Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022487.1 Corchorus olitorius cultivar O-4 contig22520, 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: 215754
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1879 original size:330 final size:330
Alignment explanation
Indices: 753--2391 Score: 1626
Period size: 330 Copynumber: 5.0 Consensus size: 330
743 ATTTAATTAA
* * * * * * *
753 AAAAATAAGAAATATGATATTAAAAGCGT-AAAATACCCTCCAATCTTTTTGGTATTGAGTTATA
1 AAAAATAGGAAAAACGATATTAAAAGCGTGAAAA-GCCCTTCAATCTTTTTGGTGTTGAATTATA
* * *
817 TATTTTTATGAGTATTTTTGCCAAAAATTGAGGAGAAATCTTTCGTGTCAATTTTTGCAAAATTT
65 TATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTT
* * *
882 TAGCCGAAATCGTGTACTAACAAACCATCACGGTTTTTGGCTAAAAACGCG-TTCCGGGTACCC-
130 TAGCCGAAATCGTG---TAA-TAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGT-CCCG
* * * * * *
945 GCTCAATTTTGCATGATTTTTTGCTCCAAAACTACTTGAAATATCTATATTCATCTAATCAATTC
190 GCTCAATTTTGCATGATTTTTGGCGCCGAAACTCCTTAAAATATCTATATTCATCTAATCAAATC
* * *
1010 TCAGCCACATTAG-ATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTTTTTCGATTTAATTAG
255 TCAGCCACATT-GCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAG
*
1074 AAATTAATTTGA-
319 AAATT-ATTTCAG
* * **
1086 AAAAATAGGAAAAAAGATATTAGAAA-CGTCAAATTCCCTTCAATCTTTTTGGTGTTGAATTATA
1 AAAAATAGGAAAAACGATATTA-AAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTATA
* * * *
1150 TATTTTTTATGAGTATTTTAGCCAAAATTTGAGGAAACATCTTTCGGGTCCATTTTTTACAAAAT
65 TA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGT-CAATTTTTGCAAAAT
* * * *
1215 GTTAGCCGAAATCGTGTAATAACCATCACAGCTTTTGGCTAAAAAAGCGTTCCGGGGTCCCGGCT
128 TTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCT
* * * * *
1280 CAATTTTGCATAATTTTTTGCGCC-AAGACTCCTTAAGATATCCATATCCATCTAATCAAATCTC
193 CAATTTTGCATGATTTTTGGCGCCGAA-ACTCCTTAAAATATCTATATTCATCTAATCAAATCTC
* * * *
1344 AGCCACATTGAATTAAAGAATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAAAAA
257 AGCCACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
**
1409 TTATTTTTG
322 TTATTTCAG
* * * * * * *
1418 AAGAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATAT
1 AAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTATAT
** * * *
1483 AAATTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTTTCTGGTCATTTTTTGCAAAATTTT
66 ATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTT
* * * * * * *
1548 AGCCAAAATCGTGTACTACCCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCTCGACTCAG
131 AGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAA
* * *
1613 TTTTGCATGATTTTTGGCGCCGAAACTCCTTAAAATATCTGTATTGATCTAAT-AAATCTTAGCC
196 TTTTGCATGATTTTTGGCGCCGAAACTCCTTAAAATATCTATATTCATCTAATCAAATCTCAGCC
* * *
1677 ACATTGCATTTATGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAT
261 ACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAT
1742 TTCAG
326 TTCAG
* * *
1747 AAAAATATGAAAAACGATAATAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATCT-TA
1 AAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAAT-TATA
* * * *
1811 TATTTTTCATGAGTATTATGGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATT
65 TATTTTT-ATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATT
* * * * * *
1876 TTAGCTGAAATCGTGTAATAATCATCACAGTTTTTTGCTAAAGACGTGTTTCGGGG-CCCGGTTC
129 TTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTC
* * * * * * *
1940 AATTTTGAATGATTTTTGACACCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAG
194 AATTTTGCATGATTTTTGGCGCCGAAACTCCTTAAAATATCTATATTCATCTAATCAAATCTCAG
* * *
2005 ---C----CA-TT----A----TTTTTACAAGTATCTGAATCATGTTTCGTTTTAATTAGAAATT
259 CCACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
*
2054 ACTTCGAGG
324 ATTTC-A-G
* * * * **
2063 AAAAATAGGAAAAA-GCTAATAGAAGCGTGAAAAGCCCTTCAACCTTTTTTATGTTGAATTATAT
1 AAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTATAT
* * * * * * *
2127 ATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTCGGGTCAGTTTTTACAAAATAT
66 A-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTT
* * **** * *
2192 TAGCCGAAATCGTGTAA-CATCATGGTTTTTCTTTTTTTTTCTTTTTGGCTAAAAACGTGTTCCG
130 TAGCCGAAATCGTGTAATAACCA-------TC------ACAGTTTTTGGCTAAAAACGCGTTTCG
* ** * *
2256 GGGCCCCGGGACAGTTTTGCATGATTTTTAGCGCC-AAGACTCCTTAAAATATCTATATTCATCT
182 GGGTCCCGGCTCAATTTTGCATGATTTTTGGCGCCGAA-ACTCCTTAAAATATCTATATTCATCT
* * * * * * * * *
2320 GATTAAAGCTCAGTCAGATTGGATTTATGGATTTATTTTTACAAGCATCTAAATCTTGTTTCGAT
246 AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGAT
2385 TTAATTA
311 TTAATTA
2392 TAATAATAAA
Statistics
Matches: 1087, Mismatches: 170, Indels: 87
0.81 0.13 0.06
Matches are distributed among these distances:
314 47 0.04
315 112 0.10
316 19 0.02
318 1 0.00
321 2 0.00
322 2 0.00
323 2 0.00
327 25 0.02
328 57 0.05
329 183 0.17
330 219 0.20
331 81 0.07
332 175 0.16
333 50 0.05
334 47 0.04
335 29 0.03
336 2 0.00
340 1 0.00
344 33 0.03
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (330 bp):
AAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTATAT
ATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTT
AGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAA
TTTTGCATGATTTTTGGCGCCGAAACTCCTTAAAATATCTATATTCATCTAATCAAATCTCAGCC
ACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAT
TTCAG
Found at i:4347 original size:332 final size:329
Alignment explanation
Indices: 2896--4951 Score: 2104
Period size: 332 Copynumber: 6.2 Consensus size: 329
2886 TCTTCAATAG
* * * *
2896 TTTTGGTGTTGAATTATATATATTTTTATGAGTATTTTA-GCAAAAAATTGAGGAAATATCTTTC
1 TTTTGGAGTTAAATTATATATA-TTTTATGAGTATTTTAGGC-AAAAATTGAGGAAAAAT-TTTT
* * * * * *
2960 CG-GTCAATTTTTGC--ATTTTTAGCTGAAATCGTGTATTAATCATCACGGTATTTGGCTTAAAA
63 CGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
* * * * * * ** * * * **
3022 CGCATTACAGGGCCCCGGGTCAGTTTTGCTTTATTTTTGACGCTAATATTCCTTGAGATATCCGT
128 CGCGTT-C-GGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTAT
* * * ** *
3087 ATTCATCTAATCAAATCTCAGCCGCATTGCATTTAAGGATTTCTTTTTAAGAAAATCTGAATATT
191 ATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTT
* * *
3152 TTTTCGATTTAATTAGAAATTAATTC--------AT-AAAAA--ATATGAAAAGCGTGAAAAGCC
256 GTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTC
*
3206 CTCTAATCT
321 CTCCAATCT
* *
3215 GTTTGGCGTTAAATTTTTATATATATATATATATATATCAAGAGTATTTTA-GCAAAAAAATTGA
1 TTTTGGAGTT-AA-----AT-TATATATAT-T-T-TAT---GAGTATTTTAGGC--AAAAATTGA
* * * *
3279 GGAAAAATTTTTC-TAGTCATTTTTTCCAAAATTTTAGGCGAAATCGTGTACAAACCATCACAGT
51 GGAAAAATTTTTCGT-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-G-
* * * * * * * *
3343 TTTTTTTGCTAAAAACGCCTTTTGGGGCCCGGGCTCAGTTTTGCATGATTTATGGCGTCGAGGCT
113 GTTTTTGGCTAAAAACG-CGTTCGGGACCC-GGCTCAGTTTTGCATGATTTTTGGCGCCGAGACT
*
3408 CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTATTTTTAC
176 CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTAC
* * * *
3473 GAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAAATGAAAAACGATTTTA
241 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTA
3538 AAAGCGTGAAAAGTCCTCCAATCT
306 AAAGCGTGAAAAGTCCTCCAATCT
* * * * ** * *
3562 TTTTGGAGTTGAGTTATATATATGTTATGAGTATTTTAGACAAAAACCGAGGAAAAATATAT-GT
1 TTTTGGAGTTAAATTATATATATTTTATGAGTATTTTAGGCAAAAATTGAGGAAAAATTTTTCGT
* * * *
3626 AGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACATTAGTCGAAGTCACGGTTTTTGACTAA
66 -GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TA-AC-CA-TCACGGTTTTTGGCTAA
* * * * ** *
3691 AAACGAGCTCCGGGACCCCGGTTCAGTTTTGCAT-TTTTTTTTCGCTGAGACTCCTTGAAATATC
125 AAACGCG-TTCGGGA-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATC
* * *** *
3755 TATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG-TAAAACAAGCATCTGAAT
188 TATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * * * *
3819 CATGTTTCGATTTAATTAGAAATTAATTCATAAAAAAATAGGGAAAACGATATTAGAAGCATGAA
253 CTTGTTTCGATTTAATTAGAAATTAATTC--AGAAAAATATGAAAAACGATATTAAAAGCGTGAA
* *
3884 AAGCCCTTCAATCT
316 AAGTCCTCCAATCT
* * * * * *
3898 TTTTGGTGTTTAATTATATATTTTTTATGAGTATTGT-GGCTAAAAATTGAGTAAATAA-CTTTC
1 TTTTGGAGTTAAATTATATATATTTTATGAGTATTTTAGGC-AAAAATTGAGGAAA-AATTTTTC
* * * *
3961 GAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAATCATCACGGTTTTTGGCTAAAAAC
64 GTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
* * * * * * *
4026 GTGTTCCAGGGACCCGACTAAGTTTTGCATGATTTTTGGCGCCAAGTCT-CTTTAAGATATCCAT
129 GCGTT-C-GGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAA-ATATCTAT
* * *
4090 ATTCATCTAATCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTT
191 ATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTT
* *
4155 GTTTCGATTTAATTAGAAATCAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTA
256 GTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTC
*
4220 TTCCAATCT
321 CTCCAATCT
* * *
4229 TTTT-GACGTCAAATTATATATATTTTATAAGTATTTTAGGCAAAAATTGACTGAAAAATTTTTC
1 TTTTGGA-GTTAAATTATATATATTTTATGAGTATTTTAGGCAAAAATTGA-GGAAAAATTTTTC
* * *
4293 GTGTCATTTTTTGCAAAATTTTAGACAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
64 GTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
* * * * *
4358 GTGTTTTGGGTCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATA
129 GCG-TTCGGG-ACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATA
* *
4423 TTCATCTAATCAAATCCCAGCCACATT---TTGAAGGATTTGTTTTTACGAGCATCTGAATCTTG
192 TTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * *
4485 TTTCGATTTAATTAGCAATTAATTCAGAAAAATAAGAAAAATGATATTAAAAGCGTGAAAAGTAC
257 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
4550 TCCAAT-T
322 TCCAATCT
** * * *
4557 TTTTCTATGTTAAATTATATATATTTTACGAGTATTTTAGCCCAAAATTGACGG-AAAATTTTAT
1 TTTTGGA-GTTAAATTATATATATTTTATGAGTATTTTAGGCAAAAATTGA-GGAAAAATTTT-T
* * * *
4621 -G-GGCCATTTTTCACAAAATTTTAGCCTAAATCGTGTACTTAACCATCACGGTTTTTGGCTAAA
63 CGTGTCAATTTTT-GCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTTTGGCTAAA
* * * *
4684 AACGCGTTTCGGGGCCCTGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTTCATGAAATATCT
126 AACGCG-TTCGGGACCC-GGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCT
* * *
4749 ATATTCATCTAATCAAATATCGGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATC
189 ATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATC
* *
4814 TTGTTTCGATTTAATTAGAAAGTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG
254 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG
4879 TCCTCCAATCT
319 TCCTCCAATCT
* * **
4890 TTTTGGAATTAAATTATATGTATTTTATGAGTATTTTAACCAAAAATTGACGGAAAAATTTT
1 TTTTGGAGTTAAATTATATATATTTTATGAGTATTTTAGGCAAAAATTGA-GGAAAAATTTT
4952 AGCCGAAATC
Statistics
Matches: 1450, Mismatches: 218, Indels: 124
0.81 0.12 0.07
Matches are distributed among these distances:
319 8 0.01
320 1 0.00
325 3 0.00
326 9 0.01
327 8 0.01
328 43 0.03
329 249 0.17
330 2 0.00
331 141 0.10
332 368 0.25
333 112 0.08
334 78 0.05
335 77 0.05
336 280 0.19
337 14 0.01
338 5 0.00
340 9 0.01
341 1 0.00
344 2 0.00
345 5 0.00
346 1 0.00
347 34 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (329 bp):
TTTTGGAGTTAAATTATATATATTTTATGAGTATTTTAGGCAAAAATTGAGGAAAAATTTTTCGT
GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGC
GTTCGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
TCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
GATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCA
ATCT
Found at i:4814 original size:661 final size:649
Alignment explanation
Indices: 2896--5559 Score: 2436
Period size: 661 Copynumber: 4.0 Consensus size: 649
2886 TCTTCAATAG
* * * *
2896 TTTTGGTGTTGAATTATATATATTTTTATGAGTATTTTAG-CAAAAAATTGAGGAAATATCTTTC
1 TTTTGGAGTTAAATTATATATA-TTTTATGAGTATTTTAGAC-AAAAA-TGATGAAA-A-ATTT-
* * * * * *
2960 CG-GTCAATTTTTGC--ATTTTTAGCTGAAATCGTGTATTAATCATCACGGTATTTGGCTTAAAA
60 CGTGTC-ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
* * * * * * ** * * * * *
3022 CGCA-TTACAGGG-CCCCGGGTCAGTTTTGCTTTATTTTTGACGCTAATATTCCTTGAGATATCC
124 CG-AGTTTC-GGGACCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCT
* * * * * ** *
3085 GTATTCATCTAATCAAATCTCAGCCGCATTGCATTTAAGGATTTCTTTTTAAGAAAATCTGAATA
187 ATATTCATCTAACCAAATCTCAGCCACATT--A-TTAAGGATTTGTTTTTACGAGCATCTGAATC
* *
3150 TTTTTTCGATTTAATTAGAAATTAATTC------AT---AAAAA--ATATGAAAAGCGTGAAAAG
249 TTGTTTCGATTTAATTAG-AATTAATTCAGAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAG
* * * * *
3204 CCCTCTAATCTGTTTGGC-GTTAAATTTTTATATATATATATATATATATCAAGAGTATTTTAGC
313 TCCTCCAATCT-TTT-TCTGTT-AA-----AT-TATATATAT-T-T-TA-C--GAGTATTATGGC
* * * * *
3268 AAAAAAATTGAGGAAAAATTTTTCTAGTCATTTTTTCCAAAATTTTAGGCGAAATCGTGTACAAA
363 -AAAAAATTGA-GAAAAA-TTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-TAA
* * * * * *
3333 CCATCACAGTTTTTTTTGCTAAAAACGCCTTTTGGGGCCCGGGCTCAGTTTTGCATGATTTATGG
423 CCATCAC-G-GTTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGG
* * * * *
3398 CGTCGAGGCTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGAT
486 CGCCAAGACTTCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGAT
* * * *
3463 TTATTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAAAATGAAA
551 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAAATGAAA
*
3528 AACGATTTTAAAAGCGTGAAAAGTCCTCCAATCT
616 AACGATATTAAAAGCGTGAAAAGTCCTCCAATCT
* * * * *
3562 TTTTGGAGTTGAGTTATATATATGTTATGAGTATTTTAGACAAAAACCGAGGAAAAATATAT-GT
1 TTTTGGAGTTAAATTATATATATTTTATGAGTATTTTAGACAAAAA-TGATGAAAAAT-T-TCGT
* * * *
3626 AGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACATTAGTCGAAGTCACGGTTTTTGACTAA
63 -GTC-ATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TA-AC-CA-TCACGGTTTTTGGCTAA
* * * ** * *
3691 AAACGAGCTCCGGGACCCCGG-TTCAGTTTTGCAT-TTTTTTTTCGCTGAGACTCCTTGAAATAT
121 AAACGAGTTTCGGGACCCCGGCTT-AGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATAT
*** *
3754 CTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG-TAAAACAAGCATCTGAA
185 CTATATTCATCTAACCAAATCTCAGCCACATT--A-TTAAGGATTTGTTTTTACGAGCATCTGAA
* * * * * *
3818 TCATGTTTCGATTTAATTAGAAATTAATTCATAAAAAAATAGGGAAAACGATATTAGAAGCATGA
247 TCTTGTTTCGATTTAATTAG-AATTAATTC--AGAAAAATAAGAAAAACGATATTAAAAGCGTGA
* * * * * * * *
3883 AAAGCCCTTCAATCTTTTTGGTGTTTAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGA
309 AAAGTCCTCCAATCTTTTT-CTGTTAAATTATATATATTTTACGAGTATTATGGCAAAAAATTGA
* * *
3948 GTAAATAACTTTCGAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAATCATCACGGTT
373 G-AAA-AATTTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ATAACCATCACGGTT
* * * * * *
4013 TTTGGCTAAAAACGTGTTCCAGGGACCC-GACTAAGTTTTGCATGATTTTTGGCGCCAAGTC-TC
434 TTTGGCTAAAAACGCGTTTC-GGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTC
* * * *
4076 TTTAAGATATCCATATTCATCTAATCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACG
498 TTGAA-ATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* * *
4141 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATCAATTCAGAAAAATATGAAAAACGATATTAA
562 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAAATGAAAAACGATATTAA
**
4206 AAGCGTGAAAAGTATTCCAATCT
627 AAGCGTGAAAAGTCCTCCAATCT
* * *
4229 TTTT-GACGTCAAATTATATATATTTTATAAGTATTTTAGGCAAAAATTGACTGAAAAATTTTTC
1 TTTTGGA-GTTAAATTATATATATTTTATGAGTATTTTAGACAAAAA-TGA-TGAAAAA--TTTC
* *
4293 GTGTCATTTTTTGCAAAATTTTAGACAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
61 GTGTCA-TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
* * *
4358 GTGTTTTGGGTCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATA
125 GAGTTTCGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATA
* *
4423 TTCATCTAATCAAATCCCAGCCACATT-TTGAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
190 TTCATCTAACCAAATCTCAGCCACATTATT-AAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* *
4487 TCGATTTAATTAGCAATTAATTCAGAAAAATAAGAAAAATGATATTAAAAGCGTGAAAAGTACTC
254 TCGATTTAATTAG-AATTAATTCAGAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGTCCTC
* * ** *
4552 CAAT-TTTTTCTATGTTAAATTATATATATTTTACGAGTATTTTAGCCCAAAATTGACGGAAAAT
318 CAATCTTTTTC--TGTTAAATTATATATATTTTACGAGTATTATGGCAAAAAATTGA-GAAAAAT
* * * * *
4616 TTTATGGGCCATTTTTCACAAAATTTTAGCCTAAATCGTGTACTTAACCATCACGGTTTTTGGCT
380 TTT-CGGTCAATTTTT-GCAAAATTTTAGCCGAAATCGTGTA--TAACCATCACGGTTTTTGGCT
* * *
4681 AAAAACGCGTTTCGGGGCCCTGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTTCATGAAATA
441 AAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATA
* * *
4746 TCTATATTCATCTAATCAAATATCGGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGA
506 TCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
* *
4811 ATCTTGTTTCGATTTAATTAGAAAGTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAA
571 ATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAAATGAAAAACGATATTAAAAGCGTGAA
4876 AAGTCCTCCAATCT
636 AAGTCCTCCAATCT
* *
4890 TTTTGGAATTAAATTATATGTATTTTATGAGTATTTTA-ACCAAAAAT--TG----A---CG-G-
1 TTTTGGAGTTAAATTATATATATTTTATGAGTATTTTAGA-CAAAAATGATGAAAAATTTCGTGT
* * *
4943 -A-------AAAATTTTAGCCGAAATCGTATACTAACCATCACGATTTTTGGCTAAAAAC-ACAT
65 CATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGA-GT
* * *
4999 TTCGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCCTGAAATATCTATATTTA
129 TTCGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATATTCA
* ** * * * *
5064 TCTAACCAAATATTTGTCACATTGAAATTAAGTATTTGTTTTTACGAGCATCTGCATCTTCTTTC
194 TCTAACCAAATCTCAGCCACATT---ATTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
* * *
5129 GATTTAAATAGAATTTAATTCAGAAAAATATGAAAAAGGATATTAAAAGCGTGAAAAGTCCTCCA
256 GATTTAATTAGAA-TTAATTCAGAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCA
** * * * *
5194 ATCTTTGGC-GTTGAATTATATATATATTTTATC-AGTATTACGGCTAAAAAACTGAATAAAAAT
320 ATCTTTTTCTGTT-AAAT-TATATATATTTTA-CGAGTATTATGGC-AAAAAATTG-AGAAAAAT
5257 ATTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTG--T-ACCATCACGGTTTTTTTTGGC
380 -TTTCGG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACGG---TTTTTGGC
* * * * *
5319 TAAAAATGCGTTTCGGGGCCCTAGG-TCAGTTTTGCATGATTTTTTGTGGCAAAACTAT-TTGAA
440 TAAAAACGCGTTTCGGGGCCCT-GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACT-TCTTGAA
* *
5382 ATATCTATATTCATCTAAACAAATCTTAG-CATCATTGGATTTAAGGATTTGTTTTTACGAGCAT
503 ATATCTATATTCATCTAATCAAATCTCAGCCA-CATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * * * *
5446 TTGAATCATGTTTCGATTTAATTAGAATTTAATTTGAAAAAAAAAAGAAAAACGATATTAGAAGC
567 CTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCAAAAAAAAATGAAAAACGATATTAAAAGC
* **
5511 GTGAAAAGCCCTTTAATCT
631 GTGAAAAGTCCTCCAATCT
* *
5530 TTTTGGCGTTGAATTATATAT-TTTTATGAG
1 TTTTGGAGTTAAATTATATATATTTTATGAG
5560 AATTGTGGCT
Statistics
Matches: 1676, Mismatches: 244, Indels: 183
0.80 0.12 0.09
Matches are distributed among these distances:
636 10 0.01
637 126 0.08
638 5 0.00
639 156 0.09
640 178 0.11
641 41 0.02
642 11 0.01
645 1 0.00
647 1 0.00
648 2 0.00
653 1 0.00
657 2 0.00
659 19 0.01
660 107 0.06
661 243 0.14
662 48 0.03
663 44 0.03
664 59 0.04
665 42 0.03
666 30 0.02
667 237 0.14
668 46 0.03
669 59 0.04
670 51 0.03
671 69 0.04
672 36 0.02
673 2 0.00
674 1 0.00
675 1 0.00
676 8 0.00
677 2 0.00
678 2 0.00
681 4 0.00
682 4 0.00
683 28 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (649 bp):
TTTTGGAGTTAAATTATATATATTTTATGAGTATTTTAGACAAAAATGATGAAAAATTTCGTGTC
ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGAGTTT
CGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATATTCATC
TAACCAAATCTCAGCCACATTATTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
AATTAGAATTAATTCAGAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTT
TTCTGTTAAATTATATATATTTTACGAGTATTATGGCAAAAAATTGAGAAAAATTTTCGGTCAAT
TTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGG
GGCCCTGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTATATTCATCTAA
TCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
AATTAGAAATTAATTCAAAAAAAAATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCT
Found at i:7314 original size:48 final size:49
Alignment explanation
Indices: 7246--7349 Score: 165
Period size: 48 Copynumber: 2.1 Consensus size: 49
7236 AGCAAATTAT
* * *
7246 ATTTGATATGAAATTGCAAACAAATTTTATTTT-TTGAGGGTCAAACAA
1 ATTTTATATGAAAATGCAAACAAATTTCATTTTATTGAGGGTCAAACAA
*
7294 ATTTTATATGAAAATGCAAACAAATTTCATTTTATTTAGGGTCAAACAA
1 ATTTTATATGAAAATGCAAACAAATTTCATTTTATTGAGGGTCAAACAA
7343 ATTTTAT
1 ATTTTAT
7350 TTAAAGCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 30 0.59
49 21 0.41
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (49 bp):
ATTTTATATGAAAATGCAAACAAATTTCATTTTATTGAGGGTCAAACAA
Found at i:14159 original size:29 final size:29
Alignment explanation
Indices: 14099--14159 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
14089 ATTAGAAATG
****
14099 AAAATGCAAACAATTTTTTTTTCTCAAAA
1 AAAATGCAAACAATTTTTTTAAAACAAAA
*
14128 AAAATGCAAACAATTTTTTTAAAACAACA
1 AAAATGCAAACAATTTTTTTAAAACAAAA
14157 AAA
1 AAA
14160 GTCTTTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATGCAAACAATTTTTTTAAAACAAAA
Found at i:14404 original size:152 final size:153
Alignment explanation
Indices: 14128--14482 Score: 482
Period size: 152 Copynumber: 2.3 Consensus size: 153
14118 TTTCTCAAAA
* * **
14128 AAAATGCAAACAATTTT-TTTAAAACAACAAAAGTCTTTTATTTATATTATTTTTTTAAAAAACA
1 AAAATGCAAACAATTTTATTT-AAA-AACAAAAGTCCTTTATTTATATCATTTTAATAAAAAACA
*
14192 AAAATTTTATTCCGCTGCCGGGATTTGAACCCGGATTCCAAATATCCATAGGAATTGCCAAGTGC
64 AAAATTTTATTCCGCTGCCAGGATTTGAACCCGGATTCCAAATATCCATAGGAATTGCCAAGTGC
14257 TACAGC-A-GATTACATTTGATATG
129 TACAGCTAGGATTACATTTGATATG
*
14280 AAAATGCAAACAATTTTATTTAAAAACAAAAGTCCTTTATTTATATCATTTCTAATAAAAAATAA
1 AAAATGCAAACAATTTTATTTAAAAACAAAAGTCCTTTATTTATATCATTT-TAATAAAAAACAA
*
14345 AAATTTTATTCTGCTGCCAGGATTTGAACCCGGATTCCAAATATCCATAGGAATTGCCAAGTGCT
65 AAATTTTATTCCGCTGCCAGGATTTGAACCCGGATTCCAAATATCCATAGGAATTGCCAAGTGCT
* *
14410 ACAGCTTATTATATGCGGATTATATTTGATGTG
130 ACAGC------TA---GGATTACATTTGATATG
* *
14443 AAAATGTAAACAATTTTATTTAAAAACAAAAGTACTTTAT
1 AAAATGCAAACAATTTTATTTAAAAACAAAAGTCCTTTAT
14483 ATGCTTCTTC
Statistics
Matches: 179, Mismatches: 11, Indels: 15
0.87 0.05 0.07
Matches are distributed among these distances:
151 25 0.14
152 98 0.55
153 3 0.02
159 1 0.01
163 52 0.29
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (153 bp):
AAAATGCAAACAATTTTATTTAAAAACAAAAGTCCTTTATTTATATCATTTTAATAAAAAACAAA
AATTTTATTCCGCTGCCAGGATTTGAACCCGGATTCCAAATATCCATAGGAATTGCCAAGTGCTA
CAGCTAGGATTACATTTGATATG
Found at i:25063 original size:42 final size:43
Alignment explanation
Indices: 25018--25102 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 43
25008 CTAAATTCTA
*
25018 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTATA--C
*
25063 CTCCATCTCTAGATAATTCATTAAAATAAAGCTAATATTA
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTA
25103 ATTGCTGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (43 bp):
CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTATAC
Found at i:27915 original size:2 final size:2
Alignment explanation
Indices: 27872--27897 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27862 TTTTAGCTTT
27872 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
27898 AATTGTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29229 original size:86 final size:85
Alignment explanation
Indices: 29135--29304 Score: 225
Period size: 86 Copynumber: 2.0 Consensus size: 85
29125 AACATCTGAA
* * *
29135 AAAAAAACACATTAC-ATCTAACTGGATCATGTCAAGGAACGTCGAACACTATATCCAGAAGTGT
1 AAAAAAA-ACATTACAATCTAACTGGATCATCTCAAGGAACATCGAACACTATATCCAAAAGTGT
* * *
29199 CATAGGAGTACCAGTGTCGAG
65 CACAGGAGTACAAGTATCGAG
* * *
29220 AAAAAAAACATTACATATCTAGCTGGATCATCTCAAGGAACATTGAACACTATGTCCAAAAGTGT
1 AAAAAAAACATTACA-ATCTAACTGGATCATCTCAAGGAACATCGAACACTATATCCAAAAGTGT
*
29285 CGCAGGAGTACAAGTATCGA
65 CACAGGAGTACAAGTATCGA
29305 ACACGGGTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
84 7 0.10
85 7 0.10
86 59 0.81
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (85 bp):
AAAAAAAACATTACAATCTAACTGGATCATCTCAAGGAACATCGAACACTATATCCAAAAGTGTC
ACAGGAGTACAAGTATCGAG
Found at i:29980 original size:25 final size:26
Alignment explanation
Indices: 29952--30009 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
29942 AAAAGATCAA
29952 AAACA-CATGTATCAGTAGTGAGAGC
1 AAACACCATGTATCAGTAGTGAGAGC
* *
29977 AAACAAACCCTGTATTAGTAGTGAGAGC
1 AAAC--ACCATGTATCAGTAGTGAGAGC
30005 AAACA
1 AAACA
30010 AACTTGCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 4 0.14
26 1 0.04
27 1 0.04
28 22 0.79
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (26 bp):
AAACACCATGTATCAGTAGTGAGAGC
Found at i:29991 original size:28 final size:28
Alignment explanation
Indices: 29959--30012 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
29949 CAAAAACACA
29959 TGTATCAGTAGTGAGAGCAAACAAACCC
1 TGTATCAGTAGTGAGAGCAAACAAACCC
*
29987 TGTATTAGTAGTGAGAGCAAACAAAC
1 TGTATCAGTAGTGAGAGCAAACAAAC
30013 TTGCCTCCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (28 bp):
TGTATCAGTAGTGAGAGCAAACAAACCC
Found at i:31828 original size:27 final size:27
Alignment explanation
Indices: 31790--31844 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
31780 TGTTTATGAG
31790 TGATTCAGAAAATGTTTCTATTGTTCA
1 TGATTCAGAAAATGTTTCTATTGTTCA
31817 TGATTCAGAAAATGTTTCTATTGTTCA
1 TGATTCAGAAAATGTTTCTATTGTTCA
31844 T
1 T
31845 TAAGTTGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (27 bp):
TGATTCAGAAAATGTTTCTATTGTTCA
Found at i:37405 original size:22 final size:22
Alignment explanation
Indices: 37374--37433 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
37364 AAACGATCAA
*
37374 ATTTCGTCATTTTTTAATACCC
1 ATTTCTTCATTTTTTAATACCC
*
37396 ATTTCTTCATTTTATAATACCC
1 ATTTCTTCATTTTTTAATACCC
*
37418 ATTCCTTCATTTTTTA
1 ATTTCTTCATTTTTTA
37434 TATATCTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.23, C:0.22, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTCTTCATTTTTTAATACCC
Found at i:38821 original size:22 final size:22
Alignment explanation
Indices: 38796--38839 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
38786 ATCTTTAAGA
38796 ATATACTTTTAAGAGTAAATTT
1 ATATACTTTTAAGAGTAAATTT
38818 ATATACTTTTAAGAGTAAATTT
1 ATATACTTTTAAGAGTAAATTT
38840 TATTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (22 bp):
ATATACTTTTAAGAGTAAATTT
Found at i:54972 original size:52 final size:52
Alignment explanation
Indices: 54906--55007 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
54896 CCTTATGTTG
*
54906 TTTTTAGTTGTTTGTATTTGAAAATTTTTAAATATCGAATTAATCTTTCAGA
1 TTTTTAGTTATTTGTATTTGAAAATTTTTAAATATCGAATTAATCTTTCAGA
* *
54958 TTTTTTGTTATTTGTATTTGAAAATTTTTAAATATCGGATTAATCTTTCA
1 TTTTTAGTTATTTGTATTTGAAAATTTTTAAATATCGAATTAATCTTTCA
55008 AATTAATCTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (52 bp):
TTTTTAGTTATTTGTATTTGAAAATTTTTAAATATCGAATTAATCTTTCAGA
Found at i:61515 original size:27 final size:27
Alignment explanation
Indices: 61477--61530 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
61467 TCAAGAAAAA
61477 TAGATGTTAATTTGGGGTTAAATCTAT
1 TAGATGTTAATTTGGGGTTAAATCTAT
61504 TAGATGTTAATTTGGGGTTAAATCTAT
1 TAGATGTTAATTTGGGGTTAAATCTAT
61531 GATTGACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (27 bp):
TAGATGTTAATTTGGGGTTAAATCTAT
Found at i:68682 original size:1 final size:1
Alignment explanation
Indices: 68676--68707 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
68666 GTAAATTTGT
68676 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
68708 CCTTCTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:69767 original size:9 final size:9
Alignment explanation
Indices: 69753--69777 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
69743 GAGATAGTGC
69753 TGAAGTTGA
1 TGAAGTTGA
69762 TGAAGTTGA
1 TGAAGTTGA
69771 TGAAGTT
1 TGAAGTT
69778 AAATATCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (9 bp):
TGAAGTTGA
Found at i:81147 original size:2 final size:2
Alignment explanation
Indices: 81140--81168 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
81130 GAAGAAAAAC
81140 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
81169 TAAAGAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:83753 original size:6 final size:6
Alignment explanation
Indices: 83742--83766 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
83732 ACTCATTAGT
83742 ACTAGA ACTAGA ACTAGA ACTAGA A
1 ACTAGA ACTAGA ACTAGA ACTAGA A
83767 TGGTGCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
ACTAGA
Found at i:96524 original size:45 final size:45
Alignment explanation
Indices: 96459--96590 Score: 201
Period size: 45 Copynumber: 2.9 Consensus size: 45
96449 GTTGATGTTG
* * *
96459 CAAGTCCTGCATCTAATTTGGCATCAAATGCTCAGTCAGTGCTTT
1 CAAGTCCTGCATCTAGTTTGGCATCAAATGCTCAGCCAGTGCTTC
*
96504 CAAGTCCTGCATCTGGTTTGGCATCAAATGCTCAGCCAGTGCTTC
1 CAAGTCCTGCATCTAGTTTGGCATCAAATGCTCAGCCAGTGCTTC
* * *
96549 CAACTCCTGCATCTAGTTTGGCGTCAAGTGCTCAGCCAGTGC
1 CAAGTCCTGCATCTAGTTTGGCATCAAATGCTCAGCCAGTGC
96591 AGCCTTCTAC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (45 bp):
CAAGTCCTGCATCTAGTTTGGCATCAAATGCTCAGCCAGTGCTTC
Found at i:99716 original size:2 final size:2
Alignment explanation
Indices: 99709--99737 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
99699 TGTCCATACT
99709 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
99738 TATTGTGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:100959 original size:32 final size:32
Alignment explanation
Indices: 100923--100985 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
100913 TTGTATGCAG
* *
100923 CAAAATTATCAGACAGCGTAAGTAATGCATTA
1 CAAAATTATCAAACAGCGTAAGTAAGGCATTA
100955 CAAAATTATCAAACAGCGTAAGTAAGGCATT
1 CAAAATTATCAAACAGCGTAAGTAAGGCATT
100986 TCAAGAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (32 bp):
CAAAATTATCAAACAGCGTAAGTAAGGCATTA
Found at i:102591 original size:3 final size:3
Alignment explanation
Indices: 102583--102625 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
102573 TATATTATAT
102583 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
102626 ATATTATTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:106761 original size:107 final size:109
Alignment explanation
Indices: 106548--106761 Score: 272
Period size: 107 Copynumber: 2.0 Consensus size: 109
106538 TGGTTCAATG
* * **
106548 TTGTTGAAGTTTAGACTAACATGGTAGACAAATGTTAAAGTTCAAAGTGTAAGTTGCATGTTTTT
1 TTGTTAAAGTTTAGACTAACATGGTAGACAAATGTTAAAGTTCAAAGTGCAAGTTGCA-GCATTT
* * *
106613 TTGTTTAGGTACTAATTTGTGCATCTAACTGTAGTTCGAGTAACA
65 TTCTTCAGATACTAATTTGTGCATCTAACTGTAGTTCGAGTAACA
*
106658 TTGTTAAAGTTTAGACTAACATGGTAGAC-AAT-TTGAAAGTTCAAGGTGCAAGTTGCA-CATTT
1 TTGTTAAAGTTTAGACTAACATGGTAGACAAATGTT-AAAGTTCAAAGTGCAAGTTGCAGCATTT
** * * *
106720 TTCTTCAGATTTTAATTTGTGCATTTCACTGTAGTTTGAGTA
65 TTCTTCAGATACTAATTTGTGCATCTAACTGTAGTTCGAGTA
106762 CAATATTTGC
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
107 37 0.41
108 2 0.02
109 23 0.26
110 28 0.31
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (109 bp):
TTGTTAAAGTTTAGACTAACATGGTAGACAAATGTTAAAGTTCAAAGTGCAAGTTGCAGCATTTT
TCTTCAGATACTAATTTGTGCATCTAACTGTAGTTCGAGTAACA
Found at i:111627 original size:19 final size:19
Alignment explanation
Indices: 111605--111642 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
111595 TTTGTATTTG
111605 TGCCTGAAGTCTGTTTCTT
1 TGCCTGAAGTCTGTTTCTT
111624 TGCCTGAAGTCTGTTTCTT
1 TGCCTGAAGTCTGTTTCTT
111643 CAGATGTTGG
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:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
TGCCTGAAGTCTGTTTCTT
Found at i:121585 original size:21 final size:18
Alignment explanation
Indices: 121547--121583 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
121537 ATCATCATTG
121547 TATTTTCCACTGTCATCA
1 TATTTTCCACTGTCATCA
*
121565 TATTTTCCACTGTCCTCA
1 TATTTTCCACTGTCATCA
121583 T
1 T
121584 CAGATTCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.30, G:0.05, T:0.46
Consensus pattern (18 bp):
TATTTTCCACTGTCATCA
Found at i:127728 original size:21 final size:20
Alignment explanation
Indices: 127704--127746 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
127694 GAAATATTTC
*
127704 ATTAGAAATTAATTTCTAATA
1 ATTACAAATT-ATTTCTAATA
* *
127725 ATTACATATTATTTTTAATA
1 ATTACAAATTATTTCTAATA
127745 AT
1 AT
127747 ATTTACTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTACAAATTATTTCTAATA
Found at i:127902 original size:21 final size:21
Alignment explanation
Indices: 127878--127939 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
127868 AATCTTAATT
127878 AACGAACATAAACGAGCTA-TA
1 AACGAACATAAACGAGC-ACTA
* *
127899 AACGAACAATAAATGAACACTA
1 AACGAAC-ATAAACGAGCACTA
*
127921 AACGAACATTAATCGAGCA
1 AACGAACA-TAAACGAGCA
127940 TGTTCGTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 9 0.27
22 24 0.73
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.15
Consensus pattern (21 bp):
AACGAACATAAACGAGCACTA
Found at i:127910 original size:11 final size:11
Alignment explanation
Indices: 127878--127928 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
127868 AATCTTAATT
127878 AACGAAC-ATA
1 AACGAACAATA
* *
127888 AACGAGCTATA
1 AACGAACAATA
127899 AACGAACAATA
1 AACGAACAATA
* *
127910 AATGAACACTA
1 AACGAACAATA
127921 AACGAACA
1 AACGAACA
127929 TTAATCGAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
10 6 0.18
11 28 0.82
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.12
Consensus pattern (11 bp):
AACGAACAATA
Found at i:129248 original size:16 final size:16
Alignment explanation
Indices: 129227--129261 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
129217 TTATATAATT
129227 TATATTCTAGCTA-TAC
1 TATATTCTAG-TAGTAC
129243 TATATTCTAGTAGTAC
1 TATATTCTAGTAGTAC
129259 TAT
1 TAT
129262 TTAACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (16 bp):
TATATTCTAGTAGTAC
Found at i:129612 original size:37 final size:38
Alignment explanation
Indices: 129544--129621 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 38
129534 TGGATTTTTC
* *
129544 GTTTGACTTAGTTTAAGTTTTTTTTCGGTAGATAAGTT
1 GTTTGACTTAATTTAAGTTTTTTTTCGGTAGATAAGCT
129582 GTTTGACTTAATTTAAG-TTTTTTTCGGTAGATAAGCT
1 GTTTGACTTAATTTAAGTTTTTTTTCGGTAGATAAGCT
129619 GTT
1 GTT
129622 AAATAAGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 22 0.58
38 16 0.42
ACGTcount: A:0.22, C:0.06, G:0.21, T:0.51
Consensus pattern (38 bp):
GTTTGACTTAATTTAAGTTTTTTTTCGGTAGATAAGCT
Found at i:131788 original size:17 final size:17
Alignment explanation
Indices: 131766--131800 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
131756 TAAATCACAA
131766 ACATTTGAAAGTCTTGG
1 ACATTTGAAAGTCTTGG
131783 ACATTTGAAAGTCTTGG
1 ACATTTGAAAGTCTTGG
131800 A
1 A
131801 GGAGAAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (17 bp):
ACATTTGAAAGTCTTGG
Found at i:135444 original size:26 final size:23
Alignment explanation
Indices: 135415--135462 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
135405 AAATTTTATC
135415 TATAAATTAAAGATATAAATAATATA
1 TATAAA-TAAA-ATAT-AATAATATA
*
135441 TATAAATAAAATCTAATAATAT
1 TATAAATAAAATATAATAATAT
135463 TATTTATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 3 0.14
25 4 0.19
26 6 0.29
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TATAAATAAAATATAATAATATA
Found at i:136121 original size:2 final size:2
Alignment explanation
Indices: 136114--136144 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
136104 TATAGATTAG
*
136114 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
136145 AATTTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:136510 original size:31 final size:32
Alignment explanation
Indices: 136469--136531 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
136459 AATTAAAAAG
* * *
136469 TTTATGAGATTGGAGATTAGATTTTGTATCCT
1 TTTATGAGATTGGAGATCAGAGTTCGTATCCT
136501 TTTAT-AGATTGGAGATCAGAGTTCGTATCCT
1 TTTATGAGATTGGAGATCAGAGTTCGTATCCT
136532 CGTACTCCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.43
Consensus pattern (32 bp):
TTTATGAGATTGGAGATCAGAGTTCGTATCCT
Found at i:137287 original size:124 final size:128
Alignment explanation
Indices: 137147--137404 Score: 389
Period size: 124 Copynumber: 2.0 Consensus size: 128
137137 CATTGTTTAA
137147 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA-A
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACA
* * *
137211 -GTTTTACCATTTTACTGTTTTAATTAAAAAAAC-T-TATATATATTAGAATTTTTTAAATAT
66 TATTTTACAATTTTACTATTTTAATTAAAAAAACATATATATATATTAGAATTTTTTAAATAT
* *
137271 ACTTTTATAGTTTTACTCAACTAAAAACTTTATTTTTGTTTAATTAAATCTAATATCCTTATACC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA-C
*
137336 TATTTTATTTTACAATTTTACTATTTTAATTAAAAAACCATATATATATATTAGAATTTTTTAAA
65 -A---TATTTTACAATTTTACTATTTTAATTAAAAAAACATATATATATATTAGAATTTTTTAAA
137401 TAT
126 TAT
137404 A
1 A
137405 TTTCTTAAAT
Statistics
Matches: 119, Mismatches: 6, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
124 61 0.51
127 1 0.01
131 29 0.24
132 1 0.01
133 27 0.23
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (128 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACA
TATTTTACAATTTTACTATTTTAATTAAAAAAACATATATATATATTAGAATTTTTTAAATAT
Found at i:137412 original size:13 final size:14
Alignment explanation
Indices: 137391--137428 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
137381 ATATATTAGA
137391 ATTTTTTAAATAT-
1 ATTTTTTAAATATC
* *
137404 ATTTCTTAAATGTC
1 ATTTTTTAAATATC
137418 ATTTTTTAAAT
1 ATTTTTTAAAT
137429 TTTACAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (14 bp):
ATTTTTTAAATATC
Found at i:139224 original size:2 final size:2
Alignment explanation
Indices: 139212--139262 Score: 66
Period size: 2 Copynumber: 25.0 Consensus size: 2
139202 TTATAAATTT
* * *
139212 TA TA TA GA TA TA TA TA TA TA TA TC TA TA TA TA CTC 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
139255 TA TA TA TA
1 TA TA TA TA
139263 GCTAATGGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 41 0.98
3 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:139800 original size:13 final size:13
Alignment explanation
Indices: 139782--139808 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
139772 TTACACTTAG
139782 TAAATATCTTTTT
1 TAAATATCTTTTT
139795 TAAATATCTTTTT
1 TAAATATCTTTTT
139808 T
1 T
139809 GGGATCCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (13 bp):
TAAATATCTTTTT
Found at i:141467 original size:331 final size:323
Alignment explanation
Indices: 140780--141646 Score: 977
Period size: 330 Copynumber: 2.6 Consensus size: 323
140770 TACAAACACC
* * * * *
140780 AGATTTAAGGGCTTTTCACGCTTTTAATATTGTGTTTCATATTTTCTGAATTAATTTCTAATTAA
1 AGATTGAAGGGCTTTTCACG-TTTTAATATCGTTTTTCATATTTTCTAAATTAAATTCTAATTAA
* * ** * * *
140845 ATCGAAACAATAATCAGATGCTCGTAAAAAGAAACCCTTAAATGCAATGTGGCTAAAATTT-ATT
65 ATCGAAACAAGATTCAGATGCTCGTAAAAA-AAAATCTTAAATCCAATGTGGCTGAGATTTGATT
* * * *
140909 TGATGAATATAGATATTTTAAGGAGTCTCGGCGCCAAAAATCATACAAAACTGAGCTGGGCCACG
129 AGATGAATATAGATA-TTTAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCGGGGCCCCG
* * *
140974 AAACACGTTTTTAGCCAAAAACCGTGATGGTTACACGATTTTGGCTAAAAATTTGCAAAAAATGA
193 -AACGCTTTTTTAGCCAAAAACCGTGATGGTTACACGATTTCGGCTAAAAATTTGCAAAAAATGA
* ** * ** ** * **
141039 CTCAAAATTTTTTTTTGTCAATTTTTGGATAAAATACTCATAAAATTTATATAATTTAATGCCAA
257 CCCAAAATGATATTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAACACCAA
141104 AA
322 AA
* * *
141106 AGATTGGAGGACTTTTCACACTTTTAATATCGTTTTTCATATTTCTCTAAATTAAATTCTAATTA
1 AGATTGAAGGGCTTTTCAC-GTTTTAATATCGTTTTTCATATTT-TCTAAATTAAATTCTAATTA
* * *
141171 AATCGAAATAAGATTCAGATGCTTGTAAAAACAAATACTTAAATCCAATGTGGCTGAGATTTGAT
64 AATCGAAACAAGATTCAGATGCTCGTAAAAAAAAAT-CTTAAATCCAATGTGGCTGAGATTTGAT
* * *
141236 TAGATGAATATGGATATCTTAAGGAGTGTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCC
128 TAGATGAATATAGATAT-TTAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG-CGGGGCCC
* * * * *
141301 CAGAACGCTTTTTTAGGCAAAAACTGTGATGGTTATTACACGATTTCGGCTTAAATTTTGTAAAA
191 C-GAACGCTTTTTTAGCCAAAAACCGTGATGG---TTACACGATTTCGGCTAAAAATTTGCAAAA
* * * *
141366 ATTGACCCGAAA-GATATTTCCTCAATTTTTTGCTAAAATACTCATAAAAAATATATAATTCAAC
252 AATGACCCAAAATGATATTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAAC
141430 ACCAAAA
317 ACCAAAA
* * * *
141437 AGATTGAAGGGCTTTTGACGTTTCTAATATCGTTTTTCCTATTTTTCCAAA-TAAATTTTAATTA
1 AGATTGAAGGGCTTTTCACGTTT-TAATATCGTTTTTCATA-TTTTCTAAATTAAATTCTAATTA
* * * *
141501 AATCGAAACAAGATTCATATGGTCGTAAAAAAAAATCTTTAAATCCAATGTGACTGAGAATTGAT
64 AATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATC-TTAAATCCAATGTGGCTGAGATTTGAT
* * * * *
141566 TAGATGAATATAAATATTTCAAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGAGTCGGGTCCC
128 TAGATGAATATAGATATTT-AAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG-CGGGGCCC
141631 CGGAACG-TGTTTTTAG
191 C-GAACGCT-TTTTTAG
141647 TAGGGATGTC
Statistics
Matches: 454, Mismatches: 72, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
326 39 0.09
327 68 0.15
328 51 0.11
329 36 0.08
330 138 0.30
331 84 0.19
332 38 0.08
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (323 bp):
AGATTGAAGGGCTTTTCACGTTTTAATATCGTTTTTCATATTTTCTAAATTAAATTCTAATTAAA
TCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCTTAAATCCAATGTGGCTGAGATTTGATTAG
ATGAATATAGATATTTAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCGGGGCCCCGAAC
GCTTTTTTAGCCAAAAACCGTGATGGTTACACGATTTCGGCTAAAAATTTGCAAAAAATGACCCA
AAATGATATTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAACACCAAAA
Found at i:143037 original size:2 final size:2
Alignment explanation
Indices: 143025--143058 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
143015 TTCGTGATTT
143025 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
143059 GCAGCTTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:144057 original size:5 final size:5
Alignment explanation
Indices: 144020--144055 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
144010 GGTAGATACA
144020 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT-TT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
144056 TTAAATCCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTCTT
Found at i:161793 original size:22 final size:22
Alignment explanation
Indices: 161765--161810 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
161755 GCATAATCTT
*
161765 ATAGGAAGTTTACCAGAATTTC
1 ATAGGAAGGTTACCAGAATTTC
*
161787 ATAGGAAGGTTATCAGAATTTC
1 ATAGGAAGGTTACCAGAATTTC
161809 AT
1 AT
161811 TACGTGGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (22 bp):
ATAGGAAGGTTACCAGAATTTC
Found at i:170853 original size:16 final size:17
Alignment explanation
Indices: 170826--170859 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
170816 ATGATTTAAC
*
170826 TCTTTTTCGTTTTTCTT
1 TCTTTTTCGTTTTGCTT
170843 TCTTTTT-GTTTTGCTT
1 TCTTTTTCGTTTTGCTT
170859 T
1 T
170860 TTCAGTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (17 bp):
TCTTTTTCGTTTTGCTT
Found at i:174763 original size:7 final size:8
Alignment explanation
Indices: 174735--174763 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
174725 AACATTATTA
174735 TTGGGAAT
1 TTGGGAAT
174743 TTGGGAAT
1 TTGGGAAT
174751 TTGGGAA-
1 TTGGGAAT
174758 TTGGGA
1 TTGGGA
174764 TCCAGATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.34
Consensus pattern (8 bp):
TTGGGAAT
Found at i:190651 original size:19 final size:19
Alignment explanation
Indices: 190620--190660 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
190610 GTTTAATTAT
*
190620 AAATGTAAATTAAAAGAAG
1 AAATGTAAATTAAAAAAAG
190639 AAATG-AAATTTAAAAAAAG
1 AAATGTAAA-TTAAAAAAAG
190658 AAA
1 AAA
190661 AAAAGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (19 bp):
AAATGTAAATTAAAAAAAG
Found at i:197372 original size:10 final size:11
Alignment explanation
Indices: 197359--197396 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
197349 CACTGTATTA
197359 TTAATTT-AAC
1 TTAATTTGAAC
197369 TTAATTATGAAC
1 TTAATT-TGAAC
197381 TT-ATTTGAAC
1 TTAATTTGAAC
197391 TTAATT
1 TTAATT
197397 AATATATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 13 0.52
11 7 0.28
12 5 0.20
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (11 bp):
TTAATTTGAAC
Found at i:199601 original size:22 final size:22
Alignment explanation
Indices: 199565--199618 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
199555 TAATAATAAC
* *
199565 AATAATAAAATAAAAC-ATATCT
1 AATAATAATAGAAAACAATA-CT
*
199587 AATAATAATAGAAAATAATACT
1 AATAATAATAGAAAACAATACT
*
199609 AATACTAATA
1 AATAATAATA
199619 TCGATTCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 24 0.89
23 3 0.11
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (22 bp):
AATAATAATAGAAAACAATACT
Found at i:199647 original size:35 final size:33
Alignment explanation
Indices: 199608--199714 Score: 97
Period size: 35 Copynumber: 3.4 Consensus size: 33
199598 AAAATAATAC
199608 TAATACTAATATCGATTCTAACTACTAACAATAAA
1 TAATACTAATATCGA-TCTAA-TACTAACAATAAA
*
199643 TAATACT-A-AT--AT-T-A-A-TAATAATAACA
1 TAATACTAATATCGATCTAATACTAACAATAA-A
199669 -AATACTAATATCGACTCTAAATACTAACAATAAA
1 TAATACTAATATCGA-TCT-AATACTAACAATAAA
199703 TAATACTAATAT
1 TAATACTAATAT
199715 TAATAATAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 24
0.69 0.02 0.29
Matches are distributed among these distances:
25 14 0.24
26 3 0.05
27 2 0.03
28 1 0.02
29 2 0.03
30 2 0.03
31 2 0.03
33 3 0.05
34 3 0.05
35 26 0.45
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (33 bp):
TAATACTAATATCGATCTAATACTAACAATAAA
Found at i:199677 original size:60 final size:60
Alignment explanation
Indices: 199600--199728 Score: 224
Period size: 60 Copynumber: 2.2 Consensus size: 60
199590 AATAATAGAA
* * *
199600 AATAAT-ACTAATACTAATATCGATTCTAACTACTAACAATAAATAATACTAATATTAAT
1 AATAATAACAAATACTAATATCGACTCTAAATACTAACAATAAATAATACTAATATTAAT
199659 AATAATAACAAATACTAATATCGACTCTAAATACTAACAATAAATAATACTAATATTAAT
1 AATAATAACAAATACTAATATCGACTCTAAATACTAACAATAAATAATACTAATATTAAT
199719 AATAATAACA
1 AATAATAACA
199729 CTAATAATTA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
59 6 0.09
60 60 0.91
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (60 bp):
AATAATAACAAATACTAATATCGACTCTAAATACTAACAATAAATAATACTAATATTAAT
Done.