Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020404.1 Corchorus olitorius cultivar O-4 contig20437, 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: 75467
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:745 original size:13 final size:13
Alignment explanation
Indices: 727--753 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
717 GCATATATAT
727 ATACTAAATACTA
1 ATACTAAATACTA
740 ATACTAAATACTA
1 ATACTAAATACTA
753 A
1 A
754 AAATTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
ATACTAAATACTA
Found at i:4899 original size:19 final size:19
Alignment explanation
Indices: 4875--4912 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4865 TTAATGATTA
4875 GCCAACTTATTTTAACTTT
1 GCCAACTTATTTTAACTTT
4894 GCCAACTTATTTTAACTTT
1 GCCAACTTATTTTAACTTT
4913 TAAACTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (19 bp):
GCCAACTTATTTTAACTTT
Found at i:5747 original size:32 final size:32
Alignment explanation
Indices: 5692--5752 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
5682 AAATATGTTT
*
5692 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGTCGATTCAATTA
*
5724 GAAAAATAAAGG-TATGATAGTCGATTCAA
1 GAAAAAT-AAGGATATAATAGTCGATTCAA
5753 AAGTTTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Found at i:14246 original size:21 final size:20
Alignment explanation
Indices: 14201--14256 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
14191 GTTTAATAAT
14201 TATACAGATGAGATT-ATAC
1 TATACAGATGAGATTAATAC
* *
14220 TGTACAGATTAGATTAAGTAC
1 TATACAGATGAGATTAA-TAC
*
14241 TATACATATGAGATTA
1 TATACAGATGAGATTA
14257 TTAGAACAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 13 0.43
20 1 0.03
21 16 0.53
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (20 bp):
TATACAGATGAGATTAATAC
Found at i:26055 original size:13 final size:13
Alignment explanation
Indices: 26037--26061 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26027 CTGGAATGTC
26037 AAAAAAAAAAAGT
1 AAAAAAAAAAAGT
26050 AAAAAAAAAAAG
1 AAAAAAAAAAAG
26062 ACCGGTTTTA
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:0.88, C:0.00, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAAAGT
Found at i:27377 original size:55 final size:55
Alignment explanation
Indices: 27293--27404 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
27283 TTGAAACGAA
27293 GTTTACACTTAAACTCCGTTTGGGGCCAAAACGGTGATAAAACGCTCAAACAATG
1 GTTTACACTTAAACTCCGTTTGGGGCCAAAACGGTGATAAAACGCTCAAACAATG
* * *
27348 GTTTATACTTAAACTCCGTTTGGGGCCAAAATGGTGATAAAACGCTCAAACGATG
1 GTTTACACTTAAACTCCGTTTGGGGCCAAAACGGTGATAAAACGCTCAAACAATG
27403 GT
1 GT
27405 GAAACGATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (55 bp):
GTTTACACTTAAACTCCGTTTGGGGCCAAAACGGTGATAAAACGCTCAAACAATG
Found at i:28175 original size:129 final size:129
Alignment explanation
Indices: 28025--28260 Score: 418
Period size: 129 Copynumber: 1.8 Consensus size: 129
28015 TTTTAGGTTC
* * * * *
28025 AAGAAAATTAGCACTAAAAAACCTTCCATGCGTTGATTAGAGTTTGACTTGATTTTATATCAGTC
1 AAGAAAATTAGCACTAAAAAACCTCCCATACATTGATTACAATTTGACTTGATTTTATATCAGTC
28090 GAAATCTAATATAACTATTGAATACTGAGATTGTACAAGAAAGGTTCAAGATTTTGTGAATGAA
66 GAAATCTAATATAACTATTGAATACTGAGATTGTACAAGAAAGGTTCAAGATTTTGTGAATGAA
*
28154 AAGAAAATTAGCATTAAAAAACCTCCCATACATTGATTACAATTTGACTTGATTTTATATCAGTC
1 AAGAAAATTAGCACTAAAAAACCTCCCATACATTGATTACAATTTGACTTGATTTTATATCAGTC
28219 GAAATCTAATATAACTATTGAATACTGAGATTGTACAAGAAA
66 GAAATCTAATATAACTATTGAATACTGAGATTGTACAAGAAA
28261 AAAATGATTA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 101 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (129 bp):
AAGAAAATTAGCACTAAAAAACCTCCCATACATTGATTACAATTTGACTTGATTTTATATCAGTC
GAAATCTAATATAACTATTGAATACTGAGATTGTACAAGAAAGGTTCAAGATTTTGTGAATGAA
Found at i:28402 original size:2 final size:2
Alignment explanation
Indices: 28359--28389 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
28349 TCTTAGTTGG
28359 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28390 CTATGACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:30501 original size:2 final size:2
Alignment explanation
Indices: 30494--30536 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
30484 AATTATTGAA
* *
30494 AT AT AT AT AT TT TT CAT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30536 A
1 A
30537 AGGTAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35363 original size:12 final size:12
Alignment explanation
Indices: 35334--35372 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35324 TTAAGCCACT
*
35334 GCCACCCTAACTA
1 GCCACCC-AACCA
*
35347 GCCACCCAGCCA
1 GCCACCCAACCA
35359 GCCACCCAACCA
1 GCCACCCAACCA
35371 GC
1 GC
35373 GCACTTCTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.28, C:0.54, G:0.13, T:0.05
Consensus pattern (12 bp):
GCCACCCAACCA
Found at i:36102 original size:202 final size:199
Alignment explanation
Indices: 35756--36157 Score: 579
Period size: 202 Copynumber: 2.0 Consensus size: 199
35746 AAATGTAAAT
* * *
35756 TAAGTTAAACCAAACAAGCATTGTAGAGAGCACAATGTGATTTGAAAAAGTTGTTTTTACATCAA
1 TAAGTTAAACCAAACAAGCATTATAGAGAGCACAATGTGATTTGAAAAAGCTGTTTTCACATCAA
* * *
35821 GAGATCGCAATCTTTCTACCAAATGTATCTTTATTTTATGTGCTGAGATGAGTCGCAATTTCTAC
66 GAAATCGCAATCTTGCTACCAAATGTATCTTTATTTTATGTGCTGAGATGAGTCGCAATCTCTAC
* * * *
35886 TAATCCTTTGATATCTCCTATTCGATAACTGCATTGAATCACAGTTAATTGGAGTCGAGTAATAT
131 TAATCCTCTGATATCTCCTATTCGATAACTGCAATGAATCACAGTTAATTAGAGTCAAGTAATAT
35951 CGGA
196 CGGA
* * *
35955 TAAGTTAAACCAAACAAGCACTATATAGAGATCACGATGTGGTTTGAAAAAGCTGTTTTCACATC
1 TAAGTTAAACCAAACAAGCA-T-TATAGAGAGCACAATGTGATTTGAAAAAGCTGTTTTCACATC
* ** * * * *
36020 AATAAATCGCAATCTTGCTATTAAATGTATTTTTTATTTTATGTGCTGAGGTGATTTGCAATCTC
64 AAGAAATCGCAATCTTGCTACCAAATGTA-TCTTTATTTTATGTGCTGAGATGAGTCGCAATCTC
*
36085 TACTAATCCTCTGATATCTCCTATTTGATAACTGCAATGAATCACAGTTAATTAGAGTCAAGTAA
128 TACTAATCCTCTGATATCTCCTATTCGATAACTGCAATGAATCACAGTTAATTAGAGTCAAGTAA
*
36150 TGTCGGA
193 TATCGGA
36157 T
1 T
36158 CCACAATTTA
Statistics
Matches: 178, Mismatches: 22, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
199 20 0.11
200 1 0.01
201 60 0.34
202 97 0.54
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (199 bp):
TAAGTTAAACCAAACAAGCATTATAGAGAGCACAATGTGATTTGAAAAAGCTGTTTTCACATCAA
GAAATCGCAATCTTGCTACCAAATGTATCTTTATTTTATGTGCTGAGATGAGTCGCAATCTCTAC
TAATCCTCTGATATCTCCTATTCGATAACTGCAATGAATCACAGTTAATTAGAGTCAAGTAATAT
CGGA
Found at i:41809 original size:21 final size:21
Alignment explanation
Indices: 41783--41822 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41773 CGCTGCTCTA
*
41783 ATAATCTTATCTGTACAGTAC
1 ATAATCTAATCTGTACAGTAC
*
41804 ATAATCTAATCTGTGCAGT
1 ATAATCTAATCTGTACAGT
41823 GTAATTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
ATAATCTAATCTGTACAGTAC
Found at i:42390 original size:11 final size:11
Alignment explanation
Indices: 42361--42415 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
42351 TGGCTAGAAC
42361 AAAAAAAAAGA
1 AAAAAAAAAGA
* *
42372 TGACAAAAAAGA
1 -AAAAAAAAAGA
42384 AAAAAAAAAGA
1 AAAAAAAAAGA
* *
42395 AAGAAGAAAGA
1 AAAAAAAAAGA
42406 AAGAAAAAAA
1 AA-AAAAAAA
42416 AGAACATGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 20 0.59
12 14 0.41
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:42404 original size:22 final size:23
Alignment explanation
Indices: 42361--42415 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
42351 TGGCTAGAAC
*
42361 AAAAAAAAAGATGACAAAAAAGA
1 AAAAAAAAAGATAACAAAAAAGA
* *
42384 AAAAAAAAAGA-AAGAAGAAAGA
1 AAAAAAAAAGATAACAAAAAAGA
42406 AAGAAAAAAA
1 AA-AAAAAAA
42416 AGAACATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAGATAACAAAAAAGA
Found at i:47975 original size:22 final size:22
Alignment explanation
Indices: 47945--48006 Score: 54
Period size: 26 Copynumber: 2.6 Consensus size: 22
47935 CGGAAATAAA
47945 CTTTGTTTTCATGAATTTATTTC
1 CTTT-TTTTCATGAATTTATTTC
*
47968 CTTTTTTTTGACACCGAATTTATTTC
1 C-TTTTTTT--CA-TGAATTTATTTC
*
47994 C-TTTTATCATGAA
1 CTTTTTTTCATGAA
48007 AAACTTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
21 3 0.09
22 2 0.06
23 5 0.16
24 8 0.25
25 2 0.06
26 12 0.38
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (22 bp):
CTTTTTTTCATGAATTTATTTC
Found at i:52623 original size:324 final size:324
Alignment explanation
Indices: 51846--53202 Score: 1699
Period size: 323 Copynumber: 4.2 Consensus size: 324
51836 AAACCGTGAT
* * * *
51846 GGCTAAAAACTGACCCGAAAAATTTTTTCGTGAAAATTTTGCAACAATACTCAGAAAAAGTATAT
1 GGCTAAAAACTAATCCGAAAAATTTTTTCGTGAAATTTTTGCAACAATACTCAGAAAAAATATAT
* * * *
51911 AACTCAACGCCAAAAAAATTGA-TGGATTTTTCATGTTTCTAATATCGATTTTCCATTT-TTATC
66 AACTCAACGCCAAAAAGATTGACTGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTCTT-TC
* * * * *
51974 CGAATTAAATTCTAATTAAATAGAATCAAGATTCAGATGCTCGTAAAAATAAATCATTAAATCTA
130 CGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCA
* * * *
52039 ATGTGGTTGAAACTTGGTTATATGGATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGC
195 ATGTGGCTGAGATTTGGTTATATGAATATAGATATTTCAAGGAGT-TTTCTGCCAAAAATCATGC
** * * *
52104 AAAACTGAGTTG-GGCCCCAAAACGCGTTTTGAGCCAAAAAACTGTGATGG-TAACGT-CACGAT
259 AAAACTGAGCCGAGGCCCCAAAACGCGTTTTTAGCCAAAAAACCGTGATGGCT-A-GTAAACGAT
52166 TTC
322 TTC
* * * *
52169 GGGTAAAAACTAATCCGAAAAATTTTTTCATGAAAATTTTGCAACAATACTCAGAAAATATATAT
1 GGCTAAAAACTAATCCGAAAAATTTTTTCGTGAAATTTTTGCAACAATACTCAGAAAAAATATAT
* * *
52234 AACTCAACGCCAAAAAGATTGAC-GGGTTTTTCACGCTTTTAATATCGTTTTCCCA-TTCTTTTC
66 AACTCAACGCCAAAAAGATTGACTGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTC-TTTC
* ** * * *
52297 CGAATTTATTTCTAATTAAACCGAAAAAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCTA
130 CGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCA
* *
52362 ATGTGGCTGAGATTTGGTTATATGGATATAGATATTTCAAGGAGTCTTTTTGCCAAAAATCATGC
195 ATGTGGCTGAGATTTGGTTATATGAATATAGATATTTCAAGGAGT-TTTCTGCCAAAAATCATGC
* * * *
52427 AAAACTGGGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAGAACCGTGATGGCTAGTAAACGATTT
259 AAAACTGAGCCGAGGCCCCAAAACGCGTTTTTAGCCAAAAAACCGTGATGGCTAGTAAACGATTT
52492 C
324 C
* * *
52493 GGCTAAAAACTGATTCGAAAAATTTTTTCGTGAAATTTTTGCAACAGTACTCAGAAAAAATATAT
1 GGCTAAAAACTAATCCGAAAAATTTTTTCGTGAAATTTTTGCAACAATACTCAGAAAAAATATAT
* * * *
52558 AACTCAACGCCAAAAAGATTGACTGG-TTTTTCGCGCTTCAAATATTGTTTTTTCATTTCTTTCC
66 AACTCAACGCCAAAAAGATTGACTGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTCTTTCC
* * *
52622 GAATTAATTTCTAATTAAATGGAAACAAGATTAAGATGCTCGT-AAAA-AAATCCTTATATCCAA
131 GAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
** *
52685 TAAGGCTGAGATTTTGTTAGT-TGAATATAGATATTTCAAGGAGTTTTTCTGCCAAAAATCATGC
196 TGTGGCTGAGATTTGGTTA-TATGAATATAGATATTTCAAGGAG-TTTTCTGCCAAAAATCATGC
* * * * * *
52749 AAAACTAAGCCGAGGCCCCGAGACGCGTTTTTAGCCCAAAAACTGTGATGGTTAG-AACACGATT
259 AAAACTGAGCCGAGGCCCCAAAACGCGTTTTTAGCCAAAAAACCGTGATGGCTAGTAA-ACGATT
52813 TC
323 TC
** * * * *
52815 GGCTAAAAACTAATATGAAAAGTTTTTTCGTGAAATTTTTTGTAATAATACTCAGCAAAAATATA
1 GGCTAAAAACTAATCCGAAAAATTTTTTCGTGAAA-TTTTTGCAACAATACTCAGAAAAAATATA
*
52880 TAACTCAACGCCAAAAAGATTGAC-GGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTT
65 TAACTCAACGCCAAAAAGATTGACTGGATTTTTCACGCTTCTAATATCGTTTTTCCA-TTTCTTT
* *
52944 CCAAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCC
129 CCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* * * * **
53009 AATGCGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTAGTCAGTTAAAAATCATG
194 AATGTGGCTGAGATTTGGTTATATGAATATAGATATTTCAAGGAGTT-TTCTGCCAAAAATCATG
* * * * *
53074 CAAAACTGAGCCGAGGCCCCAAAACGCATTTCTAGCAAAAAAAACCCGT-A--AC--GTACACGA
258 CAAAACTGAGCCGAGGCCCCAAAACGCGTTTTTAGC-CAAAAAA-CCGTGATGGCTAGTAAACGA
53134 TTTC
321 TTTC
* * *
53138 GGCTAAAAACTTATCCGAAAAATTTTTTCGCT-AAATTTTTACAACAATACTTAGAAAAAATATA
1 GGCTAAAAACTAATCCGAAAAATTTTTTCG-TGAAATTTTTGCAACAATACTCAGAAAAAATATA
53202 T
65 T
53203 GTCAATGAAC
Statistics
Matches: 901, Mismatches: 111, Indels: 45
0.85 0.11 0.04
Matches are distributed among these distances:
321 2 0.00
322 183 0.20
323 355 0.39
324 242 0.27
325 12 0.01
326 98 0.11
327 6 0.01
328 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (324 bp):
GGCTAAAAACTAATCCGAAAAATTTTTTCGTGAAATTTTTGCAACAATACTCAGAAAAAATATAT
AACTCAACGCCAAAAAGATTGACTGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTCTTTCC
GAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
TGTGGCTGAGATTTGGTTATATGAATATAGATATTTCAAGGAGTTTTCTGCCAAAAATCATGCAA
AACTGAGCCGAGGCCCCAAAACGCGTTTTTAGCCAAAAAACCGTGATGGCTAGTAAACGATTTC
Found at i:52889 original size:647 final size:645
Alignment explanation
Indices: 51527--53202 Score: 1977
Period size: 647 Copynumber: 2.6 Consensus size: 645
51517 ATATGTTAGT
* * * * * *
51527 ACACGATTTCAGCTAAAAACTGATCCGAAAAATTTTTTCGTGAAATTTTTGCAACAATACTAAGA
1 ACACGATTTCGGCTAAAAACTAATACGAAAAATTTTTTCATGAAAATTTTGCAACAATACTCAGA
* * * ***
51592 AAA-AGTATATAACTCAACGCCAAAAAAATTGACGGGTTTTTCACGTTTCTAATATCGTTTTTTA
66 AAATA-TATATAACTCAACGCCAAAAAGATTGACGGATTTTTCACGCTTCTAATATCGTTTTCCC
* * * * *
51656 ATTTTTTTTCCCGAATTTATTTCTAATTAAACCGAAAAAAGATTCAGATGCTCGTAAAAATAAAT
130 ATTTCTTTT-CCAAATTAATTTCTAATTAAACAGAAAAAAGATTCAGATGCTCGTAAAAACAAAT
* ** * * * * * * **
51721 CCTTAAATCTAATGTAGCTAAGATTTGGTTATATGGATATAGATATTTCAAGAAGTCATTTTGCC
194 CCTTAAATCCAATGCGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTAGTCAGCC
* * * * * * * * *
51786 AAAAATCATTCAAAACTGAGCCG-GAACTCCGAAACACGTTTTTAGC-TAACAAA--C----CGT
259 AAAAATCATGCAAAACTGAGCCGAG-GCCCCAAAACGCATTTCTAGCAAAAAAAACCCGTAACGT
* *
51843 ----GA--T-GGCTAAAAACTGACCCGAAAAATTTTTTCGTGAAAATTTTGCAACAATACTCAGA
323 AAACGATTTCGGCTAAAAACTGATCCGAAAAATTTTTTCGTGAAATTTTTGCAACAATACTCAGA
* * * *
51901 AAAAGTATATAACTCAACGCCAAAAAAATTGATGGATTTTTCATGTTTCTAATATCGATTTTCCA
388 AAAAATATATAACTCAACGCCAAAAAAATTGATGGATTTTTCACGCTTCAAATATCGATTTTCCA
* *
51966 TTTTTATCCGAATTAAATTCTAATTAAATAGAATCAAGATTCAGATGCTCGTAAAAATAAATCAT
453 TTTTTATCCGAATTAAATTCTAATTAAATAGAAACAAGATTAAGATGCTCGTAAAAATAAATCAT
* ** * *
52031 TAAATCTAATGTGGTTGAAACTTGGTTATATGGATATAGATATTTCAAGGAGTCTTTCTGCCAAA
518 TAAATCCAATAAGGCTGAAACTTGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAA
* **
52096 AATCATGCAAAACTGAGTTGGGCCCCAAAACGCGTTTTGAGCCAAAAAACTGTGATGGTAACG
583 AATCATGCAAAACTAAGCCGGGCCCCAAAACGCGTTTTGAGCCAAAAAACTGTGATGGTAACG
* * *
52159 TCACGATTTCGGGTAAAAACTAATCCGAAAAATTTTTTCATGAAAATTTTGCAACAATACTCAGA
1 ACACGATTTCGGCTAAAAACTAATACGAAAAATTTTTTCATGAAAATTTTGCAACAATACTCAGA
* *
52224 AAATATATATAACTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTTTAATATCGTTTTCCCA
66 AAATATATATAACTCAACGCCAAAAAGATTGACGGATTTTTCACGCTTCTAATATCGTTTTCCCA
* * * *
52289 -TTCTTTTCCGAATTTATTTCTAATTAAACCGAAAAAAGATTCAGATGCTCGTAAAAACAAATTC
131 TTTCTTTTCCAAATTAATTTCTAATTAAACAGAAAAAAGATTCAGATGCTCGTAAAAACAAATCC
* * * * * **
52353 TTAAATCTAATGTGGCTGAGATTTGGTTATATGGATATAGATATTTCAAGGAGTCT-TTTTGCCA
196 TTAAATCCAATGCGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT-TAGTCAGCCA
* * * * * * * *
52417 AAAATCATGCAAAACTGGGTCGAGGCCCCGAAACGCGTTTTTAGC-CAAAGAA-CCGTGATGGCT
260 AAAATCATGCAAAACTGAGCCGAGGCCCCAAAACGCATTTCTAGCAAAAAAAACCCGT-A--AC-
* *
52480 AGTAAACGATTTCGGCTAAAAACTGATTCGAAAAATTTTTTCGTGAAATTTTTGCAACAGTACTC
321 -GTAAACGATTTCGGCTAAAAACTGATCCGAAAAATTTTTTCGTGAAATTTTTGCAACAATACTC
* * * *
52545 AGAAAAAATATATAACTCAACGCCAAAAAGATTGACTGG-TTTTTCGCGCTTCAAATATTGTTTT
385 AGAAAAAATATATAACTCAACGCCAAAAAAATTGA-TGGATTTTTCACGCTTCAAATATCGATTT
* * *
52609 TTCATTTCTT-TCCGAATTAATTTCTAATTAAATGGAAACAAGATTAAGATGCTCGT-AAAA-AA
449 TCCATTT-TTATCCGAATTAAATTCTAATTAAATAGAAACAAGATTAAGATGCTCGTAAAAATAA
* * * * * *
52671 ATCCTTATATCCAATAAGGCTGAGATTTTGTTAGT-TGAATATAGATATTTCAAGGAGTTTTTCT
513 ATCATTAAATCCAATAAGGCTGAAACTTGGTTA-TATGAATATAGATATTTCAAGGAGTCTTTCT
* * * *
52735 GCCAAAAATCATGCAAAACTAAGCCGAGGCCCCGAGACGCGTTTTTAGCCCAAAAACTGTGATGG
577 GCCAAAAATCATGCAAAACTAAGCCG-GGCCCCAAAACGCGTTTTGAGCCAAAAAACTGTGATGG
*
52800 TTA-G
641 TAACG
* * * * * *
52804 AACACGATTTCGGCTAAAAACTAATATGAAAAGTTTTTTCGTGAAATTTTTTGTAATAATACTCA
1 -ACACGATTTCGGCTAAAAACTAATACGAAAAATTTTTTCATGAAA-ATTTTGCAACAATACTCA
*
52869 GCAAAA-ATATATAACTCAACGCCAAAAAGATTGACGGATTTTTCACGCTTCTAATATCGTTTTT
64 G-AAAATATATATAACTCAACGCCAAAAAGATTGACGGATTTTTCACGCTTCTAATATCGTTTTC
* * *
52933 CCATTTTTTTTCCAAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAA
128 CCATTTCTTTTCCAAATTAATTTCTAATTAAACAGAAAAAAGATTCAGATGCTCGTAAAAACAAA
* *
52998 TCCTTATATCCAATGCGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTAGTCAGT
193 TCCTTAAATCCAATGCGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTAGTCAGC
*
53063 TAAAAATCATGCAAAACTGAGCCGAGGCCCCAAAACGCATTTCTAGCAAAAAAAACCCGTAACGT
258 CAAAAATCATGCAAAACTGAGCCGAGGCCCCAAAACGCATTTCTAGCAAAAAAAACCCGTAACGT
* * * *
53128 ACACGATTTCGGCTAAAAACTTATCCGAAAAATTTTTTCGCT-AAATTTTTACAACAATACTTAG
323 AAACGATTTCGGCTAAAAACTGATCCGAAAAATTTTTTCG-TGAAATTTTTGCAACAATACTCAG
53192 AAAAAATATAT
387 AAAAAATATAT
53203 GTCAATGAAC
Statistics
Matches: 904, Mismatches: 108, Indels: 51
0.85 0.10 0.05
Matches are distributed among these distances:
630 155 0.17
631 8 0.01
632 115 0.13
633 1 0.00
638 1 0.00
640 2 0.00
644 2 0.00
645 146 0.16
646 82 0.09
647 224 0.25
648 158 0.17
649 6 0.01
650 4 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (645 bp):
ACACGATTTCGGCTAAAAACTAATACGAAAAATTTTTTCATGAAAATTTTGCAACAATACTCAGA
AAATATATATAACTCAACGCCAAAAAGATTGACGGATTTTTCACGCTTCTAATATCGTTTTCCCA
TTTCTTTTCCAAATTAATTTCTAATTAAACAGAAAAAAGATTCAGATGCTCGTAAAAACAAATCC
TTAAATCCAATGCGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTAGTCAGCCAA
AAATCATGCAAAACTGAGCCGAGGCCCCAAAACGCATTTCTAGCAAAAAAAACCCGTAACGTAAA
CGATTTCGGCTAAAAACTGATCCGAAAAATTTTTTCGTGAAATTTTTGCAACAATACTCAGAAAA
AATATATAACTCAACGCCAAAAAAATTGATGGATTTTTCACGCTTCAAATATCGATTTTCCATTT
TTATCCGAATTAAATTCTAATTAAATAGAAACAAGATTAAGATGCTCGTAAAAATAAATCATTAA
ATCCAATAAGGCTGAAACTTGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
CATGCAAAACTAAGCCGGGCCCCAAAACGCGTTTTGAGCCAAAAAACTGTGATGGTAACG
Found at i:61537 original size:29 final size:30
Alignment explanation
Indices: 61470--61540 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
61460 AGAGGGGGGC
* * *
61470 AAAACATCCAAAATTGAGAATTTAAGGGGT
1 AAAACGTCCAAAATTGAGAATTCAAGAGGT
* *
61500 AAAATGTCCAAAATTGA-AGTTCAAGAGGT
1 AAAACGTCCAAAATTGAGAATTCAAGAGGT
61529 AAAACGTCCAAA
1 AAAACGTCCAAA
61541 CGCTACAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (30 bp):
AAAACGTCCAAAATTGAGAATTCAAGAGGT
Found at i:63123 original size:1 final size:1
Alignment explanation
Indices: 63117--63146 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
63107 TTCAAGGCAA
63117 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
63147 ATAATTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:68681 original size:13 final size:13
Alignment explanation
Indices: 68663--68687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68653 TTCATTTTTC
68663 TAAATATTATATA
1 TAAATATTATATA
68676 TAAATATTATAT
1 TAAATATTATAT
68688 TTGGAATTCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATATTATATA
Found at i:68959 original size:22 final size:22
Alignment explanation
Indices: 68934--69335 Score: 118
Period size: 22 Copynumber: 18.3 Consensus size: 22
68924 ATTACACTAT
*
68934 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
68956 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** * *
68978 TTTTAATAACGATACTATGGAA
1 TTTTGATAACCTTCCTATGAAA
* * ** *
69000 TTTCGAGAACCTTTTTA-CAAA
1 TTTTGATAACCTTCCTATGAAA
** *
69021 TTTTTTTTAACCTTCTTATGAAA
1 -TTTTGATAACCTTCCTATGAAA
** *
69044 TTTTTTTAACC-TCTCTAAGAAA
1 TTTTGATAACCTTC-CTATGAAA
69066 TTTTGA-AGACC--CCATTATGAAA
1 TTTTGATA-ACCTTCC--TATGAAA
*
69088 TTTTGATAA-CTTCCCAATGAAA
1 TTTTGATAACCTT-CCTATGAAA
** *
69110 TTTTGATAACCAACACTATGAGA
1 TTTTGATAACCTTC-CTATGAAA
* *
69133 TGTTGATAACC-TCCATATGATA
1 TTTTGATAACCTTCC-TATGAAA
* * *
69155 TATTGATAACC-ACGTTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* * *
69177 ATTTAAAAACC-TCCATATG-AA
1 TTTTGATAACCTTCC-TATGAAA
* * *** * *
69198 TTATCAGTTTTC-ACACTCTGAAA
1 TTTTGA-TAACCTTC-CTATGAAA
* * *
69221 TGTTGATAATC-ACACTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* *
69243 TTGTGATAACC-TCTTTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* **
69265 TTTTGA-AAACTAAGCTATGAAA
1 TTTTGATAACCT-TCCTATGAAA
*
69287 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
69309 TTTTGATATCC-TCC-GTGAAA
1 TTTTGATAACCTTCCTATGAAA
69329 TTTTGAT
1 TTTTGAT
69336 TACTCCATAA
Statistics
Matches: 281, Mismatches: 77, Indels: 46
0.70 0.19 0.11
Matches are distributed among these distances:
20 13 0.05
21 18 0.06
22 214 0.76
23 34 0.12
24 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:69139 original size:45 final size:45
Alignment explanation
Indices: 69081--69197 Score: 114
Period size: 45 Copynumber: 2.6 Consensus size: 45
69071 AAGACCCCAT
* * *
69081 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACAC
* * **
69126 TATGAGATGTTGATAACCTCCATATGATATATTGATAACC-ACGT
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
* *
69170 TATGAAAAT-TTAAAAACCTCCATATGAA
1 TATG-AAATGTTGATAACCTCCATATGAA
69198 TTATCAGTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
44 25 0.42
45 34 0.58
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:69470 original size:22 final size:22
Alignment explanation
Indices: 69445--69664 Score: 121
Period size: 22 Copynumber: 10.0 Consensus size: 22
69435 AATGACATTT
*
69445 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTCTA
* *
69467 TGAAATTTTGATAACCTCTCTG
1 TGAAAATTTGATAACCTCTCTA
* *
69489 T-AAAATTTTGTTAACCCCTCTA
1 TGAAAA-TTTGATAACCTCTCTA
* * *
69511 TTAAAATTTTGATAATCACAT-TA
1 TGAAAA-TTTGATAACCTC-TCTA
* * * *
69534 TGTAATTTTGATAACCTCGCTT
1 TGAAAATTTGATAACCTCTCTA
* * ** *
69556 TGAAATTTTCATAACAACACTA
1 TGAAAATTTGATAACCTCTCTA
* *
69578 TGAAATTTTGATAATCT-TCTTA
1 TGAAAATTTGATAACCTCTC-TA
* *
69600 T-AAATTTTGATAATCCGCTCTA
1 TGAAAATTTGATAA-CCTCTCTA
* *
69622 TG-AAATTTCGATAATCACTCTA
1 TGAAAATTT-GATAACCTCTCTA
*
69644 TG-AGATTTGATAACCT-TCTA
1 TGAAAATTTGATAACCTCTCTA
69664 T
1 T
69665 CAAATGTTGG
Statistics
Matches: 153, Mismatches: 36, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
20 5 0.03
21 22 0.14
22 99 0.65
23 26 0.17
24 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:69584 original size:89 final size:89
Alignment explanation
Indices: 69425--69587 Score: 202
Period size: 89 Copynumber: 1.8 Consensus size: 89
69415 TACCACTATG
* * * * * ** * *
69425 AAATTTTGGTAATGACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTGT
1 AAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTCATAACAACACTAT
69490 AAAATTTTGTTAACCCCTCTATTA
66 AAAATTTTGTTAACCCCTCTATTA
* *
69514 AAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTCATAACAACACTA
1 AAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTCATAACAACACTA
*
69578 TGAAATTTTG
65 TAAAATTTTG
69588 ATAATCTTCT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
89 59 0.97
90 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (89 bp):
AAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTCATAACAACACTAT
AAAATTTTGTTAACCCCTCTATTA
Found at i:69585 original size:44 final size:42
Alignment explanation
Indices: 69445--69635 Score: 134
Period size: 44 Copynumber: 4.3 Consensus size: 42
69435 AATGACATTT
* * * *
69445 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAAC-CTCTC
1 TGAAATTTTGATAACCTCCTT-TGAAATTTTGATAACACACTA
* * * *
69487 TGTAAAATTTTGTTAACCCCTCTATTAAAATTTTGATAATCACATTA
1 TG--AAATTTTGATAACCTC-CT-TTGAAATTTTGATAA-CACACTA
* *
69534 TGTAATTTTGATAACCTCGCTTTGAAATTTTCATAACAACACTA
1 TGAAATTTTGATAACCTC-CTTTGAAATTTTGATAAC-ACACTA
* * * *
69578 TGAAATTTTGATAATCTTCTTAT-AAATTTTGATAATCCGCTCTA
1 TGAAATTTTGATAACCTCCTT-TGAAATTTTGATAA--CACACTA
*
69622 TGAAATTTCGATAA
1 TGAAATTTTGATAA
69636 TCACTCTATG
Statistics
Matches: 117, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
42 2 0.02
43 15 0.13
44 64 0.55
45 30 0.26
46 2 0.02
47 4 0.03
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (42 bp):
TGAAATTTTGATAACCTCCTTTGAAATTTTGATAACACACTA
Found at i:69626 original size:66 final size:66
Alignment explanation
Indices: 69445--69662 Score: 171
Period size: 67 Copynumber: 3.3 Consensus size: 66
69435 AATGACATTT
* * * * * * * * * *
69445 TGAAAATTTGATAA-CCTCTTTATGAAATTTTGATAACCTCTCTGTAAAATTTTGTTAACCCCTC
1 TGAAATTTTGATAATCTTC-TTATGAAATTTTGATAACCTCGCTTTGAAATTTCGATAATCACAC
69509 TA
65 TA
* * *
69511 TTAAAATTTTGATAATC-ACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTC-ATAA-CAA
1 -TGAAATTTTGATAATCTTC-TTATGAAATTTTGATAACCTCGCTTTGAAA-TTTCGATAATC-A
69573 CACTA
62 CACTA
* *
69578 TGAAATTTTGATAATCTTCTTAT-AAATTTTGATAATC-CGCTCTATGAAATTTCGATAATCACT
1 TGAAATTTTGATAATCTTCTTATGAAATTTTGATAACCTCGCT-T-TGAAATTTCGATAATCACA
69641 CTA
64 CTA
* *
69644 TGAGA-TTTGATAACCTTCT
1 TGAAATTTTGATAATCTTCT
69663 ATCAAATGTT
Statistics
Matches: 124, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
64 4 0.03
65 30 0.24
66 38 0.31
67 48 0.39
68 4 0.03
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (66 bp):
TGAAATTTTGATAATCTTCTTATGAAATTTTGATAACCTCGCTTTGAAATTTCGATAATCACACT
A
Found at i:69770 original size:22 final size:21
Alignment explanation
Indices: 69696--69810 Score: 70
Period size: 22 Copynumber: 5.2 Consensus size: 21
69686 AAATTGAGAC
* *
69696 TTTTATAACCTTCTTATGAAA
1 TTTTGTAACCTCCTTATGAAA
* **
69717 TTTTGAAAACCTCCCCATGAAA
1 TTTTG-TAACCTCCTTATGAAA
* *
69739 TATTAGTAACCTCCTTACGAAA
1 T-TTTGTAACCTCCTTATGAAA
*
69761 TTTTGTTAACCACAC-TATGAAA
1 TTTTG-TAACCTC-CTTATGAAA
* * *
69783 TTCTTATAAACCTCGTTATGACA
1 TT-TTGT-AACCTCCTTATGAAA
69806 TTTTG
1 TTTTG
69811 ATAATCTCTT
Statistics
Matches: 69, Mismatches: 18, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
21 7 0.10
22 43 0.62
23 19 0.28
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (21 bp):
TTTTGTAACCTCCTTATGAAA
Found at i:69999 original size:66 final size:66
Alignment explanation
Indices: 69823--70055 Score: 247
Period size: 66 Copynumber: 3.5 Consensus size: 66
69813 AATCTCTTTG
* * *** * *
69823 ATAACCTTTCTAT-AAAGTTTGTGATAACCACACTATGAAATTCCAATAACCTTCCTAAGAAATT
1 ATAACCTTCCTATGAAA-TTT-TGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
69887 TTA
64 TTA
* * *
69890 ATAATCTGATCCTATTAAATTTTGGTAACCACACTATAAAATTTTGATAACCTTCCCATGAAATT
1 ATAACCT--TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
*
69955 TTG
64 TTA
*
69958 ATAA-CTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-TCCTCATGAAATT
1 ATAACCTTCC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATT
*
70021 ATA
64 TTA
* * *
70024 ATAACCATCTTATGAAATTTTGATAACCACAC
1 ATAACCTTCCTATGAAATTTTGGTAACCACAC
70056 AGAGACAAGA
Statistics
Matches: 142, Mismatches: 18, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
65 6 0.04
66 72 0.51
67 11 0.08
68 42 0.30
69 8 0.06
70 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (66 bp):
ATAACCTTCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTT
A
Found at i:70052 original size:22 final size:22
Alignment explanation
Indices: 69819--70052 Score: 165
Period size: 22 Copynumber: 10.5 Consensus size: 22
69809 TGATAATCTC
* *
69819 TTTGATAACCTTTCTAT-AAAGT
1 TTTGATAACCATCCTATGAAA-T
69841 TTGTGATAACCA-CACTATGAAAT
1 TT-TGATAACCATC-CTATGAAAT
*** * *
69864 TCCAATAACCTTCCTAAGAAAT
1 TTTGATAACCATCCTATGAAAT
* * *
69886 TTTAATAATCTGATCCTATTAAAT
1 TTTGATAA-C-CATCCTATGAAAT
* *
69910 TTTGGTAACCA-CACTATAAAAT
1 TTTGATAACCATC-CTATGAAAT
* *
69932 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCATCCTATGAAAT
*
69954 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCATCC-TATGAAAT
* *
69976 TTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCATC-CTATGAAAT
69998 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCATCCT-ATGAAAT
* * *
70020 TATAATAACCATCTTATGAAAT
1 TTTGATAACCATCCTATGAAAT
70042 TTTGATAACCA
1 TTTGATAACCA
70053 CACAGAGACA
Statistics
Matches: 166, Mismatches: 32, Indels: 28
0.73 0.14 0.12
Matches are distributed among these distances:
21 8 0.05
22 117 0.70
23 23 0.14
24 18 0.11
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTGATAACCATCCTATGAAAT
Found at i:71372 original size:12 final size:12
Alignment explanation
Indices: 71357--71386 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
71347 CCTCAAAATT
71357 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
71369 AAAAAGAAAAAG
1 AAAAAAAAAAAG
71381 AAAAAA
1 AAAAAA
71387 GATTTAGTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:71455 original size:36 final size:36
Alignment explanation
Indices: 71408--71478 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
71398 GGTGAGTGCT
71408 ATAGCTATAGTATAATATTACTGCAACTGCAGTCTA
1 ATAGCTATAGTATAATATTACTGCAACTGCAGTCTA
71444 ATAGCTATAGTATAATATTACTGCAACTGCAGTCT
1 ATAGCTATAGTATAATATTACTGCAACTGCAGTCT
71479 TCATATACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (36 bp):
ATAGCTATAGTATAATATTACTGCAACTGCAGTCTA
Found at i:73487 original size:62 final size:62
Alignment explanation
Indices: 73421--73579 Score: 150
Period size: 60 Copynumber: 2.6 Consensus size: 62
73411 GCTAATTGCT
*
73421 CAAATAAGGGCTTAACGATTGCCAAAATGCTCAAATATAAGGA-TCCGATCTTTTAATTTAAC
1 CAAATAAGGGCTTAACGATTGCCAAAATGCTCAAATAGAAGGACT-CGATCTTTTAATTTAAC
** * * *
73483 CAAATAA-GAATCTAAC-ATTTGCCAAAATGCTC-AA-AGAAGGACTCGGTCTTTTAATTTGAT
1 CAAATAAGGGCT-TAACGA-TTGCCAAAATGCTCAAATAGAAGGACTCGATCTTTTAATTTAAC
* * * *
73543 CAAATAAGGGCCTAAAG-TTATCAAAAATGCTCAAATA
1 CAAATAAGGGCTTAACGATT-GCCAAAATGCTCAAATA
73580 AGGGCCTGAT
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
59 2 0.03
60 40 0.52
61 9 0.12
62 26 0.34
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (62 bp):
CAAATAAGGGCTTAACGATTGCCAAAATGCTCAAATAGAAGGACTCGATCTTTTAATTTAAC
Found at i:73641 original size:31 final size:31
Alignment explanation
Indices: 73603--73706 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
73593 AGTTTGGATA
73603 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
* ** * *
73634 AGGCCCTTATTTGACCAAATT--A-AAAGATC
1 AGGCCCTTATTTGAGCATTTTCGATAACG-TT
* *
73663 GGGTCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
* *
73694 ATGTCCTTATTTG
1 AGGCCCTTATTTG
73707 GCCAAATTAA
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
28 3 0.05
29 18 0.33
31 31 0.56
32 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTCGATAACGTT
Found at i:73702 original size:60 final size:60
Alignment explanation
Indices: 73607--73775 Score: 227
Period size: 60 Copynumber: 2.8 Consensus size: 60
73597 TGGATAAGGC
*
73607 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCGGGT
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGGT
* * * *
73667 CCTTATTTGAGCATTTTCGATAACGTTATGTCCTTATTTGGCCAAATTAAAAGATTAGGT
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGGT
** *
73727 CCTTATTTGAATATTTT-G-TCAAACGTTAGGCCCTTATTTGA-GAAATTAA
1 CCTTATTTGAGCATTTTCGAT--AACGTTAGGCCCTTATTTGACCAAATTAA
73776 CCTGAAGATT
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
58 1 0.01
59 8 0.08
60 87 0.91
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGGT
Found at i:73735 original size:29 final size:29
Alignment explanation
Indices: 73632--73735 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 29
73622 TTCGATAACG
* *
73632 TTAGGCCCTTATTTGACCAAATTAAAAGA
1 TTAGGTCCTTATTTGGCCAAATTAAAAGA
** ** *
73661 TCGGGTCCTTATTTGAG-CATTTTCGATAACG-
1 TTAGGTCCTTATTTG-GCCAAATT--A-AAAGA
*
73692 TTATGTCCTTATTTGGCCAAATTAAAAGA
1 TTAGGTCCTTATTTGGCCAAATTAAAAGA
73721 TTAGGTCCTTATTTG
1 TTAGGTCCTTATTTG
73736 AATATTTTGT
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 3 0.05
29 31 0.56
30 1 0.02
31 17 0.31
32 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (29 bp):
TTAGGTCCTTATTTGGCCAAATTAAAAGA
Done.