA
86576 AAA
1 AAA
86579 ACATCTCCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (22 bp):
AAATCGTTGCTCAAGTTCAAGA
Found at i:90374 original size:228 final size:223
Alignment explanation
Indices: 89977--90432 Score: 557
Period size: 228 Copynumber: 2.0 Consensus size: 223
89967 TCTGGTTGTT
* *
89977 TGTTTTAATGGAAAAAAGAAGGCAATACCATAGGATTTTGGCACACTATCCTGAGTTCAAGATTT
1 TGTTTTAATGGAAAAAAGAAGACAATACCATAGGATTTTGGCACACTATCCCGAGTTCAAGATTT
*
90042 GGGGAGAAGATCACCATGATTTTGCCGGAGAAGGAATGAACGAGGAGTCCAAGCCTCCAAGGACG
66 GGGGAGAAGATCACCATGATTTCGCCGGAGAAGGAATGAACGAGGAG--C-AG-CTCCAAGGACG
* * * *
90107 ATCTAGAACTGGTAAGGGATTCTTAAAACTTTCTTTGTTTTTTTTTTTTAAAGCTAGTAGTAATA
127 ATCTACAACTGGTAAGGGATTCTTAAAACTTTCTTTG--TTTCTTTCTAAAAGCTAGTAGTAATA
*
90172 AATTCGCTATTTTATTGCAGTTCC-CCCTGGCCA
190 AATTCGCTATTTCATTGCAGTTCCTCCCTGGCCA
* * * **
90205 TGTTTTAATGGAAGAAAGAAGACAATACTAT-GAGATTTTGGCACATTATCCCGAGTTTGAGATT
1 TGTTTTAATGGAAAAAAGAAGACAATACCATAG-GATTTTGGCACACTATCCCGAGTTCAAGATT
* *
90269 TGGGGAGAAGATCACCATGATTTCGTTC-GAGAAGGAATGGACGA-G-G-AG-TCCAAGGACGAT
65 TGGGGAGAAGATCACCATGATTTCG-CCGGAGAAGGAATGAACGAGGAGCAGCTCCAAGGACGAT
*
90329 CTACAACTGGTAAGGGATTCTTAAAATTTTCTTTGTTTCTTTGTTTCTTTCTAAAAGCTAGTGGT
129 CTACAACTGGTAAGGGATTCTTAAAA----C----TTTCTTTGTTTCTTTCTAAAAGCTAGTAGT
* *
90394 AATAACTTCTCTATTTCATTGCAGTTCCTCCCTGGCCA
186 AATAAATTCGCTATTTCATTGCAGTTCCTCCCTGGCCA
90432 T
1 T
90433 ATCCAGGCTT
Statistics
Matches: 199, Mismatches: 18, Indels: 23
0.83 0.08 0.10
Matches are distributed among these distances:
220 37 0.19
222 2 0.01
224 1 0.01
226 44 0.22
227 12 0.06
228 102 0.51
229 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (223 bp):
TGTTTTAATGGAAAAAAGAAGACAATACCATAGGATTTTGGCACACTATCCCGAGTTCAAGATTT
GGGGAGAAGATCACCATGATTTCGCCGGAGAAGGAATGAACGAGGAGCAGCTCCAAGGACGATCT
ACAACTGGTAAGGGATTCTTAAAACTTTCTTTGTTTCTTTCTAAAAGCTAGTAGTAATAAATTCG
CTATTTCATTGCAGTTCCTCCCTGGCCA
Found at i:94279 original size:2 final size:2
Alignment explanation
Indices: 94272--94299 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
94262 TAGTCTCATC
94272 AT 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 AT
94300 TGATCATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95022 original size:1 final size:1
Alignment explanation
Indices: 95016--95046 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
95006 CTCCCCACAT
95016 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
95047 GCATGTATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.