Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015454.1 Corchorus olitorius cultivar O-4 contig15487, 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: 99118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1463 original size:332 final size:330
Alignment explanation
Indices: 342--4237 Score: 3220
Period size: 332 Copynumber: 11.8 Consensus size: 330
332 CAGAACTGTA
* * * * * * *
342 ACGATTTTTGGCTAAATACGCGTTTCGGAGCCCCGTCTCAATTTTTCATGATTTTTGGCGCCGA-
1 ACGATTTTTGGCTAAAAACGCGTTCCGG-GCCCCGACTCAGTTTTGCATGATTTTTGGCACAGAT
* * * * * ** * * *
406 GACTCCTTGAAATATTTATATTCATCTAACTAAATCTTAGTTACGTTTGGATTTCAGGATTTATT
65 TA-TCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC-ATTGGATTTAAGGATTTGTT
* *
471 TTTACGAGCATGTGAATCATGTTTCGATTTAGTCAAAAATTAAATTT-GAAAAAATATG-AAAAA
128 TTTACGAGCATCTGAATCATGTTTCGATTTAATC-AAAATT-AATTTGGAAAAAATA-GAAAAAA
* ** * * * * * * *
534 TAATGCTAAAAGTGTGAAAAGCCTTTCAAATTTTTAGGATTTGAATTATATAAATT-TTATAAAT
190 TGATATTAGAAGCGTGAAAAGCCCTTC-AATTTTTTGGATTTGAATTATATATATTCTTATGAGT
** * * * * * *
598 AAAGTGGCCGAAAATTAAGGCAATATTTTTCGGATCAGTTTTTGCAAAATTTTAGGCGAACTCGT
254 ATTGTGGCCAAAAATTGAGGCAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGGCGAAATCGT
663 GTACTAACCATC
319 GTACTAACCATC
* * * * * * * *
675 ACGGTTTTTGG-TTAAAACTGCGTGCCAGGACCTCGGCTTAGTTTTGCATGATTTTTGGCACAGG
1 ACGATTTTTGGCTAAAAAC-GCGTTCC-GGGCCCCGACTCAGTTTTGCATGATTTTTGGCACAGA
* * * *
739 TTATCATTGAAATATATCTATTCATCTAACCAAATCTCAGGCACATTGGATTTAAGGATTTGTAT
64 TTATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
* * * * *
804 TTACGAGCATTTGAATCATGTTTCGATTTAATTAAAAATTAATTCGGGAAAAATA-AAAATAATA
129 TTACGAGCATCTGAATCATGTTTCGATTTAA-TCAAAATTAATTTGGAAAAAATAGAAAA-AATG
* * * * *
868 ATATTGGAAGCGTGAAAAG-CCTCTCAATATTTTTTAGA-TAGAATTATATAT-TTCTTATGGGG
192 ATATTAGAAGCGTGAAAAGCCCT-TC-A-ATTTTTTGGATTTGAATTATATATATTCTTATGAGT
* * * * * *
930 ATCGTGGTCC-AAAATTGA-GAAAAATTCTTTCGGGACAATTTTTGTAAAA-TTGAGCCGAAATC
254 ATTGTGG-CCAAAAATTGAGGCAAAATT-TTTCGGGTCAATTTTTGCAAAATTTTAGGCGAAATC
* *
992 GTATACT-ACCTATT
317 GTGTACTAACC-ATC
* * * * * * *
1006 ACGATTTTTGGCTAAAAACGCGTTCCGAAGCCTCGGCTAAGTTTTGCATGATTTTAGGCGCCGA-
1 ACGATTTTTGGCTAAAAACGCGTTCCG-GGCCCCGACTCAGTTTTGCATGATTTTTGGCACAGAT
* * *
1070 GACTCCTTGAAA-ATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
65 TA-TCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
* * * *
1134 TAACGAGTAT-TGAAGCAT-TTTCGATTTAATCAAAATTAATTTGGAAAAAATAGAAAAAAACGA
129 TTACGAGCATCTGAATCATGTTTCGATTTAATCAAAATTAATTTGGAAAAAATAG-AAAAAATGA
* * * *
1197 TGTTAGAAGTGTGAAAAGCCCTTCAATTTTTTAGGATTTTAATTATATATATAGT-TTATGAGCA
193 TATTAGAAGCGTGAAAAGCCCTTCAATTTTTT-GGATTTGAATTATATATAT--TCTTATGAGTA
* * *
1261 TTGTGGCCAAAAATTAAGGCAAAATTTTTCAGGTCAGTTTTTGCAAAATTTTAGGCGAAATCGTG
255 TTGTGGCCAAAAATTGAGGCAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGGCGAAATCGTG
1326 TACTAACCATC
320 TACTAACCATC
* * ** * *
1337 ACGATTTTTGGTTAAAAACGCATTCCTGGGTTCCGACTTAGTTTTGCATGATTTTTGGCACATAT
1 ACGATTTTTGGCTAAAAACGCGTTCC-GGGCCCCGACTCAGTTTTGCATGATTTTTGGCACAGAT
* *
1402 TATTATTGAAATATCTATATTCATTTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
65 TATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
* * * *
1467 AACAAGCATCTGAAGCAT-TTTCGATTTAATGAGAAATTAATTTGGAAAAATATAG------T-A
130 TACGAGCATCTGAATCATGTTTCGATTTAATCA-AAATTAATTTGGAAAAA-ATAGAAAAAATGA
1524 -A--A-AAGCGTGAAAAGCCCTTCAATGTTTTTGGCA-TTGAATTATATA-ATTCTTATGAGTAT
193 TATTAGAAGCGTGAAAAGCCCTTCAAT-TTTTTGG-ATTTGAATTATATATATTCTTATGAGTAT
*
1583 TGTGGCCAAAAATTGAGGCAAAAATTTTT-GGGTTAATTTTTGCAAAATTTTA-GCTGAAATCGT
256 TGTGGCCAAAAATTGAGGC-AAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGGC-GAAATCGT
1646 GTACTAACCATC
319 GTACTAACCATC
* * * * * *** * *
1658 ACGAATTTTTTTTTGGCTAAAAGCGCGATCCGGGGACTCGTCTCAGAATTTTTTTTAATTTTTGC
1 ACG-A----TTTTTGGCTAAAAACGCGTTCC-GGGCCCCGACTCAG--TTTTGCATGATTTTTGG
* * * * * * * * * *
1723 CACAAATTATCGTTGAAACATCTATATTAATCTAATCAAACCTCAGCAACAATGTATTGAAGGAT
58 CACAGATTATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGAT
* * ** * * *
1788 TTCTTTTTACGACCATCTGAATCATGTTTTAATTTAATTCGAAATTAATTCAGG-AAAACTAGGA
123 TTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAA-TCAAAATTAATT-TGGAAAAAATA-GA
* * * ** *
1852 AAAAACGAAATTAGAAGCGTGAAAAG-GCTCTCAATCTTTTTTTATATTGAACTATATAT-TTCT
185 AAAAATGATATTAGAAGCGTGAAAAGCCCT-TCAAT-TTTTTGGAT-TTGAATTATATATATTCT
* * * * * *
1915 TATGAGCATTGTGTCTAAAAATTAAGGCAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAAGCG
247 TATGAGTATTGTGGCCAAAAATTGAGGCAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGGCG
*
1980 AAATTGTGTACTAACCATC
312 AAATCGTGTACTAACCATC
* * * * * *
1999 A-GGTTTTTGGTTAAAAACGCATTCCCGGGTCCCGACTTAGTTTTGCATGATTTTTGGCATAGAT
1 ACGATTTTTGGCTAAAAACGCGTT-CCGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACAGAT
*
2063 TATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTATGGATTTGTTTT
65 TATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
* * * * *
2128 AACGAGCATTTG-A--A-G---C------AT-----TTAATTTGGAAAAAAATTGGAAAAACGAT
130 TACGAGCATCTGAATCATGTTTCGATTTAATCAAAATTAATTTGG-AAAAAATAGAAAAAATGAT
*
2175 ATTAGAAGCGTGAAAAGCCCTTCAATGTTTCTGGCA-TTGAATTATATA-ATTCTTATGAGTATT
194 ATTAGAAGCGTGAAAAGCCCTTCAAT-TTTTTGG-ATTTGAATTATATATATTCTTATGAGTATT
* *
2238 GTGGCAAAAAATTGAGGCAAAAATTTTCGGGTCAATTTTTGCAAAATTTTAGAG-GAAATCGTGT
257 GTGGCCAAAAATTGAGGCAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAG-GCGAAATCGTGT
2302 ACTAACCATC
321 ACTAACCATC
* * * * * * * *
2312 ACGGTTTTTTGGCTAAAAGCGCGTTCTGGGGACTCGTCTCAGTTTTGTATGATTTTTGGCACATA
1 AC-GATTTTTGGCTAAAAACGCGTTC-CGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACAGA
** * * * * * * * * * *
2377 TTATTGTTGAAACATCTATATTAATCTAATCAAAGCCCAGCAACAATGTATTGAAGAATTTGTTT
64 TTATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
* * * *
2442 CTACGACCATCTGAATCATGTTTC-AATT--T---AATTAA---GG-AAAAATAGGAAAAATGAT
129 TTACGAGCATCTGAATCATGTTTCGATTTAATCAAAATTAATTTGGAAAAAATAGAAAAAATGAT
**
2497 ATTAGAAGCGTGAAAAG-CCTCTCAATCTTTTTTTTATATTGAATTATATAT-TTCTTATGAGTA
194 ATTAGAAGCGTGAAAAGCCCT-TCAA--TTTTTTGGAT-TTGAATTATATATATTCTTATGAGTA
* * * * * * *
2560 TCGTGGCCAAAAAATGAGG-AATATTTTTTTTGGGTCAATTTTTTTGTAAAATATTAGCCGAAAT
255 TTGTGGCCAAAAATTGAGGCAA-A-ATTTTTCGGGTCAA--TTTTTGCAAAATTTTAGGCGAAAT
*
2624 CGTGTACGTTA-CATC
316 CGTGTAC-TAACCATC
* * *
2639 ACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACATAT
1 ACGATTTTTGGCTAAAAACGCGTTCC-GGGCCCCGACTCAGTTTTGCATGATTTTTGGCACAGAT
* * * * *
2704 TACCATTGAAATATCTACACTCATCTAACCAAATCTCAGCTACATTAGATTTAAGGATTT-TTTT
65 TATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
* * * **
2768 TACGAGCATCTGAATCATGTTACGATTTAATTAGAAATAAATTTGGAAAAAATAGGGAAAATGAT
130 TACGAGCATCTGAATCATGTTTCGATTTAATCA-AAATTAATTTGGAAAAAATAGAAAAAATGAT
* * * * * * * * ** *
2833 ATAAGAGGCGTGGAAAGCCTTTCAGTCTTTTTTGACATTGAATTATATAT-TTTTTACAAGTATC
194 ATTAGAAGCGTGAAAAGCCCTTCAAT-TTTTTGGA-TTTGAATTATATATATTCTTATGAGTATT
* * *
2897 GTGGCCAAAAATTGAGG-AAAATTCTTCCGAGTCAATTTTTGCAAAATTTTA-GCCATAATCGTG
257 GTGGCCAAAAATTGAGGCAAAATT-TTTCGGGTCAATTTTTGCAAAATTTTAGGCGA-AATCGTG
* *
2960 TACTAACTATA
320 TACTAACCATC
* *** * * * *
2971 ACGATTTTTGGCTAAAAATGCGTTTCAAAGCCCCGACTCAGTTTTACATGATCTTTGGCGCCGA-
1 ACGATTTTTGGCTAAAAACGCG-TTCCGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACAGAT
* * * * * * * ** *
3035 GACTCCTTGAAATATCTATATTCATTTAACTAAATTTCAGTCACGTTGGATTTCTGGATTTATTT
65 TA-TCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
* * *
3100 TTACGATCATCTGAATCATGTTTCGATTTAGTCGAAAATTAAATTT-GAAAAAATTGAAAAAAAA
129 TTACGAGCATCTGAATCATGTTTCGATTTAATC-AAAATT-AATTTGGAAAAAA-T-AGAAAAAA
* * * *
3164 TGATGTTAGAAGCGTGAAAAGCCCTTCAATTTTTTAGGATTTGAATTATATAAATT-TTATAAGC
190 TGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTT-GGATTTGAATTATATATATTCTTATGAGT
* * * * * **
3228 ATTATGGCCAAAAATTAAGACAAAATTTTTCGAGTCAGTTTTTGCAAAATTTTAGGTAAAATCGT
254 ATTGTGGCCAAAAATTGAGGCAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGGCGAAATCGT
3293 GTACT---CATC
319 GTACTAACCATC
* * * * * * * *
3302 GCGGTTTTTGGTTAAAAATGCGTTCCTGGGCTCCGACTTATTTTTGCATGATTTTTGGCACGGAT
1 ACGATTTTTGGCTAAAAACGCGTTCC-GGGCCCCGACTCAGTTTTGCATGATTTTTGGCACAGAT
3367 TATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
65 TATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
* * * * * * *
3432 TACGAGCACCTAAATAATGTTTCGATTTAATTAGAAATTAATTCGGGAAAAAA-AAAGAAAAATT
130 TACGAGCATCTGAATCATGTTTCGATTTAATCA-AAATTAATT-TGGAAAAAATAGA-AAAAATG
* * * *
3496 ATATTAGAAGTGTGAAAAG-CATCTCAATCTTTTTTAGA-TAGAATTATATAT-TTCTTATGAGT
192 ATATTAGAAGCGTGAAAAGCCCT-TCAA--TTTTTTGGATTTGAATTATATATATTCTTATGAGT
* * * * * *
3558 ATCGTGGTCTAAAATTGA-GAAAAATTATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTG
254 ATTGTGGCCAAAAATTGAGGCAAAATT-TTTCGGGTCAATTTTTGCAAAATTTTAGGCGAAATCG
*
3622 TGTACTAACTATC
318 TGTACTAACCATC
* * * *
3635 ATGATTTTTGGCTAAAAACGCGTT-TGAAGCCCCCG-CTCAGTTTTGCATGATTTTTGGCGTCGA
1 ACGATTTTTGGCTAAAAACGCGTTCCG--GGCCCCGACTCAGTTTTGCATGATTTTTGGC-AC-A
* * * *
3698 GA--CTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCACATTGGATATAAGGATTTGT
62 GATTATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGT
** * *
3761 TTAAACGAGCAT-TGAAGCAT-TTTCGATTTAATCAAAATTAATTTGGAAATAAAAATAGGAAAA
127 TTTTACGAGCATCTGAATCATGTTTCGATTTAATCAAAATTAATTTGG--A-AAAAATAGAAAAA
* * ** * ** *
3824 ACGATATTAGAAGCGTTAAAAGCTTTTCAAATATTTTGGCGTTGAATTATATA-ATTTTTATGAG
189 ATGATATTAGAAGCGTGAAAAGCCCTTC-AATTTTTTGGATTTGAATTATATATATTCTTATGAG
*** * * * * * *
3888 TACAATGGCAAAAAATCGAGGCAAAATTTTTCGGGTTAGTTTTTACAAAATTTTAGCCGAAATCG
253 TATTGTGGCCAAAAATTGAGGCAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGGCGAAATCG
*
3953 TGTACTAATCATC
318 TGTACTAACCATC
* * * * * *
3966 ACGGTTTTTGGCTAAAAACGCGTTTCGGGTCCTCGTCTCAGTTTTGCATGATTTTAGGCACATAT
1 ACGATTTTTGGCTAAAAACGCGTTCCGGG-CCCCGACTCAGTTTTGCATGATTTTTGGCACAGAT
* * * * *
4031 TATCATTGAAATATCTATATTCATCTAACCAAATCTCAACCATATTAGATTTAAAGA-TTATTTT
65 TATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
* * * * * * * *** *
4095 TACAAACAACTGAATCATATTTTGTTTTAATCAGAAATTAATTTGGGAAAAATAGGTTAAACGAT
130 TACGAGCATCTGAATCATGTTTCGATTTAATCA-AAATTAATTTGGAAAAAATAGAAAAAATGAT
* * * * * * * * * *
4160 ATTAGAGGCGCGGAAAGTCTTTTAA-TTTTTGGCA-TTGAATTATGTAT-TTTTTATGAATATCG
194 ATTAGAAGCGTGAAAAGCCCTTCAATTTTTTGG-ATTTGAATTATATATATTCTTATGAGTATTG
4222 TGGCCAAAAATTGAGG
258 TGGCCAAAAATTGAGG
4238 AAAGTCCTTT
Statistics
Matches: 2865, Mismatches: 530, Indels: 340
0.77 0.14 0.09
Matches are distributed among these distances:
313 92 0.03
314 43 0.02
315 117 0.04
316 1 0.00
318 1 0.00
319 2 0.00
320 4 0.00
321 73 0.03
322 51 0.02
323 39 0.01
324 51 0.02
325 36 0.01
326 136 0.05
327 61 0.02
328 134 0.05
329 105 0.04
330 228 0.08
331 493 0.17
332 517 0.18
333 275 0.10
334 126 0.04
335 122 0.04
336 37 0.01
337 3 0.00
339 4 0.00
340 32 0.01
341 80 0.03
342 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (330 bp):
ACGATTTTTGGCTAAAAACGCGTTCCGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACAGATT
ATCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
ACGAGCATCTGAATCATGTTTCGATTTAATCAAAATTAATTTGGAAAAAATAGAAAAAATGATAT
TAGAAGCGTGAAAAGCCCTTCAATTTTTTGGATTTGAATTATATATATTCTTATGAGTATTGTGG
CCAAAAATTGAGGCAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGGCGAAATCGTGTACTAA
CCATC
Found at i:5733 original size:3 final size:3
Alignment explanation
Indices: 5717--5779 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
5707 GGGGTAATGC
* * * * *
5717 TGG TGG CGG CGG TGG TGG TGA TGG TGG TGG AGG TGG TGG TGA TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
* *
5765 TGA TGG TGG CGG TGG
1 TGG TGG TGG TGG TGG
5780 CGAAGATGGA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.06, C:0.05, G:0.62, T:0.27
Consensus pattern (3 bp):
TGG
Found at i:5778 original size:21 final size:21
Alignment explanation
Indices: 5717--5766 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
5707 GGGGTAATGC
* *
5717 TGGTGGCGGCGGTGGTGGTGA
1 TGGTGGTGGAGGTGGTGGTGA
5738 TGGTGGTGGAGGTGGTGGTGA
1 TGGTGGTGGAGGTGGTGGTGA
5759 TGGTGGTG
1 TGGTGGTG
5767 ATGGTGGCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.06, C:0.04, G:0.62, T:0.28
Consensus pattern (21 bp):
TGGTGGTGGAGGTGGTGGTGA
Found at i:5861 original size:24 final size:24
Alignment explanation
Indices: 5817--5878 Score: 56
Period size: 24 Copynumber: 2.6 Consensus size: 24
5807 CATAGATATA
**
5817 GGTGGTGCAGGAGGCGATTGG-GG
1 GGTGGTGGTGGAGGCGATTGGTGG
5840 TGGTGGTGGTGGAGGC-AGTTGGTGG
1 -GGTGGTGGTGGAGGCGA-TTGGTGG
* *
5865 GGAGGAGGTGGAGG
1 GGTGGTGGTGGAGG
5879 AGGTTTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 29 0.91
25 2 0.06
ACGTcount: A:0.13, C:0.05, G:0.63, T:0.19
Consensus pattern (24 bp):
GGTGGTGGTGGAGGCGATTGGTGG
Found at i:5933 original size:18 final size:18
Alignment explanation
Indices: 5871--5941 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
5861 GTGGGGAGGA
* *
5871 GGTGGAGGAGGTTTTGAT
1 GGTGGAGGGGGTTGTGAT
*
5889 GGTGGAGGTGGTGGTTTCAGTGGT
1 GGTGGA-G-GG-GG-TT--GTGAT
5913 GGTGGAGGGGGTTGTGAT
1 GGTGGAGGGGGTTGTGAT
*
5931 GGTGGTGGGGG
1 GGTGGAGGGGG
5942 AGGAGGAGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
18 20 0.48
19 1 0.02
20 3 0.07
21 4 0.10
22 4 0.10
23 1 0.02
24 9 0.21
ACGTcount: A:0.10, C:0.01, G:0.59, T:0.30
Consensus pattern (18 bp):
GGTGGAGGGGGTTGTGAT
Found at i:8222 original size:17 final size:17
Alignment explanation
Indices: 8200--8235 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
8190 ATACAAAGAG
8200 CTATCTAGTATAACAAA
1 CTATCTAGTATAACAAA
* *
8217 CTATCTGGTGTAACAAA
1 CTATCTAGTATAACAAA
8234 CT
1 CT
8236 TTACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (17 bp):
CTATCTAGTATAACAAA
Found at i:10486 original size:332 final size:330
Alignment explanation
Indices: 9671--13403 Score: 3319
Period size: 332 Copynumber: 11.4 Consensus size: 330
9661 CCATGATGGT
* * *
9671 AAAAA-TGACCCGAAAGATTTTTCCTCAATTTTTGGCAAAAATACTCATAATATATATATATATA
1 AAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAA-A-A-A-ATATATA
* * * ** * *
9735 ATTCAATGCCAAAAGGATTGGAGAACTTTTCACACTTTTAATATCGTTTTTCATAATTTTTTCTG
62 ATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTC-G
* * * * * *
9800 AATTAATTTTTTATTAAATCGAAACAAGATTCAGATGCACATAAAAACAAATCCTTGAATCCATT
126 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * ****
9865 GT-GCATGAGATCTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGGTAATAAAAATCATGCA
191 GTGGC-TGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTC-CGGCGCCAAAAATCATGCA
* * * * * * *
9929 AACCAGAGCCGTGGTCCT-GTAATGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACG----G
254 AAACTGAGCCG-GGCCCTCG-AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC
*
9989 GGCTAAAATTTTAC
317 GGCTAAAATTTTGC
* * *
10003 AAAAATTTA-TCCGAAAGATATTTCCTTAAATTTTGGCTAAAATACTCATAAAAAATATATAATT
1 AAAAATTGACT-CGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATT
* * * ** * *
10067 CAACGACAAAAGGATTGGAGAACTTTTCACGCCTTTAATATCGTTTTTCATA-TTTTTTCTAAAT
65 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTC-GAAT
* * * * * *
10131 TAATTTCTAATTAAATCGAAACAAGATTTAGATGCACATAAAAATAAATCCTTAAATCTAATGTT
129 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * *
10196 TCTGAAATTTGATTAGATGAATAAAGATTTTTCAAGGAGTCCAGGCGTCAAAAATCATGCAAAAC
194 GCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCC-GGCGCCAAAAATCATGCAAAAC
* * * * * *
10261 AGAGTCGTGGCCCTAGAACGCGTTTTTAGCTAAAAACCGTGATGGTTTGTACACGATTTCAGCTA
258 TGAGCCG-GGCCCTCGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
*
10326 AAATTTTGG
322 AAATTTTGC
* * *
10335 AAAATTTGATTCGAAAGATATTTCCTC-ATTTATTGGCTAAAATACTCATAAAAAATATATAGTT
1 AAAAATTGACTCGAAAGATATTTCCTCAATTT-TTGGCTAAAATACTCATAAAAAATATATAATT
*** * * * * *
10399 CAACATTAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTTCAAATT
65 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCGAATT
**
10464 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTGATGTGG
130 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * * *
10529 TTAAAATTTGGTTAAATGAATATAGGTATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACT
195 CTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTC-CGGCGCCAAAAATCATGCAAAACT
* * * * *
10594 GAGCCGGGCCC-CATAATGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACATGATTTCGGCTAA
259 GAGCCGGGCCCTC-GAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
10658 AATTTTGC
323 AATTTTGC
* ** * * * * * * *
10666 AAAAATTGACTCAAAATTTTTTTTCTCGATTTCTAGCGAAATTACTCATAAAAAATATATAATTC
1 AAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * * *
10731 AATGCCAAAAA-ATTGAAAGCCTTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-GAATT
66 AACGCCAAAAAGATTGAAGGGC-TTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCGAATT
* * * *
10794 AACTTT-TAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATTCAATATC
130 AA-TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* *
10858 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGGAT-CGGCACCAAAAATCATGCAAAA
194 GCTGAAATTTGATTAGATGAATATAGATATTTCAAGGA-G-TCCGGCGCCAAAAATCATGCAAAA
* *
10922 CTGAGTC-GG-----G--C-CGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTA
257 CTGAGCCGGGCCCTCGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
10978 AAATTTTGC
322 AAATTTTGC
* * * **
10987 AAAAATTGACCCGAAAGATTTTTTCGTCAA-TTTTGGCTAAAATACTCATAAAATGTATATAATT
1 AAAAATTGACTCGAAAGA-TATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATT
* * * * *
11051 TAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-GCATT
65 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCGAATT
* * * * * **
11115 AATATCTAGTTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATTCTTCAATCCAATGTAA
130 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * * * *
11180 CTGAGATATTAGATTAAATAAATATGGATATCTCAAAGAGTCTTGGTGCCAAAAATCATGCAAAA
195 CTGA-A-ATTTGATTAGATGAATATAGATATTTCAAGGAGTC-CGGCGCCAAAAATCATGCAAAA
* * * *
11245 CTTAGCCGGGACCC-CGGAACGCGTTATTAGCCAAAAAACCGTGATGATTATTACACGATTTCGG
257 CTGAGCCGGG-CCCTC-GAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTTCGG
*
11309 CTAGAATTTTGC
319 CTAAAATTTTGC
* ** ** *** * * * *
11321 AAAAATTGAATCGAAATTTATTTCCTCAATTTTTATCCGCAATACGCATAAAAATTACATAACTC
1 AAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * * ** * *
11386 AACGCCAAAAATATTGAAGGGTTTTTCATGCTCCTAATATCGTTTTTCCTATTATTTTCCGAATT
66 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATT-TTTTTCGAATT
* * *** * *
11451 AATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT-TTTACTAATCCTTAAATCCATTGTGG
130 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * * *
11515 ATG--ATTTGGTTATATAAATATAGATATTTCAATGAGTCTCGGCGCAAAAAAATCATGCAACAC
195 CTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTC-CGGCGC-CAAAAATCATGCAAAAC
* * * * * * *
11578 TGAACTGAGGCCC-CGAACACGTTTTTAGCAAAAAAACCGTGATTTCGACTAACGTACACAATTT
258 TGAGCCG-GGCCCTCGAACGCGTTTTTAGC-CAAAAACCGTGA--T-G-GTTA-GTACACGATTT
*
11642 CGGCTAATATTTTGC
316 CGGCTAAAATTTTGC
* ** **
11657 AAAAATTGAC-CAGAAATAGGTTTCCTCAATTTTTATCTAAAATACTCATAAAATATATATATAA
1 AAAAATTGACTC-GAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAA-A-ATATATAA
* * * * * * *
11721 TTCAACTCCAAAAAGATTGGAGGACTTTTCTCGCTTTTAATTTTGTTTTTCATATTTTTCT-GAA
63 TTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCGAA
* * * *
11785 CTAATTTATTATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGT
128 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * *
11850 GGCTG--A---GATT---T-AATATAGATATTTCAAGGAGTCTCGACGCTAAAAATGATGCAAAA
193 GGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTC-CGGCGCCAAAAATCATGCAAAA
* * * *
11906 TTGAGCTGGGACCTCGAAACGCGTTTTTAGCAAAAAAAACCGTGATGGTTAGTACACGATTTCGG
257 CTGAGCCGGGCCCTCG-AACGCGTTTTTAGC--CAAAAACCGTGATGGTTAGTACACGATTTCGG
11971 CTAAAATTTTGC
319 CTAAAATTTTGC
* * * * * * * *
11983 AAAAAATGACTAGAAAAATATTCCCTCAATTATTAGCCATAATACTCATAAAAAATATATAATTC
1 AAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * *
12048 AACGCCAAAATA-ATTGAAGGGCTTTTCACG-TTTTCAATATCCTTTTTCCTATTTTTTCCGAAT
66 AACGCCAAAA-AGATTGAAGGGCTTTTCACGCTTTT-AATATCGTTTTTCATATTTTTTTCGAAT
** * * * * **
12111 TAATTTCTAATTAAAAAGAAACATGATTCACATGATTGTAAAAAC-AATGGTT-AA---AAT-T-
129 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * *
12169 --TG------G-TTAGATGGATATAGATATTTCAAGGAGTATCGGCACCAAAAATCATTCAAAAT
194 GCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGT-CCGGCGCCAAAAATCATGCAAAAC
* * * * * * *
12225 TGAACCGGGCCC-CGGAACGCATTTCTAGCCAAAAACTGTGATGATTATTACACGATTTTGGCTA
258 TGAGCCGGGCCCTC-GAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
12289 AAATTTTGC
322 AAATTTTGC
* * ** *
12298 AAAATTTGAC-CTGAAAGATACTTCCTCAATTTTCAG-TCATAATACTCATAAAAAATATATAAT
1 AAAAATTGACTC-GAAAGATATTTCCTCAATTTTTGGCT-AAAATACTCATAAAAAATATATAAT
* * * *
12361 TCAACGCCAAAAAGAATGAAGGGTTTTTCACGTTTTTAATATCGGTTTTCATATTTTATTT-GAA
64 TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTT-TTTCGAA
* *
12425 TTAA-TTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGT
128 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * ** ** *
12489 GGCT-AATTTTTATTAGATGAATATAGATATTTCAAGGAGTGTCAACGTTAAAAACCATGCAAAA
193 GGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGT-CCGGCGCCAAAAATCATGCAAAA
* * * * * * * * *
12553 CTGAGTCGGGGCCTCGAAACGCATTTTTAGACAAAAATCGTGATGGTTAATACAAGATTTTGGGT
257 CTGAGCCGGGCCCTCG-AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT
*
12618 AAAACTTTGC
321 AAAATTTTGC
** * *
12628 AAAAA---A----AAAG-T-TTTCC-CATATTTTTGAATAAAATATTCATAAAATATATATAATT
1 AAAAATTGACTCGAAAGATATTTCCTCA-ATTTTTGGCTAAAATACTCATAAAAAATATATAATT
* * * * * * * *
12683 TAACACCTAAAACATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-AAATT
65 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCGAATT
* * * * * *
12747 AATTTTTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAATAAATTCTTAAATCCAATGTAG
130 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * * * *
12812 CTGAGATTTTATTAGATGAATATGGATATCTCAAGGAGTCTTGGTGCCCAAAATCATGCAAAATT
195 CTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTC-CGGCGCCAAAAATCATGCAAAACT
* * * * * ** ** *
12877 GAGTCGGGGCCCTAGAATGCTTTTTTAGTCAAAAATTGTGATTTTTATTACACGATTTCGGCTAA
259 GAG-CCGGGCCCTCGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
*
12942 AATTTTGT
323 AATTTTGC
* * * * * * * *
12950 AAAAAATGATTAGAAAAATATTTTCTCAATTTTTGGCTAAGATATTCATAAGAAATATATAATTC
1 AAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * * * *
13015 AACGCCAAAAAAGATTGAAGGGCTTTTGACG-TTTCTAATATCATTTTTCCTA-TTTTTCCAAAT
66 AACGCC-AAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTTCATATTTTTTTCGAAT
* *
13078 TAATTTCTAATCAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
129 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * *
13143 GCTGAGATTTGATTAGTTGAATATAAATATTTCAAGTAGTCTCGGAGCCAAAAATCATGCAAAAT
194 GCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTC-CGGCGCCAAAAATCATGCAAAAC
** * *
13208 TGAGCCGGGTCCC-CGAAACGTATTTTTAGCCAAAAACCGTGATGGTTTGTTAATACACGGTTTC
258 TGAGCCGGG-CCCTCG-AACGCGTTTTTAGCCAAAAACCGTGAT-G---GTTAGTACACGATTTC
13272 GGCTAAAAATTTTGC
317 GGCT-AAAATTTTGC
* * * *
13287 AAAAATTGACACAAAAGAT-TTCTCCTCAATTTTTGGCTAAAATACTTAT-AAAAATATACAATT
1 AAAAATTGACTCGAAAGATATT-TCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATT
* * * * *
13350 CAACGCCAAAAAAATTGGAGGGCTTTTTACGCTTTTAATATCGTATTTCTTATT
65 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATT
13404 ACAATATCTT
Statistics
Matches: 2781, Mismatches: 503, Indels: 230
0.79 0.14 0.07
Matches are distributed among these distances:
314 37 0.01
315 149 0.05
316 10 0.00
317 14 0.01
318 48 0.02
319 4 0.00
320 16 0.01
321 339 0.12
322 119 0.04
323 68 0.02
324 59 0.02
325 43 0.02
326 66 0.02
327 4 0.00
328 172 0.06
329 140 0.05
330 222 0.08
331 273 0.10
332 441 0.16
333 68 0.02
334 126 0.05
335 60 0.02
336 182 0.07
337 72 0.03
338 49 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (330 bp):
AAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCGAATTA
ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
TGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCCGGCGCCAAAAATCATGCAAAACTGA
GCCGGGCCCTCGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAT
TTTGC
Found at i:13741 original size:8 final size:8
Alignment explanation
Indices: 13728--13790 Score: 69
Period size: 8 Copynumber: 7.8 Consensus size: 8
13718 TTTTATATAG
13728 TAGTAAGA
1 TAGTAAGA
13736 TAGTAAG-
1 TAGTAAGA
13743 -A-TAAGA
1 TAGTAAGA
13749 TAGTAAGA
1 TAGTAAGA
13757 TAGTAAGA
1 TAGTAAGA
13765 TAAGATAAGA
1 T-AG-TAAGA
13775 TATGATAAGA
1 TA-G-TAAGA
13785 TAGTAA
1 TAGTAA
13791 AATTGAATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.08
6 1 0.02
7 1 0.02
8 24 0.49
9 4 0.08
10 15 0.31
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.25
Consensus pattern (8 bp):
TAGTAAGA
Found at i:13749 original size:5 final size:5
Alignment explanation
Indices: 13731--13786 Score: 61
Period size: 5 Copynumber: 12.4 Consensus size: 5
13721 TATATAGTAG
13731 TAAGA T-AG- TAAGA TAAGA T-AG- TAAGA T-AG- TAAGA TAAGA TAAGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
*
13775 TATGA TAAGA TA
1 TAAGA TAAGA TA
13787 GTAAAATTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
3 3 0.07
4 12 0.28
5 28 0.65
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (5 bp):
TAAGA
Found at i:13749 original size:13 final size:13
Alignment explanation
Indices: 13731--13790 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 13
13721 TATATAGTAG
13731 TAAGATAGTAAGA
1 TAAGATAGTAAGA
13744 TAAGATAGTAAGA
1 TAAGATAGTAAGA
13757 T-AG-TAAGATAAGA
1 TAAGAT-AG-TAAGA
13770 TAAGATA-T--GA
1 TAAGATAGTAAGA
13780 TAAGATAGTAA
1 TAAGATAGTAA
13791 AATTGAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
10 9 0.22
11 2 0.05
12 5 0.12
13 20 0.50
14 3 0.08
15 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (13 bp):
TAAGATAGTAAGA
Found at i:13753 original size:21 final size:21
Alignment explanation
Indices: 13728--13771 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
13718 TTTTATATAG
13728 TAGTAAGATAGTAAGATAAGA
1 TAGTAAGATAGTAAGATAAGA
13749 TAGTAAGATAGTAAGATAAGA
1 TAGTAAGATAGTAAGATAAGA
13770 TA
1 TA
13772 AGATATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (21 bp):
TAGTAAGATAGTAAGATAAGA
Found at i:13932 original size:200 final size:194
Alignment explanation
Indices: 13595--13976 Score: 624
Period size: 200 Copynumber: 1.9 Consensus size: 194
13585 TAATTAATAA
*
13595 AAAATTGAATTAATCATCTAAAAAAAAGTTAAATGGCTAAAAAGAATACTTATTAAAAAATTTTC
1 AAAATTGAATTAATCATCTAAAAAAAAGTTAAATGGCTAAAAAGAATACTTATTAAAAAATTATC
* *
13660 ATACTATAATACTAAGGGTATTTATGAAATTTCTCAAGTATAATTTTTGAGTTCGTGCTTTTATA
66 ATACTATAATACTAAGGATATTTATGAAATTTCTCAAGTAGAATTTTTGAGTTCGTGCTTTTATA
* *
13725 TAGTAGTAAGATAGTAAGATAAGAT-AG-TAAGATAGTAAGATAAGATAAGATATGATAAGATAG
131 TAGTAGTAAGATAATAAAATAAGATAAGATAAGATAGTAAGAT-AG-TAAGATATGATAAGATAG
13788 T
194 T
13789 AAAATTGAATTAATCATCTAAAAAAATAAAAAAGTTAAATGGCTAAAAAGAATACTTATTAAAAA
1 AAAATTGAATTAATCATCT-----AA-AAAAAAGTTAAATGGCTAAAAAGAATACTTATTAAAAA
*
13854 ATTATCATACTATAATACTAAGGATATTTATGAAATTTCTCAATTAGAATTTTTGAGTTCGTGCT
60 ATTATCATACTATAATACTAAGGATATTTATGAAATTTCTCAAGTAGAATTTTTGAGTTCGTGCT
13919 TTTATATAGTAGTAAGATAATAAAATAAGATAAGATAAGATAGTAAGATAGTAAGATA
125 TTTATATAGTAGTAAGATAATAAAATAAGATAAGATAAGATAGTAAGATAGTAAGATA
13977 ACTAGTTAGT
Statistics
Matches: 174, Mismatches: 6, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
194 19 0.11
199 2 0.01
200 135 0.78
201 4 0.02
202 14 0.08
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.34
Consensus pattern (194 bp):
AAAATTGAATTAATCATCTAAAAAAAAGTTAAATGGCTAAAAAGAATACTTATTAAAAAATTATC
ATACTATAATACTAAGGATATTTATGAAATTTCTCAAGTAGAATTTTTGAGTTCGTGCTTTTATA
TAGTAGTAAGATAATAAAATAAGATAAGATAAGATAGTAAGATAGTAAGATATGATAAGATAGT
Found at i:13965 original size:8 final size:8
Alignment explanation
Indices: 13928--13976 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
13918 TTTTATATAG
13928 TAGTAAGA
1 TAGTAAGA
*
13936 TAATAA-A
1 TAGTAAGA
13943 -A-TAAGA
1 TAGTAAGA
13949 TAAGATAAGA
1 T-AG-TAAGA
13959 TAGTAAGA
1 TAGTAAGA
13967 TAGTAAGA
1 TAGTAAGA
13975 TA
1 TA
13977 ACTAGTTAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 1 0.03
8 21 0.60
9 2 0.06
10 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.24
Consensus pattern (8 bp):
TAGTAAGA
Found at i:14824 original size:24 final size:24
Alignment explanation
Indices: 14788--14836 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
14778 TGGAGGAGGT
*
14788 GATGGTGGTGGTGGGGATGGTGGA
1 GATGGTGGGGGTGGGGATGGTGGA
*
14812 GATGGTGGGGGTGGTGATGGTGGA
1 GATGGTGGGGGTGGGGATGGTGGA
14836 G
1 G
14837 GAGGCGGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.63, T:0.24
Consensus pattern (24 bp):
GATGGTGGGGGTGGGGATGGTGGA
Found at i:19081 original size:2 final size:2
Alignment explanation
Indices: 19074--19101 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19064 AAATCAAATA
19074 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
19102 GCTTTTACCA
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:20605 original size:9 final size:9
Alignment explanation
Indices: 20591--20628 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
20581 TTTATCTTAC
20591 TATTACTAT
1 TATTACTAT
20600 TATTACTAT
1 TATTACTAT
*
20609 TATTAATAT
1 TATTACTAT
20618 TATTACTAT
1 TATTACTAT
20627 TA
1 TA
20629 CTATACTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (9 bp):
TATTACTAT
Found at i:20607 original size:15 final size:15
Alignment explanation
Indices: 20587--20632 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 15
20577 CATGTTTATC
20587 TTACTATTACTATTA
1 TTACTATTACTATTA
*
20602 TTACTATTATTAATATTA
1 TTAC---TATTACTATTA
20620 TTACTATTACTAT
1 TTACTATTACTAT
20633 ACTATACTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 12 0.46
18 14 0.54
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (15 bp):
TTACTATTACTATTA
Found at i:22506 original size:14 final size:14
Alignment explanation
Indices: 22484--22513 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22474 AGGAAATATC
*
22484 TTTCGAGTCAATTT
1 TTTCAAGTCAATTT
22498 TTTCAAGTCAATTT
1 TTTCAAGTCAATTT
22512 TT
1 TT
22514 GCAAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.53
Consensus pattern (14 bp):
TTTCAAGTCAATTT
Found at i:23296 original size:333 final size:330
Alignment explanation
Indices: 21280--24520 Score: 2254
Period size: 333 Copynumber: 9.7 Consensus size: 330
21270 TTTAATAGTT
* *** * * * * *
21280 TATA-TCATCTAACCAAATCTCAATAACACTGAATTTAAGAATTTGTTTTTACAAGCATTTGAAT
1 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * *
21344 CTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAACGT-AAA
66 CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAA
* * *
21408 AAGCCCTCCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTTTTTTAGCCAAAAATTGAG
131 AA-CCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAG-CAAAAATTGAG
* * * * * * *
21472 AAAAAAAAAATCTTT-CGTTTCAATTTTTGCAAAATTTTAGCTGAAAATCGTGCAGTAACAAACC
194 ----GAAATATCTTTCCG-GTCAATTTTTGAAAAATTTTAGCCG-AAATCGT---GTAA-TAATC
* * * *
21536 ATCACGGTTTTTGGCTAAAAACGCGTTCCGAGGACCCGGCTCAATTTTGCATGATTTCTGGCTCC
249 ATCACGGTTTTTGGCTAAAAACGCGTTCCG-GGCCCCGGCTCAGTTTTGCATGATTTTTGGCTCT
* *
21601 GAGACTACTTGAAATATC
313 AAGACTCCTTGAAATATC
* * * *
21619 TATATTCATCTAATCAAATCTCACCCACCTTAGATTTAACGATTTGTTTTTACGAGCATCTGAAT
1 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
** * *
21684 CTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAATGATATTGAAAA-CGTCAA
66 CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATT-AAAAGCGTGAA
* * *
21748 AAACCCTTCAATTTTTTTGGTGTTTAGA-TATAT-TTTTTTATGAGTATTTTAGCCAAAAATTGA
130 AAACCCTTCAATCTTTTTGGCG-TTAAATTATATATTTTTTATGAGTATTTTAG-CAAAAATTGA
* * * ** * **
21811 GAAAATATCTTTCGGGTCAATTTTT-ACAAAAATTTAGCCGAAATCGCATAATAACCATCACAAT
193 GGAAATATCTTTCCGGTCAATTTTTGA-AAAATTTTAGCCGAAATCGTGTAATAATCATCACGGT
* * * * *
21875 TTTTGGATAAAAA-GCGTTCTGGGGCCCCGACCCA-TTTTGCATGATTTTTGGCGTC-AATACTC
257 TTTTGGCTAAAAACGCGTTC-CGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC-TCTAAGACTC
21937 CTATTG--ATATC
320 C--TTGAAATATC
* * *
21948 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAA-AATTTTGTTTTTACAAGCATCTAAA
1 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGA-TTTGTTTTTACGAGCATCTGAA
* * *
22012 TCTTGTTTCGATATAATT-GAAAATTAATACA-AAAAAACTATGAAAAACGATATTAAAAGCGTG
65 TCTTGTTTCGATTTAATTAG-AAATTAATTCAGAAAAAA-TAGGAAAAACGATATTAAAAGCGTG
** * * * *
22075 AAAAGTCCTCCAAT-ATTTTGGCCGTTAAATTATATA-TATTT-TGAGTATTTTAGGAAAAAATT
128 AAAAACCCTTCAATCTTTTTGG-CGTTAAATTATATATTTTTTATGAGTATTTTA-GCAAAAATT
* * * * * * *
22137 -AGGAAAAAAT-TTTCGGGTCTTTTTATTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACC
191 GAGG-AAATATCTTTCCGGTC-----A-ATTTTTGAAAAATTTTAGCCGAAATCGTGTAATAATC
* * * * ** * **
22200 ATCACGAG-TTTTGGTTAAAAACACGTTTCGGGGCACCAACTTAGTTTTGCATGATTTTTGATTC
249 ATCACG-GTTTTTGGCTAAAAACGCG-TTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCTC
** * *
22264 CGACATTCCTTGAAATAAT-
312 TAAGACTCCTTGAAAT-ATC
* * * * *
22283 TATATTCATTTAAT-AGAATCTTATCCACATTGCATTTAA-TATTT-TTCTTTACGAGCATCTGA
1 TATATTCATCTAATCA-AATCTCAGCCACATTGGATTTAAGGATTTGTT-TTTACGAGCATCTGA
* * * * *
22345 ATCATGTTTCGATTTAATTAGAAATTAATCCAGAAAAAATATGAAAAACGATATTAAAAACGTCA
64 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGA
* * * *
22410 AAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGA
129 AAAACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAGC-AAAAATTGA
*
22475 GGAAATATCTTT-CGAGTCAATTTTTTCAAGTCAATTTTTGCAAAATTTTAGCCCAAATC-T-TA
193 GGAAATATCTTTCCG-GTCAA-TTTTT---G---A-------AAAATTTTAGCCGAAATCGTGTA
* * * *** * *
22537 ATAATCATCATGGTTTTTGG---AAAACGCGATCCGGGGCCCATTTTAGTTTTGAATGATTTTTG
243 ATAATCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTG
*
22599 GCTC-AGAGTCTCCTTGAAATATC
308 GCTCTA-AGACTCCTTGAAATATC
* * ** *
22622 TATATTCATCTAACCAAAT-T----C-CA---G---T---CA-TTGTTTTTATAAGTATCTGAAT
1 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * * * * **
22671 CATGCTTCGTTTTAATTAAAAATTAATTCAGAAAAAATAGGAAAAACGGTATTAGAAGTATGAAA
66 CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAA
* * * *
22736 AACCATTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGA-G
131 AACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAGC-AAAAATTGAGG
* * * * * * * ***
22800 AAATAATATTTCGGGTCATTTTTTGCAAAATATTAGCCAAAATCGTGTAA-CATCA-CGATTTTT
195 AAAT-ATCTTTCCGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTAATAATCATC-A-CGGT
** * * * * *
22863 TTTTTTCTAAAAACACGTTCCGGGACCCCGGGTCAGTATTGCATGATTTTTTG-TTTCAAGACTC
257 TTTTGGCTAAAAACGCGTTCCGGG-CCCCGGCTCAGTTTTGCATGATTTTTGGCTCT-AAGACTC
* *
22927 CTTTAACTATC
320 CTTGAAATATC
* *
22938 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTAAAT
1 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * *
23003 CTTGTTTCGATTTAATATTGAAATTAATTCGGAAAAAAGTAGGAAAAACAATATTAGAAGCGT-A
66 CTTGTTTCGATTTAAT-TAGAAATTAATTCAGAAAAAA-TAGGAAAAACGATATTAAAAGCGTGA
* * * *
23067 AAAACCCTTCAATATTTTTGGCATAAAATTATATATTTTTTAATGA-TAATTTAGCAAAAATTTG
129 AAAACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTT-ATGAGTATTTTAGCAAAAA-TTG
* *
23131 AGGAAATATCTTTCCGGTCAATTTTTGAAAAATTTTAGCCGAAATTGTGTAATAATCAGCACGGT
192 AGGAAATATCTTTCCGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGT
* * * * *
23196 TTTTGGCTAAAAATGCGTTCCAGGGCCCCGGGTTAGTTTTGCATGATTTTTGGCGCTAAGACTAC
257 TTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCTCTAAGACTCC
*
23261 TTGAGATATC
321 TTGAAATATC
* * * * * *
23271 CATATACATCTAATTAAATCTCAGCCACATTGCATTTGAGGATTTGTTTTTACGAGCATCTAAAT
1 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * * * *
23336 CTTATTTTCTATTTAATTAAAAATTAATTCATAAAAAATATGAAAAGCG---TTAAAA--GT---
66 CTT-GTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAA
* ** * *
23393 ----CCTCCAATCTTTTTGATGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAATTGAG
130 AAACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAG-CAAAAATTGAG
* * * * * * * * * ** *****
23454 GAAAAATTTTTCAGTTCATTTTTTACAAAAATTTTAGGCGAAATCGTGTTACAA-GGTTTTTTTT
194 GAAATATCTTTCCGGTCAATTTTT-GAAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTT
* * * * *
23518 TTTTGCTAAAAACGTGTTTCGGGACCCCTGCTCAGTTTTGCATGATTTTTGGCATC-GAGACTCC
258 TTTGGCTAAAAACGCGTTCCGGG-CCCCGGCTCAGTTTTGCATGATTTTTGGC-TCTAAGACTCC
*
23582 TTGAAATATA
321 TTGAAATATC
* * * * * *
23592 TATATTCATCTAATCAAATCTCATCCATATTGCATTTAAAGATTTATTTTTACAAGCATCTGAAT
1 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* *
23657 CTTGTTTCGATTTAATTAGAAATTAATTTAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAA
66 CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAA
** * * * * *
23721 AGTCCTTTAATATTTTTGGAGTTGAATTATATATATTTTATGAGTATTTTAGACAAAAATTGAGG
131 AACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAG-CAAAAATTGAGG
* * * * * * *
23786 AAA-A-CTATATCTGGTCAATTTTTGCAAAATATTAGTCGAAATCATGTACGTTAGTCGAAATCA
195 AAATATCT-T-TCCGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTA--ATAATC---ATCA
* * ** * * * * * * * **
23849 TGGTTTTTTGCTAAAAACTTGTTACGGGGTCCCGGTTCAATGTTGCATGATTTTTTGCACCGAGA
253 CGGTTTTTGGCTAAAAACGCGTT-CCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCTCTAAGA
*
23914 CTCATTGAAATATC
317 CTCCTTGAAATATC
* * * * ***
23928 TATATTAATCTAACCAAATCTCAATATCCACAATGGATTTAAGGATTTGTAAAATA--AGCATCT
1 TATATTCATCTAATCAAATCTC---AGCCACATTGGATTTAAGGATTTGT-TTTTACGAGCATCT
* * * * *
23991 TAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAATAATAGGAAAAACGATATTAGAAGCA
62 GAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAA-AATAGGAAAAACGATATTAAAAGCG
* * * * * * *
24056 TG-AAAAGCCTTTAATCTTGTTGGTGTTAAATTATATA-ATTTTATGAGTATTGTGGCTAAAAAT
126 TGAAAAACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAGC-AAAAAT
* *
24119 TGAGGAAATAACTTT-CGAGTCAATTTTTTATCACCACAATTTTTGCAAACTTCTAGCCGAAAAA
190 TGAGGAAATATCTTTCCG-GTCAATTTTTGA--A--A-AA----T------TT-TAGCCG--AAA
* * * * * *
24183 TCTTGTAATAATCATCACGATTTTTTGCTAAAAACGCGTTCCGGGGCCTCGCCTAAGTTTTGCAT
236 TCGTGTAATAATCATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCAT
* * *
24248 GATTTTTGACGTC-AAGACTCTTTGAGATATC
300 GATTTTTGGC-TCTAAGACTCCTTGAAATATC
* * * * * * * *
24279 CATATTTATCTAATCAAATCCCAGCTACAATAGATTTAAGAATTTGTTTTTACGAGCTTCTGAAT
1 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * * * *
24344 CTTATTTCGATTTAATTAAAAATTAATTCAG-AAAAATATG-AAAACGATAGTAAAAGCATGAAA
66 CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAA
** * * * * *
24407 AGTCCTCCAATCTTGTTGGCATTAAATTTTATATATTTTATGAGTA-TTTATGCCAAAAATTGAC
131 AACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTA-G-CAAAAATTGA-
* * * * * * *
24471 AGAAAAATTTTTCAGGTC-ATTTTTTACAAAATTTTATCTGAAATCGTGTA
193 GGAAATATCTTTCCGGTCAATTTTTGA-AAAATTTTAGCCGAAATCGTGTA
24521 TATCAAATCT
Statistics
Matches: 2314, Mismatches: 420, Indels: 344
0.75 0.14 0.11
Matches are distributed among these distances:
310 17 0.01
311 6 0.00
312 9 0.00
315 14 0.01
316 52 0.02
317 2 0.00
319 15 0.01
320 31 0.01
321 176 0.08
322 39 0.02
323 10 0.00
324 141 0.06
325 5 0.00
327 14 0.01
328 46 0.02
329 153 0.07
330 38 0.02
331 104 0.04
332 54 0.02
333 296 0.13
334 158 0.07
335 87 0.04
336 134 0.06
337 15 0.01
338 82 0.04
339 113 0.05
340 188 0.08
341 12 0.01
342 2 0.00
343 19 0.01
344 3 0.00
345 18 0.01
346 18 0.01
347 40 0.02
348 54 0.02
349 48 0.02
350 2 0.00
351 79 0.03
352 1 0.00
353 1 0.00
354 9 0.00
356 9 0.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (330 bp):
TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAA
AACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTAGCAAAAATTGAGGA
AATATCTTTCCGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTT
GGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCTCTAAGACTCCTTGAA
ATATC
Found at i:23561 original size:654 final size:644
Alignment explanation
Indices: 21392--23827 Score: 1952
Period size: 654 Copynumber: 3.7 Consensus size: 644
21382 AAGAAATACG
* * * * * * * *
21392 ATATTAAAAACGTAAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTTTTT
1 ATATGAAAAGCGTTAAAAGTCCTCCAATCTTTTTGACGTTAAATTATATATATTTATGAGTATTT
* * * * *
21457 TAGCCAAAAATTGAGAAAAAAAAAATCTTTC-GTTTCAATTTTTGCAAAATTTTAGCTGAAAATC
66 TAGCAAAAAATTGAG----GAAAAATTTTTCAG-TTCATTTTTTGCAAAATTTTAGC-CAAAATC
* * ***** * *
21521 GTGCAGTAACAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAGGA-CCCGGCTCAATTTTG
125 GT---GTTAC-AA-CGTTTTTTTTTTTGGCTAAAAACACGTTCCG-GGACCCCGGCTCAGTTTTG
* * * * *
21585 CATGATTTCTGGCTCCGAGACTACTTGAAATATCTATATTCATCTAATCAAATCTCACCCACCTT
184 CATGATTTTTGGCTTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCATCCACATT
**
21650 AG-ATTTAACGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTG
249 -GCATTTAA-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA
* * * ** *
21714 GAAAAAATAGGAAAAATGATATTGAAAACGTCAAAAACCCTTCAATTTTTTTGGTGTTTAGA-TA
312 GAAAAAATAGGAAAAACGATATTAAAAACGTCAAAAACCCTTCAATATTTTTGG-CATTAAATTA
* * * * *
21778 TAT-TTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAATATCTTTCGGGTCAATTTTT-ACAAA
376 TATATTTTTTATGAGTAATTTAGACAAAAATTGAGGAAATATCTTTCCGGTCAATTTTTGATAAA
* * * * ** *
21841 AATTTAGCCGAAATCGCATAATAACCATCACAATTTTTGGATAAAAAGCGTTCTGGGGCCCCGAC
441 ATTTTAGCCGAAATTG-TTAATAATCATCACGGTTTTTGG-TAAAAAGCGTTC-CGGGCCCCGAC
** * *
21906 CCA-TTTTGCATGATTTTTGGCG-TCAATACTCCTAT-TGATATCTATATTCATCTAATCAAATC
503 TTAGTTTTGCATGATTTTTGGCGCT-AAGACTCCT-TGAGATATCTATATTCATCTAATCAAATC
* * * * * *
21968 TCAGCCACATTGGATTTAAAATTTTGTTTTTACAAGCATCTAAATCTT-GTTTCGATATAATTGA
566 TCAGCCACATTGCATTT-AGA-TTTGTTTTTAC-AGCATCTAAATCTTATTTTCTATTTAATTAA
*
22032 AAATTAATACAAAAAAACTATGAAAAA
628 AAATTAAT--------TC-AT-AAAAA
* * * * *
22059 CGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTGGCCGTTAAATTATATATATTT-TGAGTAT
1 --ATATGAAAAGCGTTAAAAGTCCTCCAATCTTTTTGACGTTAAATTATATATATTTATGAGTAT
* ** *
22123 TTTAGGAAAAAATT-AGGAAAAAATTTTCGGGTCTTTTTATTTTTTTGCAAAATTTTAGCCAAAA
64 TTTAGCAAAAAATTGAGG-AAAAATTTT----TCAGTTCA-TTTTTTGCAAAATTTTAGCCAAAA
* ****** * * * * ** *
22187 TCGTG-TACTAACCATCACGAGTTTTGGTTAAAAACACGTTTCGGGGCACCAACTTAGTTTTGCA
123 TCGTGTTAC-AA-CGTTTTTTTTTTTGGCTAAAAACACGTTCCGGGACCCCGGCTCAGTTTTGCA
* * * * *
22251 TGATTTTT-GATTCCGACATTCCTTGAAATAAT-TATATTCATTTAAT-AGAATCTTATCCACAT
186 TGATTTTTGGCTT-CGAGACTCCTTGAAAT-ATCTATATTCATCTAATCA-AATCTCATCCACAT
* * *
22313 TGCATTTAATATTT-TTCTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATCCA
248 TGCATTTAAGATTTGTT-TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA
* * * * *
22377 GAAAAAATATGAAAAACGATATTAAAAACGTCAAAAGCCCTTCAATCTTTTTGGCGTTGAATTAT
312 GAAAAAATAGGAAAAACGATATTAAAAACGTCAAAAACCCTTCAATATTTTTGGCATTAAATTAT
*
22442 ATATTTTTTATGAGT-A-TTATGGCTAAAAATTGAGGAAATATCTTT-CGAGTCAATTTTTTCAA
377 ATATTTTTTATGAGTAATTTA-GAC-AAAAATTGAGGAAATATCTTTCCG-GTCAA-TTTTT---
* * * * *
22504 GTCAATTTTTGCAAAATTTTAGCCCAAA-TCTTAATAATCATCATGGTTTTTGG-AAAACGCGAT
435 G---A----T--AAAATTTTAGCCGAAATTGTTAATAATCATCACGGTTTTTGGTAAAAAGCGTT
* * * * * *
22567 CCGGGGCCC-ATTTTAGTTTTGAATGATTTTTGGCTC-AGAGTCTCCTTGAAATATCTATATTCA
491 CCGGGCCCCGA-CTTAGTTTTGCATGATTTTTGGCGCTA-AGACTCCTTGAGATATCTATATTCA
* * * * * *
22630 TCTAACCAAAT-T----C-CAGT-CA-TT-G--TT-TTTATA-AGTATCTGAATC--ATGCTTCG
554 TCTAATCAAATCTCAGCCACATTGCATTTAGATTTGTTTTTACAGCATCTAAATCTTAT-TTTC-
*
22680 T-TTTAATTAAAAATTAATTCAGAAAAA
617 TATTTAATTAAAAATTAATTCATAAAAA
* * * * * * *
22707 ATAGGAAAAACGGTATTAGAAGTATGAAAAACCATTCAATCTTTTTGGCGTTGAATTATATATTT
1 ATATGAAAAGC-G--TTA-AA--A-G----TCC-TCCAATCTTTTTGACGTTAAATTATATA-TA
* * * * * * *
22772 TTTATGAGTATTGTGGCTAAAAATTGA-GAAATAATATTTCGGGTCATTTTTTGCAAAATATTAG
53 TTTATGAGTATTTTAGCAAAAAATTGAGGAAA-AATTTTTCAGTTCATTTTTTGCAAAATTTTAG
* *
22836 CCAAAATCGTGTAACATCACGATTTTTTTTTTT--CTAAAAACACGTTCCGGGACCCCGGGTCAG
117 CCAAAATCGTGTTACA--ACG-TTTTTTTTTTTGGCTAAAAACACGTTCCGGGACCCCGGCTCAG
* * * * * * *
22899 TATTGCATGATTTTTTGTTTCAAGACTCCTTTAACTATCTATATTCATCTAATCAAATCTCAGCC
179 TTTTGCATGATTTTTGGCTTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCATCC
* * * *
22964 ACATTGGATTTAAGGATTTGCTTTTACGAGCATCTAAATCTTGTTTCGATTTAATATTGAAATTA
244 ACATTGCATTTAA-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT-TAGAAATTA
* * * * *
23029 ATTCGGAAAAAAGTAGGAAAAACAATATTAGAAGCGT-AAAAACCCTTCAATATTTTTGGCATAA
307 ATTCAGAAAAAA-TAGGAAAAACGATATTAAAAACGTCAAAAACCCTTCAATATTTTTGGCATTA
23093 AATTATATATTTTTTAATGA-TAATTTAG-CAAAAATTTGAGGAAATATCTTTCCGGTCAATTTT
371 AATTATATATTTTTT-ATGAGTAATTTAGACAAAAA-TTGAGGAAATATCTTTCCGGTCAATTTT
*
23156 TGA-AAAATTTTAGCCGAAATTGTGTAATAATCAGCACGGTTTTTGGCTAAAAATGCGTTCCAGG
434 TGATAAAATTTTAGCCGAAATTGT-TAATAATCATCACGGTTTTTGG-TAAAAA-GCGTTCC-GG
** * * *
23220 GCCCCGGGTTAGTTTTGCATGATTTTTGGCGCTAAGACTACTTGAGATATCCATATACATCTAAT
495 GCCCCGACTTAGTTTTGCATGATTTTTGGCGCTAAGACTCCTTGAGATATCTATATTCATCTAAT
*
23285 TAAATCTCAGCCACATTGCATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTATTTTCTATTT
560 CAAATCTCAGCCACATTGCATTT-A-GATTTGTTTTTAC-AGCATCTAAATCTTATTTTCTATTT
23350 AATTAAAAATTAATTCATAAAAA
622 AATTAAAAATTAATTCATAAAAA
*
23373 ATATGAAAAGCGTTAAAAGTCCTCCAATCTTTTTGATGTTAAATTATATATATTTCATGAGTATT
1 ATATGAAAAGCGTTAAAAGTCCTCCAATCTTTTTGACGTTAAATTATATATATTT-ATGAGTATT
* * * *
23438 TTAGCCAAAAATTGAGGAAAAATTTTTCAGTTCATTTTTTACAAAAATTTTAGGCGAAATCGTGT
65 TTAGCAAAAAATTGAGGAAAAATTTTTCAGTTCATTTTTTGC-AAAATTTTAGCCAAAATCGTGT
* * ** * *
23503 TACAAGGTTTTTTTTTTTTGCTAAAAACGTGTTTCGGGACCCCTGCTCAGTTTTGCATGATTTTT
129 TACAACGTTTTTTTTTTTGGCTAAAAACACGTTCCGGGACCCCGGCTCAGTTTTGCATGATTTTT
* * *
23568 GGCATCGAGACTCCTTGAAATATATATATTCATCTAATCAAATCTCATCCATATTGCATTTAAAG
194 GGCTTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCATCCACATTGCATTT-AAG
* * * *
23633 ATTTATTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAG-AAAAATATG
258 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGG
* * ** * * *
23697 AAAAACGATATTAAAAGCGTGAAAAGTCCTTTAATATTTTTGG-AGTTGAATTATATATATTTTA
323 AAAAACGATATTAAAAACGTCAAAAACCCTTCAATATTTTTGGCA-TTAAATTATATATTTTTTA
* * * * *
23761 TGAGTATTTTAGACAAAAATTGAGGAAA-A-CTATATCTGGTCAATTTTTG-CAAAATATTAGTC
387 TGAGTAATTTAGACAAAAATTGAGGAAATATCT-T-TCCGGTCAATTTTTGATAAAATTTTAGCC
23823 GAAAT
450 GAAAT
23828 CATGTACGTT
Statistics
Matches: 1416, Mismatches: 239, Indels: 241
0.75 0.13 0.13
Matches are distributed among these distances:
643 15 0.01
644 2 0.00
645 20 0.01
646 8 0.01
647 5 0.00
648 11 0.01
649 60 0.04
650 8 0.01
651 28 0.02
652 96 0.07
653 26 0.02
654 193 0.14
655 142 0.10
656 58 0.04
657 89 0.06
658 79 0.06
659 11 0.01
660 30 0.02
661 3 0.00
662 12 0.01
663 118 0.08
664 139 0.10
665 20 0.01
666 39 0.03
667 5 0.00
668 34 0.02
669 66 0.05
672 2 0.00
673 10 0.01
674 55 0.04
676 18 0.01
678 14 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (644 bp):
ATATGAAAAGCGTTAAAAGTCCTCCAATCTTTTTGACGTTAAATTATATATATTTATGAGTATTT
TAGCAAAAAATTGAGGAAAAATTTTTCAGTTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTTA
CAACGTTTTTTTTTTTGGCTAAAAACACGTTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTGG
CTTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCATCCACATTGCATTTAAGATT
TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAA
AACGATATTAAAAACGTCAAAAACCCTTCAATATTTTTGGCATTAAATTATATATTTTTTATGAG
TAATTTAGACAAAAATTGAGGAAATATCTTTCCGGTCAATTTTTGATAAAATTTTAGCCGAAATT
GTTAATAATCATCACGGTTTTTGGTAAAAAGCGTTCCGGGCCCCGACTTAGTTTTGCATGATTTT
TGGCGCTAAGACTCCTTGAGATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAGA
TTTGTTTTTACAGCATCTAAATCTTATTTTCTATTTAATTAAAAATTAATTCATAAAAA
Found at i:25191 original size:11 final size:11
Alignment explanation
Indices: 25175--25199 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25165 CTTTCTCCTC
25175 CAGATAGTTGG
1 CAGATAGTTGG
25186 CAGATAGTTGG
1 CAGATAGTTGG
25197 CAG
1 CAG
25200 CCTTGAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.12, G:0.36, T:0.24
Consensus pattern (11 bp):
CAGATAGTTGG
Found at i:25327 original size:84 final size:84
Alignment explanation
Indices: 25186--25341 Score: 296
Period size: 84 Copynumber: 1.9 Consensus size: 84
25176 AGATAGTTGG
25186 CAGATAGTTGGCAGCCTTGAGCATCGCCACCAACGTCTCGTGGTTTTGAGCTCTGACGAAATTTT
1 CAGATAGTTGGCAGCCTTGAGCATCGCCACCAACGTCTCGTGGTTTTGAGCTCTGACGAAATTTT
25251 CGTCGAATTACTTCTCCTC
66 CGTCGAATTACTTCTCCTC
25270 CAGATAGTTGGCAGCCTTGAGCATCGCCACCAACGTCTCGTGGTTTTGAGC-CTTGACGAAATTT
1 CAGATAGTTGGCAGCCTTGAGCATCGCCACCAACGTCTCGTGGTTTTGAGCTC-TGACGAAATTT
25334 TCGTCGAA
65 TCGTCGAA
25342 CTCCTTAGCT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
83 1 0.01
84 70 0.99
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.29
Consensus pattern (84 bp):
CAGATAGTTGGCAGCCTTGAGCATCGCCACCAACGTCTCGTGGTTTTGAGCTCTGACGAAATTTT
CGTCGAATTACTTCTCCTC
Found at i:33769 original size:13 final size:13
Alignment explanation
Indices: 33751--33775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33741 CTTGTGTCCA
33751 TATAAAAAGATAG
1 TATAAAAAGATAG
33764 TATAAAAAGATA
1 TATAAAAAGATA
33776 TTTTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
TATAAAAAGATAG
Found at i:44078 original size:90 final size:91
Alignment explanation
Indices: 43951--44131 Score: 319
Period size: 90 Copynumber: 2.0 Consensus size: 91
43941 ATCAGTAAAA
* * *
43951 TTTCAATAATAATAAGTCAGACTTGTGTTGGTAAAATTTCAATGGATCTGTAAATCTCC-AATGA
1 TTTCAATAATAACAAGTCAAACTCGTGTTGGTAAAATTTCAATGGATCTGTAAATCTCCAAATGA
*
44015 TATTGTAGATGAGATAAACTACTGTG
66 CATTGTAGATGAGATAAACTACTGTG
44041 TTTCAATAATAACAAGTCAAACTCGTGTTGGTAAAATTTCAATGGATCTGTAAATCTCCAAATGA
1 TTTCAATAATAACAAGTCAAACTCGTGTTGGTAAAATTTCAATGGATCTGTAAATCTCCAAATGA
44106 CATTGTAGATGAGATAAACTACTGTG
66 CATTGTAGATGAGATAAACTACTGTG
44132 CTGCTAAACA
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
90 56 0.65
91 30 0.35
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (91 bp):
TTTCAATAATAACAAGTCAAACTCGTGTTGGTAAAATTTCAATGGATCTGTAAATCTCCAAATGA
CATTGTAGATGAGATAAACTACTGTG
Found at i:44512 original size:61 final size:60
Alignment explanation
Indices: 44424--44550 Score: 211
Period size: 61 Copynumber: 2.1 Consensus size: 60
44414 CTAATTATTT
*
44424 AACT-TTTTTTTTACAAGGCTATGCGCACACTACTCTTGTACACTATCAATTTGAATAAC
1 AACTGTTTTTTTTACAAGGCTATGCGCACACTACTCTTGTACACTACCAATTTGAATAAC
*
44483 AACTGTTTTGTTTTGCAAGGCTATGCGCACACTACTCTTGTACACTACCAATTTGAATAAC
1 AACTGTTTT-TTTTACAAGGCTATGCGCACACTACTCTTGTACACTACCAATTTGAATAAC
*
44544 AAATGTT
1 AACTGTT
44551 GGATATAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 4 0.06
60 4 0.06
61 55 0.87
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (60 bp):
AACTGTTTTTTTTACAAGGCTATGCGCACACTACTCTTGTACACTACCAATTTGAATAAC
Found at i:45977 original size:35 final size:35
Alignment explanation
Indices: 45931--46002 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
45921 TAGAAGAAAA
45931 AGCTTGACTCTAGTATTATTCCTCTTACACCAGAT
1 AGCTTGACTCTAGTATTATTCCTCTTACACCAGAT
*
45966 AGCTTGACTCTAGTATTATTCCTCTTACATCAGAT
1 AGCTTGACTCTAGTATTATTCCTCTTACACCAGAT
46001 AG
1 AG
46003 TATAAGAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (35 bp):
AGCTTGACTCTAGTATTATTCCTCTTACACCAGAT
Found at i:46220 original size:31 final size:31
Alignment explanation
Indices: 46185--46248 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
46175 ACAACACACA
46185 AGTACTAGAGTCAATAGAAATATACCAGTTG
1 AGTACTAGAGTCAATAGAAATATACCAGTTG
46216 AGTACTAGAGTCAATAGAAATATACCAGTTG
1 AGTACTAGAGTCAATAGAAATATACCAGTTG
46247 AG
1 AG
46249 AAGCCTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (31 bp):
AGTACTAGAGTCAATAGAAATATACCAGTTG
Found at i:46397 original size:33 final size:33
Alignment explanation
Indices: 46355--46420 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
46345 AGGCACCTTC
46355 AAATTCCTATGCCTTAAAGTATCATAAACAACA
1 AAATTCCTATGCCTTAAAGTATCATAAACAACA
46388 AAATTCCTATGCCTTAAAGTATCATAAACAACA
1 AAATTCCTATGCCTTAAAGTATCATAAACAACA
46421 GAAGTCTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.27
Consensus pattern (33 bp):
AAATTCCTATGCCTTAAAGTATCATAAACAACA
Found at i:46545 original size:41 final size:41
Alignment explanation
Indices: 46488--46572 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
46478 AATGCAACCT
46488 CTCGAAGTTAAGCACCTTTTAGCCTTTGTTTGAACTAAAAG
1 CTCGAAGTTAAGCACCTTTTAGCCTTTGTTTGAACTAAAAG
46529 CTCGAAGTTAAGCACCTTTTAGCCTTTGTTTGAACTAAAAG
1 CTCGAAGTTAAGCACCTTTTAGCCTTTGTTTGAACTAAAAG
46570 CTC
1 CTC
46573 AAAATCAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (41 bp):
CTCGAAGTTAAGCACCTTTTAGCCTTTGTTTGAACTAAAAG
Found at i:56547 original size:77 final size:77
Alignment explanation
Indices: 56451--56676 Score: 382
Period size: 76 Copynumber: 2.9 Consensus size: 77
56441 TCATTATGTA
* * *
56451 AGTAGTTTTTTGTATTTTTTTTTTAAATGTGTAGCTTTTTAAAATGATATAAATAAAATTTAAAT
1 AGTAGTTTTTGGTAGTTTTTTTTTAAATGGGTAGCTTTTTAAAATGATATAAATAAAATTTAAAT
56516 ACTTATATCGTG
66 ACTTATATCGTG
* *
56528 AGTAGTTTTTGGCAG-TTTTTTTTAAATGGGTAACTTTTTAAAATGATATAAATAAAATTTAAAT
1 AGTAGTTTTTGGTAGTTTTTTTTTAAATGGGTAGCTTTTTAAAATGATATAAATAAAATTTAAAT
56592 ACTTATATCGTG
66 ACTTATATCGTG
* *
56604 AGTAGTTTTTGATAGTTTTTTTTTAAAGGGGTAGCTTTTTAAAATGATATAAATAAAATTTAAAT
1 AGTAGTTTTTGGTAGTTTTTTTTTAAATGGGTAGCTTTTTAAAATGATATAAATAAAATTTAAAT
56669 ACTTATAT
66 ACTTATAT
56677 TTATCCTCTA
Statistics
Matches: 139, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
76 72 0.52
77 67 0.48
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.47
Consensus pattern (77 bp):
AGTAGTTTTTGGTAGTTTTTTTTTAAATGGGTAGCTTTTTAAAATGATATAAATAAAATTTAAAT
ACTTATATCGTG
Found at i:59221 original size:332 final size:328
Alignment explanation
Indices: 57676--59928 Score: 2029
Period size: 332 Copynumber: 6.8 Consensus size: 328
57666 TAAACGGGAT
* * * **
57676 CCCG-GAACGCGTTTTTTAGCCAAAAATCGTGATGATTATTACAAGATTTCGGCTAGAATTTTAC
1 CCCGCGAACGCG-TTTTTAGCCAAAAACCGTGATG-TTATTACACGATTTCGGCTAAAATTTTGT
** * * * *
57740 AAAAATTGACTCGAAAGTTATTTCCTCAATTTTTATCCACAATACTCATAAAA-ATTATATAATT
64 AAAAATTGAC-CGAAAAATATCTCCTCAATTTTTAGCTAAAATACTCATAAAATA-TATATAATT
** * * *
57804 CAACGCCAAAAAGATTGAAGGGTTTTTCATGCTTATAATATCGTTTTTCCA-ATTATTTTCTGAA
127 CAACGCCAAAAAGATTGAAGGACTTTTCA-CCTTTTAATATCGTTTTT-CATATT-TTTTCTAAA
* ***
57868 TTAATTTCTAATTAAATCGAAACATGATTCAGATGCT--TATTTTACAAATCCTTAAATCCAATG
189 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA-AAAACAAATCC-TAAATCCAATG
** * * * * * *
57931 TGGTTGAGATTTGATTAGATAAATGTAGATATTTCAAGGAGTCTCGGCACAAAAAATCATGCAAC
252 TGCCTGAGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAA
* * *
57996 AGTGAACCAGGG
317 ATTGAGCCGGGG
* * * *
58008 CCC-CATAACGCATTTGTAGCCAAAAACCGTGAT-TTCAACTAACATACACGATTTCGGCTAATA
1 CCCGC-GAACGCGTTTTTAGCCAAAAACCGTGATGTT--A-T----TACACGATTTCGGCTAAAA
* ** * * **
58071 TTTTGCAAAAATTGACCAGAAATGTTTTTCCTCAATTTTTCTCTAAAATACTCATAAAATATATA
58 TTTTGTAAAAATTGACC-GAAAAATATCTCCTCAATTTTTAGCTAAAATACTCATAAAATATATA
* * * * * *
58136 TAATTCAACTCCAAAAAAGATTGGAGGACTTTTCTCACTTCTAGTATCATTTTTCATA-TTTTTC
122 TAATTCAACGCC-AAAAAGATTGAAGGACTTTTCAC-CTTTTAATATCGTTTTTCATATTTTTTC
*
58200 TAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCA
185 TAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC-TAAATCCA
* * * * *
58265 ATGTGGCTGAGA--T--TTA-AT--ATA-A-ATATTTCGAGGAGTCTTGACACCAACAAA-CATG
249 ATGTGCCTGAGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAA-AAATCATG
* **
58320 CAAAACTGAGTTGGGG
313 CAAAATTGAGCCGGGG
* *
58336 CCC-CGAAACGCGTTTTTAGCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTT
1 CCCGCG-AACGCGTTTTTAGC--CAAAAACCGTGAT-GTTATTACACGATTTCGGCTAAAATTTT
* * * * * *
58400 GCAAAAAATGACCAGAAAAATAT-TCTCTCAATTTTTGGCCATAATACTCATAAAAAATATATAA
62 GTAAAAATTGACC-GAAAAATATCTC-CTCAATTTTTAGCTAAAATACTCATAAAATATATATAA
* * * *
58464 TTCAACGTCGAAAAA-ATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTTC-TATTTTTTCCA
125 TTCAACG-CCAAAAAGATTGAAGGACTTTTCAC-CTTTTAATATCG-TTTTTCATATTTTTTCTA
* * * * *
58527 AATTAATTTCTAATTAAAACGAAATATGATTCAGATGTTTGT-------AA----AAA--CAATG
187 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAAATCCAATG
* * ** * * * *
58579 -G-TTGGGATTTGGTTAAATGAATATAGATATTTCAAGGAGTATCGGCGCCAAAAATCGTTCAAA
252 TGCCTGAGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAA
**
58642 ATTGAATC-GGG
317 ATTGAGCCGGGG
* *
58653 CCC-CTGAACGCGTTTTTCGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGC
1 CCCGC-GAACGCGTTTTTAGCCAAAAACCGTGATG-TTATTACACGATTTCGGCTAAAATTTTGT
*
58717 AAAAATTGATCCGAAAGAA-ATCTCCTCAATTTTTAG-TCATAATACTCATAAAATATATATAAT
64 AAAAATTGA-CCGAAA-AATATCTCCTCAATTTTTAGCT-AAAATACTCATAAAATATATATAAT
* * *
58780 TCAACGCCAAAAGGATTGAAGGACTTTTCAAACTTTTAATATCGTTTTTCATATTTTTTTCTGAA
126 TCAACGCCAAAAAGATTGAAGGACTTTTC-ACCTTTTAATATCGTTTTTCATA-TTTTTTCTAAA
* *
58845 TTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTAAATTGCAATGT
189 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAAA-TCCAATGT
* * * * * *
58910 GGCTAAGATTTCATTTGATGAATATAGATATTTTAAGGAGTGTCGGCGCCAAAAACCATGCAAAA
253 GCCTGAGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
* *
58975 CT-ACGTCGGGG
318 TTGA-GCCGGGG
* * * *
58986 CCC-CGATACGCGTTTTTAGTCAAAAACCGTGATAGTTAGTACACGATTTTGGCTAAAACTTTGC
1 CCCGCGA-ACGCGTTTTTAGCCAAAAACCGTGAT-GTTATTACACGATTTCGGCTAAAATTTTG-
* * * * * * * * *
59050 AAAAAAATGACCTGAAAATTTTTTGCC-CTATTTCTGGATAAAATACTCATAAAATATATATAAT
63 TAAAAATTGACC-GAAAAATATCT-CCTCAATTTTTAGCTAAAATACTCATAAAATATATATAAT
** * * *
59114 TTTACGTCAAAAAGATTGGAGGACTTTTCATCCTTTTAATATCGTTTTTCATA-TTTTTCTGAAT
126 TCAACGCCAAAAAGATTGAAGGACTTTTCA-CCTTTTAATATCGTTTTTCATATTTTTTCTAAAT
* * * * *
59178 TAATTTCTAATTAAACCGAAATAAGATTCAGTTGCTTGTAAAAACAAATTCTTAAATCCAATGTG
190 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA-TCCTAAATCCAATGTG
* * * * * * *
59243 CCTGATATTTTATTGGATGAATATGGATATCTCAAGGAGTCTTGGCGCCCAAAATCATGCAAAAT
254 CCTGAGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAT
59308 TGAGCCGGGG
319 TGAGCCGGGG
** * *
59318 CCCTAGAACGCTTTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTA
1 CCCGCGAACGCGTTTTTAGCCAAAAACCGTGAT-GTTATTACACGATTTCGGCTAAAATTTTGTA
** * * *
59383 AAAATTGATTAGAAAAATATTTCCTCAATTTTTAGCTAAAATATTCATAAAAAATATATAATTCA
65 AAAATTGA-CCGAAAAATATCTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTCA
* * * * * * *
59448 AAGCCAAAAATATTGAAGGGCTTTTGACGTTTCTAATATCGTTTTTCCTA-TTTTTCCAAATTAA
129 ACGCCAAAAAGATTGAAGGACTTTTCACCTTT-TAATATCGTTTTTCATATTTTTTCTAAATTAA
* * *
59512 TTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTGAAAACAAATCCTTAAATCCAATGTGTCT
193 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC-TAAATCCAATGTGCCT
* * *
59577 GAGATTTGC-TTAGTTGAATATAGATATTTCAAGTAGTCTCGGAGCC-AAAATCATGCAAAATTG
257 GAGATTT-CATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAATTG
*
59640 AGCCGGGT
321 AGCCGGGG
* * *
59648 CCCGGGAACGCGTTTTTAGCCAAAATCCGTTGATGGTTTGTTAATACACGATTTCGGCTAAAATT
1 CCCGCGAACGCGTTTTTAGCCAAAAACCG-TGA-----TGTTATTACACGATTTCGGCTAAAATT
* *
59713 TTGTAAAAATTGACAC-AAAAGATTTCTCCTCAATTTTTGGCTAAAATACTCATAAAA-ATATAT
60 TTGTAAAAATTGAC-CGAAAA-ATATCTCCTCAATTTTTAGCTAAAATACTCATAAAATATATAT
* * * * *
59776 AATTCAACG-C-TAAAGATTGGAGGACTTTTTACGCTTTTAATATCGTATTTCTTATTTTTTCTA
123 AATTCAACGCCAAAAAGATTGAAGGACTTTTCAC-CTTTTAATATCGTTTTTCATATTTTTTCTA
* * * *
59839 AATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTGGTAAAAAAAAAATTTCTTAAATCCA
187 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAAACAAA--TCCTAAATCCA
**
59904 ATGTTG-CTGAGATTTGGTTAGATGA
249 ATG-TGCCTGAGATTTCATTAGATGA
59929 TGTAAAGTAT
Statistics
Matches: 1589, Mismatches: 237, Indels: 187
0.79 0.12 0.09
Matches are distributed among these distances:
309 4 0.00
310 1 0.00
311 6 0.00
313 6 0.00
314 14 0.01
315 122 0.08
316 53 0.03
317 24 0.02
318 34 0.02
323 2 0.00
324 28 0.02
325 135 0.08
326 1 0.00
327 3 0.00
328 51 0.03
329 4 0.00
330 78 0.05
331 193 0.12
332 288 0.18
333 128 0.08
334 116 0.07
335 101 0.06
336 50 0.03
337 111 0.07
338 36 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (328 bp):
CCCGCGAACGCGTTTTTAGCCAAAAACCGTGATGTTATTACACGATTTCGGCTAAAATTTTGTAA
AAATTGACCGAAAAATATCTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTCAAC
GCCAAAAAGATTGAAGGACTTTTCACCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTT
CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAAATCCAATGTGCCTGAGA
TTTCATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAATTGAGCCG
GGG
Found at i:60062 original size:12 final size:12
Alignment explanation
Indices: 60045--60069 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60035 TGGCATAGAA
60045 ACTTTAATCTTG
1 ACTTTAATCTTG
60057 ACTTTAATCTTG
1 ACTTTAATCTTG
60069 A
1 A
60070 TAGGCTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (12 bp):
ACTTTAATCTTG
Found at i:84964 original size:31 final size:31
Alignment explanation
Indices: 84926--84984 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
84916 TTTCTTCAGT
*
84926 GTGCTCCATGCAACTATATCGAACACTTCCC
1 GTGCTCCATGCAACTACATCGAACACTTCCC
**
84957 GTGCTCCATGCGCCTACATCGAACACTT
1 GTGCTCCATGCAACTACATCGAACACTT
84985 ACCGGACTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.24, C:0.36, G:0.15, T:0.25
Consensus pattern (31 bp):
GTGCTCCATGCAACTACATCGAACACTTCCC
Found at i:98448 original size:31 final size:31
Alignment explanation
Indices: 98371--98476 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 31
98361 TGAACTGGTG
* * **
98371 TCAAGACGTTTTATCCTCTGGA-TTTCAAA-
1 TCAAGACATTTTATCCTTTAAATTTTCAAAT
* *
98400 TCAAGACGTTTTGTCCTTTAAATTTTCAAAT
1 TCAAGACATTTTATCCTTTAAATTTTCAAAT
*
98431 TCAAGACATTTTATCC-TTAAATTTCCCAAAT
1 TCAAGACATTTTATCCTTTAAATTT-TCAAAT
*
98462 TCAACACATTTTATC
1 TCAAGACATTTTATC
98477 TCCTGACGGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.27
30 15 0.23
31 33 0.50
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (31 bp):
TCAAGACATTTTATCCTTTAAATTTTCAAAT
Done.