Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019331.1 Corchorus olitorius cultivar O-4 contig19364, 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: 47791
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:526 original size:21 final size:20
Alignment explanation
Indices: 480--522 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
470 CTCTCACAAG
* *
480 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
500 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
520 TTT
1 TTT
523 TCTACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:1586 original size:30 final size:31
Alignment explanation
Indices: 1550--1608 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1540 GTTAATAAAC
* *
1550 CATTAAAATTTGAGGATATTAGA-GAAAAGT
1 CATTAAAATTCGAGGATATGAGAGGAAAAGT
*
1580 CATTAAAATTCGAGGTTATGAGAGGAAAA
1 CATTAAAATTCGAGGATATGAGAGGAAAA
1609 TCAAGATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (31 bp):
CATTAAAATTCGAGGATATGAGAGGAAAAGT
Found at i:3898 original size:2 final size:2
Alignment explanation
Indices: 3891--3922 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3881 ATCTCACAAA
3891 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3923 TTTACTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5129 original size:21 final size:21
Alignment explanation
Indices: 5088--5131 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5078 AATTTTGTTG
**
5088 TTTATTTATTTATTTTTAATA
1 TTTATTTATTTATTTGCAATA
5109 TTTA-TTATTTAATTTGCAATA
1 TTTATTTATTT-ATTTGCAATA
5130 TT
1 TT
5132 ATCCCTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTATTTATTTATTTGCAATA
Found at i:5964 original size:42 final size:43
Alignment explanation
Indices: 5912--6005 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
5902 AGTGCATTAT
*
5912 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
5953 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
5998 CTAATATT
1 CTAATATT
6006 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:15993 original size:40 final size:40
Alignment explanation
Indices: 15948--16028 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
15938 ACTTGACCCT
* *
15948 CCTAATAATTAAGGAAATAAATTAAATCCAGGTTTAGCCC
1 CCTAATAACTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
*
15988 CCTAATAACTAAGGTAAGAAATTAAATCCAGGTTTAGCCC
1 CCTAATAACTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
16028 C
1 C
16029 TAGTTATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.26
Consensus pattern (40 bp):
CCTAATAACTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
Found at i:16524 original size:16 final size:16
Alignment explanation
Indices: 16505--16558 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
16495 GGAATAATTT
*
16505 ATTTCTATAATAAAAA
1 ATTTATATAATAAAAA
16521 ATTTATATAATAAAAA
1 ATTTATATAATAAAAA
*
16537 A-TTATA-ATTAAAAA
1 ATTTATATAATAAAAA
16551 ATGTTATA
1 AT-TTATA
16559 CACTAAATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 8 0.24
15 5 0.15
16 21 0.62
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTTATATAATAAAAA
Found at i:16764 original size:19 final size:19
Alignment explanation
Indices: 16721--16757 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16711 TTAGAAAACT
*
16721 TCAAAATTGAAAAAAAAAG
1 TCAAAATTAAAAAAAAAAG
*
16740 TAAAAATTAAAAAAAAAA
1 TCAAAATTAAAAAAAAAA
16758 TGCAAAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (19 bp):
TCAAAATTAAAAAAAAAAG
Found at i:17295 original size:4 final size:4
Alignment explanation
Indices: 17279--17336 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
17269 TTAAACATAG
* * *
17279 CTAA CTAA ATAA CTAA CTAA CTAA CTAA CTTA GTAA -TAA -TCAA CTAA
1 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CT-AA CTAA
17326 CT-A CTAA CTAA
1 CTAA CTAA CTAA
17337 TTAGTATAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
3 7 0.15
4 38 0.83
5 1 0.02
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.28
Consensus pattern (4 bp):
CTAA
Found at i:17337 original size:19 final size:21
Alignment explanation
Indices: 17279--17337 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 21
17269 TTAAACATAG
* *
17279 CTAACTAAATAACTAACTAA-
1 CTAACTAACTTACTAACTAAT
*
17299 CTAACTAACTTAGTAA-TAAT
1 CTAACTAACTTACTAACTAAT
17319 C-AACTAAC-TACTAACTAAT
1 CTAACTAACTTACTAACTAAT
17338 TAGTATAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 5 0.15
19 14 0.42
20 14 0.42
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (21 bp):
CTAACTAACTTACTAACTAAT
Found at i:20645 original size:21 final size:20
Alignment explanation
Indices: 20617--20682 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
20607 GCTAAGTCTT
20617 GAAAATTCTCTGTAAATTAA
1 GAAAATTCTCTGTAAATTAA
* * *
20637 GAAATATTCAACT-CAAATCATA
1 GAAA-ATTC-TCTGTAAATTA-A
*
20659 GAAAATTCTTTGTAAATTAA
1 GAAAATTCTCTGTAAATTAA
20679 GAAA
1 GAAA
20683 TACTCAACTC
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
20 10 0.29
21 18 0.51
22 7 0.20
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (20 bp):
GAAAATTCTCTGTAAATTAA
Found at i:20676 original size:42 final size:42
Alignment explanation
Indices: 20617--20699 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
20607 GCTAAGTCTT
*
20617 GAAAATTCTCTGTAAATTAAGAAATATTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
20659 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCAT
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCAT
20700 GATCCTTAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:20835 original size:56 final size:57
Alignment explanation
Indices: 20763--20879 Score: 191
Period size: 56 Copynumber: 2.0 Consensus size: 57
20753 TTTATTTTGT
*
20763 AGAATAATTAAGTAGAGACAGGGGGATAGG-ATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGACAGGGGGATAGGAATTTATTATAACATTTATTATGTGAA
*
20819 AGAATAATTAAGTAGAGATAGGGGGATAGGAATATTTATTATAACATTTATTATGTGAA
1 AGAATAATTAAGTAGAGACAGGGGGATAGG-A-ATTTATTATAACATTTATTATGTGAA
20878 AG
1 AG
20880 GAAACTAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
56 29 0.52
59 27 0.48
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGACAGGGGGATAGGAATTTATTATAACATTTATTATGTGAA
Found at i:24402 original size:15 final size:17
Alignment explanation
Indices: 24382--24414 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
24372 GGCCAACGTG
24382 AAAACCA-CA-AACCAA
1 AAAACCACCAGAACCAA
24397 AAAACCACCAGAACCAA
1 AAAACCACCAGAACCAA
24414 A
1 A
24415 TTATGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.64, C:0.33, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAACCACCAGAACCAA
Found at i:26732 original size:15 final size:16
Alignment explanation
Indices: 26707--26736 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
26697 AATAATTATT
26707 TTTAGATTATAATATA
1 TTTAGATTATAATATA
26723 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
26737 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:27822 original size:332 final size:332
Alignment explanation
Indices: 27088--29227 Score: 1767
Period size: 337 Copynumber: 6.4 Consensus size: 332
27078 GTTTAATACT
* * * *
27088 AAATCTCAGTCACATTGCATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTATTTCGATTTAA
1 AAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTTGATTTAA
* * ** * * ** *
27153 TTAGAAATTAATTTA-AAAAATATAAGAAATGCTATATTAAAAGCGTGAAAGGCCCCCCCAATAT
66 TTAGAAATTAATTCAGAAAAA-ATAGGAAAAACGATATTAAAAGCGTGAAAAG-CCCTTCAAT-C
* * * * * *
27217 TTTTTGGCATTG-AATTATATATTTTTATGAGTTTTTTAGTCAAAAATTGAGGAGAA-ATCTTTC
128 TTTTTGGCGTTGAAATTATATAATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATATCTTTT
* * * *
27280 GTGTCAATTTTTGCAAAAATTTAGCCGAAAT-AGTGTACTAACTAACCATAACGGTTTTTGGCTA
193 GGGTCATTTTTTGCAAAATTTTAGCCGAAATCA-TG---TAACTAACCATCACGGTTTTTGGCTA
* * * * * * *
27344 AAAATGCGTTCCGGGGATCCGCCTCAATTTTGCATGATTTTTGACTCCGAGACTACTTGAAATAT
254 AAAACGCGTT-CGGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATAT
27409 CTATATTCATCTAATC
317 CTATATTCATCTAATC
* * * * * * *
27425 AAATCTCAACCACATAGGACTTAAGGATTTGTTTTTACGAGCATCTTAATCTTATTTTCGATTTA
1 AAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTT-GATTTA
*
27490 ATTATG-AATTAATTCAGAAAAAATAGGAAAAACGATATTAGAAA-CGTCAAAAGCCCTTCAATC
65 ATTA-GAAATTAATTCAGAAAAAATAGGAAAAACGATATTA-AAAGCGTGAAAAGCCCTTCAATC
* *
27553 TTTTTAGCGTTGAAA-TATATAGTTTTATGAGTATTTTAGCCAAAAATTGA-GAAAATATCTTTT
128 TTTTTGGCGTTGAAATTATATAATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATATCTTTT
* * * ** *
27616 GGGCCCATTTTTTACAAAATTTCAGCCGAAATCATGTAA-TAACCATCACAATTTTTGACTAAAA
193 GGG-TCATTTTTTGCAAAATTTTAGCCGAAATCATGTAACTAACCATCACGGTTTTTGGCTAAAA
* * * * *
27680 AAGCGTTATGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAGATATCCAT
257 ACGCGTT-CGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTAT
* *
27745 ATTTATTTAATC
321 ATTCATCTAATC
** * *
27757 AAATCTCAGCCACATTTAAATTTAATGATTTGCTTTTACAAGCATCTGAATCTTGTTTTGATTTA
1 AAATCTCAGCCACA-TTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTTGATTTA
* * *
27822 ATTAGAAATTGATTCAG-AAAAATATGG-AAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCT
65 ATTAGAAATTAATTCAGAAAAAATA-GGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCT
* * *
27885 TTTTGGTGTT-AAATTATATATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAA-ATTTTTT
129 TTTTGGCGTTGAAATTATATA-ATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATATCTTTT
** * * *
27948 GGGTCATTTTTTTTTAAAAAAATTTTAGCCAAAATCGTGT-ACTATAATCATCACGGTTTTTTTT
193 GGGTCA---TTTTTT-GCAAAATTTTAGCCGAAATCATGTAAC--TAACCATCACGG----TTTT
* * **
28012 TGGCAAAAAACGCGTTTCGGGAGCCCGGCTCAGTTTTGCATGATTTTTAGCATCGAGACTCCTCT
248 TGGCTAAAAACGCG-TTCGGG-GCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCT-T
*
28077 -AAA-ATCTATATTCATCTAATA
310 GAAATATCTATATTCATCTAATC
* * *
28098 AAATCTTAGCTACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGGATCTTGTTTTGATTTAA
1 AAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTTGATTTAA
** * * *
28163 TTAGAAATTAATTTTGAAAAAATATGAAAAACGATATTAAATGCGTGAAAAGCCCTTCAATGTTT
66 TTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTT
* * * * * * * *
28228 TTGGTGTAG-AATTATATATTTTTTATGAGTATTGTGGCTAAAATTTGAGG-CAATATCTTTTGG
131 TTGGCGTTGAAATTATATA-ATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATATCTTTTGG
* * * * *
28291 GTTAATTTTTGCAAAATTTTAGCTGAAA--ATCGT-A-T-ATCATCACAGTTTTTGGCTAAAAAC
195 GTCATTTTTTGCAAAATTTTAGCCGAAATCAT-GTAACTAACCATCACGGTTTTTGGCTAAAAAC
* * * * *
28351 GCATTCCGGGG-CCGGTTCAGTTTTGCATGATTCTTGGCGCTGAGACTCCTTGATATATCTATAT
259 GCGTT-CGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATAT
* *
28415 TTATCTAACC
323 TCATCTAATC
* * * *
28425 AAA--T----CACA---C---T----A-TTG-TTTTATAAGCGTCTGAATCATGTTTTAATTTAA
1 AAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTTGATTTAA
* * * *
28472 TTAGAAATTAGTT-AGGGAAAAAATAGGTAAAAACGATATTAAAAGCATGAAAACCCCTTCGATC
66 TTAGAAATTAATTCA--GAAAAAATAGG-AAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATC
* * *
28536 TTTTTGGCGTTGTATTATAAATTTTTTTATAAAAATTGTGGGTAAACATTGAGGAAAAATATTTC
128 TTTTTGGCGTTG------AAA-----TTAT-ATAATT-T---T----A-TGA-G---TAT-TTTA
* * * * *
28601 GCAAAAAATTGAGGAGAAAT-T-TTTTGGGTCATTTTCTGCAAAATTTAAGCTGGAATC--GTAA
167 GCCAAAAATTGAGGA-AAATATCTTTTGGGTCATTTTTTGCAAAATTTTAGCCGAAATCATGT-A
* *
28662 ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTAGGCTTAGTTTTGCATGATTTT
230 ACTAACCATCACGGTTTTTGGCTAAAAACGCG-TTCGGGGCC-CGGCTCAGTTTTGCATGATTTT
* *
28727 TGGCGCCGAAACTCCTTGAAATGTCTATATTCATCTAATC
293 TGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATC
* *
28767 AAATCTCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTA
1 AAATCTCAGCCACA-TTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTTGATTTA
* *
28832 ATTAGAAATTAATTCAG-----AT------AA--ATATGAAAAGC-TCGAAAAGTCCTTCAA-CT
65 ATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGT-GAAAAGCCCTTCAATC-
* * * **
28882 TTTTTGGTGTT-AAATTATAT-ATTTCATAAGTATTTTAGCCAAAAAATTGAATAAAA-AT-TTT
128 TTTTTGGCGTTGAAATTATATAATTTTATGAGTATTTTAGCC-AAAAATTGAGGAAAATATCTTT
* * *
28943 CAGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTG-AACTAACCATCACGGTTTTTTGCTAAA
192 -TGGGTCATTTTTTGCAAAATTTTAGCCGAAATCATGTAACTAACCATCACGGTTTTTGGCTAAA
* * **
29007 AACGCATTACGGGGCTCCGACTCAGTTTTGCATGATTTTTGGCGTTGAGACTCCTTGAAATATTC
256 AACGCGTT-CGGGGC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATA-TC
*
29072 TATATTCATTTAATC
318 TATATTCATCTAATC
* * ** * *
29087 AAATCTCAG-CACATTGCGTTTAAGGATTTGTTTATATGAGCATTTGAATCTTGTTTCGATTTAA
1 AAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTTGATTTAA
* * * *
29151 TTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAACCGTGAAAAGTCCTCCAA-CATT
66 TTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATC-TT
*
29214 TTTGGTGTT-AAATT
130 TTTGGCGTTGAAATT
29228 CACTGTTTTC
Statistics
Matches: 1461, Mismatches: 221, Indels: 249
0.76 0.11 0.13
Matches are distributed among these distances:
309 40 0.03
310 13 0.01
311 42 0.03
315 1 0.00
318 78 0.05
319 119 0.08
320 26 0.02
321 4 0.00
322 3 0.00
323 8 0.01
324 4 0.00
325 2 0.00
326 35 0.02
327 22 0.02
328 22 0.02
330 45 0.03
331 56 0.04
332 139 0.10
333 74 0.05
334 14 0.01
335 25 0.02
336 57 0.04
337 149 0.10
338 48 0.03
339 16 0.01
340 92 0.06
341 141 0.10
342 96 0.07
343 1 0.00
344 1 0.00
345 2 0.00
346 31 0.02
348 6 0.00
355 3 0.00
359 1 0.00
360 4 0.00
361 40 0.03
362 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (332 bp):
AAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTTGATTTAA
TTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTT
TTGGCGTTGAAATTATATAATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATATCTTTTGGG
TCATTTTTTGCAAAATTTTAGCCGAAATCATGTAACTAACCATCACGGTTTTTGGCTAAAAACGC
GTTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
TCTAATC
Found at i:30264 original size:335 final size:333
Alignment explanation
Indices: 29638--31202 Score: 2071
Period size: 328 Copynumber: 4.7 Consensus size: 333
29628 AAAAACAATG
* *
29638 GTTAAA-T-TATATATTTTATGACTATTTTAGCCAAAAATTGAGGAAAAATTTTCGGGCCATTTT
1 GTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATTTTCGGGCCATTTT
* *
29701 CTGCAAAATTTAAGTTGGAATCGTGTACTAACCATCACCGTTTTTTTTTGCTAAAAACGCGTTTA
66 CTGCAAAATTTAAGCTGGAATCGTGTACTAACCATCA-CGTTTGTTTTTGCTAAAAACGCGTTT-
* *
29766 CGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCGCCGCGAAATCCTTGAAATATCTATACTCAT
129 CGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCGCCGAG-ACTCCTTGAAATATCTATACTCAT
*
29831 CTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATATTGTTTT
193 CTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATATTATTTT
*
29896 GATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAACCATGAAAAGTCCTCCA
258 GATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCA
* *
29961 ATATTTTTGGT
323 ATCTTTTTGGC
* *
29972 GTTAAATTATATATATTTTATGACTATTTTAGC-CAAAATTGAGGAGAAAATTTTCGGGCCATTT
1 GTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGA-AAAATTTTCGGGCCATTT
* * *
30036 TCTGCAAAATTTAAGTTGGAATCGTGTAGTAACCATCACCGTTTTTTTTTGGCTAAAAACGCGTT
65 TCTGCAAAATTTAAGCTGGAATCGTGTACTAACCATCA-CGTTTGTTTTT-GCTAAAAACGCGTT
* *
30101 TCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCGCCGCGATTCCTTGAAATATCTATACTCAT
128 TCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATACTCAT
30166 CTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATATTATTTT
193 CTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATATTATTTT
* * *
30231 GATTTAATTAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGCTTGAAAAGTCCTTCA
258 GATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCA
*
30296 ACCTTTTTGGC
323 ATCTTTTTGGC
* *
30307 GTTAAA-T-TATATATTTTATGAGTATTTTAGCAAAAAATTGAAGAAAAACTTTTCGGGCCATTT
1 GTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAA-TTTTCGGGCCA-TT
* ** * * **
30370 TTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCA--TGGGTTTTTGCTAAAAACGCGTTT
64 TTCTGCAAAATTTAAGCTGGAATCGTGTACTAACCATCACGTTTGTTTTTGCTAAAAACGCGTTT
** * * *
30433 TAGGGCTCC-GACTTAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCAT
129 CGGGGCCCCAG-CTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATACTCAT
* * * * *
30497 CTAATCAAATCTCAGCCACA-TTGCATTTAATGATTTGTTTATACGAGCATTTGAATCTTATTTC
193 CTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATATTATTTT
* * * *
30561 GATTTAATTAGAAATTAATTCTGAAAAATATGAAAAACGATATTAAAAGCGTAAAAAATCCTCCA
258 GATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCA
*
30626 ATCTTTTTGAC
323 ATCTTTTTGGC
* *
30637 GTTAAATTATATATATATTATGAGTATTTTAGCTAAAAATTGAGGAAAAATTTGTCGGGTCATTT
1 GTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATTT-TCGGGCCATTT
30702 TCTGCAAAATTTAAGCTGGAATCGTG---TAACCATCACG---GTTTTTGGCTAAAAACGCGTTT
65 TCTGCAAAATTTAAGCTGGAATCGTGTACTAACCATCACGTTTGTTTTT-GCTAAAAACGCGTTT
* *
30761 CGGGGCCCCGGCTTAGTTTTGTATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATACTCATC
129 CGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATACTCATC
* *
30826 TAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTTG
194 TAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATATTATTTTG
* *
30891 ATTTAATTAGAAATTGATTCAG-AAAATATGGAAAACGATATTAAAAGCATGAAAAGTCCTCCAA
259 ATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAA
*
30955 TCTTTTTGGA
324 TCTTTTTGGC
* * * * *
30965 GTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTCGGTTCTATT
1 GTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAAT-TTTCGG-GCCATT
** * * * * * * *
31030 TT-TGCAAAATTTTGGCCGAAATCGTG---T-ACCATCACGATT-TTTTGGCTTAAAACACGTTC
64 TTCTGCAAAATTTAAGCTGGAATCGTGTACTAACCATCACGTTTGTTTTTGCTAAAAACGCGTTT
* * * * * * * * * *
31089 CGGGGTCCCGGGTCAGTTTTGCATGATTTTTTTGTGGCAAAACTCCTCT-AAATATCTATAGTCA
129 CGGGGCCCCAGCTTAGTTTTGCATGA-TTTTTGGCGCCGAGACTCCT-TGAAATATCTATACTCA
* * * * * *
31153 TCTAACCTAATCTTAGCCACAATAG-ATTTAAAGATTTGTTTTTACGAGCA
192 TCTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCA
31203 GTAGAGCAAG
Statistics
Matches: 1105, Mismatches: 103, Indels: 52
0.88 0.08 0.04
Matches are distributed among these distances:
327 15 0.01
328 276 0.25
329 121 0.11
330 115 0.10
331 118 0.11
332 51 0.05
333 27 0.02
334 28 0.03
335 208 0.19
336 131 0.12
337 15 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (333 bp):
GTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATTTTCGGGCCATTTT
CTGCAAAATTTAAGCTGGAATCGTGTACTAACCATCACGTTTGTTTTTGCTAAAAACGCGTTTCG
GGGCCCCAGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATACTCATCTA
ATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATATTATTTTGAT
TTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATC
TTTTTGGC
Found at i:31235 original size:659 final size:660
Alignment explanation
Indices: 29638--31235 Score: 1902
Period size: 659 Copynumber: 2.4 Consensus size: 660
29628 AAAAACAATG
* * * *
29638 GTTAAATTATATATTTTATGACTATTTTAGCCAAAAATTGAGGAAAAA-TTTTCGGGCCAT-TTT
1 GTTAAATTATATATTTTATGAGTATTGTAGCAAAAAATTGAAGAAAAACTTTTCGGGCCATATTT
* ** ** * ** * *
29701 CTGCAAAATTTAAGTTGGAATCGTGTACTAACCATCACCGTTTTTTTTTGCTAAAAACGCGTTTA
66 TTGCAAAATTTTGGCCGAAATCGTG-A-TAACCATCA-CG--AGTTTTTGCTAAAAACACG-TTC
* * * * *
29766 CGGGGC-CCCAGCTTAGTTTTGCATGATTTTTGGCGCCGCGAAA-TCCTTGAAATATCTATACTC
125 CAGGGCTCCGA-CTCAGTTTTGCATGATTTTTGGCG--GCAAAACTCCTTGAAATATCTATAGTC
* * * * * * ***
29829 ATCTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCA-TCTGAATA-TTG
187 ATCTAACCAAATCTCAGCCACA-TAGCATTTAAAGATTTGTTTATACGAGCAGT-AGAA-ACAAA
* ** * * *
29892 TTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAACCATGAAAAGTCC
249 TTTCGATCCAATAAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAACCATAAAAAATCC
** * *
29957 TCCAATATTTTTGGTGTTAAATTATATATATTTTATGACTATTTTAGCCAAAATTGAGGAGAAAA
314 TCCAATATTTTTGACGTTAAATTATATATATATTATGACTATTTTAGCAAAAATTGAGGAGAAAA
* *
30022 TTTTCGGGCCATTTTCTGCAAAATTTAAGTTGGAATCGTGTAGTAACCATCACCGTTTTTTTTTG
379 TTTTCGGGCCATTTTCTGCAAAATTTAAGCTGGAATCG-GTAGTAACCATCACCG--TGTTTTTG
* *
30087 GCTAAAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCGCCGCGATTCCTTGAA
441 GCTAAAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAA
30152 ATATCTATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCAT
506 ATATCTATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCAT
* *
30217 CTGAATATTATTTTGATTTAATTAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGCT
571 CTGAATATTATTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCA
* *
30282 TGAAAAGTCCTTCAACCTTTTTGGC
636 TGAAAAGTCCTCCAACCTTTTTGGA
* *
30307 GTTAAATTATATATTTTATGAGTATTTTAGCAAAAAATTGAAGAAAAACTTTTCGGGCCATTTTT
1 GTTAAATTATATATTTTATGAGTATTGTAGCAAAAAATTGAAGAAAAACTTTTCGGGCCATATTT
* * * **
30372 TTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCATGGGTTTTTGCTAAAAACGCGTTTTAGG
66 TTGCAAAATTTTGGCCGAAATCGTG-A-TAACCATCACGAGTTTTTGCTAAAAACACGTTCCAGG
* * * * * *
30437 GCTCCGACTTAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAAT
129 GCTCCGACTCAGTTTTGCATGATTTTTGGCGGCAAAACTCCTTGAAATATCTATAGTCATCTAAC
* * * * * ** **
30502 CAAATCTCAGCCACATTGCATTTAATGATTTGTTTATACGAGCATTTGAATCTTATTTCGATTTA
194 CAAATCTCAGCCACATAGCATTTAAAGATTTGTTTATACGAGCAGTAGAAACAAATTTCGATCCA
* * * * *
30567 ATTAGAAATTAATTCTGAAAAATATGAAAAACGATATTAAAAGCGTAAAAAATCCTCCAATCTTT
259 ATAAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAACCATAAAAAATCCTCCAATATTT
*
30632 TTGACGTTAAATTATATATATATTATGAGTATTTTAGCTAAAAATTGAGGA-AAAATTTGTCGGG
324 TTGACGTTAAATTATATATATATTATGACTATTTTAGC-AAAAATTGAGGAGAAAATTT-TCGGG
*
30696 TCATTTTCTGCAAAATTTAAGCTGGAATC-GT-GTAACCATCA-CG-GTTTTTGGCTAAAAACGC
387 CCATTTTCTGCAAAATTTAAGCTGGAATCGGTAGTAACCATCACCGTGTTTTTGGCTAAAAACGC
* *
30757 GTTTCGGGGCCCCGGCTTAGTTTTGTATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATACT
452 GTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATACT
* *
30822 CATCTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATCTTGT
517 CATCTAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATATTAT
* *
30887 TTTGATTTAATTAGAAATTGATTCAG-AAAATATGGAAAACGATATTAAAAGCATGAAAAGTCCT
582 TTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCT
*
30951 CCAATCTTTTTGGA
647 CCAACCTTTTTGGA
* * * * **
30965 GTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAA-TATTTCGGTTC-TA
1 GTT-AAAT-TATATATTTTATGAGTATTGTAGCAAAAAATTGAAGAAAAACT-TTTCGGGCCATA
* *
31028 TTTTTGCAAAATTTTGGCCGAAATCGTG-T-ACCATCACGATTTTTTGGCTTAAAACACGTTCC-
63 TTTTTGCAAAATTTTGGCCGAAATCGTGATAACCATCACGAGTTTTT-GCTAAAAACACGTTCCA
* ** * *
31090 GGGGTCCCGGGTCAGTTTTGCATGATTTTTTTGTGGCAAAACTCCTCT-AAATATCTATAGTCAT
127 GGGCT-CCGACTCAGTTTTGCATGA-TTTTTGGCGGCAAAACTCCT-TGAAATATCTATAGTCAT
* * * *
31154 CTAACCTAATCTTAGCCACAATAG-ATTTAAAGATTTGTTTTTACGAGCAGTAGAGCAAGAAATT
189 CTAACCAAATCTCAGCCAC-ATAGCATTTAAAGATTTGTTTATACGAGCAGTAGA--AACAAATT
*
31218 TCGGTCCAATAAGAAATT
251 TCGATCCAATAAGAAATT
31236 TTCTACAAAT
Statistics
Matches: 819, Mismatches: 92, Indels: 46
0.86 0.10 0.05
Matches are distributed among these distances:
655 17 0.02
656 29 0.04
657 72 0.09
658 54 0.07
659 216 0.26
660 44 0.05
662 2 0.00
663 10 0.01
664 2 0.00
665 146 0.18
666 85 0.10
667 30 0.04
668 20 0.02
669 45 0.05
670 13 0.02
671 34 0.04
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (660 bp):
GTTAAATTATATATTTTATGAGTATTGTAGCAAAAAATTGAAGAAAAACTTTTCGGGCCATATTT
TTGCAAAATTTTGGCCGAAATCGTGATAACCATCACGAGTTTTTGCTAAAAACACGTTCCAGGGC
TCCGACTCAGTTTTGCATGATTTTTGGCGGCAAAACTCCTTGAAATATCTATAGTCATCTAACCA
AATCTCAGCCACATAGCATTTAAAGATTTGTTTATACGAGCAGTAGAAACAAATTTCGATCCAAT
AAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAACCATAAAAAATCCTCCAATATTTTT
GACGTTAAATTATATATATATTATGACTATTTTAGCAAAAATTGAGGAGAAAATTTTCGGGCCAT
TTTCTGCAAAATTTAAGCTGGAATCGGTAGTAACCATCACCGTGTTTTTGGCTAAAAACGCGTTT
CGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATACTCATC
TAATCAAATCTCAGCCACATTTGAATTTAATGATTTGTTTTTACGAGCATCTGAATATTATTTTG
ATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAA
CCTTTTTGGA
Found at i:31644 original size:37 final size:40
Alignment explanation
Indices: 31601--31710 Score: 127
Period size: 37 Copynumber: 2.7 Consensus size: 40
31591 ATTATTGAAA
*
31601 GAAGATCCACGTATGTGGAGGATTATT-TC-CA-AAGATT
1 GAAGATCCACGTATGTGGAGGATTATTATCAAAGAAGATT
*
31638 GAAGATCCACGTATATGGAGGATTATTATCAAAGAAGATT
1 GAAGATCCACGTATGTGGAGGATTATTATCAAAGAAGATT
**
31678 GAAAAAAGATCCACGTATGTGGAAAATTATTAT
1 G----AAGATCCACGTATGTGGAGGATTATTAT
31711 TCTTGAAGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
37 26 0.43
38 2 0.03
39 1 0.02
40 7 0.11
44 25 0.41
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (40 bp):
GAAGATCCACGTATGTGGAGGATTATTATCAAAGAAGATT
Found at i:32808 original size:336 final size:331
Alignment explanation
Indices: 32113--32927 Score: 947
Period size: 336 Copynumber: 2.5 Consensus size: 331
32103 TGTGTGTTAC
* *
32113 ACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATTAATTT-GAAAAAGAAATAGAAAAAACG
1 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAG-AAAA-AAATAGAAAAAACG
*
32177 ATATTAGAAGCGTG-AGAAGCCCTTAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATT
64 ATATTAGAAGCGTGAAAAAGCCCTTAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATT
* *
32241 GTGGCTAAAAATTGAGATAAATATTTAGGATCAATTTTTGCAAAACTTTAGCCAAAATCGTGTAC
129 GTCGCTAAAAATTGAGAAAAATATTTAGGATCAATTTTTGCAAAACTTTAGCCAAAATCGTGTAC
* *
32306 CATCACGGTTTTTTGGCTAAAAACGCGATTTGGGGCCCCAGGTCAGTTTTGCATGAGTTTTGACG
194 CATCACGGTTTTTTGGCTAAAAACGCGATTTGGGGCCACAGGTCAGTTTTGCATGAGTTTTGACA
* * * * *
32371 CCGAGACTCCTTAAAATATATCTTTATTCATGTAACCAAATCTCGGCCACATTGTATTTAAGAAT
259 CCAAGACTCCTTAAAATATATCTTTATTCATCTAACCAAACCTCAGCCACATTGGATTTAAGAAT
32436 TTGTTTTT
324 TTGTTTTT
* *
32444 ACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAATAAAATAGAAAAAACGA
1 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAA-AAAATAGAAAAAACGA
* * * *
32509 TATTAGAAGCGTGAAAAATG-CTTTCAATTTTTTTGGTGTTGATTTATATA-TTTTTATTAGTAT
65 TATTAGAAGCGTGAAAAA-GCCCTT-AATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTAT
* * * * * * *
32572 TTTCGCTAGAAATTGTGGAAAAATCTTT-TGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
128 TGTCGCTAAAAATTG-AGAAAAATATTTAGGA-TCAATTTTTGCAAAACTTTAGCCAAAATC--G
**
32636 TTCGTTAACCATCACGG-TTTTTGGCTAAAAACGCG-TTCTGGGGCCAC-GGCTTTGTTTTGCAT
189 -T-G-T-ACCATCACGGTTTTTTGGCTAAAAACGCGATT-TGGGGCCACAGG-TCAGTTTTGCAT
* * *
32698 GATTTTTTG-CACCAAGACTCCTT-GAA-ATATCTTTATTCATCTAATCAAACCTCAGCCACATT
248 GA-GTTTTGACACCAAGACTCCTTAAAATATATCTTTATTCATCTAACCAAACCTCAGCCACATT
*
32760 GGATTTAAGGATTTGTTTTT
312 GGATTTAAGAATTTGTTTTT
* * *
32780 ACGTGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAG-AAAAAATATG-AAAAACGA
1 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAATA-GAAAAAACGA
* ** * * ** * * *
32843 TATTAAAAGCGTG-AAAAGTACTCCAGTCTTTTTGGCATTGAATTTTATATATATTATGAGTATT
65 TATTAGAAGCGTGAAAAAGCCCT-TAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATT
* * *
32907 TTTGCCAAAAATTGAGAAAAA
129 GTCGCTAAAAATTGAGAAAAA
32928 ATCTTTCCGG
Statistics
Matches: 411, Mismatches: 53, Indels: 38
0.82 0.11 0.08
Matches are distributed among these distances:
331 70 0.17
332 35 0.09
333 90 0.22
334 48 0.12
335 4 0.01
336 91 0.22
337 7 0.02
338 51 0.12
339 15 0.04
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (331 bp):
ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAATAGAAAAAACGAT
ATTAGAAGCGTGAAAAAGCCCTTAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTGT
CGCTAAAAATTGAGAAAAATATTTAGGATCAATTTTTGCAAAACTTTAGCCAAAATCGTGTACCA
TCACGGTTTTTTGGCTAAAAACGCGATTTGGGGCCACAGGTCAGTTTTGCATGAGTTTTGACACC
AAGACTCCTTAAAATATATCTTTATTCATCTAACCAAACCTCAGCCACATTGGATTTAAGAATTT
GTTTTT
Found at i:34567 original size:17 final size:17
Alignment explanation
Indices: 34545--34580 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
34535 GCAATAGTGA
34545 TTGAACTTCTTTCATGT
1 TTGAACTTCTTTCATGT
34562 TTGAACTTCTTTCATGT
1 TTGAACTTCTTTCATGT
34579 TT
1 TT
34581 CGGATAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.56
Consensus pattern (17 bp):
TTGAACTTCTTTCATGT
Found at i:34879 original size:16 final size:15
Alignment explanation
Indices: 34858--34887 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
34848 TTATGTGAAT
34858 AATAAAATAAATAAAC
1 AATAAAAT-AATAAAC
34874 AATAAAATAATAAA
1 AATAAAATAATAAA
34888 ATTAAGCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAAAATAATAAAC
Found at i:34898 original size:24 final size:25
Alignment explanation
Indices: 34855--34908 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
34845 GAATTATGTG
* *
34855 AATAATAAAATAAATAAACAATA-A
1 AATAATAAAATAAAGAAACAAGATA
* *
34879 AATAATAAAATTAAGCAACAAGATA
1 AATAATAAAATAAAGAAACAAGATA
34904 AATAA
1 AATAA
34909 ATACTCCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (25 bp):
AATAATAAAATAAAGAAACAAGATA
Found at i:38111 original size:26 final size:26
Alignment explanation
Indices: 38075--38126 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
38065 TAATTTATAA
38075 GTATCACTATAATCCCTTTCAGAGGC
1 GTATCACTATAATCCCTTTCAGAGGC
38101 GTATCACTATAATCCCTTTCAGAGGC
1 GTATCACTATAATCCCTTTCAGAGGC
38127 TTGTGGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (26 bp):
GTATCACTATAATCCCTTTCAGAGGC
Found at i:38284 original size:117 final size:118
Alignment explanation
Indices: 38078--38313 Score: 420
Period size: 117 Copynumber: 2.0 Consensus size: 118
38068 TTTATAAGTA
*
38078 TCACTATAATCCCTTTCAGAGGCGTATCACTATAATCCCTTTCAGAGGCTTGTGGTATATCTTGA
1 TCACTATAATCCCTTTCAGAGGCGTATCACTATAATCCCTTTCAGAGGCTTGTGGTATACCTTGA
* * *
38143 CCCTGAACCGTAACAACCTCCTCTCATCTAAACTTTTGAGGACCG-AAATTTT
66 CCCTGAACCATAACAACCTCCTCTCATCTAAACTTTTAAGAACCGAAAATTTT
38195 TCACTATAATCCCTTTCAGAGGCGTATCACTATAATCCCTTTCAGAGGCTTGTGGTATACCTTGA
1 TCACTATAATCCCTTTCAGAGGCGTATCACTATAATCCCTTTCAGAGGCTTGTGGTATACCTTGA
*
38260 CCCTGAACTATAACAACCTCCTCTCATCTAAACTTTTAAGAACCGAAAATTTT
66 CCCTGAACCATAACAACCTCCTCTCATCTAAACTTTTAAGAACCGAAAATTTT
38313 T
1 T
38314 TTTTTTTTGG
Statistics
Matches: 113, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
117 105 0.93
118 8 0.07
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (118 bp):
TCACTATAATCCCTTTCAGAGGCGTATCACTATAATCCCTTTCAGAGGCTTGTGGTATACCTTGA
CCCTGAACCATAACAACCTCCTCTCATCTAAACTTTTAAGAACCGAAAATTTT
Found at i:43831 original size:18 final size:18
Alignment explanation
Indices: 43787--43886 Score: 62
Period size: 18 Copynumber: 5.3 Consensus size: 18
43777 ACCGACCGCC
*
43787 TAATATATATAATATTTTTAA
1 TAATATATAT-ATA-TTAT-A
*
43808 TAAATATTTATATATTATA
1 T-AATATATATATATTATA
*
43827 TAATATATATCT-TATATA
1 TAATATATATATAT-TATA
*
43845 TAAAATATATATA-TATA
1 TAATATATATATATTATA
*
43862 GGAATATATAATTATATTA-A
1 -TAATATAT-A-TATATTATA
43882 TAATA
1 TAATA
43887 ATTTATAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
17 5 0.08
18 29 0.46
19 7 0.11
20 8 0.13
21 6 0.10
22 8 0.13
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (18 bp):
TAATATATATATATTATA
Found at i:43871 original size:2 final size:2
Alignment explanation
Indices: 43789--43861 Score: 50
Period size: 2 Copynumber: 39.5 Consensus size: 2
43779 CGACCGCCTA
* * * *
43789 AT AT AT AT A- AT AT TT TT A- AT AA AT AT TT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
43828 A- AT AT AT AT CT -T AT AT AT A- AA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43862 GGAATATATA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
1 6 0.11
2 51 0.89
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43883 original size:16 final size:16
Alignment explanation
Indices: 43816--43899 Score: 59
Period size: 18 Copynumber: 5.2 Consensus size: 16
43806 AATAAATATT
43816 TATAT-ATTATA-TAA
1 TATATAATTATATTAA
*
43830 TATATATCTTATATATAA
1 TATATA-ATTATAT-TAA
* **
43848 AATATATATATATAGGAA
1 TATATA-AT-TATATTAA
43866 TATATAATTATATTAA
1 TATATAATTATATTAA
*
43882 TA-ATAATT-TATAAA
1 TATATAATTATATTAA
43896 TATA
1 TATA
43900 AAAAATTAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
14 12 0.22
15 7 0.13
16 13 0.24
17 2 0.04
18 17 0.31
19 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (16 bp):
TATATAATTATATTAA
Found at i:46456 original size:13 final size:13
Alignment explanation
Indices: 46417--46458 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
46407 AGGCCAAGCA
46417 CGCTGGGCCAGCG
1 CGCTGGGCCAGCG
* *
46430 CGC-AGCCCAGGCG
1 CGCTGGGCCA-GCG
46443 CGCTGGGCCAGCG
1 CGCTGGGCCAGCG
46456 CGC
1 CGC
46459 GGCCCAGCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.17
13 15 0.65
14 4 0.17
ACGTcount: A:0.10, C:0.43, G:0.43, T:0.05
Consensus pattern (13 bp):
CGCTGGGCCAGCG
Found at i:47434 original size:28 final size:27
Alignment explanation
Indices: 47394--47467 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
47384 TAATATGTCA
*
47394 AAATTACTGTTTTACCCTTGG-TCATCT
1 AAATTACAGTTTTACCCTTGGTTCA-CT
* *
47421 AAAATTAACA-TTTTACCCCTGGTTGACT
1 -AAATT-ACAGTTTTACCCTTGGTTCACT
47449 AAATTACAGTTTTACCCTT
1 AAATTACAGTTTTACCCTT
47468 AAATGCCGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 3 0.08
27 14 0.36
28 18 0.46
29 4 0.10
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
AAATTACAGTTTTACCCTTGGTTCACT
Done.