Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008893.1 Hibiscus syriacus cultivar Beakdansim tig00112159_pilon, 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: 2797279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 13
Found at i:967 original size:21 final size:22
Alignment explanation
Indices: 920--972 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
910 AAGACAATCA
*
920 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGATC
* *
942 A-AGTCGTAGAGAAACTCGA-G
1 AGAGTCGAAGAGAAACTCGATC
962 AGAGTCGAAGA
1 AGAGTCGAAGA
973 TACACTCAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.42, C:0.13, G:0.30, T:0.15
Consensus pattern (22 bp):
AGAGTCGAAGAGAAACTCGATC
Found at i:1058 original size:33 final size:33
Alignment explanation
Indices: 1016--1081 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1006 AAATAGATGG
*
1016 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1049 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1082 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2887 original size:19 final size:19
Alignment explanation
Indices: 2863--2911 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
2853 AATGTCGAGT
2863 TAATTTTGTATA-AGATTTA
1 TAATTTTGTATACA-ATTTA
2882 TAATTTTGTATACAATTTA
1 TAATTTTGTATACAATTTA
*
2901 TATTTTTGTAT
1 TAATTTTGTAT
2912 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATACAATTTA
Found at i:4565 original size:198 final size:199
Alignment explanation
Indices: 3029--4588 Score: 2802
Period size: 199 Copynumber: 7.9 Consensus size: 199
3019 ACAATATGGC
* * *
3029 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
3094 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
3158 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGA
3222 ATTAAA
194 ATTAAA
*
3228 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
3293 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
3358 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
3423 TTAAA
195 TTAAA
* *
3428 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
3493 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGG-TTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
3556 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
3621 TAAA
196 TAAA
*
3625 AACAAGGTGCACCCATAAAGTGTTGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
3688 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACTGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
* *
3752 AATATGTCTAAATAATGTGTCGACACAAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
3817 TAAA
196 TAAA
3821 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
3886 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
3950 TATATGTCT-AATAATGTGTCGACACTAATATAG-TTGTGTCGATA-TTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
**
4012 GGAA
196 TAAA
4016 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
4081 CAAAAGTATAATGTAATATGTATTTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
4146 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATTAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
**
4211 GGAA
196 TAAA
4215 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
4280 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
4345 TATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
**
4410 GGAA
196 TAAA
4414 AACAAGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
4478 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
4543 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
4589 CTAATTTAAA
Statistics
Matches: 1325, Mismatches: 25, Indels: 23
0.97 0.02 0.02
Matches are distributed among these distances:
194 13 0.01
195 136 0.10
196 207 0.16
197 195 0.15
198 316 0.24
199 384 0.29
200 74 0.06
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
TAAA
Found at i:4565 original size:397 final size:398
Alignment explanation
Indices: 3029--4588 Score: 2811
Period size: 397 Copynumber: 3.9 Consensus size: 398
3019 ACAATATGGC
* * *
3029 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
3094 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
3158 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGA
*
3222 ATTAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
194 ATGAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
*
3287 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
259 CG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
3352 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAG
323 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAG
3417 AATGAATTAAA
388 AATGAATTAAA
* *
3428 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
3493 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGG-TTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
3556 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
* *
3621 TAAAAACAAGGTGCACCCATAAAGTGTTGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCG
196 GAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
*
3684 AACCCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACTGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
*
3748 AGAGAATATGTCTAAATAATGTGTCGACACAAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
3813 GAATTAAA
391 GAATTAAA
3821 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
3886 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
3950 TATATGTCT-AATAATGTGTCGACACTAATATAG-TTGTGTCGATA-TTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
*
4012 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
*
4077 AACCCAAAAGTATAATGTAATATGTATTTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
*
4142 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
* **
4207 TAATGGAA
391 GAATTAAA
4215 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
4280 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
4345 TATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
*
4410 GGAAAACAAGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
4474 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
4539 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
4589 CTAATTTAAA
Statistics
Matches: 1127, Mismatches: 23, Indels: 24
0.96 0.02 0.02
Matches are distributed among these distances:
391 53 0.05
392 62 0.06
393 246 0.22
394 214 0.19
395 81 0.07
396 102 0.09
397 277 0.25
398 57 0.05
399 35 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (398 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
GAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
GAATTAAA
Found at i:5350 original size:184 final size:184
Alignment explanation
Indices: 5041--5461 Score: 797
Period size: 184 Copynumber: 2.3 Consensus size: 184
5031 ACCTGGGTTT
5041 CTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACA
1 CTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACA
5106 TCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTT
66 TCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTT
*
5171 TATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTA
131 TATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTATCGGTA
5225 CTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACA
1 CTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACA
5290 TCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTT
66 TCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTT
5355 TATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTATCGGTA
131 TATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTATCGGTA
* * * *
5409 CTTTATGTCCAGATTGGAATAAAAATGTGTCGATACCATTGAAAAAAGTGTCG
1 CTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCG
5462 GTAATTTGAA
Statistics
Matches: 232, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 232 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (184 bp):
CTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACA
TCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTT
TATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTATCGGTA
Found at i:7959 original size:25 final size:25
Alignment explanation
Indices: 7925--7989 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
7915 TTATCATTAA
7925 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
7950 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
7975 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
7990 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:8307 original size:23 final size:23
Alignment explanation
Indices: 8276--8339 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
8266 ATAGGTAAAC
*
8276 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
8299 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
8322 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
8340 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:8346 original size:23 final size:23
Alignment explanation
Indices: 8276--8348 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
8266 ATAGGTAAAC
* **
8276 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
8299 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
8322 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
8345 ATAT
1 ATAT
8349 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:8651 original size:25 final size:25
Alignment explanation
Indices: 8617--8667 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
8607 ACAACAAATC
*
8617 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
8642 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
8667 A
1 A
8668 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:8983 original size:18 final size:18
Alignment explanation
Indices: 8962--8998 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8952 GTAATTGGAG
8962 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
8980 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
8998 T
1 T
8999 ATTTATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:9006 original size:24 final size:23
Alignment explanation
Indices: 8953--9003 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
8943 ATTTCATATG
*
8953 TAATTGGAGTTTGAATTTAAATT
1 TAATTTGAGTTTGAATTTAAATT
8976 TCAATTTGAGTTTGAATTTCAATATT
1 T-AATTTGAGTTTGAATTT-AA-ATT
9002 TA
1 TA
9004 TTTCGGCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 1 0.04
24 16 0.67
25 3 0.12
26 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (23 bp):
TAATTTGAGTTTGAATTTAAATT
Found at i:9713 original size:23 final size:23
Alignment explanation
Indices: 9682--9745 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
9672 ATAGGTAAAC
*
9682 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
9705 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
9728 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
9746 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:9752 original size:23 final size:23
Alignment explanation
Indices: 9682--9754 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
9672 ATAGGTAAAC
* **
9682 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
9705 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
9728 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
9751 ATAT
1 ATAT
9755 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:23505 original size:60 final size:60
Alignment explanation
Indices: 23394--23507 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
23384 CTATAATGTA
* *
23394 TTGCTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATGGTCATCCGACTATAGAATG
1 TTGCTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATGATCAGCCGACTATAGAATG
* * * *
23454 TTGCTTTGTTGAGTCCCTCGGCTATTAAAAGTTACACAATGAT-AGCTCGACTAT
1 TTGCTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATGATCAGC-CGACTAT
23508 TCATTATATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (60 bp):
TTGCTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATGATCAGCCGACTATAGAATG
Found at i:24236 original size:17 final size:17
Alignment explanation
Indices: 24214--24263 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
24204 AAATTCTTCT
24214 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
24231 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
24245 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
24262 AA
1 AA
24264 ACATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:24585 original size:20 final size:19
Alignment explanation
Indices: 24560--24626 Score: 118
Period size: 20 Copynumber: 3.5 Consensus size: 19
24550 TATTTTTTTA
24560 ATATATATATATAATAT-T
1 ATATATATATATAATATAT
24578 ATATATATATATAATATAT
1 ATATATATATATAATATAT
24597 ATATATATAATATAATATAT
1 ATATATAT-ATATAATATAT
24617 ATATATATAT
1 ATATATATAT
24627 GGATGGATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
18 17 0.36
19 11 0.23
20 19 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATATATATATAATATAT
Found at i:24602 original size:33 final size:33
Alignment explanation
Indices: 24560--24623 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
24550 TATTTTTTTA
*
24560 ATATATATATATAATATTATATATATATATAAT
1 ATATATATATATAATATAATATATATATATAAT
24593 ATATATATATATAATATAATATATATATATA
1 ATATATATATATAATATAATATATATATATA
24624 TATGGATGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
ATATATATATATAATATAATATATATATATAAT
Found at i:24642 original size:2 final size:2
Alignment explanation
Indices: 24560--24626 Score: 99
Period size: 2 Copynumber: 36.0 Consensus size: 2
24550 TATTTTTTTA
24560 AT AT AT AT AT AT A- AT AT -T AT AT AT AT AT AT A- 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
24599 AT AT AT A- 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
24627 GGATGGATAG
Statistics
Matches: 60, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
1 5 0.08
2 55 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24648 original size:20 final size:22
Alignment explanation
Indices: 24615--24654 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
24605 AATATAATAT
24615 ATATATATATATGGATGGATAG
1 ATATATATATATGGATGGATAG
*
24637 ATATAT-TA-ATGGGTGGAT
1 ATATATATATATGGATGGAT
24655 GGATGCTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (22 bp):
ATATATATATATGGATGGATAG
Found at i:25626 original size:18 final size:20
Alignment explanation
Indices: 25603--25646 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
25593 ATTATGAAAA
25603 TATTTTAAAAT-AT-TTATT
1 TATTTTAAAATCATATTATT
25621 TATTTTTAAAATCATATTATT
1 TA-TTTTAAAATCATATTATT
25642 TATTT
1 TATTT
25647 GAAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.09
19 9 0.39
20 5 0.22
21 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTTAAAATCATATTATT
Found at i:25629 original size:19 final size:21
Alignment explanation
Indices: 25605--25646 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
25595 TATGAAAATA
25605 TTTTAAAAT-AT-TTATTTAT
1 TTTTAAAATCATATTATTTAT
25624 TTTTAAAATCATATTATTTAT
1 TTTTAAAATCATATTATTTAT
25645 TT
1 TT
25647 GAAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.43
20 2 0.10
21 10 0.48
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAAAATCATATTATTTAT
Found at i:26402 original size:18 final size:19
Alignment explanation
Indices: 26381--26416 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
26371 CTAAAATTAA
26381 ATAAAAATT-ATAATTTAG
1 ATAAAAATTAATAATTTAG
26399 ATAAAAATTAATAATTTA
1 ATAAAAATTAATAATTTA
26417 TTATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
ATAAAAATTAATAATTTAG
Found at i:30444 original size:2 final size:2
Alignment explanation
Indices: 30418--30502 Score: 75
Period size: 2 Copynumber: 41.5 Consensus size: 2
30408 ATCTCAACTC
* * * *
30418 TA TA TGA TA TA TG TA TA TCA AA TA TA TA TA TCA TG TA CGA TA TA
1 TA TA T-A TA TA TA TA TA T-A TA TA TA TA TA T-A TA TA -TA TA TA
*
30462 TA TA TA -A CA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30502 T
1 T
30503 TGCTATGATA
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
1 2 0.03
2 61 0.88
3 6 0.09
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:30551 original size:22 final size:22
Alignment explanation
Indices: 30510--30575 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
30500 TATTGCTATG
* *
30510 ATAAATTATTTAAATTAAAATAAA
1 ATAATTTAATTAAA-TAAAA-AAA
30534 ATAATGTT-A-TAAATAAAAAAA
1 ATAAT-TTAATTAAATAAAAAAA
*
30555 TTAATTTAATTAAATAAAAAA
1 ATAATTTAATTAAATAAAAAA
30576 TTAATTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 2 0.06
21 8 0.22
22 16 0.44
23 4 0.11
24 4 0.11
25 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATAATTTAATTAAATAAAAAAA
Found at i:30573 original size:21 final size:21
Alignment explanation
Indices: 30512--30582 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
30502 TTGCTATGAT
*
30512 AAATT-ATTTAAATTAAA-ATA
1 AAATTAATTT-AATTAAATAAA
30532 AAA-TAATGTT-A-TAAATAAAA
1 AAATTAAT-TTAATTAAAT-AAA
30552 AAATTAATTTAATTAAATAAA
1 AAATTAATTTAATTAAATAAA
30573 AAATTAATTT
1 AAATTAATTT
30583 TTCAAGTCGA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
18 4 0.09
19 2 0.05
20 12 0.28
21 20 0.47
22 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (21 bp):
AAATTAATTTAATTAAATAAA
Found at i:42604 original size:22 final size:21
Alignment explanation
Indices: 42576--42624 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
42566 TTGGAAAGTG
*
42576 TCGATACCCTAGCTCGAG-AGTA
1 TCGATA-CCTAG-TCCAGCAGTA
42598 TCGATA-CTAGTCCAGCAGTA
1 TCGATACCTAGTCCAGCAGTA
42618 TCGATAC
1 TCGATAC
42625 TACTCGCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
22 6 0.25
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGATACCTAGTCCAGCAGTA
Found at i:46306 original size:14 final size:14
Alignment explanation
Indices: 46289--46331 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
46279 TTTTATTTAT
46289 GTTCATTTATGTTC
1 GTTCATTTATGTTC
46303 GTTCATTTATGTTC
1 GTTCATTTATGTTC
* *
46317 ATTTATTTATGTTC
1 GTTCATTTATGTTC
46331 G
1 G
46332 AACAGAGGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:46330 original size:24 final size:24
Alignment explanation
Indices: 46253--46322 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
46243 TGTTCGTGAA
*
46253 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTC-ATT-TATGTTCATTTATGTT
* *
46279 -TTTTATTTATGTTCATTTATGTT
1 CGTTCATTTATGTTCATTTATGTT
46302 CGTTCATTTATGTTCATTTAT
1 CGTTCATTTATGTTCATTTAT
46323 TTATGTTCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 15 0.39
24 21 0.55
25 2 0.05
ACGTcount: A:0.17, C:0.10, G:0.13, T:0.60
Consensus pattern (24 bp):
CGTTCATTTATGTTCATTTATGTT
Found at i:46587 original size:28 final size:28
Alignment explanation
Indices: 46556--46615 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
46546 TACATTCATT
*
46556 TGTTGTGT-TCGAATAAGTTTGTTTTTTG
1 TGTT-TGTATCGAATAAGTTTGTTTATTG
** *
46584 TGTTTGTATCGTTTATGTTTGTTTATTG
1 TGTTTGTATCGAATAAGTTTGTTTATTG
46612 TGTT
1 TGTT
46616 CGTTTATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.12, C:0.03, G:0.23, T:0.62
Consensus pattern (28 bp):
TGTTTGTATCGAATAAGTTTGTTTATTG
Found at i:46619 original size:23 final size:23
Alignment explanation
Indices: 46592--46642 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
46582 TGTGTTTGTA
** *
46592 TCGTTTATGTTTGTTTATTGTGT
1 TCGTTTATGTTCCTTTATTATGT
46615 TCGTTTATGTTCCTTTATTATGT
1 TCGTTTATGTTCCTTTATTATGT
46638 TCGTT
1 TCGTT
46643 CATTTGTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.10, C:0.10, G:0.18, T:0.63
Consensus pattern (23 bp):
TCGTTTATGTTCCTTTATTATGT
Found at i:46621 original size:13 final size:13
Alignment explanation
Indices: 46592--46658 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 13
46582 TGTGTTTGTA
46592 TCGTTTA-TGT-T
1 TCGTTTATTGTGT
46603 T-GTTTATTGTGT
1 TCGTTTATTGTGT
46615 TCGTTTA---TGT
1 TCGTTTATTGTGT
* *
46625 TCCTTTATTATGT
1 TCGTTTATTGTGT
*
46638 TCGTTCATTTGTGT
1 TCGTTTA-TTGTGT
46652 TCGTTTA
1 TCGTTTA
46659 CGTTCGTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
10 14 0.32
11 4 0.09
12 2 0.05
13 13 0.30
14 11 0.25
ACGTcount: A:0.10, C:0.10, G:0.18, T:0.61
Consensus pattern (13 bp):
TCGTTTATTGTGT
Found at i:46652 original size:37 final size:36
Alignment explanation
Indices: 46596--46669 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
46586 TTTGTATCGT
* * *
46596 TTATGTTTGTTTATTGTGTTCGTTTATGTTCCTTTA
1 TTATGTTCGTTCATTGTGTTCGTTTACGTTCCTTTA
*
46632 TTATGTTCGTTCATTTGTGTTCGTTTACGTTCGTTTA
1 TTATGTTCGTTCA-TTGTGTTCGTTTACGTTCCTTTA
46669 T
1 T
46670 GTTCATTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 11 0.33
37 22 0.67
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.61
Consensus pattern (36 bp):
TTATGTTCGTTCATTGTGTTCGTTTACGTTCCTTTA
Found at i:46672 original size:20 final size:20
Alignment explanation
Indices: 46639--46678 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
46629 TTATTATGTT
* *
46639 CGTTCATTTGTGTTCGTTTA
1 CGTTCATTTATGTTCATTTA
*
46659 CGTTCGTTTATGTTCATTTA
1 CGTTCATTTATGTTCATTTA
46679 TCATTTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.55
Consensus pattern (20 bp):
CGTTCATTTATGTTCATTTA
Found at i:53350 original size:38 final size:38
Alignment explanation
Indices: 53284--53371 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
53274 TTTTGTTATG
*
53284 GTCGGGTCTGG-TTTTTTAAGTGTAATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGA
* *
53321 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGA
*
53359 GTCAGGTCGGGTT
1 GTCGGGTCGGGTT
53372 CGGGTTTAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 10 0.22
38 36 0.78
ACGTcount: A:0.12, C:0.11, G:0.38, T:0.39
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGA
Found at i:53600 original size:38 final size:37
Alignment explanation
Indices: 53546--53627 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 37
53536 TGTTCGGGTT
*
53546 GGGTTGGATTTTTTAAGTGTGATATTCGGGTC-GAGTC
1 GGGTCGGATTTTTTAAGTGTGATATTCGGGTCAG-GTC
53583 GGGTCGGATTTTTTTAAGTGTGATATTCGGGTCAGGTC
1 GGGTCGGA-TTTTTTAAGTGTGATATTCGGGTCAGGTC
53621 GGGTCGG
1 GGGTCGG
53628 GTTCGGGCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
37 7 0.17
38 34 0.81
39 1 0.02
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (37 bp):
GGGTCGGATTTTTTAAGTGTGATATTCGGGTCAGGTC
Found at i:53605 original size:259 final size:261
Alignment explanation
Indices: 53050--53677 Score: 940
Period size: 259 Copynumber: 2.4 Consensus size: 261
53040 ACTTTATTTT
* * * * * *
53050 GGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTGGGTTCAGTTTAGGGTTT
1 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGG-TCGGGTTCGGGTTT
* *
53115 AGGGTGAAAAAAACCTGACCGATCCGAAAATATATATAATTCAAGTCGGGTCGGATAAAGTCACT
65 AGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAAGTCGGGTCGGATAAAGTCACT
* *
53180 GTTTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTGGATTTCTAATTCAT
130 GTTTTTATTAAATAAAAATAATTTTTTATTATTT---GTCGGGTCGGGTCGGATTTCTAATTCAT
* *
53245 ATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTATGGTCGGGTCTGGTTTTTTAAGTGTAAT
192 ATATTCGGGTCGGATCGGATGAAACTTTATTTTGTTAGGGTCGGGTCTGGTTTTTTAAGTGTAAT
53310 ATTCG
257 ATTCG
*
53315 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCAGGTCGGGTTCGGGTTTA
1 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTCGGGTTCGGGTTTA
* ** * *
53380 GGGTGAAAAAAACCGGATCGACCCGAAAATATATATAATTCGGGTTGGGTCGGATTAAGTCACTG
66 GGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAAGTCGGGTCGGATAAAGTCACTG
*
53445 TTTTTATTAAATAAAAATAATTTTTTATTATTT-T-GGGTCGGGTCGGATTTTTAATTCATATAT
131 TTTTTATTAAATAAAAATAATTTTTTATTATTTGTCGGGTCGGGTCGGATTTCTAATTCATATAT
* * *
53508 TCGGGTCGGATCGGATGAAACTTTATTTTGTTCGGGTTGGGT-TGGATTTTTTAAGTGTGATATT
196 TCGGGTCGGATCGGATGAAACTTTATTTTGTTAGGGTCGGGTCTGG-TTTTTTAAGTGTAATATT
53572 CG
260 CG
* * *
53574 GGTCGAGTCGGGTCGGATTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGGGTTCGGGCTTA
1 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTCGGGTTCGGGTTTA
* *
53639 GGGTGAAAAAAA-CGGGCCGACCCGAAAAAATATATAATT
66 GGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATT
53678 TTACCTTATA
Statistics
Matches: 333, Mismatches: 29, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
258 27 0.08
259 157 0.47
260 1 0.00
264 102 0.31
265 46 0.14
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.36
Consensus pattern (261 bp):
GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTCGGGTTCGGGTTTA
GGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAAGTCGGGTCGGATAAAGTCACTG
TTTTTATTAAATAAAAATAATTTTTTATTATTTGTCGGGTCGGGTCGGATTTCTAATTCATATAT
TCGGGTCGGATCGGATGAAACTTTATTTTGTTAGGGTCGGGTCTGGTTTTTTAAGTGTAATATTC
G
Found at i:54228 original size:16 final size:18
Alignment explanation
Indices: 54207--54252 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
54197 TATGGAATTG
54207 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
54223 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
54241 GATTCCAATTCC
1 GATTCCAATTCC
54253 CTCATAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 12 0.43
17 1 0.04
18 15 0.54
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:54390 original size:19 final size:19
Alignment explanation
Indices: 54366--54405 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
54356 CATTATGTCA
54366 ACCTTAAATAATATTGTGC
1 ACCTTAAATAATATTGTGC
54385 ACCTTAAATAATATTGTGC
1 ACCTTAAATAATATTGTGC
54404 AC
1 AC
54406 ATTTAACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (19 bp):
ACCTTAAATAATATTGTGC
Found at i:68176 original size:3 final size:3
Alignment explanation
Indices: 68168--68247 Score: 63
Period size: 3 Copynumber: 25.7 Consensus size: 3
68158 ATTTTATTTA
* * * *
68168 TAT TAT TAT TAT TAT AAT TAT AAT TAT TA- TATT TAT AAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* *
68213 TAT TAT TAA TAT ATAT TATT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT -TAT TA-T TA-T TAT TAT TAT TA
68248 CAAAACCCAG
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 2 0.03
3 49 0.78
4 12 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:68239 original size:21 final size:22
Alignment explanation
Indices: 68161--68245 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 22
68151 AATTTTAATT
*
68161 TTATTTATATTATTATTATTATAA
1 TTATTTAT-TTATTAATA-TATAA
*
68185 TTATAATTATTATATTTATA-ATAA
1 TTAT--TTATT-TATTAATATATAA
68209 TTA-TTA-TTATTAATATAT-A
1 TTATTTATTTATTAATATATAA
68228 TTATTTATTTATTAATAT
1 TTATTTATTTATTAATAT
68246 TACAAAACCC
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
19 11 0.21
20 6 0.12
21 13 0.25
24 11 0.21
25 1 0.02
26 10 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTTATTTATTAATATATAA
Found at i:69618 original size:26 final size:26
Alignment explanation
Indices: 69576--69627 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
69566 ATTGTTTTAA
**
69576 TTTTACTTATTTATATTTTTAAATAT
1 TTTTACTTATTTATATTCATAAATAT
*
69602 TTTTA-TTATTATGTATTCATAAATAT
1 TTTTACTTATT-TATATTCATAAATAT
69628 ATATATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTACTTATTTATATTCATAAATAT
Found at i:73686 original size:15 final size:15
Alignment explanation
Indices: 73666--73697 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
73656 ATCAATACCT
73666 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
73681 TTTTGCATACATTCA
1 TTTTGCATACATGCA
73696 TT
1 TT
73698 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:81051 original size:9 final size:9
Alignment explanation
Indices: 81028--81084 Score: 71
Period size: 9 Copynumber: 6.2 Consensus size: 9
81018 ATGCTTGAAG
81028 AAAAA-AAA
1 AAAAAGAAA
*
81036 AAGAAGAAA
1 AAAAAGAAA
81045 AAAAAGAGAA
1 AAAAAGA-AA
81055 AAAAAGAAA
1 AAAAAGAAA
*
81064 AAAGAGAAA
1 AAAAAGAAA
81073 AAAGAAGAAA
1 AAA-AAGAAA
81083 AA
1 AA
81085 GGGGGGGTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 4 0.10
9 22 0.52
10 16 0.38
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:81061 original size:19 final size:19
Alignment explanation
Indices: 81028--81084 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
81018 ATGCTTGAAG
81028 AAAA-AAAAAAGAAGAAAA
1 AAAAGAAAAAAGAAGAAAA
81046 AAAAGAGAAAAA-AAGAAAA
1 AAAAGA-AAAAAGAAGAAAA
*
81065 AAGAGAAAAAAGAAGAAAA
1 AAAAGAAAAAAGAAGAAAA
81084 A
1 A
81085 GGGGGGGTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 9 0.26
19 21 0.60
20 5 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAGAAGAAAA
Found at i:81068 original size:26 final size:26
Alignment explanation
Indices: 81024--81084 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
81014 TATTATGCTT
*
81024 GAAGAAAAAAAAAAGAAGAAAAAAAA
1 GAAGAAAAAAAAAAAAAGAAAAAAAA
*
81050 G-AGAAAAAAAGAAAAAAGAGAAAAAA
1 GAAGAAAAAAA-AAAAAAGAAAAAAAA
81076 GAAGAAAAA
1 GAAGAAAAA
81085 GGGGGGGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 9 0.29
26 15 0.48
27 7 0.23
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
GAAGAAAAAAAAAAAAAGAAAAAAAA
Found at i:82362 original size:83 final size:83
Alignment explanation
Indices: 82223--82707 Score: 781
Period size: 83 Copynumber: 5.8 Consensus size: 83
82213 ACATTAGCTG
*
82223 GAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
82288 AAACCAATCATTGAAATT
66 AAACCAATCATTGAATTT
*
82306 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
82371 AAACCAATCATTGAATTT
66 AAACCAATCATTGAATTT
82389 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* *
82454 AAACCAGTTATTGAATTT
66 AAACCAATCATTGAATTT
* *
82472 GGAACAAATGAATGTGCTCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTG
1 -GAA-AGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
*
82537 GTAAAACGAATCATTGAATTT
63 GTAAAACCAATCATTGAATTT
* *
82558 GAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTTGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* * *
82623 AAACTAGTTATTGAATTT
66 AAACCAATCATTGAATTT
* * *
82641 GGAAAGACGAATATGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 -GAAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
82706 TA
64 TA
82708 TGAACCCCAA
Statistics
Matches: 375, Mismatches: 22, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
83 221 0.59
84 29 0.08
85 63 0.17
86 62 0.17
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACCAATCATTGAATTT
Found at i:82564 original size:169 final size:168
Alignment explanation
Indices: 82223--82707 Score: 830
Period size: 169 Copynumber: 2.9 Consensus size: 168
82213 ACATTAGCTG
82223 GAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* * * *
82288 AAACCAATCATTGAAATT-GAAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAA
66 AAACCAGTTATTGAATTTGGAAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAG
82351 TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTT
131 TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTT
*
82389 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* *
82454 AAACCAGTTATTGAATTTGGAACAAATGAATGTGCTCAATAGCATCTTCTGGAAATGTTCTTTGA
66 AAACCAGTTATTGAATTTGGAA-AGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
*
82519 GTTATCTGATCTGGTTTGGTAAAACGAATCATTGAATTT
130 GTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTT
*
82558 GAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTTGTA
1 GAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* * * *
82623 AAACTAGTTATTGAATTTGGAAAGACGAATATGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
66 AAACCAGTTATTGAATTTGGAAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAG
82688 TTATCTGATCTGGTTTGGTA
131 TTATCTGATCTGGTTTGGTA
82708 TGAACCCCAA
Statistics
Matches: 300, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
166 79 0.26
167 3 0.01
168 71 0.24
169 147 0.49
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (168 bp):
GAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACCAGTTATTGAATTTGGAAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAG
TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTT
Found at i:83732 original size:113 final size:113
Alignment explanation
Indices: 83548--84175 Score: 989
Period size: 113 Copynumber: 5.6 Consensus size: 113
83538 ATCAGCATTA
* *
83548 CCAGGTCGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 CCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGATGAAGAAGTTCATAATGAGA
83613 AGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTT
63 AGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTT
*
83664 CCAGTTCGAGTTTATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGA
1 CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGA
*
83729 ATTTGTTCAACCTTTTGCTTAAATCTATCACTTGATGGATTATCTTTT
66 ATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTT
*
83777 CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGATGAAGTTCATAATGAGAAGA
1 CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGA
83842 ATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTT
66 ATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTT
83890 CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGA
1 CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGA
***
83955 ATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTAAAATTT
66 ATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTT
* * * *
84003 CCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGA
* * * *
84068 ATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGGTCAGT-TTTT
66 ATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTA-TCTTTT
*** * *
84116 CCAG-GAAAGTTCATAATGAGAAGAACTCATCAGGAGAA-GA--AA-AAGTTCATAATGAGAAGA
1 CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGA
84176 GCTTATTCAA
Statistics
Matches: 486, Mismatches: 25, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
108 18 0.04
109 2 0.00
111 2 0.00
112 30 0.06
113 409 0.84
114 1 0.00
116 24 0.05
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (113 bp):
CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGA
ATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTT
Found at i:84274 original size:226 final size:226
Alignment explanation
Indices: 83556--84274 Score: 668
Period size: 226 Copynumber: 3.2 Consensus size: 226
83546 TACCAGGTCG
83556 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG-GAAGAAGAAGTTCATAATGAGAAGAATTT
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAGAAGAAGAAGTTCATAATGAGAAGAATTT
* * *** *
83620 GTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTTATAATGAG
63 GTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCATCTTTTCCAGTGAAAGTTCATAATGAG
* * * *** *
83685 AAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTA
128 AAGAACTCATCAGAAGAAGGA-GAAGAAGTTCATAATGAGAAGAACTTATTCAACCAAATGCTCA
** **** * * *** ** ****
83750 AATCTATCACTTGATGGATTATCTTTTCCAGTTCG
192 AATCTAGAAAGAAAAGGATCAAAATCCCCAGGGAA
* *
83785 AGTTCATAATGAGAAGAACTCATCTGAAGAAG-GATGATGAAGTTCATAATGAGAAGAATTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * ***
83849 CAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAG
66 CAACCTTTTGCTCAAATCCATCACTTGATGGATCATCTTTTCCAGTGAAAGTTCATAATGAGAAG
* * * ***
83914 AACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
131 AACTCATCAGAAGAAGGA-GAAGAAGTTCATAATGAGAAGAACTTATTCAACCAAATGCTCAAAT
** **** * * ** * *
83979 CTATCACTTGATGGATTAAAATTTCCAGGTAG
195 CTAGAAAGAAAAGGATCAAAATCCCCAGGGAA
84011 AGTTCATAATGAGAAGAACTCATCTGAAGAA-AGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* *
84075 CAACTTTTTGCTCAAATCCATCACTTGATGGGTCAGT-TTTTCCAG-GAAAGTTCATAATGAGAA
66 CAACCTTTTGCTCAAATCCATCACTTGATGGATCA-TCTTTTCCAGTGAAAGTTCATAATGAGAA
* * ** **
84138 GAACTCATCAGGAGAA-GA-AA-AAGTTCATAATGAGAAGAGCTTATTCAATGAAATGACTCTCA
130 GAACTCATCAGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCAAATG-CTCAAA
84200 -C-AGAAAGAAAAGG-TCAACATCATCCCCAGCGGAA
194 TCTAGAAAGAAAAGGATCAA-A--ATCCCCAG-GGAA
*
84234 AGTTCATAATGAGAAGAACTCACCTGACAGAAAGAGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGA-AG-AAGAGAAGAA
84275 TTTATTCAAT
Statistics
Matches: 437, Mismatches: 43, Indels: 23
0.87 0.09 0.05
Matches are distributed among these distances:
219 3 0.01
220 6 0.01
221 28 0.06
222 12 0.03
223 28 0.06
224 4 0.01
225 31 0.07
226 305 0.70
227 2 0.00
229 18 0.04
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (226 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTGCTCAAATCCATCACTTGATGGATCATCTTTTCCAGTGAAAGTTCATAATGAGAAG
AACTCATCAGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCAAATGCTCAAATC
TAGAAAGAAAAGGATCAAAATCCCCAGGGAA
Found at i:84427 original size:9 final size:8
Alignment explanation
Indices: 84419--84484 Score: 68
Period size: 9 Copynumber: 8.2 Consensus size: 8
84409 TTAATTTTAT
84419 TTATATTA
1 TTATATTA
84427 TTATTATTA
1 TTA-TATTA
84436 TTATTATTA
1 TTA-TATTA
84445 TTATA-T-
1 TTATATTA
84451 TTATAATTA
1 TTAT-ATTA
84460 TTATTATTA
1 TTA-TATTA
84469 TTATA-TA
1 TTATATTA
84476 TTAT-TTA
1 TTATATTA
84483 TT
1 TT
84485 TAAATATTAC
Statistics
Matches: 52, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
6 4 0.08
7 12 0.23
8 8 0.15
9 27 0.52
10 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATATTA
Found at i:84430 original size:3 final size:3
Alignment explanation
Indices: 84422--84480 Score: 84
Period size: 3 Copynumber: 19.3 Consensus size: 3
84412 ATTTTATTTA
*
84422 TAT TAT TAT TAT TAT TAT TAT TAT TA- TATT TAT AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
84467 TAT TAT ATAT TAT T
1 TAT TAT -TAT TAT T
84481 TATTTAAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 2 0.04
3 44 0.86
4 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:88116 original size:15 final size:15
Alignment explanation
Indices: 88096--88124 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
88086 TAACACCTTT
88096 GGTTTAGATAACGAG
1 GGTTTAGATAACGAG
88111 GGTTTAGATAACGA
1 GGTTTAGATAACGA
88125 AAAAGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.31, T:0.28
Consensus pattern (15 bp):
GGTTTAGATAACGAG
Found at i:88961 original size:23 final size:23
Alignment explanation
Indices: 88935--88983 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
88925 TGTTAAAATA
*
88935 TTTTGGATGTTTGGA-TTGATATG
1 TTTTGGATGTTTGAACTTGA-ATG
88958 TTTTGGATGTTTGAACTTGAATG
1 TTTTGGATGTTTGAACTTGAATG
88981 TTT
1 TTT
88984 ATATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.18, C:0.02, G:0.27, T:0.53
Consensus pattern (23 bp):
TTTTGGATGTTTGAACTTGAATG
Found at i:88990 original size:2 final size:2
Alignment explanation
Indices: 88983--89009 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
88973 CTTGAATGTT
88983 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
89010 TTGGTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:89046 original size:19 final size:20
Alignment explanation
Indices: 89008--89047 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
88998 ATATATATAT
**
89008 ATTTGGTTTTGATTGTTTTA
1 ATTTGGTTTTGATTAATTTA
89028 ATTT-GTTTTGATTAATTTA
1 ATTTGGTTTTGATTAATTTA
89047 A
1 A
89048 ACTTAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (20 bp):
ATTTGGTTTTGATTAATTTA
Found at i:89325 original size:21 final size:22
Alignment explanation
Indices: 89296--89336 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
89286 GAGAATATAG
*
89296 TAAGAGGGAGTAATTTTCAATT
1 TAAGAGGGAGCAATTTTCAATT
89318 TAAG-GGGAGCAATTTTCAA
1 TAAGAGGGAGCAATTTTCAA
89337 AATTGAGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (22 bp):
TAAGAGGGAGCAATTTTCAATT
Found at i:92771 original size:20 final size:20
Alignment explanation
Indices: 92738--92775 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
92728 TTTAGTTCAC
*
92738 AGAATGTAAAATTATCAGTG
1 AGAATATAAAATTATCAGTG
*
92758 AGAATATAAGATTATCAG
1 AGAATATAAAATTATCAG
92776 AGAATAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (20 bp):
AGAATATAAAATTATCAGTG
Found at i:92795 original size:15 final size:16
Alignment explanation
Indices: 92763--92796 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
92753 CAGTGAGAAT
92763 ATAAGATTATCAGAGA
1 ATAAGATTATCAGAGA
*
92779 ATAAGATTA-CTGAGA
1 ATAAGATTATCAGAGA
92794 ATA
1 ATA
92797 TTGTATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (16 bp):
ATAAGATTATCAGAGA
Found at i:94010 original size:20 final size:19
Alignment explanation
Indices: 93945--94030 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 19
93935 GTTTCCAAAT
93945 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAA-TTGTAAA
* * **
93965 TCGTAACAC-AAAAGTCAAA
1 TCGCAACGCGAATTGT-AAA
93984 TTCGCAACGCGAATCTGTAAA
1 -TCGCAACGCGAAT-TGTAAA
94005 TCGCAACGCGAAATTGTAAA
1 TCGCAACGCG-AATTGTAAA
94025 TCGCAA
1 TCGCAA
94031 TACAGAAGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.04
19 5 0.09
20 36 0.68
21 8 0.15
22 2 0.04
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (19 bp):
TCGCAACGCGAATTGTAAA
Found at i:94098 original size:19 final size:19
Alignment explanation
Indices: 94072--94137 Score: 96
Period size: 19 Copynumber: 3.5 Consensus size: 19
94062 AATTCGTAAC
94072 ACTGAATTTCAAATTTGCA
1 ACTGAATTTCAAATTTGCA
*
94091 ATTGAATTTCAAATTTGCA
1 ACTGAATTTCAAATTTGCA
**
94110 ACTGAATTTCAAATCCGCA
1 ACTGAATTTCAAATTTGCA
*
94129 ACTCAATTT
1 ACTGAATTT
94138 TCTAATTCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (19 bp):
ACTGAATTTCAAATTTGCA
Found at i:94148 original size:20 final size:19
Alignment explanation
Indices: 94076--94169 Score: 82
Period size: 19 Copynumber: 4.9 Consensus size: 19
94066 CGTAACACTG
* * *
94076 AATTTCAAATTTGCAATTG
1 AATTTCAAATTCGCAACTC
* *
94095 AATTTCAAATTTGCAACTG
1 AATTTCAAATTCGCAACTC
*
94114 AATTTCAAATCCGCAACTC
1 AATTTCAAATTCGCAACTC
* *
94133 AATTTTCTAATTCGCAACAC
1 AA-TTTCAAATTCGCAACTC
*
94153 GAATTT-AATTTCGCAAC
1 -AATTTCAAATTCGCAAC
94170 AGGTTTTAGT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 45 0.70
20 17 0.27
21 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (19 bp):
AATTTCAAATTCGCAACTC
Found at i:94167 original size:19 final size:18
Alignment explanation
Indices: 94143--94188 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
94133 AATTTTCTAA
94143 TTCGCAACACGAATTTAAT
1 TTCGCAACA-GAATTTAAT
** *
94162 TTCGCAACAGGTTTTAGT
1 TTCGCAACAGAATTTAAT
94180 TTCGCAACA
1 TTCGCAACA
94189 TAAATGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (18 bp):
TTCGCAACAGAATTTAAT
Found at i:94342 original size:16 final size:16
Alignment explanation
Indices: 94323--94362 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
94313 TTCCCATCTC
*
94323 TAATTTTTTTTTTACA
1 TAATTTTTTTTCTACA
* *
94339 TAATTTTATTTCTATA
1 TAATTTTTTTTCTACA
94355 TAATTTTT
1 TAATTTTT
94363 CAATGATTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TAATTTTTTTTCTACA
Found at i:94978 original size:12 final size:12
Alignment explanation
Indices: 94957--94990 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
94947 ACCACATTTC
*
94957 CAATACCAAACA
1 CAATATCAAACA
94969 CAATATCAAACA
1 CAATATCAAACA
*
94981 CAATCTCAAA
1 CAATATCAAA
94991 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:95143 original size:24 final size:24
Alignment explanation
Indices: 95116--95169 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
95106 GTATTCGAAA
95116 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
95140 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
95164 TTTGAT
1 TTTGAT
95170 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:97454 original size:18 final size:18
Alignment explanation
Indices: 97431--97471 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
97421 AGCAAAAGGA
*
97431 AATCAAAATAAAAATCGC
1 AATCAAAATAAAAATCCC
*
97449 AATCAAAATCAAAATCCC
1 AATCAAAATAAAAATCCC
97467 AATCA
1 AATCA
97472 CAACCGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.59, C:0.22, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATAAAAATCCC
Found at i:97893 original size:66 final size:64
Alignment explanation
Indices: 97811--97954 Score: 252
Period size: 66 Copynumber: 2.2 Consensus size: 64
97801 AATTTAAAAC
97811 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTACACATC-AATT
97876 A
64 A
* *
97877 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
97941 AACAAATCAACTTT
1 AACAAATCAACTTT
97955 CAATGTAAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
64 19 0.25
65 23 0.30
66 34 0.45
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:99331 original size:20 final size:20
Alignment explanation
Indices: 99306--99452 Score: 201
Period size: 20 Copynumber: 7.3 Consensus size: 20
99296 TGTGAATCGG
99306 GTTGCGAATTTGACTTCAGT
1 GTTGCGAATTTGACTTCAGT
*
99326 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCAGT
*
99346 GTTGTGAATTTGACTATC-GT
1 GTTGCGAATTTGACT-TCAGT
99366 GTTGCGAATTTGACTTCAGT
1 GTTGCGAATTTGACTTCAGT
99386 GTTGCGAATTTGACTTCAGT
1 GTTGCGAATTTGACTTCAGT
*
99406 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCAGT
* *
99426 TTTTCGAATTTGACTT-ATGT
1 GTTGCGAATTTGACTTCA-GT
99446 GTTGCGA
1 GTTGCGA
99453 TTTACAAATT
Statistics
Matches: 114, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
19 2 0.02
20 110 0.96
21 2 0.02
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCAGT
Found at i:99474 original size:20 final size:20
Alignment explanation
Indices: 99446--99492 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
99436 TGACTTATGT
99446 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
99466 GTTGTGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
99486 GTTGCGA
1 GTTGCGA
99493 ATTTGGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:99544 original size:19 final size:19
Alignment explanation
Indices: 99482--99556 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
99472 ATTTACAGAT
99482 TCGCGTTGCGAATTTGGAAA
1 TCGCGTTGCGAATTT-GAAA
* * * **
99502 -CTGGGTTGTGAAATTGGAGT
1 TC-GCGTTGCG-AATTTGAAA
*
99522 TCGCGTTGTGAATTTGAAA
1 TCGCGTTGCGAATTTGAAA
99541 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
99557 TTGTCATTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
19 22 0.52
20 15 0.36
21 5 0.12
ACGTcount: A:0.21, C:0.12, G:0.32, T:0.35
Consensus pattern (19 bp):
TCGCGTTGCGAATTTGAAA
Found at i:126984 original size:21 final size:20
Alignment explanation
Indices: 126945--126984 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
126935 AAGTGTGAAG
*
126945 TCTAAAGTTAAGGGACTAGA
1 TCTAAAGTTAAGGCACTAGA
*
126965 TCTAAAGTTTAAGGCTCTAG
1 TCTAAAG-TTAAGGCACTAG
126985 TTATTAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (20 bp):
TCTAAAGTTAAGGCACTAGA
Found at i:134336 original size:2 final size:2
Alignment explanation
Indices: 134329--134353 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
134319 TAAATTTAGA
134329 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
134354 AGTATTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134922 original size:18 final size:18
Alignment explanation
Indices: 134899--134952 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
134889 CGAATATTAA
134899 ATTTACACTTTTAAGTAG
1 ATTTACACTTTTAAGTAG
134917 ATTTACA-TATTT-A--A-
1 ATTTACACT-TTTAAGTAG
*
134931 ATTTAAACTTTTAAGTAG
1 ATTTACACTTTTAAGTAG
134949 ATTT
1 ATTT
134953 TATATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
14 9 0.31
15 3 0.10
17 3 0.10
18 14 0.48
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (18 bp):
ATTTACACTTTTAAGTAG
Found at i:134961 original size:31 final size:32
Alignment explanation
Indices: 134895--134966 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
134885 TTTACGAATA
*
134895 TTAAATTTACACTTTTAAGTAGATTTACATAT
1 TTAAATTTAAACTTTTAAGTAGATTTACATAT
*
134927 TTAAATTTAAACTTTTAAGTAGATTT-TATAT
1 TTAAATTTAAACTTTTAAGTAGATTTACATAT
134958 TTAAATTTA
1 TTAAATTTA
134967 CGAATCAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 13 0.34
32 25 0.66
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (32 bp):
TTAAATTTAAACTTTTAAGTAGATTTACATAT
Found at i:143340 original size:15 final size:15
Alignment explanation
Indices: 143297--143341 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
143287 ATAAAATAAT
143297 AATGAAAATGAAATAA
1 AATGAAAATGAAA-AA
* *
143313 AATAAAAAGGAAAAA
1 AATGAAAATGAAAAA
*
143328 AATGTAAATGAAAA
1 AATGAAAATGAAAA
143342 TTCTAATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (15 bp):
AATGAAAATGAAAAA
Found at i:144522 original size:19 final size:19
Alignment explanation
Indices: 144493--144540 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
144483 AAAGAACAAA
144493 AAATAAAAA-ATAAAGATAAT
1 AAATAAAAATAT-AA-ATAAT
*
144513 AAATAAAAATATTAATAAT
1 AAATAAAAATATAAATAAT
144532 AAATAAAAA
1 AAATAAAAA
144541 GAAAAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 14 0.54
20 10 0.38
21 2 0.08
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (19 bp):
AAATAAAAATATAAATAAT
Found at i:146725 original size:29 final size:29
Alignment explanation
Indices: 146683--146741 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
146673 ATTTTCACCT
146683 AACTAAATTGATGTAAACAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
*
146712 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
146741 A
1 A
146742 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAACAATGACATCAA
Found at i:151400 original size:29 final size:29
Alignment explanation
Indices: 151358--151416 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
151348 ATTTTCACCT
151358 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
151387 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
151416 A
1 A
151417 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:158991 original size:14 final size:14
Alignment explanation
Indices: 158972--158999 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
158962 TTGACTTGTC
158972 ATCAATCTAATTAA
1 ATCAATCTAATTAA
158986 ATCAATCTAATTAA
1 ATCAATCTAATTAA
159000 GAGATATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
ATCAATCTAATTAA
Found at i:160160 original size:22 final size:22
Alignment explanation
Indices: 160129--160193 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
160119 GAGTCGAGGG
*
160129 ATATATAGTGGTCTTTCGGGAC
1 ATATACAGTGGTCTTTCGGGAC
*
160151 ATATACAGTGGTCCTTCGGGAC
1 ATATACAGTGGTCTTTCGGGAC
160173 ATATACAGTGGTCTTTCGGGA
1 ATATACAGTGGTCTTTCGGGA
160194 TAAATTTCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (22 bp):
ATATACAGTGGTCTTTCGGGAC
Found at i:166272 original size:3 final size:3
Alignment explanation
Indices: 166264--166321 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
166254 ATTATATCTA
* *
166264 TAT TAT TAT TAT TAT T-T TAAT T-T TAT TAA TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
166308 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
166322 ATTTACAACC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.08
3 42 0.88
4 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:167633 original size:51 final size:50
Alignment explanation
Indices: 167534--167633 Score: 114
Period size: 51 Copynumber: 2.0 Consensus size: 50
167524 TTTAATTTAG
* *
167534 TCACTGTTAGTTTCTGATTTAGCTACTGTTATTTTAATTTTTGCATTTTGC
1 TCACTGTTAGTTTCTGATTTAGCTAC-GTAATTTTAATTTTTGAATTTTGC
* *
167585 TCACTGTTTA-TTTCTGATTTAGTTAC-TAACTTTTATTTTCTTGAATTTT
1 TCACTG-TTAGTTTCTGATTTAGCTACGTAA-TTTTAATTT-TTGAATTTT
167634 AGTCATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
49 2 0.05
50 8 0.19
51 29 0.69
52 3 0.07
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (50 bp):
TCACTGTTAGTTTCTGATTTAGCTACGTAATTTTAATTTTTGAATTTTGC
Found at i:167769 original size:6 final size:6
Alignment explanation
Indices: 167758--167807 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
167748 GGTCATCATA
*
167758 TTTTAT TTTTA- TTTTAT GTTTT-T TTACTAT TTTTATT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT -TTTTAT TT-TTAT TTTTA-T TTTTAT TTTTAT
167807 T
1 T
167808 ATGTTTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 7 0.19
6 17 0.46
7 13 0.35
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:167803 original size:13 final size:13
Alignment explanation
Indices: 167758--167807 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
167748 GGTCATCATA
167758 TTTTATTTTTA--
1 TTTTATTTTTATT
167769 TTTTATGTTTT-TT
1 TTTTAT-TTTTATT
**
167782 TACTATTTTTATT
1 TTTTATTTTTATT
167795 TTTTATTTTTATT
1 TTTTATTTTTATT
167808 ATGTTTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 6 0.19
12 8 0.26
13 17 0.55
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:168857 original size:25 final size:24
Alignment explanation
Indices: 168812--168875 Score: 85
Period size: 23 Copynumber: 2.6 Consensus size: 24
168802 ATTATTTGAC
*
168812 TATAATTAAAATTAATTATTATAAAA
1 TATAATTAAAATTAA-TAAT-TAAAA
168838 TATAATT-AAATTAATAATTAAAA
1 TATAATTAAAATTAATAATTAAAA
*
168861 TATATTTAAAATTAA
1 TATAATTAAAATTAA
168876 GTTTATTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 11 0.31
24 10 0.29
25 7 0.20
26 7 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TATAATTAAAATTAATAATTAAAA
Found at i:168871 original size:11 final size:11
Alignment explanation
Indices: 168833--168872 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
168823 TTAATTATTA
168833 TAAAATATAAT
1 TAAAATATAAT
*
168844 TAAATTAATAAT
1 TAAAAT-ATAAT
*
168856 TAAAATATATT
1 TAAAATATAAT
168867 TAAAAT
1 TAAAAT
168873 TAAGTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAAATATAAT
Found at i:169600 original size:77 final size:77
Alignment explanation
Indices: 169416--169870 Score: 402
Period size: 77 Copynumber: 5.9 Consensus size: 77
169406 TCCGGTGGTG
* * *
169416 CCAAAAATGTCATGATTCACTAAGAAATAGATTGC--GATATGAAATGTTAATATTTTTTTATTA
1 CCAAGAATGTCATGATTCACTAAGAAATA-AGT-CATGATATGGAATGTTAATA--TTTTTATTA
169479 ATAAAATGGGTTGTGC
62 ATAAAATGGGTTGTGC
* * * *
169495 CCAAAGAATGTCATGGTTCACTAAGAAATAAGTCATGATCTGGAATGCTAATATTTTTATTGATA
1 CC-AAGAATGTCATGATTCACTAAGAAATAAGTCATGATATGGAATGTTAATATTTTTATTAATA
*
169560 AAATGGGTTGTGT
65 AAATGGGTTGTGC
* ** ** *
169573 CCAAGAATATCATGATTCACTAAGAAAT-AGATTGTGATCCGCAATGTTAATATTTTTATTAATA
1 CCAAGAATGTCATGATTCACTAAGAAATAAG-TCATGATATGGAATGTTAATATTTTTATTAATA
169637 AAATGGGTTGTGC
65 AAATGGGTTGTGC
** * * *
169650 AAAAGAATGTTATGATTCACTAAGAAATATATTGCA--ATATAGAATGTTAATA-TTTTATTAAT
1 CCAAGAATGTCATGATTCACTAAGAAATA-AGT-CATGATATGGAATGTTAATATTTTTATTAAT
** * ***
169712 AAAATATGCTACAC
64 AAAATGGGTTGTGC
* * * * * *
169726 CCAAATAATGTCATGGTTTACTAAGAAATAAATTATGATACGGAATGTTAATATTTTTATTAATA
1 CC-AAGAATGTCATGATTCACTAAGAAATAAGTCATGATATGGAATGTTAATATTTTTATTAATA
* *
169791 AAATAGGTTGGGC
65 AAATGGGTTGTGC
* * * ** * * *
169804 GCAAGAATGTTATGGTTCACTAAGAAACTAAGTTGTGATATGAAATGCTAATAATTTTATT-ATA
1 CCAAGAATGTCATGATTCACTAAGAAA-TAAGTCATGATATGGAATGTTAATATTTTTATTAATA
169868 AAA
65 AAA
169871 AATTTGAAAG
Statistics
Matches: 305, Mismatches: 59, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
75 1 0.00
76 22 0.07
77 164 0.54
78 74 0.24
79 5 0.02
80 39 0.13
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (77 bp):
CCAAGAATGTCATGATTCACTAAGAAATAAGTCATGATATGGAATGTTAATATTTTTATTAATAA
AATGGGTTGTGC
Found at i:169740 original size:154 final size:153
Alignment explanation
Indices: 169416--169870 Score: 495
Period size: 154 Copynumber: 2.9 Consensus size: 153
169406 TCCGGTGGTG
* *
169416 CCAAAAATGTCATGATTCACTAAGAAATAGATTGCGATATGAAATGTTAATATTTTTTTATTAAT
1 CCAAAAATGTCATGATTCACTAAGAAATAGATTGTGATACGAAATGTTAATA--TTTTTATTAAT
* * * *
169481 AAAATGGGTTGTGCCCAAAGAATGTCATGGTTCACTAAGAAATAAGTCATGATCTGGAATGCTAA
64 AAAATGGGTTGTG-CAAAAGAATGTTATGGTTCACTAAGAAATAAGTCA-GATATAGAATGCTAA
* * * ****
169546 TATTTTTATTGATAAAATGGGTTGTGT
127 TATTTTTATTAATAAAATAGGCTACAC
* * * *
169573 CCAAGAATATCATGATTCACTAAGAAATAGATTGTGATCCGCAATGTTAATATTTTTATTAATAA
1 CCAAAAATGTCATGATTCACTAAGAAATAGATTGTGATACGAAATGTTAATATTTTTATTAATAA
* * *
169638 AATGGGTTGTGCAAAAGAATGTTATGATTCACTAAGAAATATATTGCA-ATATAGAATGTTAATA
66 AATGGGTTGTGCAAAAGAATGTTATGGTTCACTAAGAAATA-AGT-CAGATATAGAATGCTAATA
*
169702 -TTTTATTAATAAAATATGCTACAC
129 TTTTTATTAATAAAATAGGCTACAC
* * * * *
169726 CCAAATAATGTCATGGTTTACTAAGAAATAAATTATGATACGGAATGTTAATATTTTTATTAATA
1 CCAAA-AATGTCATGATTCACTAAGAAATAGATTGTGATACGAAATGTTAATATTTTTATTAATA
* * ** **
169791 AAATAGGTTGGGCGCAAGAATGTTATGGTTCACTAAGAAACTAAGTTGTGATAT-GAAATGCTAA
65 AAATGGGTTGTGCAAAAGAATGTTATGGTTCACTAAGAAA-TAAG-TCAGATATAG-AATGCTAA
*
169855 TAATTTTATT-ATAAAA
127 TATTTTTATTAATAAAA
169871 AATTTGAAAG
Statistics
Matches: 252, Mismatches: 38, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
153 20 0.08
154 129 0.51
155 48 0.19
156 9 0.04
157 46 0.18
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (153 bp):
CCAAAAATGTCATGATTCACTAAGAAATAGATTGTGATACGAAATGTTAATATTTTTATTAATAA
AATGGGTTGTGCAAAAGAATGTTATGGTTCACTAAGAAATAAGTCAGATATAGAATGCTAATATT
TTTATTAATAAAATAGGCTACAC
Found at i:171789 original size:32 final size:32
Alignment explanation
Indices: 171680--171789 Score: 123
Period size: 32 Copynumber: 3.4 Consensus size: 32
171670 ATTAGTCTTA
* ** * *
171680 CATTTAGATAATACACAACAGA-GTCAGTGTTG
1 CATTTAGATAATGCACATGA-ATGTCAGTATCG
* * *
171712 CATTTAGATAATGAACATGAATGTCAATATCT
1 CATTTAGATAATGCACATGAATGTCAGTATCG
171744 CATTTAGATAATGCACATGAATGTCAGTATCG
1 CATTTAGATAATGCACATGAATGTCAGTATCG
*
171776 CATTTTGATAATGC
1 CATTTAGATAATGC
171790 GTATCAGATA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 1 0.02
32 64 0.98
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (32 bp):
CATTTAGATAATGCACATGAATGTCAGTATCG
Found at i:176804 original size:37 final size:37
Alignment explanation
Indices: 176763--176864 Score: 177
Period size: 37 Copynumber: 2.8 Consensus size: 37
176753 AACATAACGT
*
176763 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
176800 TAGAGTTTTATTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
176837 TAAAGTTTTACTATGATTCAAACTCCTA
1 TAGAGTTTTACTATGATTCAAACTCCTA
176865 TTGTAACTCA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:177190 original size:3 final size:3
Alignment explanation
Indices: 177179--177227 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
177169 TCAATTTTTT
*
177179 TTA TATA TTA TT- TTC TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
177224 TTA T
1 TTA T
177228 ATTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:178135 original size:80 final size:80
Alignment explanation
Indices: 177762--178400 Score: 719
Period size: 80 Copynumber: 7.8 Consensus size: 80
177752 TGACAAATAT
* * * * * *
177762 CCCTTCTTGCCTTGAGCTATGTTGTAAATTTGATTTGCCTCTGAGCTGAATGTAATCGAACTCGA
1 CCCTTCTTGCCTTGAGTTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
* *
177827 AGGTCTTTGATGATAGACAA
64 AGGTCTTTG--G-CAGATAA
* * * * * * * * *
177847 CCTTTCTCGTCTTGAGTTATGTTGTAAATGATGCGCCTTGGAGCTGAGTGTAATCAAACTCTAAG
1 CCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
177912 GTCTTGTGTTGGCAGATAA
66 GTC---T-TTGGCAGATAA
* * * * *
177931 CCCTTATAGCCTTGACTTATGCTGCAAATGATGTGCCTTAGAGCTGAGAT-TAATTGAACTCGAA
1 CCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAG-TGTAATCGAACTCGAA
*
177995 GGTCTTGTGTTGGAAGATAA
65 GGTC---T-TTGGCAGATAA
*
178015 CCCTTCTAGCCTTGAGTTATG-TAGCAAATGATGTGCCTTTGAGCTGAGTGTAAAT-GAACTCGA
1 CCCTTCTTGCCTTGAGTTATGCT-GCAAATGATGTGCCTTTGAGCTGAGTGT-AATCGAACTCGA
* *
178078 AGGACTTTGGCAGATAG
64 AGGTCTTTGGCAGATAA
* * *
178095 CCTTTATTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAACTGAGTGTAATCGAACTC-AAG
1 CCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* **
178159 GTATTTTACAGATAA
66 GTCTTTGGCAGATAA
* * *
178174 CCCTTCTTTCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAG
1 CCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* *
178239 GTCTTTGGCGGATAG
66 GTCTTTGGCAGATAA
* *
178254 TCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
178319 GTCTTTGGCAGATAG
66 GTCTTTGGCAGATAA
* * *
178334 CCCTTCTTTCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
178399 GT
66 GT
178401 ATTTTGTTGG
Statistics
Matches: 483, Mismatches: 60, Indels: 27
0.85 0.11 0.05
Matches are distributed among these distances:
79 71 0.15
80 212 0.44
81 2 0.00
83 35 0.07
84 130 0.27
85 29 0.06
86 1 0.00
87 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (80 bp):
CCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
GTCTTTGGCAGATAA
Found at i:178216 original size:159 final size:160
Alignment explanation
Indices: 177763--178400 Score: 727
Period size: 159 Copynumber: 3.9 Consensus size: 160
177753 GACAAATATC
* * * * * *
177763 CCTTCTTGCCTTGAGCTATGTTGTAAATTTGATTTGCCTCTGAGCTGAATGTAATCGAACTCGAA
1 CCTTATTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
* * * * * * * *
177828 GGTCTTTGATGATAGACAACCTTTCTCGT-CTTGAGTTATGTTGTAAATGATGCGCCTTGGAGCT
64 GGTCTTT--TGACAGATAACCCTTCT-TTCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCT
* *
177892 GAGTGTAATCAAACTCTAAGGTCTTGTGTTGGCAGATAAC
126 GAGTGTAATCAAACTCGAAGGTC---T-TTGGCAGAT-AG
* * *
177932 CCTTATAGCCTTGA-CTTATGCTGCAAATGATGTGCCTTAGAGCTGAGAT-TAATTGAACTCGAA
1 CCTTATTGCCTTGAGC-TATGCTGCAAATGATGTGCCTTTGAGCTGAG-TGTAATCGAACTCGAA
**
177995 GGTCTTGTGTTGGA-AGATAACCCTTCTAGCCTTGAGTTATG-TAGCAAATGATGTGCCTTTGAG
64 GGTC-T-T-TT-GACAGATAACCCTTCTTTCCTTGAGTTATGCT-GCAAATGATGTGCCTTTGAG
* *
178058 CTGAGTGTAAAT-GAACTCGAAGGACTTTGGCAGATAG
124 CTGAGTGT-AATCAAACTCGAAGGTCTTTGGCAGATAG
* *
178095 CCTTTATTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAACTGAGTGTAATCGAACTC-AAG
1 CC-TTATTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* *
178159 GTATTTT-ACAGATAACCCTTCTTTCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGT
65 GTCTTTTGACAGATAACCCTTCTTTCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
178223 GTAATCAAACTCGAAGGTCTTTGGCGGATAG
130 GTAATCAAACTCGAAGGTCTTTGGCAGATAG
*
178254 TCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 -CCTTATTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* * * *
178319 GTC-TTTGGCAGATAGCCCTTCTTTCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGT
65 GTCTTTTGACAGATAACCCTTCTTTCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
178383 GTAATCGAACTCGAAGGT
130 GTAATCAAACTCGAAGGT
178401 ATTTTGTTGG
Statistics
Matches: 410, Mismatches: 41, Indels: 45
0.83 0.08 0.09
Matches are distributed among these distances:
158 4 0.01
159 132 0.32
160 80 0.20
161 1 0.00
162 1 0.00
163 9 0.02
164 59 0.14
165 1 0.00
167 34 0.08
168 61 0.15
169 27 0.07
170 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (160 bp):
CCTTATTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
TCTTTTGACAGATAACCCTTCTTTCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
TAATCAAACTCGAAGGTCTTTGGCAGATAG
Found at i:178327 original size:239 final size:242
Alignment explanation
Indices: 177762--178406 Score: 773
Period size: 239 Copynumber: 2.6 Consensus size: 242
177752 TGACAAATAT
* * * *
177762 CCCTTCTTGCCTTGAGCTATGTTGTAAATTTGATTTGCCTCTGAGCTGAATGTAATCGAACTCGA
1 CCCTTCTTGCCTTGAGCTATG-TGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
* * * * * * * * *
177827 AGGTCTTTGATGATAGACAACCTTTCTCGTCTTGAGTTATGTTGTAAATGATGCGCCTTGGAGCT
63 AGGTCTTTG--G-CAGATAGCCTTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCT
* * * * *
177892 GAGTGTAATCAAACTCTAAGGTCTTGTGTTGGCAGATAACCCTTATAGCCTTGACTTATGCTGCA
125 GAGTGTAATCGAACTCGAAGGT-AT-T-TTGACAGATAACCCTTATAGCCTTGACATATGCTGCA
**
177957 AATGATGTGCCTTAGAGCTGAGATTAATTGAACTCGAAGGTCTTGTGTTGGAAGATAA
187 AATGATGTGCCTTAGAGCTGAGATTAATCAAACTCGAAGGTCTTGTG-TGG-AGATAA
* *
178015 CCCTTCTAGCCTTGAGTTATGTAGCAAATGATGTGCCTTTGAGCTGAGTGTAAAT-GAACTCGAA
1 CCCTTCTTGCCTTGAGCTATGT-GCAAATGATGTGCCTTTGAGCTGAGTGT-AATCGAACTCGAA
* * *
178079 GGACTTTGGCAGATAGCCTTTATTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAACTGAGT
64 GGTCTTTGGCAGATAGCCTTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* ** *
178144 GTAATCGAACTC-AAGGTATTTT-ACAGATAACCCTTCTTTCCTTGAGATATGCTGCAAATGATG
129 GTAATCGAACTCGAAGGTATTTTGACAGATAACCCTTATAGCCTTGACATATGCTGCAAATGATG
* *
178207 TGCCTTTGAGCTGAG-TGTAATCAAACTCGAAGGTCTT-TG-GCG-GATAG
194 TGCCTTAGAGCTGAGAT-TAATCAAACTCGAAGGTCTTGTGTG-GAGATAA
*
178254 TCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATG-TGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* * * *
178319 GTCTTTGGCAGATAGCCCTTCTTTCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTG
65 GTCTTTGGCAGATAGCCTTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
178384 TAATCGAACTCGAAGGTATTTTG
130 TAATCGAACTCGAAGGTATTTTG
178407 TTGGTAGATA
Statistics
Matches: 344, Mismatches: 40, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
238 3 0.01
239 129 0.38
240 12 0.03
241 1 0.00
242 3 0.01
243 67 0.19
244 2 0.01
245 1 0.00
246 1 0.00
247 5 0.01
248 56 0.16
249 1 0.00
251 36 0.10
252 4 0.01
253 23 0.07
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (242 bp):
CCCTTCTTGCCTTGAGCTATGTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
TCTTTGGCAGATAGCCTTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
AATCGAACTCGAAGGTATTTTGACAGATAACCCTTATAGCCTTGACATATGCTGCAAATGATGTG
CCTTAGAGCTGAGATTAATCAAACTCGAAGGTCTTGTGTGGAGATAA
Found at i:183470 original size:10 final size:9
Alignment explanation
Indices: 183449--183576 Score: 51
Period size: 9 Copynumber: 14.2 Consensus size: 9
183439 ATATAATAAT
183449 AATAAAATA
1 AATAAAATA
183458 AATAAAGATA
1 AATAAA-ATA
183468 AATAAAATTTA
1 AATAAAA--TA
183479 GCAATAAAAT-
1 --AATAAAATA
183489 AATAATAAT-
1 AATAA-AATA
183498 AATAAAGAT-
1 AATAAA-ATA
183507 AA-AAAA-A
1 AATAAAATA
183514 AATAAAA-A
1 AATAAAATA
*
183522 ACA-AAAACA
1 A-ATAAAATA
183531 AA-AAAA-A
1 AATAAAATA
** *
183538 AACGAAATG
1 AATAAAATA
*
183547 AACAAAATA
1 AATAAAATA
183556 AATAATAAT-
1 AATAA-AATA
183565 AATAATAATA
1 AATAA-AATA
183575 AA
1 AA
183577 AGGTTAAATT
Statistics
Matches: 99, Mismatches: 5, Indels: 29
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.06
8 27 0.27
9 42 0.42
10 14 0.14
11 3 0.03
13 7 0.07
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (9 bp):
AATAAAATA
Found at i:183537 original size:17 final size:17
Alignment explanation
Indices: 183507--183540 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
183497 TAATAAAGAT
183507 AAAAAAAAATAAAAAAC
1 AAAAAAAAATAAAAAAC
183524 AAAAACAAAA-AAAAAAC
1 AAAAA-AAAATAAAAAAC
183541 GAAATGAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (17 bp):
AAAAAAAAATAAAAAAC
Found at i:183789 original size:5 final size:5
Alignment explanation
Indices: 183779--183803 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
183769 ATAAATCGCC
183779 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
183804 ATGTAGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:190198 original size:2 final size:2
Alignment explanation
Indices: 190191--190215 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
190181 TGCGAATTTG
190191 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
190216 CACACACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:190536 original size:23 final size:25
Alignment explanation
Indices: 190490--190568 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 25
190480 GTTCTACGCA
*
190490 GTCCTTCGGGACAAA--A-TGATGTG
1 GTCCTTCGGGACAAATTACT-ACGTG
*
190513 GTCCTTCTGGAC-AATTA-TACGTG
1 GTCCTTCGGGACAAATTACTACGTG
* **
190536 GTCGTTCGGGACAAATTACTATATG
1 GTCCTTCGGGACAAATTACTACGTG
190561 GTCCTTCG
1 GTCCTTCG
190569 AGAAAAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 2 0.04
23 25 0.56
24 7 0.16
25 11 0.24
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (25 bp):
GTCCTTCGGGACAAATTACTACGTG
Found at i:190716 original size:19 final size:20
Alignment explanation
Indices: 190684--190722 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
190674 ATGGGCTAAA
*
190684 TAAACTAATGGATAT-GAAT
1 TAAACAAATGGATATAGAAT
*
190703 TAAACAAATTGATATAGAAT
1 TAAACAAATGGATATAGAAT
190723 GAAAAGTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (20 bp):
TAAACAAATGGATATAGAAT
Found at i:192636 original size:186 final size:186
Alignment explanation
Indices: 192322--192695 Score: 732
Period size: 186 Copynumber: 2.0 Consensus size: 186
192312 GAAATAAAAG
192322 AAAAATTAAATTGAAATATGTATGTAGATAAAAAAATTTAATTGATAATAGATCAGGAATTAGAA
1 AAAAATTAAATTGAAATATGTATGTAGATAAAAAAATTTAATTGATAATAGATCAGGAATTAGAA
192387 TACCAAGTTCTTTTCAAAGAAAATTTGGTAAATGGGATTGAAAGATTTGTCAGAAATTTTACTAG
66 TACCAAGTTCTTTTCAAAGAAAATTTGGTAAATGGGATTGAAAGATTTGTCAGAAATTTTACTAG
192452 TTGAATGAGAAAAGTAAACTTATAGGTAGATACATATTTGAA-TTATTTTATGGATC
131 TTGAATGAGAAAAGTAAA-TTATAGGTAGATACATATTTGAATTTATTTTATGGATC
192508 AAAAATTAAATTGAAATATGTATGTAGATAAAAAAATTTAATTGATAATAGATCAGGAATTAGAA
1 AAAAATTAAATTGAAATATGTATGTAGATAAAAAAATTTAATTGATAATAGATCAGGAATTAGAA
192573 TACCAAGTTCTTTTCAAAGAAAATTTGGTAAATGGGATTGAAAGATTTGTCAGAAATTTTACTAG
66 TACCAAGTTCTTTTCAAAGAAAATTTGGTAAATGGGATTGAAAGATTTGTCAGAAATTTTACTAG
192638 TTGAATGAGAAAAGTAAATTATAGGTAGATACATATTTGAATTTATTTTATGGATC
131 TTGAATGAGAAAAGTAAATTATAGGTAGATACATATTTGAATTTATTTTATGGATC
192694 AA
1 AA
192696 GTGGGGAAAC
Statistics
Matches: 187, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
185 23 0.12
186 164 0.88
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (186 bp):
AAAAATTAAATTGAAATATGTATGTAGATAAAAAAATTTAATTGATAATAGATCAGGAATTAGAA
TACCAAGTTCTTTTCAAAGAAAATTTGGTAAATGGGATTGAAAGATTTGTCAGAAATTTTACTAG
TTGAATGAGAAAAGTAAATTATAGGTAGATACATATTTGAATTTATTTTATGGATC
Found at i:197003 original size:23 final size:23
Alignment explanation
Indices: 196977--197072 Score: 111
Period size: 23 Copynumber: 4.1 Consensus size: 23
196967 GGTTCTACGC
196977 GGTCCTTCAGGACAATTCTATGT
1 GGTCCTTCAGGACAATTCTATGT
* *
197000 GGTCATTCAGGACAATTCTACGT
1 GGTCCTTCAGGACAATTCTATGT
* * *
197023 GGTCCTTCGGGATAAATTTCTATGC
1 GGTCCTTCAGGA-CAA-TTCTATGT
* *
197048 GGTCCTTCGGGACAAATCTATGT
1 GGTCCTTCAGGACAATTCTATGT
197071 GG
1 GG
197073 CACTTCGGTG
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
23 39 0.64
24 4 0.07
25 18 0.30
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
GGTCCTTCAGGACAATTCTATGT
Found at i:197088 original size:48 final size:48
Alignment explanation
Indices: 196970--197088 Score: 120
Period size: 48 Copynumber: 2.5 Consensus size: 48
196960 AGTCGAGGGT
* * * *
196970 TCTACGCGGTCCTTCAGGAC-AA-TTCTATGTGGTCATTCAGGACAAT
1 TCTACGTGGTCCTTCGGGACAAATTTCTATGCGGTCATTCAGGACAAA
* * *
197016 TCTACGTGGTCCTTCGGGATAAATTTCTATGCGGTCCTTCGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAATTTCTATGCGGTCATTCAGGACAAA
*
197064 TCTATGTGG-CACTTCGGTG-CAAATT
1 TCTACGTGGTC-CTTCGG-GACAAATT
197089 ATATGAGCAG
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
46 17 0.28
47 3 0.05
48 39 0.65
49 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.32
Consensus pattern (48 bp):
TCTACGTGGTCCTTCGGGACAAATTTCTATGCGGTCATTCAGGACAAA
Found at i:204925 original size:31 final size:33
Alignment explanation
Indices: 204836--204932 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
204826 TTGGCAAGTT
*
204836 GAAAATTTCATCTTGGTTGGTAGCCAACTTATTG
1 GAAAA-TTCATCTTGGTTGGTGGCCAACTTATTG
*
204870 GAAAATTCATCTTAGTTGGTGGCCAACTTATTG
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTG
*
204903 GAAAATTC-T-TTGGTAGGTGGCCAACTTATT
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATT
204933 TTCATCATTG
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
31 19 0.32
32 1 0.02
33 34 0.58
34 5 0.08
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (33 bp):
GAAAATTCATCTTGGTTGGTGGCCAACTTATTG
Found at i:208530 original size:21 final size:21
Alignment explanation
Indices: 208513--208594 Score: 94
Period size: 23 Copynumber: 3.7 Consensus size: 21
208503 ATAAATTGCA
208513 CCGAAGTG-CCACATAATTGTC
1 CCGAAG-GACCACATAATTGTC
* *
208534 CCGAAGGACCACATAGGTTTGTT
1 CCGAAGGACCACATA--ATTGTC
208557 CCGAAGGACCACATAATTTTGTC
1 CCGAAGGACCACATAA--TTGTC
208580 CCGAAGGACCACATA
1 CCGAAGGACCACATA
208595 GAACCCTCGA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
20 1 0.02
21 13 0.25
23 38 0.73
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (21 bp):
CCGAAGGACCACATAATTGTC
Found at i:208560 original size:23 final size:23
Alignment explanation
Indices: 208529--208595 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
208519 TGCCACATAA
208529 TTGTCCCGAAGGACCACATAGGT
1 TTGTCCCGAAGGACCACATAGGT
* **
208552 TTGTTCCGAAGGACCACATAATT
1 TTGTCCCGAAGGACCACATAGGT
208575 TTGTCCCGAAGGACCACATAG
1 TTGTCCCGAAGGACCACATAG
208596 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.24
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAGGT
Found at i:216551 original size:4 final size:4
Alignment explanation
Indices: 216542--216811 Score: 79
Period size: 4 Copynumber: 67.5 Consensus size: 4
216532 AAAAGGTAAG
* *
216542 AAAT AAAT AAAT AAAATT AAAAT GAAG AAA- AAAT AAATT AAAT AAA-
1 AAAT AAAT AAAT -AAA-T -AAAT AAAT AAAT AAAT AAA-T AAAT AAAT
* * * * * *
216588 AGAT AAGAT AAAG AAAGT AAAG ATA- AAAT -AGT AAGT AAAAT AAAT AAAT
1 AAAT AA-AT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT
* * *
216637 AAAT -ATT AAA- AAAT -ATT AAA- AAAT AAGA- AAA- AGAAG AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT A-AAT AAAT AAAT
* *
216680 AAAT AAAT AAAAC AAAT AAAT AAA- ATAAT -AAT AAA- AAAGT AAAA ATAAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAA-T AAAT A-AAT
* * * * *
216729 ATAT ATAT ATAT ATAAT AAAT AAAT AAAT ACAT AAA- AAAT -AGT AAAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
216776 ATAT ATAT AAATT AAAA AACAT ATAAT AAA- AAAT AA
1 AAAT AAAT AAA-T AAAT AA-AT A-AAT AAAT AAAT AA
216812 CATATATATA
Statistics
Matches: 204, Mismatches: 30, Indels: 64
0.68 0.10 0.21
Matches are distributed among these distances:
3 39 0.19
4 118 0.58
5 41 0.20
6 6 0.03
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:216564 original size:15 final size:15
Alignment explanation
Indices: 216542--216752 Score: 59
Period size: 15 Copynumber: 14.1 Consensus size: 15
216532 AAAAGGTAAG
216542 AAAT-AAATAAATAA
1 AAATAAAATAAATAA
*
216556 AATTAAAATGAAGA-AA
1 AAATAAAAT-AA-ATAA
*
216572 AAATAAATTAAATAA
1 AAATAAAATAAATAA
* *
216587 AAGATAAGATAAA-GA
1 AA-ATAAAATAAATAA
* *
216602 AAGTAAAGATAAAATAGT
1 AAATAAA-AT-AAATA-A
*
216620 AAGTAAAATAAAT--
1 AAATAAAATAAATAA
216633 AAATAAATATTAAA-AA
1 AAATAAA-A-TAAATAA
* *
216649 ATATTAAA-AAATAA
1 AAATAAAATAAATAA
* *
216663 GAAA-AAGA-AGA-AA
1 -AAATAAAATAAATAA
216676 AAAT-AAATAAATAA
1 AAATAAAATAAATAA
*
216690 AACAAATAAATAAAATAA
1 AA-ATA-AAAT-AAATAA
* *
216708 TAATAAAA-AAGTAA
1 AAATAAAATAAATAA
* * *
216722 AAATAATATATATAT
1 AAATAAAATAAATAA
* *
216737 ATATATAATAAATAA
1 AAATAAAATAAATAA
216752 A
1 A
216753 TAAATACATA
Statistics
Matches: 141, Mismatches: 33, Indels: 45
0.64 0.15 0.21
Matches are distributed among these distances:
12 5 0.04
13 13 0.09
14 29 0.21
15 37 0.26
16 34 0.24
17 9 0.06
18 14 0.10
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.22
Consensus pattern (15 bp):
AAATAAAATAAATAA
Found at i:216577 original size:26 final size:26
Alignment explanation
Indices: 216539--216691 Score: 85
Period size: 25 Copynumber: 5.9 Consensus size: 26
216529 ATAAAAAGGT
216539 AAGAAATAAATAAATAAAATTAAAATG
1 AAGAAATAAATAAATAAAA-TAAAATG
*
216566 AAGAAA-AAATAAATTAAATAAAA-G
1 AAGAAATAAATAAATAAAATAAAATG
* *
216590 ATA-AGATAAAGAAAGTAAAGATAAAATAG
1 A-AGAAATAAATAAA-TAAA-ATAAAAT-G
216619 TAAGTAAAATAAATAAATAAATATTAAAA--
1 -AAG--AAATAAATAAATAAA-A-TAAAATG
* * *
216648 AA-TATTAAA-AAATAAGA-AAAA-G
1 AAGAAATAAATAAATAAAATAAAATG
216670 AAGAAA-AAATAAAT-AAATAAAA
1 AAGAAATAAATAAATAAAATAAAA
216692 CAAATAAATA
Statistics
Matches: 98, Mismatches: 13, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
21 4 0.04
22 7 0.07
23 10 0.10
24 10 0.10
25 17 0.17
26 14 0.14
27 12 0.12
28 2 0.02
29 2 0.02
30 1 0.01
31 5 0.05
32 14 0.14
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (26 bp):
AAGAAATAAATAAATAAAATAAAATG
Found at i:216652 original size:10 final size:10
Alignment explanation
Indices: 216632--216661 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
216622 GTAAAATAAA
216632 TAAATAAATAT
1 TAAA-AAATAT
216643 TAAAAAATAT
1 TAAAAAATAT
216653 TAAAAAATA
1 TAAAAAATA
216662 AGAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:216696 original size:13 final size:13
Alignment explanation
Indices: 216675--216704 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
216665 AAAAGAAGAA
*
216675 AAAATAAATAAAT
1 AAAACAAATAAAT
216688 AAAACAAATAAAT
1 AAAACAAATAAAT
216701 AAAA
1 AAAA
216705 TAATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAACAAATAAAT
Found at i:216778 original size:41 final size:40
Alignment explanation
Indices: 216733--216825 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 40
216723 AATAATATAT
* **
216733 ATATATATATAA-TAAATAAATAAATACATAAAAAATAGTAA
1 ATATATATATAATTAAA-AAACAAATA-ATAAAAAATAACAA
* *
216774 ATATATATATAAATTAAAAAACATATAATAAAAAATAACAT
1 ATATATATAT-AATTAAAAAACAAATAATAAAAAATAACAA
216815 ATATATATATA
1 ATATATATATA
216826 TGTAATCTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
40 1 0.02
41 31 0.69
42 9 0.20
43 4 0.09
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (40 bp):
ATATATATATAATTAAAAAACAAATAATAAAAAATAACAA
Found at i:216897 original size:22 final size:24
Alignment explanation
Indices: 216859--216903 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
216849 ATATATTAAA
216859 GTAAAAAAGAAAATACAT-AAAAT
1 GTAAAAAAGAAAATACATGAAAAT
*
216882 GTAAAAAA-AAATTACATGAAAA
1 GTAAAAAAGAAAATACATGAAAA
216904 AAAGAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (24 bp):
GTAAAAAAGAAAATACATGAAAAT
Found at i:217434 original size:37 final size:37
Alignment explanation
Indices: 217384--217495 Score: 197
Period size: 37 Copynumber: 3.0 Consensus size: 37
217374 ATGCTTCTAG
* *
217384 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
217421 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
*
217458 ATCATATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
217495 A
1 A
217496 ACGCTATGTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:218149 original size:83 final size:84
Alignment explanation
Indices: 217992--218236 Score: 309
Period size: 83 Copynumber: 2.9 Consensus size: 84
217982 TTTGTTGGCA
* * * * * *
217992 GATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTGCCTCT-GAGTTGAATGTAATCGA
1 GATAACCCTTCTTGCCTTGAGTTATGCTGCAAA--TGATGTGCCT-TGGAGCTGAGTGTAATCGA
218056 ACTCGAAGGTCTTTGATGAC-T
63 ACTCGAAGGTCTTTGATGACAT
* * *
218077 GATAACCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
1 GATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACT
*
218142 CGAAGGTCTTTGTTGACAT
66 CGAAGGTCTTTGATGACAT
* * *
218161 -ATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAAC
1 GATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAATCGAAC
218225 TCGAAGG-CTTTG
65 TCGAAGGTCTTTG
218237 TGTTTCAAGA
Statistics
Matches: 141, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
82 1 0.01
83 82 0.58
84 29 0.21
85 29 0.21
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (84 bp):
GATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACT
CGAAGGTCTTTGATGACAT
Found at i:218294 original size:28 final size:28
Alignment explanation
Indices: 218239--218297 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
218229 AGGCTTTGTG
* *
218239 TTTCAAGAGAAACATTTTCAAAGTTTTT
1 TTTCAAGAGAAACAATTTCAAAGGTTTT
* *
218267 TTTCAAGAGAAACAATTTCGAGGGTTTT
1 TTTCAAGAGAAACAATTTCAAAGGTTTT
218295 TTT
1 TTT
218298 TGTGTTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (28 bp):
TTTCAAGAGAAACAATTTCAAAGGTTTT
Found at i:218394 original size:37 final size:36
Alignment explanation
Indices: 218301--218416 Score: 135
Period size: 36 Copynumber: 3.2 Consensus size: 36
218291 TTTTTTTTGT
* * * *
218301 GTTTCAAGAGAAACTGTCTCAATAGGGACAAAATTT
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTA
*
218337 GTTTCAAAAGAAACTATCTCAAGAGAGACAAAACTTA
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTA
* * *
218374 G-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATTT
1 GTTTC-AAAAGAAACTGTCTCAAGAGAGACAAAATTA
218410 GTTTCAA
1 GTTTCAA
218417 GGAAAAGATA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
36 37 0.54
37 31 0.46
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (36 bp):
GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTA
Found at i:219706 original size:32 final size:32
Alignment explanation
Indices: 219670--219750 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
219660 CTCAATATTC
*
219670 GATGTTGAATCTCAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATCT
* *
219702 GATGTTAAATCTAAAAAAATGCCCCAACATCT
1 GATGTTGAATCTCAAAAAATGCCCCAACATCT
219734 GATGTTGAATCTTCAAA
1 GATGTTGAATC-TCAAA
219751 GATGCCCTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 39 0.91
33 4 0.09
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAACATCT
Found at i:220925 original size:27 final size:25
Alignment explanation
Indices: 220884--220935 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
220874 TTTTTCTTCA
220884 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
220909 ATTTTCTCTTTGCTTTTTTCTCTTTTT
1 ATTTTC-CTTTG-TTTTTTCTCTTTTT
220936 TTCTGATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Done.