Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012659.1 Corchorus olitorius cultivar O-4 contig12692, 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: 62722
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3239 original size:333 final size:332
Alignment explanation
Indices: 17--5406 Score: 6377
Period size: 334 Copynumber: 16.2 Consensus size: 332
7 GTTGAATTAT
*
17 ATATTTCGGGTCAATTTTTTGGAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
* * * * * *
82 TTAAAAAACATGTTTCAGGACCCCGACTCAGTTTTGCATGATTTTTGGGGCCAGGACTTCTTGAA
66 CTAAAAAAC-TGTTCCGGGA-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAA
* * *
147 ATATCTTTATTCTTCTAACCAAATCTCAGCGACATTAGATTTAAGGATTTGTTTTTACGAGCATC
129 ATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATC
* *
212 TGAATCTTGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAAAAGCG
194 TGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAGCG
* *
277 TGAAAATCTCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAAAT
259 TGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAAAT
342 TTAGGAGAAA
324 TTAGGA-AAA
** *
352 ACT-TTT-GGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAATTATTACAGTTTTTG
1 A-TATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTG
* * *
415 GCTAAAAAACATGTTCCGGGACCCCGGCTCAGTTTTGCATGAGTTTTGGCGCCATGACTCCTTGA
65 GCTAAAAAAC-TGTTCCGGGA-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGA
* * ** * * * *
480 AATATATATATTCATCGAACCATTTCTCAACCACATTGGACTTAAGGATTTGTTTTTACAAG-AT
128 AATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCA-
* * * * * *
544 TCTGAATCATGTCTCAATTTAATCTGAAA-TAGATTCAAATAAAATTGGAAAAACGATATTGGAA
192 TCTGAATCATGTTTCGATTTAATCAGAAATTA-ATTCAGATAAAATTGGAAAAACAATATTAGAA
* * * * ** * * * *
608 GCATGAAAAGCTATTCATTCTCTTTGTTGTTTAATTATCTATTTTTTATGAGTGTTGTGGCTAAA
256 GCGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAA
*
673 AATTTAAGAAAA
321 AATTTAGGAAAA
* * ** * *
685 ATATTTCTGGTCAATTTTTTGCAAAATTGTAGCTGAAATCATGTACTAACCATCACAGTTTTTGC
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
* * * *
750 CT-AAAAACGCGTTCCGGGGCCCCCTGCTCAATTTTGCATGATTTTTGGCGCCAAGACTTCTTGA
66 CTAAAAAAC-TGTTCC-GGG-ACCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGA
* *
814 AATATCTTTATTCTTCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCAT
128 AATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCAT
*
879 CTGAATCTTGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAGC
193 CTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAGC
*
944 GTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAAA
258 GTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAAA
*
1009 TTCAGGAAAA
323 TTTAGGAAAA
* *
1019 ATCTTTCGGGTCAATTTCTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
* * * *
1084 CTAAATAACATGTTCCAGAACTCCGGCTCAGTTTTGCATGATTTTTGGCGCCAGGA-TTCCTTGA
66 CTAAAAAAC-TGTTCCGGGAC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTT-CTTGA
* * * * * *
1148 AATATTTATATTCATCTAACCAATTCTCAGCCACATTGGATTTAAGAATTTGTGTTTACAAG-AT
128 AATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCA-
* * * * * *
1212 TCTGAATCATTTTTCAATTTAATCTGAAATTAATTCAAATAAAATTGGAAAAACGATATTGGAAG
192 TCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAG
* * ** * *
1277 CGTGAAAAGCTATTCATTCTTTTTGTTGTTGAATTATATATTTTTTATGAGTGTTGTGGCTAAAA
257 CGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAA
*
1342 TTTTAGGAAAA
322 ATTTAGGAAAA
* **
1353 ATATTTCGGATCAATTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACAGTTTTTGG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
* *
1418 CTAAAAAACGCGTTCCGAGG-CCCTAGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGA
66 CTAAAAAAC-TGTTCCG-GGACCC-GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGA
* * * * * *
1482 AATATCTTTATTCTTCTAACCAAATCTAAGTCACATTAGACTTAAGGATTTGTTTTTACGAGTAT
128 AATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCAT
** * * *
1547 CAAAATCATGTTTCTATTAAATCAGAAATTAATTTAGATAAAATTGGAAAAACAATATTAGAAGC
193 CTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAGC
* *
1612 GTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATACATTTTTTATGAGTATAGTGGCTAAAAA
258 GTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAAA
1677 TTTTA-GAAAA
323 -TTTAGGAAAA
* *
1687 ATATTTCGGTTCAATTTTTTGCAAAATTTTAACCAAAATCGTGTACTAACCATCACAGTTTTTGG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
* * *
1752 CTAAAGAACAC-GTTTCGGGACCACGGCTGAGTTTTGCATGATTTTTGGCGCGAAGA-TTCATTG
66 CTAAA-AA-ACTGTTCCGGGACC-CGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTC-TTG
* * * * * *
1815 AAATATCTATAATCAACTAACAAAATCTCAGCTACATTAGTTTTAAGGATTTGTTTTTACGACCA
127 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCA
* * * * *
1880 TTTAAATCATGTTTCGATTTAATCAGAAATTAATTTAGATTAAATTGGAGAAACAATATTAGAAG
192 TCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAG
* *
1945 CGTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGATAAAA
257 CGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAA
*
2010 ATTTAGAAAAA
322 ATTTAGGAAAA
* * * *
2021 ATCTTTCGGGTCAATTTTTTGGAAAATTTTAGCCAAAATCGTGTACAAACCCATCACAGTTTTAG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAA-CCATCACAGTTTTTG
* * * *
2086 G-TTAAAAACATGTTCCAGGACCCCGGCTCAGTTTTGCATGATTTTTGGCGCCATGACTCCTTGA
65 GCTAAAAAAC-TGTTCCGGGA-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGA
* * * * * *
2150 AATATATATATTCATCTAACCAATTCTCAGCCACATTGGATTTAAGAATTTGTGTTTACAAG-AT
128 AATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCA-
* * * * * *
2214 TCTGAATCATTTTTCAATTTAATCTGAAATTAATTCAAATAAAATTGGAAAAACGATATTGGAAG
192 TCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAG
* * ** * * *
2279 CGTGAAAAGCTATTCATTCTTTTTGTTGTTGAATTATATGTTTTTTATGAGTGTTGTGGCTAAAA
257 CGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAA
2344 ATTTAGGAAAA
322 ATTTAGGAAAA
* ** *
2355 ATATTTCGGATCAATTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACAGTTTTTGC
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
* * * * *
2420 CTAAAAAACGCGTTCCGGGGCCCCCCAGCTCAATTTTGCATGATTTTTGGGGCCAAGACTTCTTG
66 CTAAAAAAC-TGTTCC-GGG--ACCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTG
* * * * * *
2485 AAATATCTTTATTCTTCTAACAAAATCTCAGCCACATTAGATTTAAGGATTCGCTTTTACGAGAA
127 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCA
* * * * *
2550 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGATAAAATTGGAAAAACATTATTAGGAC
192 TCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAG
*
2615 CGTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAA
257 CGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAA
*
2680 ATTTAGAAAAA
322 ATTTAGGAAAA
* * *
2691 ATCTTTCGGGTCAATTTTTTGGAAAATTTTAGCCAAAATCATGTACTAACCATCACAGTTTTTGG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
* * * *
2756 TTAAAAAACATGTTCCAGGACCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAGGACTCCTTGAA
66 CTAAAAAAC-TGTTCCGGGA-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAA
* * * * *
2821 ATATATATATTCATCTAACCAATTCTCAACCACATTGGATTTAAGGATTTGTTTTTACAAG-ATT
129 ATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCA-T
* * * * * * *
2885 CTAAATCATGTCTCAATTTAATTAGAAATTAATTCAAATAAAATTGGAAAAACGATATTGGAAGC
193 CTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAGC
* * * * ** * * * * *
2950 GTGAAAAGCTATTTATTTTTTTTGTTGTTAAATTATATGTTTTTTATGAGTGTTGTGGCTTAAAA
258 GTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAAA
3015 TTTAGGAAAA
323 TTTAGGAAAA
* **
3025 ATATTTCGGATCAATTTTTTGCAAAATTTTAGCTGAAATCGTGTACT-ACCATCACAGTTTTTGG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
* * ** * *
3089 CTAAAAAACTCGTTCTGGGGCCCTAACTCAGTTTTGCATGATTTTTGGCGCTAAGATTTCTTGAA
66 CTAAAAAACT-GTTCCGGGACCC-GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAA
* *
3154 ATATCTTTATTCTTCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATC
129 ATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATC
* * *
3219 TGAATCTTGTTTCGATTTAATCAGAAATTAATTCGGATAAAATTGGAAAAATAATATTAGAAGCG
194 TGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAGCG
* * *
3284 TGAAAATCTCTTCAATCTTATTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGTTAAAAAT
259 TGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAAAT
3349 TTAGGAAAA
324 TTAGGAAAA
* * ** * *
3358 ATCTTCCAAGTCAATTTCTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTTG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
*
3423 CTAAAAAAACATGTTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
66 CT-AAAAAAC-TGTTCCGGGA-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGA
* * * * *
3488 AATATATATATTCATCTAACCAATTCTCAGTCACATTGGATTTAAGGATTTGTTTTTACAAG-AT
128 AATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCA-
* * * * * *
3552 TCTGAATCAAGTTTCAATTTAATCTGAAATTAATTCAAATAAAATTGGAAAAACGATATTGGAAG
192 TCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAG
* * * ** * * *
3617 CGTGAAAAGTTATTCATTCTTTTTGTTGTTGAATTATATGTTTTTTATGAGTGTTGTGGC-----
257 CGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAA
3677 ---T-----AA
322 ATTTAGGAAAA
* * * *
3680 ATATTTCAGGTCAAATTTTTTGCAAAATTTTAGCTAAAATCATGTACTAATCATCACAGTTTTTG
1 ATATTTCGGGTC-AATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTG
* * * *
3745 CCTAAAAAACGCGTTCCGGG-CGCCAGCTCAGTTTTGCATGATTTTTGGCGTCAAGACTTCTTGA
65 GCTAAAAAAC-TGTTCCGGGAC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGA
* * *
3809 AATATCTTTATTCCTCTAACCAAATCTTAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCAT
128 AATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCAT
* * * *
3874 CTGAATCTTATTTTGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAGA
193 CTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAGC
*
3939 GTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAAA
258 GTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAAA
4004 TTTAGGAAAA
323 TTTAGGAAAA
* * * *
4014 ATCTTTCAGTTCAATTTTTTTGCAAAATTTTAACCAAAATCGTGTACTAACCATCACAGTTTTTG
1 ATATTTCGGGTCAA-TTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTG
** * * *
4079 GCTAAAAAAC-GCATT-TTGGACCACGGCTCAGTTTTGCATGATTTTTGGCGCGAAAAC-TCAAT
65 GCTAAAAAACTG--TTCCGGGACC-CGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTC-TT
* * ** * *
4141 GAAATATCTATAATAATCTAACCAAATCTCAGTTACATTAGATTTATGTATTTGTTTTTACGAGC
126 GAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGC
*
4206 ATCTGAATCATGTTTCGATTTAATCAGAAATTAATTTAGATAAAATT-GAAAAACAATATTAGAA
191 ATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAA
*
4270 GCGTGAAAATCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAA
256 GCGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAA
4335 AATTTAGGAAAA
321 AATTTAGGAAAA
* * * *
4347 ATCTTTCTGTTCAATTTTTTGCAAAATTTTAACCAAAATCGTGTACTAACCATCACAGTTTTTGG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
* * * * * *
4412 CTAAAAAACGCGTTTCGGGACCACGACTCCGTTTTGCATGATTTTTGGTGCGAAGAC-TCATTGA
66 CTAAAAAAC-TGTTCCGGGACC-CGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTC-TTGA
* * * * *
4476 AATATCTATAATCATCTAACCAAATCTCAGCTACATTAGATTTAAGGATTTGATTTTAAGAACAT
128 AATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCAT
* * *
4541 CTGAATCATGTTTCGATTTAATCATAAATTACA-TCAGATATAATTGGAAAAAAAATATTAGAAG
193 CTGAATCATGTTTCGATTTAATCAGAAATTA-ATTCAGATAAAATTGGAAAAACAATATTAGAAG
* * * * * * * ** *
4605 TGTAAAAAGCTCTTCATTCTTTTTGCCGCTGAATTATATATTTTTTTATCATTATTTTGTCTAAA
257 CGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTTATGAGTATAGTGGCTAAA
4670 AATTTAGG-AAA
321 AATTTAGGAAAA
* * *
4681 ATCTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTTG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAG-TTTTTG
** * * * * * *
4746 GCTAAAAGAGGTGTTCCAGGACTCCGACTCAGTTTTGCATGATTTTTTGTGCCTAGACTCCTTGA
65 GCTAAAA-AACTGTTCCGGGAC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGA
* * * * * *
4811 TATATTTATATTCATCTAATCAAATCTCAGCCACGTT-GCATTTATGGATTTGTTTTTATGAGCA
128 AATATCTATATTCATCTAACCAAATCTCAGCCACATTAG-ATTTAAGGATTTGTTTTTACGAGCA
* * * * * * * *
4875 TCTAAATTATGTTACGATTTAGTCAG------ATTCAGATAAAATTAGAAAAGCGATATTGGAAG
192 TCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAG
* * * * *
4934 CGTGAAAAGCTCTTCATTATTTTTGTCGTTGAATTATATATTTTTTATGAGTATTGTGACTAAAA
257 CGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAA
* *
4999 ATTTTGAAAAA
322 ATTTAGGAAAA
* * * * * * * * *
5010 ATATTTCGGGTTAACTTTTTGCAAAATTTTGGACGAAATCATGTACTTACCATAACTGTTTTTGG
1 ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
* * * *
5075 CTAAAAAACATGTTTCAGAACCCAGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCAAGACT
66 CTAAAAAAC-TGTTCCGGGACCCGGCTCAGTTTTGCATGATTTTTGG---C--G---CCAAGACT
* * * * *
5140 TCTTCAAATATCTATATTCATCTAACCAAATTTCAGCTACGTT-GTATTTAAGGATTTTCTTTTT
122 TCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAG-ATTTAAGGA--TT-TGTTT
** * * * * *
5204 TTACGAATATCTAAATAATCTTACGAATTAATCAG------ATTCAGATAAAATT-GAAAAAGCA
183 TTACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAA-CA
* * * * * *
5262 ATATTGGAAGCGTGAAAAGCTCTTCATTATTTTTGTCGTTGAATTATATATTTTTTATCAGTATT
247 ATATTAGAAGCGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATA
*
5327 GTGGCTAAAAATTTAGAAAAA
312 GTGGCTAAAAATTTAGGAAAA
* ** * * *
5348 ATCTTTCGCATCAATTTTTTTACAAAATTTTGGCCAAAATCGTGTA-TAAACCATAACAG
1 ATATTTCGGGTCAA-TTTTTTGCAAAATTTTAGCCAAAATCGTGTACT-AACCATCACAG
5407 AGGCCTCCGC
Statistics
Matches: 4324, Mismatches: 636, Indels: 186
0.84 0.12 0.04
Matches are distributed among these distances:
320 1 0.00
321 199 0.05
322 27 0.01
323 49 0.01
327 25 0.01
328 49 0.01
329 112 0.03
332 71 0.02
333 583 0.13
334 2266 0.52
335 467 0.11
336 291 0.07
337 8 0.00
338 141 0.03
339 35 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (332 bp):
ATATTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGG
CTAAAAAACTGTTCCGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAAT
ATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTG
AATCATGTTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACAATATTAGAAGCGTG
AAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATAGTGGCTAAAAATTT
AGGAAAA
Found at i:5538 original size:50 final size:53
Alignment explanation
Indices: 5403--5869 Score: 672
Period size: 50 Copynumber: 9.1 Consensus size: 53
5393 ATAAACCATA
* *
5403 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAAACACGAAGCTACATGAGAAG
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
* *
5456 ACAGAGGCCTCCGCAGCGAGGCGAGGCTAGCAGACACGAAGCTACACGAG-A-
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
*
5507 A-AGAGGCCTCCGCAGTGAGGCAAGGCCAGCAGACACGAAGCTACACGAGAAG
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
5559 ACAGAGGCCTCCGCAGTGAGGCGAGGCCA--A-ACACGAAGCTACACGAGAAG
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
* * **
5609 ATAGAGGCCTCCGCAATGAGGCGAGGCCA--A-ACACGAAGCTACACCCGAAG
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
*
5659 ATAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
* * *
5712 ACAGAGACCTCCGCAGTGAGGCGAGGCCA--ACACACAAAGCTACACGAGAAG
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
* * *
5763 ACAGAGGCCTCCGCCGTGAGGCGAGGCCA--ACACACAAAGCTACACGAGAAG
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
* * *
5814 ACAGAGGCCTCCGCAGTGAAGTGAGGCCAGCAGACACGAAGCTACATGAGAAG
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
5867 ACA
1 ACA
5870 CACACGACAC
Statistics
Matches: 379, Mismatches: 27, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
50 139 0.37
51 98 0.26
52 3 0.01
53 139 0.37
ACGTcount: A:0.34, C:0.28, G:0.31, T:0.07
Consensus pattern (53 bp):
ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
Found at i:5584 original size:103 final size:105
Alignment explanation
Indices: 5403--5869 Score: 668
Period size: 103 Copynumber: 4.5 Consensus size: 105
5393 ATAAACCATA
* *
5403 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAAACACGAAGCTACATGAGAAGACAGAGGCCTCC
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAGACAGAGGCCTCC
* *
5468 GCAGCGAGGCGAGGCTAGCAGACACGAAGCTACACGAG-A-
66 GCAGTGAGGCGAGGCCA-CAGACACGAAGCTACACGAGAAG
*
5507 A-AGAGGCCTCCGCAGTGAGGCAAGGCCAGCAGACACGAAGCTACACGAGAAGACAGAGGCCTCC
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAGACAGAGGCCTCC
5571 GCAGTGAGGCGAGGCCA-A-ACACGAAGCTACACGAGAAG
66 GCAGTGAGGCGAGGCCACAGACACGAAGCTACACGAGAAG
* * ** *
5609 ATAGAGGCCTCCGCAATGAGGCGAGGCCA--A-ACACGAAGCTACACCCGAAGATAGAGGCCTCC
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAGACAGAGGCCTCC
5671 GCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAG
66 GCAGTGAGGCGAGGCCA-CAGACACGAAGCTACACGAGAAG
* * *
5712 ACAGAGACCTCCGCAGTGAGGCGAGGCCA--ACACACAAAGCTACACGAGAAGACAGAGGCCTCC
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAGACAGAGGCCTCC
* * *
5775 GCCGTGAGGCGAGGCCA-ACACACAAAGCTACACGAGAAG
66 GCAGTGAGGCGAGGCCACAGACACGAAGCTACACGAGAAG
* * *
5814 ACAGAGGCCTCCGCAGTGAAGTGAGGCCAGCAGACACGAAGCTACATGAGAAGACA
1 ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAGACA
5870 CACACGACAC
Statistics
Matches: 328, Mismatches: 26, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
100 63 0.19
101 3 0.01
102 48 0.15
103 147 0.45
104 67 0.20
ACGTcount: A:0.34, C:0.28, G:0.31, T:0.07
Consensus pattern (105 bp):
ACAGAGGCCTCCGCAGTGAGGCGAGGCCAGCAGACACGAAGCTACACGAGAAGACAGAGGCCTCC
GCAGTGAGGCGAGGCCACAGACACGAAGCTACACGAGAAG
Found at i:5897 original size:31 final size:30
Alignment explanation
Indices: 5847--5930 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 30
5837 AGGCCAGCAG
* *
5847 ACACGAAGCTACATGAGAAGACACACACGAC
1 ACACGAAGGTACACGAGAAGACACACAC-AC
* * *
5878 ACACGAAGGTACACAAGAAGATAGGACACAC
1 ACACGAAGGTACACGAGAAGACA-CACACAC
5909 ACA--AAGGTACACGAGAAGACAC
1 ACACGAAGGTACACGAGAAGACAC
5931 GGTGGTGCTC
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
29 16 0.36
31 24 0.55
32 4 0.09
ACGTcount: A:0.48, C:0.25, G:0.21, T:0.06
Consensus pattern (30 bp):
ACACGAAGGTACACGAGAAGACACACACAC
Found at i:7888 original size:31 final size:31
Alignment explanation
Indices: 7852--7916 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
7842 CGAAGAAACG
7852 AAATCAAGAAAAGAAAATAAAAAGAAATACA
1 AAATCAAGAAAAGAAAATAAAAAGAAATACA
7883 AAATCAAGAAAAGAAAATAAAAAGAAATACA
1 AAATCAAGAAAAGAAAATAAAAAGAAATACA
7914 AAA
1 AAA
7917 AATCAGATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.75, C:0.06, G:0.09, T:0.09
Consensus pattern (31 bp):
AAATCAAGAAAAGAAAATAAAAAGAAATACA
Found at i:10135 original size:19 final size:20
Alignment explanation
Indices: 10111--10150 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
10101 TTCACAGAAG
10111 TTTG-TTTTTTCCATCAAAC
1 TTTGTTTTTTTCCATCAAAC
10130 TTTGTTTTTTTCCATCAAAC
1 TTTGTTTTTTTCCATCAAAC
10150 T
1 T
10151 ATTACAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTGTTTTTTTCCATCAAAC
Found at i:17451 original size:11 final size:11
Alignment explanation
Indices: 17435--17460 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17425 TTATGCTCAA
17435 AAAATTAAGAT
1 AAAATTAAGAT
17446 AAAATTAAGAT
1 AAAATTAAGAT
17457 AAAA
1 AAAA
17461 GTAGGCAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (11 bp):
AAAATTAAGAT
Found at i:20040 original size:35 final size:35
Alignment explanation
Indices: 20000--20074 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
19990 AGTTCGTTTA
20000 TGTTCACGAACATGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACATGCTCGTTTATTGTTCATTTAAG
* *
20035 TGTTCATGAATATGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACATGCTCGTTTATTGTTCATTTAAG
20070 TGTTC
1 TGTTC
20075 GTTTATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (35 bp):
TGTTCACGAACATGCTCGTTTATTGTTCATTTAAG
Found at i:20137 original size:16 final size:16
Alignment explanation
Indices: 20116--20147 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20106 TATAATTATT
20116 TATATATTAATAATAA
1 TATATATTAATAATAA
*
20132 TATATATTATTAATAA
1 TATATATTAATAATAA
20148 AAATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:20142 original size:19 final size:19
Alignment explanation
Indices: 20100--20152 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
20090 GAACGTTCAT
* *
20100 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
20120 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
*
20138 TTATTAATAAAAATA
1 TTATTAATAATAATA
20153 ATAATATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:20154 original size:25 final size:27
Alignment explanation
Indices: 20124--20173 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
20114 TTTATATATT
20124 AATAATAATA-TATATTAT-TAATAAA
1 AATAATAATATTATATTATCTAATAAA
*
20149 AATAATAATATTCTATTATCTAATA
1 AATAATAATATTATATTATCTAATA
20174 TATTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
AATAATAATATTATATTATCTAATAAA
Found at i:20297 original size:18 final size:18
Alignment explanation
Indices: 20270--20304 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20260 AATTATTACA
20270 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
20288 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
20305 CAAATTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:24209 original size:19 final size:19
Alignment explanation
Indices: 24185--24222 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
24175 CGCTGCTCTA
24185 ATAATCTCATATGTACAGT
1 ATAATCTCATATGTACAGT
24204 ATAATCTCATATGTACAGT
1 ATAATCTCATATGTACAGT
24223 TGCTAAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
ATAATCTCATATGTACAGT
Found at i:25314 original size:19 final size:19
Alignment explanation
Indices: 25290--25336 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
25280 TTTTTAAGGA
25290 TACAATATTCAAATCTCAT
1 TACAATATTCAAATCTCAT
*
25309 TACAATATTATTCAAATCTTAT
1 TAC-A-A-TATTCAAATCTCAT
25331 TACAAT
1 TACAAT
25337 CAAATAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 4 0.17
20 2 0.08
21 2 0.08
22 16 0.67
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
TACAATATTCAAATCTCAT
Found at i:25323 original size:22 final size:22
Alignment explanation
Indices: 25295--25336 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
25285 AAGGATACAA
25295 TATTCAAATCTCATTACAATAT
1 TATTCAAATCTCATTACAATAT
*
25317 TATTCAAATCTTATTACAAT
1 TATTCAAATCTCATTACAAT
25337 CAAATAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTCAAATCTCATTACAATAT
Found at i:31374 original size:21 final size:19
Alignment explanation
Indices: 31348--31404 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
31338 TGCTGCTCTA
31348 ATAATCTCATCTGTACAAT
1 ATAATCTCATCTGTACAAT
* *
31367 ACATAATCTAATCTGTACAGT
1 --ATAATCTCATCTGTACAAT
*
31388 GTAATCTCATCTGTACA
1 ATAATCTCATCTGTACA
31405 GTTGTCAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (19 bp):
ATAATCTCATCTGTACAAT
Found at i:31394 original size:19 final size:19
Alignment explanation
Indices: 31370--31406 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31360 GTACAATACA
31370 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
31389 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
31407 TGTCAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:36566 original size:28 final size:27
Alignment explanation
Indices: 36534--36603 Score: 117
Period size: 25 Copynumber: 2.6 Consensus size: 27
36524 CCAAATCCAG
36534 AATCCTAAAACTGTTTTTTTTTAGGTA
1 AATCCTAAAACTGTTTTTTTTTAGGTA
36561 TAATCCTAAAACTG--TTTTTTTAGGTA
1 -AATCCTAAAACTGTTTTTTTTTAGGTA
36587 AATCCTAAAACTGTTTT
1 AATCCTAAAACTGTTTT
36604 AATTACCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
25 13 0.32
26 12 0.30
27 2 0.05
28 13 0.32
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (27 bp):
AATCCTAAAACTGTTTTTTTTTAGGTA
Found at i:45477 original size:60 final size:60
Alignment explanation
Indices: 45411--45537 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
45401 GCTAATTGCT
** * *
45411 CAAATAAAGATTTAACGTTTGCCAAAATGCTCAAATATGGGTCTAATCTTTTAATTTGAC
1 CAAATAAAGACCTAACGTTTGCCAAAATGCTCAAATAAGAGTCTAATCTTTTAATTTGAC
* * * * * * *
45471 CAAATAAGGGCCTAATGTTTGTCAAAATGCTCAAATAAGAGTCTGATCTTTTGATTTGGC
1 CAAATAAAGACCTAACGTTTGCCAAAATGCTCAAATAAGAGTCTAATCTTTTAATTTGAC
45531 CAAATAA
1 CAAATAA
45538 GGGCCGGCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (60 bp):
CAAATAAAGACCTAACGTTTGCCAAAATGCTCAAATAAGAGTCTAATCTTTTAATTTGAC
Found at i:45485 original size:29 final size:28
Alignment explanation
Indices: 45442--45542 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 28
45432 CCAAAATGCT
* *
45442 CAAATATGGGTCTAATCTTTTAATTTGAC
1 CAAATAAGGGCCTAATCTTTTAATTTG-C
* **
45471 CAAATAAGGGCCTAATGTTTGTCAAAATGC
1 CAAATAAGGGCCTAATCTTT-T-AATTTGC
* * * *
45501 TCAAATAAGAGTCTGATCTTTTGATTTGGC
1 -CAAATAAGGGCCTAATCTTTTAATTT-GC
45531 CAAATAAGGGCC
1 CAAATAAGGGCC
45543 GGCAAATAAG
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
29 29 0.54
30 5 0.09
31 20 0.37
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (28 bp):
CAAATAAGGGCCTAATCTTTTAATTTGC
Found at i:45538 original size:60 final size:60
Alignment explanation
Indices: 45427--45542 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
45417 AAGATTTAAC
* *
45427 GTTTGCCAAAATGCTCAAATATGGGTCTAATCTTTTAATTTGACCAAATAAGGGCCTAAT
1 GTTTGCCAAAATGCTCAAATAAGAGTCTAATCTTTTAATTTGACCAAATAAGGGCCTAAT
* * * *
45487 GTTTGTCAAAATGCTCAAATAAGAGTCTGATCTTTTGATTTGGCCAAATAAGGGCC
1 GTTTGCCAAAATGCTCAAATAAGAGTCTAATCTTTTAATTTGACCAAATAAGGGCC
45543 GGCAAATAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (60 bp):
GTTTGCCAAAATGCTCAAATAAGAGTCTAATCTTTTAATTTGACCAAATAAGGGCCTAAT
Found at i:45682 original size:60 final size:59
Alignment explanation
Indices: 45600--45733 Score: 189
Period size: 60 Copynumber: 2.2 Consensus size: 59
45590 GATACCAGGC
*
45600 CCTTATTTGAACATTTTCGATAACATTAGGCCCTTATTTCGCCAAATTAAGAGATCAGA
1 CCTTATTTGAACATTTTCGATAACATTAGGCCCTTATTTCGCCAAATTAAAAGATCAGA
* * *
45659 TCCTTATTTGAGCAGTTTT-GATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
1 -CCTTATTTGAACA-TTTTCGATAACATTAGGCCCTTATTTCGCCAAATTAAAAGATCAGA
*
45719 CCTTTATTTAAACAT
1 CC-TTATTTGAACAT
45734 CTTGACAAAC
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
59 3 0.05
60 59 0.89
61 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (59 bp):
CCTTATTTGAACATTTTCGATAACATTAGGCCCTTATTTCGCCAAATTAAAAGATCAGA
Found at i:45745 original size:60 final size:60
Alignment explanation
Indices: 45625--45759 Score: 175
Period size: 60 Copynumber: 2.2 Consensus size: 60
45615 TTCGATAACA
* * * * * *
45625 TTAGGCCCTTATTTCGCCAAATTAAGAGATCAGATCCTTATTTGAGCAGTTTTGATAACG
1 TTAGGCCCTTATTTGGCCAAATTAAAAGATCAGATCCTTATTTAAACAGTCTTGAAAACG
45685 TTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA-CCTTTATTTAAACA-TCTTGACAAACG
1 TTAGGCCCTTATTTGGCCAAATTAAAAGATCAGATCC-TTATTTAAACAGTCTTGA-AAACG
*
45745 TTAGACCCTTATTTG
1 TTAGGCCCTTATTTG
45760 AGCAATTAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 7 0.11
60 59 0.89
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (60 bp):
TTAGGCCCTTATTTGGCCAAATTAAAAGATCAGATCCTTATTTAAACAGTCTTGAAAACG
Found at i:50308 original size:6 final size:6
Alignment explanation
Indices: 50297--50323 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
50287 TAATAAATGC
50297 AATACT AATACT AATACT AATACT AAT
1 AATACT AATACT AATACT AATACT AAT
50324 GTACTATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
AATACT
Found at i:50872 original size:7 final size:7
Alignment explanation
Indices: 50862--50888 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
50852 TAGTAGTAAG
50862 TATAAAC
1 TATAAAC
50869 TATAAAC
1 TATAAAC
50876 TATAAAC
1 TATAAAC
50883 TATAAA
1 TATAAA
50889 GAGCTAAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (7 bp):
TATAAAC
Found at i:53427 original size:31 final size:31
Alignment explanation
Indices: 53392--53453 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
53382 AATTCAATCT
53392 TATCCCATTATCTTATTTTGGGTGAATGAAA
1 TATCCCATTATCTTATTTTGGGTGAATGAAA
53423 TATCCCATTATCTTATTTTGGGTGAATGAAA
1 TATCCCATTATCTTATTTTGGGTGAATGAAA
53454 ATATTAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (31 bp):
TATCCCATTATCTTATTTTGGGTGAATGAAA
Found at i:55844 original size:13 final size:13
Alignment explanation
Indices: 55826--55857 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
55816 TGACACGTCA
55826 GGAGGGACAAATT
1 GGAGGGACAAATT
*
55839 GGAGGGACAAGTT
1 GGAGGGACAAATT
55852 GGAGGG
1 GGAGGG
55858 TCATATAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.50, T:0.12
Consensus pattern (13 bp):
GGAGGGACAAATT
Found at i:61045 original size:18 final size:18
Alignment explanation
Indices: 61022--61080 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
61012 GAAGCTTCTT
61022 AAGATTTTGCACAATAAA
1 AAGATTTTGCACAATAAA
* *
61040 AAGATTTCTGGCAAAAAAAAAA
1 AAGATTT-T-GC--ACAATAAA
*
61062 AAGATTTTGCACATTAAA
1 AAGATTTTGCACAATAAA
61080 A
1 A
61081 GGTGTAGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
18 13 0.41
19 1 0.03
20 4 0.12
21 1 0.03
22 13 0.41
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (18 bp):
AAGATTTTGCACAATAAA
Found at i:61861 original size:19 final size:19
Alignment explanation
Indices: 61837--61873 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
61827 GTACAGTACA
61837 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
61856 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
61874 TACCAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Done.