Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013180.1 Kokia drynarioides strain JFW-HI SEQ_128199, 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: 197382
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:69 original size:3 final size:3
Alignment explanation
Indices: 61--151 Score: 139
Period size: 3 Copynumber: 30.0 Consensus size: 3
51 TTAATGATAT
**
61 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA CTGC T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA -TAA TAA TAA TAA TAA
107 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
152 ATAAAAAATT
Statistics
Matches: 82, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
2 1 0.01
3 77 0.94
4 4 0.05
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1183 original size:30 final size:30
Alignment explanation
Indices: 1147--1466 Score: 300
Period size: 29 Copynumber: 10.8 Consensus size: 30
1137 CTAAATTACC
**
1147 CAAAAATTCTATTTTTAACCTTGAAACTTT
1 CAAAAATTCTATTTTTAACCCCGAAACTTT
*
1177 CAAAAATTCTATTTTT-ACCCTC-AAACTTC
1 CAAAAATTCTATTTTTAACCC-CGAAACTTT
* * * *
1206 CAAAAATCCCATTTTTAACCCCAAAACTCT
1 CAAAAATTCTATTTTTAACCCCGAAACTTT
1236 CAAAAATTCTATTTTT-ACTCCCG-AAC-TT
1 CAAAAATTCTATTTTTAAC-CCCGAAACTTT
* * * *
1264 CTAAAAATCCCATTTTTAACCTCGAAACTCT
1 C-AAAAATTCTATTTTTAACCCCGAAACTTT
*
1295 CAAAAATTCTATTTTTACCCCCG-AAC-TT
1 CAAAAATTCTATTTTTAACCCCGAAACTTT
* * * *
1323 CTAAAAATCCCATTTTTAACCTCGAAACTCT
1 C-AAAAATTCTATTTTTAACCCCGAAACTTT
*
1354 CAAAAATTCTATTTTT-ACCCTCGAAA-TTC
1 CAAAAATTCTATTTTTAACCC-CGAAACTTT
* * * *
1383 CAAAAATCCCATTTTTAACCCCAAAACTCT
1 CAAAAATTCTATTTTTAACCCCGAAACTTT
* *
1413 CAAAAATTCTATTTTT-ACCCCTAAACTTC
1 CAAAAATTCTATTTTTAACCCCGAAACTTT
* *
1442 CAAAAATCCCATTTTTAACCCCGAA
1 CAAAAATTCTATTTTTAACCCCGAA
1467 TTTTCTCGAA
Statistics
Matches: 232, Mismatches: 43, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.02
29 112 0.48
30 112 0.48
31 4 0.02
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (30 bp):
CAAAAATTCTATTTTTAACCCCGAAACTTT
Found at i:1239 original size:59 final size:58
Alignment explanation
Indices: 1146--1466 Score: 464
Period size: 59 Copynumber: 5.4 Consensus size: 58
1136 CCTAAATTAC
* * ** *
1146 CCAAAAATTCTATTTTTAACCTTGAAACTTTCAAAAATTCTATTTTTACCCTCAAACTT
1 CCAAAAATCCCATTTTTAACCCCGAAACTCTCAAAAATTCTATTTTTACCC-CAAACTT
* *
1205 CCAAAAATCCCATTTTTAACCCCAAAACTCTCAAAAATTCTATTTTTACTCCCGAACTT
1 CCAAAAATCCCATTTTTAACCCCGAAACTCTCAAAAATTCTATTTTTAC-CCCAAACTT
* * *
1264 CTAAAAATCCCATTTTTAACCTCGAAACTCTCAAAAATTCTATTTTTACCCCCGAACTT
1 CCAAAAATCCCATTTTTAACCCCGAAACTCTCAAAAATTCTATTTTTA-CCCCAAACTT
* *
1323 CTAAAAATCCCATTTTTAACCTCGAAACTCTCAAAAATTCTATTTTTACCCTCGAAA-TT
1 CCAAAAATCCCATTTTTAACCCCGAAACTCTCAAAAATTCTATTTTTACCC-C-AAACTT
*
1382 CCAAAAATCCCATTTTTAACCCCAAAACTCTCAAAAATTCTATTTTTACCCCTAAACTT
1 CCAAAAATCCCATTTTTAACCCCGAAACTCTCAAAAATTCTATTTTTACCCC-AAACTT
1441 CCAAAAATCCCATTTTTAACCCCGAA
1 CCAAAAATCCCATTTTTAACCCCGAA
1467 TTTTCTCGAA
Statistics
Matches: 241, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
58 7 0.03
59 229 0.95
60 5 0.02
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (58 bp):
CCAAAAATCCCATTTTTAACCCCGAAACTCTCAAAAATTCTATTTTTACCCCAAACTT
Found at i:13263 original size:207 final size:207
Alignment explanation
Indices: 12842--13403 Score: 785
Period size: 207 Copynumber: 2.7 Consensus size: 207
12832 ATTCTCGAGT
* * * * * * * *
12842 AACGCGGTCATCTTCCTAATGAGATAATGAGAAGTACACCAAGT-CAAGTCCACGCTTGATATGA
1 AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAA-CCCACGCTCGATATGA
* * * *
12906 GCAAATCTTCGAATCCCAGCTTCCTGATGAGACACGGAGAAGCAGGTCGAAGC-A-ACAAACGGT
65 GTAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGT
* * *
12969 TAGCTTCCGGAGGAGATACTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCG
130 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCG
13034 AATTGAAACAAAC
195 AATTGAAACAAAC
*
13047 AATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
1 AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
* * *
13112 TAAATCTTCGAACCCC-GACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAAACGAT
66 TAAATCTTCGAACCCCAG-CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGT
13176 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGT-TTTCCTGATGAGATACAGAGAAGC
130 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTT-CTGATGAGATACAGAGAAGC
13240 GAATTGAAACAAAC
194 GAATTGAAACAAAC
* * * * * * *
13254 GACGCAGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATGTAAG
1 AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
**
13319 TAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAAT-AAAGTGGTT
66 TAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGTT
* *
13383 AACTCCCTGATGAGATACTGA
131 AGCTTCCTGATGAGATACTGA
13404 AAAGGCCAAG
Statistics
Matches: 317, Mismatches: 34, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
204 1 0.00
205 97 0.31
206 32 0.10
207 186 0.59
208 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (207 bp):
AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
TAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGTT
AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCGA
ATTGAAACAAAC
Found at i:13753 original size:17 final size:17
Alignment explanation
Indices: 13728--13809 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 17
13718 CTGGGCCCAA
*
13728 TAAACTTAAATTTATTT
1 TAAATTTAAATTTATTT
* * *
13745 TAAAATTAAGTTTATTC
1 TAAATTTAAATTTATTT
**
13762 TAAATTTAAATTTGGTT
1 TAAATTTAAATTTATTT
* * *
13779 GAAATTTAAGTTTATTA
1 TAAATTTAAATTTATTT
13796 TAAATTTAAATTTA
1 TAAATTTAAATTTA
13810 AAATTTATTT
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:23957 original size:207 final size:207
Alignment explanation
Indices: 23536--24097 Score: 785
Period size: 207 Copynumber: 2.7 Consensus size: 207
23526 ATTCTCGAGT
* * * * * * * *
23536 AACGCGGTCATCTTCCTAATGAGATAATGAGAAGTACACCAAGT-CAAGTCCACGCTTGATATGA
1 AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAA-CCCACGCTCGATATGA
* * * *
23600 GCAAATCTTCGAATCCCAGCTTCCTGATGAGACACGGAGAAGCAGGTCGAAGC-A-ACAAACGGT
65 GTAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGT
* * *
23663 TAGCTTCCGGAGGAGATACTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCG
130 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCG
23728 AATTGAAACAAAC
195 AATTGAAACAAAC
*
23741 AATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
1 AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
* * *
23806 TAAATCTTCGAACCCC-GACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAAACGAT
66 TAAATCTTCGAACCCCAG-CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGT
23870 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGT-TTTCCTGATGAGATACAGAGAAGC
130 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTT-CTGATGAGATACAGAGAAGC
23934 GAATTGAAACAAAC
194 GAATTGAAACAAAC
* * * * * * *
23948 GACGCAGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATGTAAG
1 AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
**
24013 TAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAAT-AAAGTGGTT
66 TAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGTT
* *
24077 AACTCCCTGATGAGATACTGA
131 AGCTTCCTGATGAGATACTGA
24098 AAAGGCCAAG
Statistics
Matches: 317, Mismatches: 34, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
204 1 0.00
205 97 0.31
206 32 0.10
207 186 0.59
208 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (207 bp):
AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
TAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGTT
AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCGA
ATTGAAACAAAC
Found at i:24447 original size:17 final size:17
Alignment explanation
Indices: 24422--24503 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 17
24412 CTGGGCCCAA
*
24422 TAAACTTAAATTTATTT
1 TAAATTTAAATTTATTT
* * *
24439 TAAAATTAAGTTTATTC
1 TAAATTTAAATTTATTT
**
24456 TAAATTTAAATTTGGTT
1 TAAATTTAAATTTATTT
* * *
24473 GAAATTTAAGTTTATTA
1 TAAATTTAAATTTATTT
24490 TAAATTTAAATTTA
1 TAAATTTAAATTTA
24504 AAATTTATTT
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:34651 original size:207 final size:207
Alignment explanation
Indices: 34230--34791 Score: 785
Period size: 207 Copynumber: 2.7 Consensus size: 207
34220 ATTCTCGAGT
* * * * * * * *
34230 AACGCGGTCATCTTCCTAATGAGATAATGAGAAGTACACCAAGT-CAAGTCCACGCTTGATATGA
1 AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAA-CCCACGCTCGATATGA
* * * *
34294 GCAAATCTTCGAATCCCAGCTTCCTGATGAGACACGGAGAAGCAGGTCGAAGC-A-ACAAACGGT
65 GTAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGT
* * *
34357 TAGCTTCCGGAGGAGATACTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCG
130 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCG
34422 AATTGAAACAAAC
195 AATTGAAACAAAC
*
34435 AATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
1 AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
* * *
34500 TAAATCTTCGAACCCC-GACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAAACGAT
66 TAAATCTTCGAACCCCAG-CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGT
34564 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGT-TTTCCTGATGAGATACAGAGAAGC
130 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTT-CTGATGAGATACAGAGAAGC
34628 GAATTGAAACAAAC
194 GAATTGAAACAAAC
* * * * * * *
34642 GACGCAGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATGTAAG
1 AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
**
34707 TAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAAT-AAAGTGGTT
66 TAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGTT
* *
34771 AACTCCCTGATGAGATACTGA
131 AGCTTCCTGATGAGATACTGA
34792 AAAGGCCAAG
Statistics
Matches: 317, Mismatches: 34, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
204 1 0.00
205 97 0.31
206 32 0.10
207 186 0.59
208 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (207 bp):
AACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCCAACCCACGCTCGATATGAG
TAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAACGGTT
AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCGA
ATTGAAACAAAC
Found at i:35141 original size:17 final size:17
Alignment explanation
Indices: 35116--35197 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 17
35106 CTGGGCCCAA
*
35116 TAAACTTAAATTTATTT
1 TAAATTTAAATTTATTT
* * *
35133 TAAAATTAAGTTTATTC
1 TAAATTTAAATTTATTT
**
35150 TAAATTTAAATTTGGTT
1 TAAATTTAAATTTATTT
* * *
35167 GAAATTTAAGTTTATTA
1 TAAATTTAAATTTATTT
35184 TAAATTTAAATTTA
1 TAAATTTAAATTTA
35198 AAATTTATTT
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:35858 original size:3 final size:3
Alignment explanation
Indices: 35850--35907 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
35840 TTAATGATAT
**
35850 TAA TAA TAA TAA TAA -AA -AA TAA TAA TAA CTGC T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
35893 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
35908 ATAAATAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
2 5 0.10
3 43 0.88
4 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:36938 original size:30 final size:31
Alignment explanation
Indices: 36903--37395 Score: 437
Period size: 29 Copynumber: 16.7 Consensus size: 31
36893 CTAAATTGCC
36903 CAAAAATTCTATTTTTAACCCCAAAACTTCT
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
* * *
36934 -AAAAATCCCATTTTTAACCCTAAAACTT-T
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
*
36963 CAAAAATTCTATTTTT-ACCCCCAAACTTC-
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
* * * *
36992 CAAAAATCCCATTTTTAACCTCGAAACTTC-
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
*
37022 CAAAAATTCCA-TTTTAACCCCAAAACTT-T
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
**
37051 CAAAAATTCTATTTTT-ACCCCCGAACTTC-
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
* * *
37080 CAAAAATCCCA-TTTTAACCCTAAAAC-TCT
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
*
37109 CAAAAATTCTATTTTT-ACCCCCAAACTTCT
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
* * * **
37139 -AAAAATCCCATTTTTTTAACCTCGTAAC-TCT
1 CAAAAAT-TC-TATTTTTAACCCCAAAACTTCT
**
37170 CAAAAATTCTATTTTT-ACCCCTGAACTTCT
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
* **
37200 -AAAAA-CCTCA-TTTTAACCGTAAAAC-TCT
1 CAAAAATTCT-ATTTTTAACCCCAAAACTTCT
*
37228 CAAAAATTCTATTTTT-ACCCCTAAACTTCT
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
* *
37258 -AAAAATCCCATTTTTAACCCCAAAAC-TCT
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
* *
37287 CAAATATTCTATTTTT-ACCCCTAAACTTC-
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
* * *
37316 CAAAAATCCCATTTTTAACCCTAAAACTT-T
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
*
37346 CAAAAATTCTATTTTT-ACCCCCAAACTT-T
1 CAAAAATTCTATTTTTAACCCCAAAACTTCT
* * *
37375 AAAAAATCCCATTTTTAACCC
1 CAAAAATTCTATTTTTAACCC
37396 TGAATTTTGT
Statistics
Matches: 371, Mismatches: 64, Indels: 55
0.76 0.13 0.11
Matches are distributed among these distances:
28 15 0.04
29 193 0.52
30 140 0.38
31 10 0.03
32 13 0.04
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.34
Consensus pattern (31 bp):
CAAAAATTCTATTTTTAACCCCAAAACTTCT
Found at i:37363 original size:59 final size:59
Alignment explanation
Indices: 36902--37396 Score: 558
Period size: 59 Copynumber: 8.4 Consensus size: 59
36892 CCTAAATTGC
* * * * * *
36902 CCAAAAATTCTATTTTTAACCCCAAAACT-TCTAAAAATCCCATTTTTAACCCTAAAACTT
1 CCAAAAATCCCATTTTTAACCCTAAAACTCTC-AAAAATTCTATTTTTACCCCT-AAACTT
* * * ** * * * *
36962 TCAAAAATTCTATTTTT-ACCCCCAAACT-TCCAAAAATCCCATTTTTAACCTCGAAACTT
1 CCAAAAATCCCATTTTTAACCCTAAAACTCT-CAAAAATTCTATTTTT-ACCCCTAAACTT
* * * **
37021 CCAAAAATTCCA-TTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCCGAACTT
1 CCAAAAATCCCATTTTTAACCCTAAAACTCTCAAAAATTCTATTTTTACCCCTAAACTT
*
37079 CCAAAAATCCCA-TTTTAACCCTAAAACTCTCAAAAATTCTATTTTTACCCCCAAACTT
1 CCAAAAATCCCATTTTTAACCCTAAAACTCTCAAAAATTCTATTTTTACCCCTAAACTT
* *
37137 CTAAAAATCCCATTTTTTTAACCTCGT--AACTCTCAAAAATTCTATTTTTACCCCTGAACTT
1 CCAAAAATCCCA--TTTTTAACC-C-TAAAACTCTCAAAAATTCTATTTTTACCCCTAAACTT
* *
37198 CTAAAAA-CCTCA-TTTTAACCGTAAAACTCTCAAAAATTCTATTTTTACCCCTAAACTT
1 CCAAAAATCC-CATTTTTAACCCTAAAACTCTCAAAAATTCTATTTTTACCCCTAAACTT
* * *
37256 CTAAAAATCCCATTTTTAACCCCAAAACTCTCAAATATTCTATTTTTACCCCTAAACTT
1 CCAAAAATCCCATTTTTAACCCTAAAACTCTCAAAAATTCTATTTTTACCCCTAAACTT
* *
37315 CCAAAAATCCCATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTACCCCCAAACTT
1 CCAAAAATCCCATTTTTAACCCTAAAACTCTCAAAAATTCTATTTTTACCCCTAAACTT
**
37374 TAAAAAATCCCATTTTTAACCCT
1 CCAAAAATCCCATTTTTAACCCT
37397 GAATTTTGTC
Statistics
Matches: 389, Mismatches: 32, Indels: 29
0.86 0.07 0.06
Matches are distributed among these distances:
56 1 0.00
58 128 0.33
59 186 0.48
60 23 0.06
61 49 0.13
62 1 0.00
63 1 0.00
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.34
Consensus pattern (59 bp):
CCAAAAATCCCATTTTTAACCCTAAAACTCTCAAAAATTCTATTTTTACCCCTAAACTT
Found at i:40927 original size:20 final size:20
Alignment explanation
Indices: 40898--40937 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40888 TATTCCTGCA
* *
40898 TAAAATTGAAAAGGTAAAAG
1 TAAAAGTGAAAAAGTAAAAG
40918 TAAAAGTGAAAAAGTAAAAG
1 TAAAAGTGAAAAAGTAAAAG
40938 GAAATGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.20, T:0.17
Consensus pattern (20 bp):
TAAAAGTGAAAAAGTAAAAG
Found at i:40930 original size:14 final size:13
Alignment explanation
Indices: 40906--40941 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
40896 CATAAAATTG
*
40906 AAAAGGTAAAAGT
1 AAAAGGAAAAAGT
40919 AAAAGTGAAAAAGT
1 AAAAG-GAAAAAGT
40933 AAAAGGAAA
1 AAAAGGAAA
40942 TGTAAAATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (13 bp):
AAAAGGAAAAAGT
Found at i:59095 original size:47 final size:47
Alignment explanation
Indices: 59044--59136 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
59034 CGAGTCAATC
*
59044 CAATGAGAATTCTTTTTCATCAATCAACTACACATTAGTTTCAATGT
1 CAATGAGAATTCTTTGTCATCAATCAACTACACATTAGTTTCAATGT
59091 CAATGAGAATTCTTTGTCATCAATCAACTACACATTAGTTTCAATG
1 CAATGAGAATTCTTTGTCATCAATCAACTACACATTAGTTTCAATG
59137 CATTATTGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (47 bp):
CAATGAGAATTCTTTGTCATCAATCAACTACACATTAGTTTCAATGT
Found at i:62891 original size:26 final size:26
Alignment explanation
Indices: 62850--62916 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
62840 GACCCTTTTA
* *
62850 TGCAGCGACAACTCTGGACATA-TTCAC
1 TGCAGCGACAATTCTGAACA-AGTTC-C
*
62877 -GCAGCGATAATTCTGAACAAGTTCC
1 TGCAGCGACAATTCTGAACAAGTTCC
62902 TGCAGCGACAATTCT
1 TGCAGCGACAATTCT
62917 AGACGCAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 2 0.06
26 32 0.94
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (26 bp):
TGCAGCGACAATTCTGAACAAGTTCC
Found at i:70795 original size:18 final size:18
Alignment explanation
Indices: 70772--70812 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
70762 TCACAGATAC
70772 TTCCTTTGTTCATACATA
1 TTCCTTTGTTCATACATA
*
70790 TTCCTTTGTTTATACATA
1 TTCCTTTGTTCATACATA
70808 TTCCT
1 TTCCT
70813 ACCCTTAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.05, T:0.54
Consensus pattern (18 bp):
TTCCTTTGTTCATACATA
Found at i:71184 original size:27 final size:27
Alignment explanation
Indices: 71154--71208 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
71144 GCTTTTCCTA
* *
71154 CATAATTCGTCGCAAAGGCTACTCTTT
1 CATAATTCATCACAAAGGCTACTCTTT
* *
71181 CATATTTTATCACAAAGGCTACTCTTT
1 CATAATTCATCACAAAGGCTACTCTTT
71208 C
1 C
71209 CTAACGTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36
Consensus pattern (27 bp):
CATAATTCATCACAAAGGCTACTCTTT
Found at i:75998 original size:62 final size:59
Alignment explanation
Indices: 75927--76044 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 59
75917 AGTGATTATC
* * *
75927 TTAATATTAAATTTAATGTAATGTTTATCTTGTAGATAAATATTCTATTAATTTAATATGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-TA-ATAAATATTCTAATAATTTAATATGAT
* *
75989 TTAATATTAAATTTAATCTAATATTTATCTTAATAATTATTGTAATAATTTAATAT
1 TTAATATTAAATTTAATCTAATATTTATCTTAATAAATATTCTAATAATTTAATAT
76045 TAAAGTGATT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
59 21 0.41
60 2 0.04
61 1 0.02
62 27 0.53
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTAATAAATATTCTAATAATTTAATATGAT
Found at i:76184 original size:14 final size:14
Alignment explanation
Indices: 76138--76175 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
76128 TGAATTCAAC
*
76138 AGAAAGTTCTAAAG
1 AGAAAATTCTAAAG
76152 AGAAAATTCTAAAG
1 AGAAAATTCTAAAG
76166 AGAAAATTCT
1 AGAAAATTCT
76176 CTAAAGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.53, C:0.08, G:0.16, T:0.24
Consensus pattern (14 bp):
AGAAAATTCTAAAG
Found at i:79525 original size:27 final size:26
Alignment explanation
Indices: 79484--79546 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
79474 AAATATTCTC
79484 TAAATAAT-AAATATTAATTTATAAA
1 TAAATAATAAAATATTAATTTATAAA
* **
79509 TAAATTAATAAAATATTCATTTATCGA
1 TAAA-TAATAAAATATTAATTTATAAA
79536 TAAACTAATAA
1 TAAA-TAATAA
79547 CCTCAATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 4 0.12
26 4 0.12
27 24 0.75
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (26 bp):
TAAATAATAAAATATTAATTTATAAA
Found at i:86692 original size:18 final size:18
Alignment explanation
Indices: 86658--86693 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
86648 CAGTTTCTAA
*
86658 AGGATCTTCTTCATCTTC
1 AGGATCTTCCTCATCTTC
*
86676 AGGATCTTCCTCTTCTTC
1 AGGATCTTCCTCATCTTC
86694 TTCAGCTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.31, G:0.11, T:0.44
Consensus pattern (18 bp):
AGGATCTTCCTCATCTTC
Found at i:86817 original size:24 final size:24
Alignment explanation
Indices: 86790--86839 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
86780 TCATGTTCGT
86790 AAGAATTTTAGCTTTTAAGCATAA
1 AAGAATTTTAGCTTTTAAGCATAA
86814 AAGAATTTTAGCTTTTAAGCATAA
1 AAGAATTTTAGCTTTTAAGCATAA
86838 AA
1 AA
86840 CTATGATCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (24 bp):
AAGAATTTTAGCTTTTAAGCATAA
Found at i:88145 original size:13 final size:14
Alignment explanation
Indices: 88112--88146 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
88102 AATTTATTAA
88112 AAATAA-ATAAAAT
1 AAATAACATAAAAT
88125 AAATAACATAAAAT
1 AAATAACATAAAAT
88139 AAA-AACAT
1 AAATAACAT
88147 TTATTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAACATAAAAT
Found at i:88218 original size:26 final size:28
Alignment explanation
Indices: 88166--88221 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
88156 GCTATTTTAA
*
88166 AATATTTACAAAAAAAGACAACTAATTTT
1 AATATTTACAAAAAAAGAC-ACAAATTTT
88195 AATATTTACAAAAAAA-AC-CAAATTTT
1 AATATTTACAAAAAAAGACACAAATTTT
88221 A
1 A
88222 TAAAAAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.31
28 2 0.08
29 16 0.62
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (28 bp):
AATATTTACAAAAAAAGACACAAATTTT
Found at i:100106 original size:10 final size:10
Alignment explanation
Indices: 100087--100122 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
100077 ATATGACTGA
100087 ATGTGATTAT
1 ATGTGATTAT
*
100097 ATGTGCTTAT
1 ATGTGATTAT
100107 ATGTGATTATT
1 ATGTGATTA-T
100118 ATGTG
1 ATGTG
100123 TCAGAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:103440 original size:22 final size:22
Alignment explanation
Indices: 103412--103460 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
103402 TAAGCAACCA
*
103412 TTTTTTTCTT-CTTTTTCTCTTT
1 TTTTTTTCTTCCTTTTT-TCTAT
*
103434 TTTTTTTTTTCCTTTTTTCTAT
1 TTTTTTTCTTCCTTTTTTCTAT
103456 TTTTT
1 TTTTT
103461 GTTGTTCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTTCTTCCTTTTTTCTAT
Found at i:103458 original size:9 final size:8
Alignment explanation
Indices: 103412--103460 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 8
103402 TAAGCAACCA
103412 TTTTTTTC
1 TTTTTTTC
103420 TTCTTTTTC
1 TT-TTTTTC
103429 TCTTTTTT-
1 T-TTTTTTC
103437 TTTTTTTC
1 TTTTTTTC
*
103445 CTTTTTTC
1 TTTTTTTC
103453 TATTTTTT
1 T-TTTTTT
103461 GTTGTTCGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
7 6 0.17
8 10 0.29
9 18 0.51
10 1 0.03
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTC
Found at i:103504 original size:16 final size:16
Alignment explanation
Indices: 103478--103542 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
103468 GTACGAGCAG
* *
103478 TTTTCTCTTTTCTTTTT
1 TTTTCTATTTT-TTTCT
103495 TTTTCT-TTTTTTTGC-
1 TTTTCTATTTTTTT-CT
*
103510 TGTTCTATTTTTTTCT
1 TTTTCTATTTTTTTCT
103526 TCTTT-TATTTTTTTCT
1 T-TTTCTATTTTTTTCT
103542 T
1 T
103543 CTTTATTCGA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 9 0.22
16 24 0.59
17 8 0.20
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTCTATTTTTTTCT
Found at i:103549 original size:15 final size:16
Alignment explanation
Indices: 103515--103546 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
103505 TTTGCTGTTC
103515 TATTTTTTTCTTCTTT
1 TATTTTTTTCTTCTTT
103531 TATTTTTTTCTTCTTT
1 TATTTTTTTCTTCTTT
103547 ATTCGAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (16 bp):
TATTTTTTTCTTCTTT
Found at i:109260 original size:17 final size:19
Alignment explanation
Indices: 109228--109265 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
109218 GTTTCTGTAA
109228 AATGAAAATGAAAATAACT
1 AATGAAAATGAAAATAACT
109247 AATG-AAAT-AAAATAACT
1 AATGAAAATGAAAATAACT
109264 AA
1 AA
109266 ACCTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 4 0.21
19 4 0.21
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.21
Consensus pattern (19 bp):
AATGAAAATGAAAATAACT
Found at i:110153 original size:99 final size:99
Alignment explanation
Indices: 109982--110179 Score: 360
Period size: 99 Copynumber: 2.0 Consensus size: 99
109972 ACACTATAGT
*
109982 AATGAAATAAAAAAGTTATATGTGTATTAATTTATCGATATAAGATGAACATGATGCGAGACAGT
1 AATGAAATAAAAAAGTTATATGTGTATTAATTTATCGATATAAGACGAACATGATGCGAGACAGT
110047 GGTGTGGCATCCTAGTATTCGGGCTCGACGATCG
66 GGTGTGGCATCCTAGTATTCGGGCTCGACGATCG
*
110081 AATGAAATAAAAAAGTTATTTGTGTATTAATTTATCGATATAAGACGAACATGATGCGAGACAGT
1 AATGAAATAAAAAAGTTATATGTGTATTAATTTATCGATATAAGACGAACATGATGCGAGACAGT
* *
110146 GGTGTGGCGTCCTAGTATTCGGGCTTGACGATCG
66 GGTGTGGCATCCTAGTATTCGGGCTCGACGATCG
110180 GGCTGGGTAT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (99 bp):
AATGAAATAAAAAAGTTATATGTGTATTAATTTATCGATATAAGACGAACATGATGCGAGACAGT
GGTGTGGCATCCTAGTATTCGGGCTCGACGATCG
Found at i:111260 original size:47 final size:47
Alignment explanation
Indices: 111175--111293 Score: 111
Period size: 47 Copynumber: 2.5 Consensus size: 47
111165 CAGTAATGTA
** *
111175 AATAAACTGCCACTTAATAATATTGCGGACTAGCCACCACTTTTGAT
1 AATAAACTGCCACTTAATAATATTGCGGAAAAGCCACCAATTTTGAT
* * *
111222 AATATACTGCCACTTAGA-AATATT-CTGGAAAAGGCACCAATTTT-ACA
1 AATAAACTGCCACTTA-ATAATATTGC-GGAAAAGCCACCAATTTTGA-T
*
111269 AATAAACTGTCACATT-ATAATATTG
1 AATAAACTGCCAC-TTAATAATATTG
111294 TGGACATGCC
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
46 3 0.05
47 52 0.90
48 3 0.05
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (47 bp):
AATAAACTGCCACTTAATAATATTGCGGAAAAGCCACCAATTTTGAT
Found at i:137873 original size:15 final size:15
Alignment explanation
Indices: 137833--137873 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
137823 TTACCGGATG
*
137833 TAAAAAATATTTTTT
1 TAAAAAAAATTTTTT
**
137848 TAAAACTAATTTTTT
1 TAAAAAAAATTTTTT
137863 TAAAAAAAATT
1 TAAAAAAAATT
137874 ATGAAATAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAAAAAAATTTTTT
Found at i:139308 original size:24 final size:23
Alignment explanation
Indices: 139274--139462 Score: 94
Period size: 24 Copynumber: 8.4 Consensus size: 23
139264 CTGCAACGAA
*
139274 ACCACCTCCCTCTCCTACTGGTAC
1 ACCACCACCCTCTCCTACT-GTAC
*
139298 ACCACCACCCTCTCCTACTGTGGC
1 ACCACCACCCTCTCCTACTGT-AC
* * *
139322 ACCACCATCAC-CTGCTAC--TAA
1 ACCACCA-CCCTCTCCTACTGTAC
* *
139343 ACCACCTCCCACTCCTACTGGTAC
1 ACCACCACCCTCTCCTACT-GTAC
* * * *
139367 ACCA-C-CTC-CTGCTA-T-AAA
1 ACCACCACCCTCTCCTACTGTAC
*
139385 ACCACCACCCTCTCCTACTGTGGC
1 ACCACCACCCTCTCCTACTGT-AC
* * *
139409 ACCACCATCAC-CTGCTAC--TAA
1 ACCACCA-CCCTCTCCTACTGTAC
*
139430 ACCACCTCCCTCTCCTACTGGTAC
1 ACCACCACCCTCTCCTACT-GTAC
139454 ACCACCACC
1 ACCACCACC
139463 TGCTATAAAA
Statistics
Matches: 120, Mismatches: 28, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
18 5 0.04
19 1 0.01
20 7 0.06
21 34 0.28
22 5 0.04
23 3 0.03
24 61 0.51
25 4 0.03
ACGTcount: A:0.23, C:0.48, G:0.08, T:0.21
Consensus pattern (23 bp):
ACCACCACCCTCTCCTACTGTAC
Found at i:139358 original size:45 final size:45
Alignment explanation
Indices: 139298--139490 Score: 233
Period size: 42 Copynumber: 4.4 Consensus size: 45
139288 CTACTGGTAC
139298 ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTACT-AA
1 ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTA-TAAA
* * *
139343 ACCACCTCCCACTCCTACTG-GTACACCACC-T--CCTGCTATAAA
1 ACCACCACCCTCTCCTACTGTG-GCACCACCATCACCTGCTATAAA
139385 ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTACT-AA
1 ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTA-TAAA
* * *
139430 ACCACCTCCCTCTCCTAC--TGGTA-CACCACCACCTGCTATAAA
1 ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTATAAA
*
139472 ACCACCAGCCTCTCCTACT
1 ACCACCACCCTCTCCTACT
139491 CTCACACCAC
Statistics
Matches: 128, Mismatches: 11, Indels: 20
0.81 0.07 0.13
Matches are distributed among these distances:
41 2 0.02
42 66 0.52
43 6 0.05
44 2 0.02
45 51 0.40
46 1 0.01
ACGTcount: A:0.25, C:0.47, G:0.08, T:0.21
Consensus pattern (45 bp):
ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTATAAA
Found at i:139502 original size:87 final size:87
Alignment explanation
Indices: 139298--139490 Score: 359
Period size: 87 Copynumber: 2.2 Consensus size: 87
139288 CTACTGGTAC
139298 ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTACTAAACCACCTCCCACTCCTACTG
1 ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTACTAAACCACCTCCCACTCCTACTG
*
139363 GTACACCACCTCCTGCTATAAA
66 GTACACCACCACCTGCTATAAA
*
139385 ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTACTAAACCACCTCCCTCTCCTACTG
1 ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTACTAAACCACCTCCCACTCCTACTG
139450 GTACACCACCACCTGCTATAAA
66 GTACACCACCACCTGCTATAAA
*
139472 ACCACCAGCCTCTCCTACT
1 ACCACCACCCTCTCCTACT
139491 CTCACACCAC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 103 1.00
ACGTcount: A:0.25, C:0.47, G:0.08, T:0.21
Consensus pattern (87 bp):
ACCACCACCCTCTCCTACTGTGGCACCACCATCACCTGCTACTAAACCACCTCCCACTCCTACTG
GTACACCACCACCTGCTATAAA
Found at i:139571 original size:27 final size:27
Alignment explanation
Indices: 139524--139597 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
139514 GCCAATTGTG
* * *
139524 CCTCCACCACCACGACATCAA-CCATT
1 CCTCCACCTCCACCACCTCAATCCATT
*
139550 CCATCCACCTCCACCACCTCAATCTATT
1 CC-TCCACCTCCACCACCTCAATCCATT
*
139578 TCTCCACCAT-CACCACCTCA
1 CCTCCACC-TCCACCACCTCA
139598 TGTAATTCCG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 2 0.05
27 32 0.80
28 6 0.15
ACGTcount: A:0.27, C:0.51, G:0.01, T:0.20
Consensus pattern (27 bp):
CCTCCACCTCCACCACCTCAATCCATT
Found at i:145250 original size:10 final size:10
Alignment explanation
Indices: 145235--145280 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
145225 AAAATTTGCC
145235 TTTTTTCATT
1 TTTTTTCATT
145245 TTTTTT--TT
1 TTTTTTCATT
*
145253 TTTTTTCAAT
1 TTTTTTCATT
145263 TTTTTTCAACTT
1 TTTTTTC-A-TT
145275 TTTTTT
1 TTTTTT
145281 TTCTAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 8 0.27
10 14 0.47
11 1 0.03
12 7 0.23
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:146444 original size:38 final size:34
Alignment explanation
Indices: 146364--146447 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
146354 TCTTTACATG
*
146364 TTTATGCAGCGACATTCCTGGGTGCAATTGAATA
1 TTTATGCAGCGACATTCCTGGATGCAATTGAATA
* **
146398 CTTATGCAGCGACATTTTTGGATGCAATTTGAAGAATA
1 TTTATGCAGCGACATTCCTGGATGCAA-TT---GAATA
146436 TTTATGCAGCGA
1 TTTATGCAGCGA
146448 TAGTCTTGGG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 23 0.56
35 2 0.05
38 16 0.39
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (34 bp):
TTTATGCAGCGACATTCCTGGATGCAATTGAATA
Found at i:152160 original size:6 final size:6
Alignment explanation
Indices: 152140--152352 Score: 177
Period size: 6 Copynumber: 34.3 Consensus size: 6
152130 AGTGCATAAT
* * *
152140 AAAAT- AAAATA AAAA-A TAAAATA AAACTA AAAACTA AAACT- AAACTA
1 AAAATA AAAATA AAAATA -AAAATA AAAATA AAAA-TA AAAATA AAAATA
* *
152187 AAACTA AAACTA AAAATA AAAATA AAAATA AAAAT- AAAATGA AAAATGA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A AAAAT-A
152236 AAAATGA AAAATGA AAAATGA AAAATGA AAAATGA AAAATGA AAAATGA
1 AAAAT-A AAAAT-A AAAAT-A AAAAT-A AAAAT-A AAAAT-A AAAAT-A
* * * * *
152285 AAAATGA AAAATGA AAAAGA AAAA-G AAAA-A GAAATG AAAATG AAAATA
1 AAAAT-A AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
152333 AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AA
152353 TGTACTATTT
Statistics
Matches: 189, Mismatches: 11, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
5 23 0.12
6 86 0.46
7 80 0.42
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:152232 original size:7 final size:7
Alignment explanation
Indices: 152198--152349 Score: 199
Period size: 7 Copynumber: 23.9 Consensus size: 7
152188 AACTAAAACT
152198 AAAAAT-
1 AAAAATG
152204 AAAAAT-
1 AAAAATG
152210 AAAAAT-
1 AAAAATG
152216 AAAAAT-
1 AAAAATG
152222 -AAAATG
1 AAAAATG
152228 AAAAATG
1 AAAAATG
152235 AAAAATG
1 AAAAATG
152242 AAAAATG
1 AAAAATG
152249 AAAAATG
1 AAAAATG
152256 AAAAATG
1 AAAAATG
152263 AAAAATG
1 AAAAATG
152270 AAAAATG
1 AAAAATG
152277 AAAAATG
1 AAAAATG
152284 AAAAATG
1 AAAAATG
152291 AAAAATG
1 AAAAATG
152298 AAAAA-G
1 AAAAATG
152304 AAAAA-G
1 AAAAATG
152310 AAAAA-G
1 AAAAATG
152316 --AAATG
1 AAAAATG
152321 -AAAATG
1 AAAAATG
152327 -AAAAT-
1 AAAAATG
152332 AAAAAT-
1 AAAAATG
152338 AAAAAT-
1 AAAAATG
152344 AAAAAT
1 AAAAAT
152350 AAATGTACTA
Statistics
Matches: 141, Mismatches: 0, Indels: 10
0.93 0.00 0.07
Matches are distributed among these distances:
4 3 0.02
5 6 0.04
6 58 0.41
7 74 0.52
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:170732 original size:14 final size:14
Alignment explanation
Indices: 170708--170740 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
170698 AATAATGCAA
170708 TCAAA-GTTAAATG
1 TCAAAGGTTAAATG
170721 TCAAAGGTTAAATG
1 TCAAAGGTTAAATG
170735 TCAAAG
1 TCAAAG
170741 CAACGGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (14 bp):
TCAAAGGTTAAATG
Found at i:172462 original size:25 final size:25
Alignment explanation
Indices: 172408--172453 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
172398 GTTGGATCCA
172408 AATTAAATTCTAAAAAAATAATTAG
1 AATTAAATTCTAAAAAAATAATTAG
*
172433 AATTAAA-TCT-AAACAATAATT
1 AATTAAATTCTAAAAAAATAATT
172454 TCGTAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (25 bp):
AATTAAATTCTAAAAAAATAATTAG
Found at i:172548 original size:13 final size:13
Alignment explanation
Indices: 172527--172560 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
172517 TAAACAATAT
172527 AATAATAATCCTA
1 AATAATAATCCTA
*
172540 AATATTAATCCTA
1 AATAATAATCCTA
*
172553 AAAAATAA
1 AATAATAA
172561 ATTTTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:179710 original size:25 final size:25
Alignment explanation
Indices: 179662--179873 Score: 228
Period size: 25 Copynumber: 8.4 Consensus size: 25
179652 ATTTATCTCA
* *
179662 TACGAGCCTAGATAGAATAACGCTCT
1 TACGAGCC-AGACAGAATATCGCTCT
*
179688 TACGAGCCAAACAGAATATCGCTCT
1 TACGAGCCAGACAGAATATCGCTCT
*
179713 TATGAGCCAGACAGAATATCGCTCT
1 TACGAGCCAGACAGAATATCGCTCT
** *
179738 TACGAGTTAGACAGAATATCACTCT
1 TACGAGCCAGACAGAATATCGCTCT
* *
179763 TACGAGCCAAATAGAATATCGCTCT
1 TACGAGCCAGACAGAATATCGCTCT
** *
179788 TATTAGCCTA-ACAGAATATAGCTCT
1 TACGAGCC-AGACAGAATATCGCTCT
* * *
179813 TACAAGCTAGATAGAATATCGCTCT
1 TACGAGCCAGACAGAATATCGCTCT
* ** *
179838 TACGATCTGGACAAAATATCGCTCT
1 TACGAGCCAGACAGAATATCGCTCT
179863 TACGAGCCAGA
1 TACGAGCCAGA
179874 GTTTAGAGTC
Statistics
Matches: 153, Mismatches: 31, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
24 1 0.01
25 143 0.93
26 9 0.06
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (25 bp):
TACGAGCCAGACAGAATATCGCTCT
Found at i:179763 original size:75 final size:75
Alignment explanation
Indices: 179669--179873 Score: 268
Period size: 75 Copynumber: 2.7 Consensus size: 75
179659 TCATACGAGC
* *
179669 CTAGATAGAATAACGCTCTTACGAGCCAAACAGAATATCGCTCTTATGAGCCAGACAGAATATCG
1 CTAGATAGAATATCGCTCTTACGAGCCAAACAGAATATCGCTCTTATGAGCCAGACAGAATATAG
*
179734 CTCTTACGAG
66 CTCTTACAAG
* * * * *
179744 TTAGACAGAATATCACTCTTACGAGCCAAATAGAATATCGCTCTTATTAGCCTA-ACAGAATATA
1 CTAGATAGAATATCGCTCTTACGAGCCAAACAGAATATCGCTCTTATGAGCC-AGACAGAATATA
179808 GCTCTTACAAG
65 GCTCTTACAAG
* *** * *
179819 CTAGATAGAATATCGCTCTTACGATCTGGACAAAATATCGCTCTTACGAGCCAGA
1 CTAGATAGAATATCGCTCTTACGAGCCAAACAGAATATCGCTCTTATGAGCCAGA
179874 GTTTAGAGTC
Statistics
Matches: 109, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
74 1 0.01
75 107 0.98
76 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (75 bp):
CTAGATAGAATATCGCTCTTACGAGCCAAACAGAATATCGCTCTTATGAGCCAGACAGAATATAG
CTCTTACAAG
Found at i:195566 original size:17 final size:17
Alignment explanation
Indices: 195534--195592 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
195524 ATAATTATCC
* *
195534 TTGCATTATTAATGTCA
1 TTGCATTTTTATTGTCA
*
195551 TTGCATTTTTATTGTCG
1 TTGCATTTTTATTGTCA
* * **
195568 CTGCATCTACATTGTCA
1 TTGCATTTTTATTGTCA
195585 TTGCATTT
1 TTGCATTT
195593 CCATATATAT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (17 bp):
TTGCATTTTTATTGTCA
Done.