Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005912.1 Hibiscus syriacus cultivar Beakdansim tig00013883_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: 72670
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7912 original size:20 final size:20
Alignment explanation
Indices: 7887--7924 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
7877 ACTTGCATAG
7887 GGGTATCGGTACCCTATGAT
1 GGGTATCGGTACCCTATGAT
7907 GGGTATCGGTACCCTATG
1 GGGTATCGGTACCCTATG
7925 GGTAATCGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (20 bp):
GGGTATCGGTACCCTATGAT
Found at i:7938 original size:74 final size:76
Alignment explanation
Indices: 7838--8012 Score: 218
Period size: 74 Copynumber: 2.3 Consensus size: 76
7828 CCAGGGGATC
* * *
7838 TCGGTACCC-ATAGGGCATTCT-ATTTTTCTCGGAG-TTAAAACTTG-CATAGGGGTATCGGT-A
1 TCGGTACCCTAT-GGGCAATCTGGTTTTTCTCGGAGCCT-AAA-TTGACATAGGGGTATCGGTAA
*
7898 CCCTATGATGGGTA
63 CCCTATGAGGGGTA
*
7912 TCGGTACCCTATGGGTAATC-GGTTTTTCTCGGAGCCTAAATTGACATAGGGGTATCGGTACACC
1 TCGGTACCCTATGGGCAATCTGGTTTTTCTCGGAGCCTAAATTGACATAGGGGTATCGGTA-ACC
7976 CTATGAGGGGTA
65 CTATGAGGGGTA
*
7988 TCGGTACCCTCTGGGCAATCTGGTT
1 TCGGTACCCTATGGGCAATCTGGTT
8013 GTCTCGAAGC
Statistics
Matches: 87, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
73 3 0.03
74 45 0.52
75 3 0.03
76 32 0.37
77 4 0.05
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (76 bp):
TCGGTACCCTATGGGCAATCTGGTTTTTCTCGGAGCCTAAATTGACATAGGGGTATCGGTAACCC
TATGAGGGGTA
Found at i:8018 original size:76 final size:74
Alignment explanation
Indices: 7882--8023 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 74
7872 TTAAAACTTG
* * * *
7882 CATAGGGGTATCGGTACCCTATGATGGGTATCGGTACCCTATGGGTAATCGGTTTTTCTCGGAGC
1 CATAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCCTATGGGCAATCGGTTTGTCTCGAAGC
7947 CTAAATTGA
66 CTAAATTGA
*
7956 CATAGGGGTATCGGTACACCCTATGAGGGGTATCGGTACCCTCTGGGCAATCTGG-TTGTCTCGA
1 CATAGGGGTATCGGT--ACCCTATGAGGGGTATCGGTACCCTATGGGCAATC-GGTTTGTCTCGA
8020 AGCC
63 AGCC
8024 CTTTTATAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
74 15 0.25
76 43 0.72
77 2 0.03
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (74 bp):
CATAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCCTATGGGCAATCGGTTTGTCTCGAAGC
CTAAATTGA
Found at i:9545 original size:134 final size:135
Alignment explanation
Indices: 9365--9613 Score: 360
Period size: 134 Copynumber: 1.8 Consensus size: 135
9355 AAAAAGATTA
* * * * * *
9365 TCGGGTTTCGAATTTGACGAAACGGACTTCGGATTTGGATTCAGGACGTCCAAAAACATAAAATA
1 TCGGGTTTCGAATTTGAC-AAACAGACTTCGGAATCGGACTCAGGACATCAAAAAACATAAAATA
* *
9430 TGACTTTTCGAAAATTTTGACTTTTTGGTCGAAGTCGAA-GTCAACGGGTTTGATTGACAATTTC
65 TGACTTTTCGAAAATTTTGACGTTTTGGTCAAAGTC-AACGTCAACGGGTTTGATTGACAATTTC
9494 GAGGCTT
129 GAGGCTT
9501 TCGGG-TTCGAATTTGGA-AAACAGACTTCGGAATCGGACTCAGGACATCAAAAAACATAAAATA
1 TCGGGTTTCGAATTT-GACAAACAGACTTCGGAATCGGACTCAGGACATCAAAAAACATAAAATA
*
9564 TTACTTTTCGAAAATTTTGACGTTTTGGTCAAAGTCAACGGTCAACGGGT
65 TGACTTTTCGAAAATTTTGACGTTTTGGTCAAAGTCAAC-GTCAACGGGT
9614 CGGATCGGGT
Statistics
Matches: 101, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
133 2 0.02
134 73 0.72
135 19 0.19
136 7 0.07
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (135 bp):
TCGGGTTTCGAATTTGACAAACAGACTTCGGAATCGGACTCAGGACATCAAAAAACATAAAATAT
GACTTTTCGAAAATTTTGACGTTTTGGTCAAAGTCAACGTCAACGGGTTTGATTGACAATTTCGA
GGCTT
Found at i:12045 original size:19 final size:19
Alignment explanation
Indices: 12000--12046 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
11990 TTATTTTATT
*
12000 TGAAAATAACAAAAAATAG
1 TGAAAATGACAAAAAATAG
12019 TGAAAATGACAAAAAATAG
1 TGAAAATGACAAAAAATAG
12038 TGAAAATGA
1 TGAAAATGA
12047 TCAACCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.64, C:0.04, G:0.15, T:0.17
Consensus pattern (19 bp):
TGAAAATGACAAAAAATAG
Found at i:17564 original size:3 final size:3
Alignment explanation
Indices: 17552--17644 Score: 89
Period size: 3 Copynumber: 30.3 Consensus size: 3
17542 AATTTGGCCT
* * *
17552 ATA ATAA ATA ATA ATA ATA TTA AT- ATA ATA ATG ATA TTA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
17597 TTA ATAA ATA ATA ATT ATA ATA TTG ATA ATA ATA ATA ATAA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
17644 A
1 A
17645 ATAGTCTCCG
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
2 2 0.03
3 61 0.85
4 9 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:17969 original size:134 final size:134
Alignment explanation
Indices: 17820--18667 Score: 753
Period size: 134 Copynumber: 6.3 Consensus size: 134
17810 CAGATCGAGA
* * * * * *
17820 AACGTTGATTCATTCCATTGTT-CTTTAGGGAAGATTGAATCGTGGTAGACTTGTTCTACTATTA
1 AACGTTGATTCATTCCACTATTAC-TCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTA
* * *
17884 CTCACGGAATATCAAATCTTGAAAGAGAGGGATCTACTCCGTTTCTTCTCGAGGGAAAATCAGAT
65 CTCACGGAATATCAAATCTTGAAAGAGAGGGATCTATTCCGCTTCTTCTTGAGGGAAAATCAGAT
*
17949 TTGGG
130 ATGGG
* * * * * * *
17954 GACGTTGATTTATTCCACTATT-CTTTAGGAAAGATTGAATTGAGGTAGATTTGTTCAACTGTTA
1 AACGTTGATTCATTCCACTATTAC-TCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTA
* * * * * * *
18018 CTTAGGGAATATTAAATCTTGAAAAGAGAGGGATCCACTT-TGCTTCTTCTTAAGGAAAAATCAG
65 CTCACGGAATATCAAATCTTG-AAAGAGAGGGATCTA-TTCCGCTTCTTCTTGAGGGAAAATCAG
*
18082 ATATGGA
128 ATATGGG
* * * *
18089 AACATTGATTCATTCCA-TAATTACTCAGTGAAGATTGAATCGGGGTAGTCTTGTTCCACTGTTA
1 AACGTTGATTCATTCCACT-ATTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTA
** * *
18153 CTCATAGAATATCAAATC-TGAAAGGAGAGGGATCTGTTCCACTTCTTCTTGAGGGAAAATCAGA
65 CTCACGGAATATCAAATCTTGAAA-GAGAGGGATCTATTCCGCTTCTTCTTGAGGGAAAATCAGA
18217 TATGGG
129 TATGGG
* * * * * * * *
18223 GACGTTGATTCATTCCATTATTACTTAGGGAAGATTGAATCGAGGCAAACTTATTCCATTGTCAC
1 AACGTTGATTCATTCCACTATTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTAC
* * * * * * *
18288 TTA-GGAAATATCAAATCTTGAAAGAGAGGGATATGTTCTGATTATTCTTGAGGGAAAATCATAT
66 TCACGG-AATATCAAATCTTGAAAGAGAGGGATCTATTCCGCTTCTTCTTGAGGGAAAATCAGAT
*
18352 CTGGG
130 ATGGG
* * * * * *
18357 AACTTTGATTCATTCAACTGTTACTCAGGGAAAATTGAATCGAAGCT-GACTTATTCCACTGTTA
1 AACGTTGATTCATTCCACTATTACTCAGGGAAGATTGAATCG-AGGTAGACTTGTTCCACTGTTA
* * * * ** *
18421 CTCAC-AAACTATCAAATCTTGAAAGAAAAGGATTTATTATGCTTCTTCTTGAGGGAATATCAGA
65 CTCACGGAA-TATCAAATCTTGAAAGAGAGGGATCTATTCCGCTTCTTCTTGAGGGAAAATCAGA
* *
18485 TCTGGA
129 TATGGG
* * ** * *
18491 AATGTTGATTCATTCCACTGTT-CTTCATAGAAGATTGAATCGAGGCAGACTTGTTCCATTGTTA
1 AACGTTGATTCATTCCACTATTAC-TCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTA
** * * * * * * ***
18555 CTCAAAGAATATCAAATCTAGAAAAATAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATTTTAT
65 CTCACGGAATATCAAATCTTGAAAGAGAGGGATCTATTCCGCTTCTTCTTGAGGGAAAATCAGAT
*
18620 ATGGA
130 ATGGG
* * * *
18625 AATGTTGATTCATTCCACT-TTTCTTCATGGATGATTGAATCGA
1 AACGTTGATTCATTCCACTATTAC-TCAGGGAAGATTGAATCGA
18668 ATTCGATATG
Statistics
Matches: 583, Mismatches: 115, Indels: 32
0.80 0.16 0.04
Matches are distributed among these distances:
133 13 0.02
134 457 0.78
135 111 0.19
136 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (134 bp):
AACGTTGATTCATTCCACTATTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTAC
TCACGGAATATCAAATCTTGAAAGAGAGGGATCTATTCCGCTTCTTCTTGAGGGAAAATCAGATA
TGGG
Found at i:18292 original size:269 final size:266
Alignment explanation
Indices: 17818--18667 Score: 897
Period size: 268 Copynumber: 3.2 Consensus size: 266
17808 ATCAGATCGA
* * * *
17818 GAAACGTTGATTCATTCCATTGTT-CTTTAGGGAAGATTGAATCGTGGTAGACTTGTTCTACTAT
1 GAAACGTTGATTCATTCCA-TGTTAC-TCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGT
* * * *
17882 TACTCACGGAATATCAAATCTTGAAAGAGAGGGATCTACTCCGTTTCTTCTCGAGGGAAAATCAG
64 TACTCACAGAATATCAAATCTTGAAAGAGAGGGATCTATTCCGCTTCTTCTTGAGGGAAAATCAG
* * * * * * *
17947 ATTTGGGGACGTTGATTTATTCCACTATTCTTTAGGAAAGATTGAATTGAGGTAGATTTGTTCAA
129 ATATGGGGACGTTGATTCATTCCACTATTC-TTAGGGAAGATTGAATCGAGGCAGACTTGTTCCA
* * * * *
18012 CTGTTACTTAGGGAATATTAAATCTTGAAAAGAGAGGGATCCA-CTTTGCTTCTTCTTAAGGAAA
193 TTGTTACTTAGGGAATATCAAATCTTGAAAAGAGAGGGAT--ATGTTTGCTTCTTCTTGAGGGAA
*
18076 AATCAGATATG
256 AATCATATATG
* * * * *
18087 GAAACATTGATTCATTCCATAATTACTCAGTGAAGATTGAATCGGGGTAGTCTTGTTCCACTGTT
1 GAAACGTTGATTCATTCCAT-GTTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTT
* * *
18152 ACTCATAGAATATCAAATC-TGAAAGGAGAGGGATCTGTTCCACTTCTTCTTGAGGGAAAATCAG
65 ACTCACAGAATATCAAATCTTGAAA-GAGAGGGATCTATTCCGCTTCTTCTTGAGGGAAAATCAG
* * *
18216 ATATGGGGACGTTGATTCATTCCATTATTACTTAGGGAAGATTGAATCGAGGCAAACTTATTCCA
129 ATATGGGGACGTTGATTCATTCCACTATT-CTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCA
* * * *
18281 TTGTCACTTAGGAAATATCAAATCTTG-AAAGAGAGGGATATGTTCTGATTATTCTTGAGGGAAA
193 TTGTTACTTAGGGAATATCAAATCTTGAAAAGAGAGGGATATGTT-TGCTTCTTCTTGAGGGAAA
*
18345 ATCATATCTG
257 ATCATATATG
* * * * * *
18355 GGAACTTTGATTCATTCAACTGTTACTCAGGGAAAATTGAATCGAAGCT-GACTTATTCCACTGT
1 GAAACGTTGATTCATTCCA-TGTTACTCAGGGAAGATTGAATCG-AGGTAGACTTGTTCCACTGT
* * * ** *
18419 TACTCACA-AACTATCAAATCTTGAAAGAAAAGGATTTATTATGCTTCTTCTTGAGGGAATATCA
64 TACTCACAGAA-TATCAAATCTTGAAAGAGAGGGATCTATTCCGCTTCTTCTTGAGGGAAAATCA
* ** * * **
18483 GATCTGGAAATGTTGATTCATTCCACTGTTCTTCATAGAAGATTGAATCGAGGCAGACTTGTTCC
128 GATATGGGGACGTTGATTCATTCCACTATTCTT-AGGGAAGATTGAATCGAGGCAGACTTGTTCC
* ** * *
18548 ATTGTTACTCAAAGAATATCAAATCTAGAAAA-ATAGGGATATGTTTCGCTTCTTCTTGAGGGAA
192 ATTGTTACTTAGGGAATATCAAATCTTGAAAAGAGAGGGATATGTTT-GCTTCTTCTTGAGGGAA
**
18612 AATTTTATATG
256 AATCATATATG
* * * *
18623 GAAATGTTGATTCATTCCACT-TTTCTTCATGGATGATTGAATCGA
1 GAAACGTTGATTCATTCCA-TGTTAC-TCAGGGAAGATTGAATCGA
18668 ATTCGATATG
Statistics
Matches: 482, Mismatches: 85, Indels: 30
0.81 0.14 0.05
Matches are distributed among these distances:
266 1 0.00
267 12 0.02
268 276 0.57
269 191 0.40
270 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (266 bp):
GAAACGTTGATTCATTCCATGTTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTA
CTCACAGAATATCAAATCTTGAAAGAGAGGGATCTATTCCGCTTCTTCTTGAGGGAAAATCAGAT
ATGGGGACGTTGATTCATTCCACTATTCTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCATTG
TTACTTAGGGAATATCAAATCTTGAAAAGAGAGGGATATGTTTGCTTCTTCTTGAGGGAAAATCA
TATATG
Found at i:22842 original size:23 final size:23
Alignment explanation
Indices: 22773--22842 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
22763 TGAAAACAAG
* **
22773 CAATCACATACTTTCATAACACA
1 CAATCACATACTTTCATATCTTA
* * * *
22796 CATTTACATGCTTTCATATTTTA
1 CAATCACATACTTTCATATCTTA
*
22819 CAATCACATACTTTCATCTCTTA
1 CAATCACATACTTTCATATCTTA
22842 C
1 C
22843 CTGAATCATT
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.27, G:0.01, T:0.39
Consensus pattern (23 bp):
CAATCACATACTTTCATATCTTA
Found at i:23146 original size:42 final size:42
Alignment explanation
Indices: 23048--23188 Score: 138
Period size: 42 Copynumber: 3.3 Consensus size: 42
23038 GCCATATAAA
* ** * ** *
23048 ATGTTCCGAAGGACCACATATATATCCCAAAAGACCGCATAGA
1 ATGTCCCGAAGGACCACATATATATTACAAAGGACCAAATA-T
* * *
23091 ATTATCCCTAAGGACCACATATATGTTACAAAGGACCAAATAT
1 A-TGTCCCGAAGGACCACATATATATTACAAAGGACCAAATAT
* * * *
23134 ATGTCCCGAAGGACCGCATATATATTTCAAAGGATCACATAT
1 ATGTCCCGAAGGACCACATATATATTACAAAGGACCAAATAT
23176 ATGTCCCGAAGGA
1 ATGTCCCGAAGGA
23189 TCGCGCAGAA
Statistics
Matches: 80, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
42 47 0.59
43 2 0.03
44 31 0.39
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (42 bp):
ATGTCCCGAAGGACCACATATATATTACAAAGGACCAAATAT
Found at i:23190 original size:21 final size:21
Alignment explanation
Indices: 23056--23188 Score: 104
Period size: 21 Copynumber: 6.2 Consensus size: 21
23046 AAATGTTCCG
*
23056 AAGGACCACATATATATCCCA
1 AAGGACCACATATATGTCCCA
* * * * *
23077 AAAGACCGCATAGAATTATCCCT
1 AAGGACCACATA-TA-TGTCCCA
**
23100 AAGGACCACATATATGTTACA
1 AAGGACCACATATATGTCCCA
* *
23121 AAGGACCAAATATATGTCCCG
1 AAGGACCACATATATGTCCCA
* * **
23142 AAGGACCGCATATATATTTCA
1 AAGGACCACATATATGTCCCA
* *
23163 AAGGATCACATATATGTCCCG
1 AAGGACCACATATATGTCCCA
23184 AAGGA
1 AAGGA
23189 TCGCGCAGAA
Statistics
Matches: 83, Mismatches: 27, Indels: 4
0.73 0.24 0.04
Matches are distributed among these distances:
21 65 0.78
22 2 0.02
23 16 0.19
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.22
Consensus pattern (21 bp):
AAGGACCACATATATGTCCCA
Found at i:24037 original size:35 final size:35
Alignment explanation
Indices: 23991--24060 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
23981 CATTCTAAAA
* * *
23991 ATGGTACCGATACTTCCACATT-GGTATCGATACCC
1 ATGGTAACGATACTACCAC-TTCAGTATCGATACCC
24026 ATGGTAACGATACTACCACTTCAGTATCGATACCC
1 ATGGTAACGATACTACCACTTCAGTATCGATACCC
24061 CATGAAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (35 bp):
ATGGTAACGATACTACCACTTCAGTATCGATACCC
Found at i:25092 original size:15 final size:15
Alignment explanation
Indices: 25035--25092 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
25025 AAATACTTGA
25035 CTTTTTTCTCCTTTTT
1 CTTTTTTCT-CTTTTT
*
25051 CTTTTTCCTCTTTTT
1 CTTTTTTCTCTTTTT
*
25066 CTTCCTTT-TCTTTTT
1 CTT-TTTTCTCTTTTT
*
25081 CTTTTTTATCTT
1 CTTTTTTCTCTT
25093 ATTTTTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 3 0.08
15 23 0.64
16 10 0.28
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTTTCTCTTTTT
Found at i:25098 original size:24 final size:24
Alignment explanation
Indices: 25037--25098 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
25027 ATACTTGACT
**
25037 TTTTTCTCCTTTTTCTTTTTCCTC
1 TTTTTCTTATTTTTCTTTTTCCTC
** *
25061 TTTTTCTTCCTTTTCTTTTT-CTT
1 TTTTTCTTATTTTTCTTTTTCCTC
25084 TTTTATCTTATTTTT
1 TTTT-TCTTATTTTT
25099 TTCTATTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 6 0.19
24 26 0.81
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTCTTATTTTTCTTTTTCCTC
Found at i:29449 original size:56 final size:58
Alignment explanation
Indices: 29389--29502 Score: 144
Period size: 56 Copynumber: 2.0 Consensus size: 58
29379 TTTTTGGGGC
* * *
29389 TATGTCGAGGAGCGATCCAACTTAATC-TCGGAAAGGTTGGGCTTT-AAA-AAATGTAT
1 TATGTCG-GGAACGATCCAAATTAATCTTCGAAAAGGTTGGGCTTTAAAATAAATGTAT
* * *
29445 TATGTCGGGAATGATCCAAATTAATCTTTGAAAAGGTTGGGTTTTAAAATAAATGTAT
1 TATGTCGGGAACGATCCAAATTAATCTTCGAAAAGGTTGGGCTTTAAAATAAATGTAT
29503 AAATAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
55 16 0.33
56 22 0.45
57 3 0.06
58 8 0.16
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (58 bp):
TATGTCGGGAACGATCCAAATTAATCTTCGAAAAGGTTGGGCTTTAAAATAAATGTAT
Found at i:30269 original size:16 final size:16
Alignment explanation
Indices: 30219--30270 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
30209 TATTGGGTGT
30219 TAAAATTACAAAT-AA-
1 TAAAATTA-AAATAAAC
30234 TAAAA-T-AAATAACAC
1 TAAAATTAAAATAA-AC
30249 T-AAATTAAAATAAAC
1 TAAAATTAAAATAAAC
30264 TAAAATT
1 TAAAATT
30271 GTGTGGCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
12 4 0.13
13 1 0.03
14 5 0.16
15 10 0.32
16 11 0.35
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAATTAAAATAAAC
Found at i:31399 original size:13 final size:13
Alignment explanation
Indices: 31381--31405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31371 TGGGCTTGGA
31381 TGCTTGTTGGGTT
1 TGCTTGTTGGGTT
31394 TGCTTGTTGGGT
1 TGCTTGTTGGGT
31406 CGGATGACTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.40, T:0.52
Consensus pattern (13 bp):
TGCTTGTTGGGTT
Found at i:31486 original size:20 final size:21
Alignment explanation
Indices: 31461--31517 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
31451 GCCTGTAATA
*
31461 AATAATAATATTATTATTA-T
1 AATAATAATATTAATATTATT
*
31481 AATAATGATATTAATATTATT
1 AATAATAATATTAATATTATT
*
31502 AATAAATAATAATAAT
1 AAT-AATAATATTAAT
31518 TATAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 17 0.55
21 4 0.13
22 10 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATAATAATATTAATATTATT
Found at i:31519 original size:20 final size:20
Alignment explanation
Indices: 31456--31527 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 20
31446 ATTTGGCCTG
31456 TAATAAATAATAAT-ATTAT
1 TAATAAATAATAATAATTAT
*
31475 TATTATAATAATGATATTAATATTAT
1 TAATA-AATAAT-A-A-T-A-ATTAT
31501 TAATAAATAATAATAATTAT
1 TAATAAATAATAATAATTAT
*
31521 AAATAAA
1 TAATAAA
31528 AAAGGGTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
19 4 0.09
20 17 0.40
21 2 0.05
22 2 0.05
23 2 0.05
24 1 0.02
25 6 0.14
26 9 0.21
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
TAATAAATAATAATAATTAT
Found at i:33031 original size:2 final size:2
Alignment explanation
Indices: 33026--33054 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33016 ATATTATTCA
33026 AT AT 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 AT AT A
33055 GATGCCTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36072 original size:15 final size:16
Alignment explanation
Indices: 36042--36082 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
36032 GGGTTTTAAG
36042 CCGATCCGA-TCTGAT
1 CCGATCCGATTCTGAT
36057 CCGATCCGATTC-GAT
1 CCGATCCGATTCTGAT
* *
36072 CAGATCAGATT
1 CCGATCCGATT
36083 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (16 bp):
CCGATCCGATTCTGAT
Found at i:41845 original size:20 final size:21
Alignment explanation
Indices: 41817--41858 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
41807 TTTTTTTTCC
*
41817 AAAA-AAAAAAAG-GCAAAAA
1 AAAACAAAAAAAGAGCCAAAA
41836 A-AACAAAAAAAGAGCCAAAA
1 AAAACAAAAAAAGAGCCAAAA
41856 AAA
1 AAA
41859 GCCAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
18 2 0.11
19 9 0.47
20 7 0.37
21 1 0.05
ACGTcount: A:0.81, C:0.10, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAACAAAAAAAGAGCCAAAA
Found at i:41865 original size:21 final size:21
Alignment explanation
Indices: 41819--41858 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41809 TTTTTTCCAA
*
41819 AAAAAAAAAGGCAAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAAC
*
41840 AAAAAAAGAGCCAAAAAAA
1 AAAAAAAAAGCCAAAAAAA
41859 GCCAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGCCAAAAAAAAC
Found at i:48954 original size:15 final size:15
Alignment explanation
Indices: 48931--48960 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48921 CGGCGGCGGT
48931 GGTTGGAAACCCTAG
1 GGTTGGAAACCCTAG
*
48946 GGTTTGAAACCCTAG
1 GGTTGGAAACCCTAG
48961 TGGCTTTGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (15 bp):
GGTTGGAAACCCTAG
Found at i:49511 original size:20 final size:20
Alignment explanation
Indices: 49486--49524 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
49476 CATCATGCTC
49486 GAAGGTCTTATAGATAGCCT
1 GAAGGTCTTATAGATAGCCT
49506 GAAGGTCTTATAGATAGCC
1 GAAGGTCTTATAGATAGCC
49525 CAAAGGACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (20 bp):
GAAGGTCTTATAGATAGCCT
Found at i:49530 original size:20 final size:20
Alignment explanation
Indices: 49487--49536 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
49477 ATCATGCTCG
**
49487 AAGGTCTTATAGATAGCCTG
1 AAGGTCTTATAGATAGCCCA
49507 AAGGTCTTATAGATAGCCCA
1 AAGGTCTTATAGATAGCCCA
*
49527 AAGGACTTAT
1 AAGGTCTTAT
49537 CATCTTGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (20 bp):
AAGGTCTTATAGATAGCCCA
Found at i:50009 original size:258 final size:256
Alignment explanation
Indices: 49284--52445 Score: 1073
Period size: 258 Copynumber: 11.7 Consensus size: 256
49274 CTGACAGGTG
* *
49284 ACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTTATGGCCCGAAGAACTTACCAATTTTG
1 ACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTG
* *
49349 GAAATAGTTTACTAAGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCTTTTTTT
66 GAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTT-AAAAATTTC--ATTTT
*
49414 TTGAAAATACTAAATGAAAACTTTGAAAATCGCTTTCTCATTTTCAAATTATCACATGAAAGCAT
128 CTGAAAATACTAAATGAAAACTTTGAAAATCGCTTTCTCATTTTCAAATTATCACATGAAAGCAT
* *
49479 CATG-CTCGAAGGTCTTATAGATAGCCTGAAGGTCTTATAGATAGCCCAAAGGACTTATCATCTT
193 CTTGCCT-GAAGGTC---T---T-G--T--A---C--AT-G---GCCCGAAGGACTTATCATCTT
*
49543 GCTTGAAAGACTGAAAGACTGAAAGATG
237 GCTTGAAAGACT----GA--G--AGATA
* ** * * *
49571 ACCCGAATAATTTAATCATCATGCTTGAAAGACTTATTGATGGCCCGAATGG-CTTACTAATTTT
1 ACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAA-GGACTTACCAATTTT
* * * *
49635 GGAAATAGTTTACTTGGTAAGAAACTTTGGAAATTGCTTTCATACTTTTCAACAATTTCATTTTC
65 GGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTT-AAAAATTTCATTTTC
* *
49700 TGAAAACACTAAATGATAAACTTTGAAAATCACTTTCTCATTTTCAAATTATCACATGAAAGCAT
129 TGAAAATACTAAATGA-AAACTTTGAAAATCGCTTTCTCATTTTCAAATTATCACATGAAAGCAT
* *
49765 CTTGCCTGAAGGTCTTGTACATGGCCCGAAGGACTTACCATCTTGCTT-AGAAGGCTGAGAGATA
193 CTTGCCTGAAGGTCTTGTACATGGCCCGAAGGACTTATCATCTTGCTTGA-AAGACTGAGAGATA
* * *
49829 ACCCAAAGGATTTAATAATCATGCTCGAAAGATTTACTGATGGCCCGAAGGATTTACCAATTTTG
1 ACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTG
* * *
49894 GAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTTAAAATTACATTTTGTG
66 GAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTAAAAATTTCATTTTCTG
* *
49959 AAAATACTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTAAATTATCACATGAAAACATC
131 AAAATACTAAATGA-AAACTTTGAAAATCGCTTTCTCA-TTTTCAAATTATCACATGAAAGCATC
** * * * *
50024 TTGCCCAAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATA
194 TTGCCTGAAGGTCTTGTACATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTGAGAGATA
* *
50087 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAACAATTTTG
1 ACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTG
** * * *** * * * * * * * **
50152 G-GCTTGTTGAC-CCCT-TGTAA-TTAGGCCCAA---CTTGGGCTT-GTTGT---AATGCGCATG
66 GAAATAGTTTACTAGGTAAGAAACTTTGG--AAATCGCTT--TCTTACTTTTAAAAAT-TTCAT-
***** * * * * ** *** **
50206 TAAAAAAAAATAATAATTATTAATAA-TAATAATTATAAT-AATAAAT-ATTAACAAAATATATG
125 TTTCTGAAAATACTAA--ATGAA-AACT--T--TGAAAATCGCTTTCTCATTTTC-AAAT-TAT-
** * * * * * * * ** * **
50268 GGCGA-AAAAG-AGTGTT---T-AATGCTACCCT-T-CTTTGCCC-ATGCTTGTGTTAACAAGAA
180 CAC-ATGAAAGCA-TCTTGCCTGAA-GGT--CTTGTACATGGCCCGAAG---GACTTATC-A-TC
* * * * *
50324 TAG--GGAAAAGA-T-AAAAAAA
235 TTGCTTG-AAAGACTGAGAGATA
** * * * ** * * * *
50343 AGACAATGTTTTTTGTCTGGTTTCATCCTGATGTTGACTC-AAATGAGTCTGACAGATGACCCAA
1 ACCCAA-------AG---GATTTAAT-C--ATCATG-CTCGAAA-GA--CTTACTGATGGCCCGA
* * ** * * * *
50407 AGGATTTAATCATCATACTCGAAAGA-CTTACTTATGGCCTGGAGAACTTACCAATTTTGGAAAT
49 AGGACTT-ACCA--ATTTTGGAAATAGTTTAC-TA-GG--T-AAGAA---A-C---TTTGGAAAT
** * ** *
50471 -ATTTTACTAGGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTC-AAAAATTTCTTTTTTCTGA
99 CGCTTT-CT---T-----ACTTT-TAAA--AATTTC--A-TTTTCTGAAAA-----------T--
* *
50534 AAAATACTAAATGAAAACTTTGAAAATCACTTTCTCATTTTCAAATTATCACATGAAATCATCTT
136 -A----CTAAATGAAAACTTTGAAAATCGCTTTCTCATTTTCAAATTATCACATGAAAGCATCTT
* * * * * * * * *
50599 G-CTCGAAGGACTTATAGATAGCCCGAAGGACTTATCATCTTTCTTGAAAGACTCACATATG
196 GCCT-GAAGGTCTTGTACATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTGAGAGATA
* *
50660 ACCCGAAA-GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAATGACTTACCAATTTT
1 ACCC-AAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTT
* * * *
50724 GGAAATAGTTTACTTGGTAAGAAACTTTGGAAATTGCTTTCATACTTTTCAACAATTTCATTTTC
65 GGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTT-AAAAATTTCATTTTC
*
50789 TGAAAATACTAAATGATAAACTTTGAAAATCGTTTTCTCATTTTCAAATTATCACATGAAAGCAT
129 TGAAAATACTAAATGA-AAACTTTGAAAATCGCTTTCTCATTTTCAAATTATCACATGAAAGCAT
* * * * * * * *
50854 CTTGCCCGAAGGTCTTATAGATGGCCCGATGGACTTACCATATTGCTCGGAAAG-TTGAGAGATA
193 CTTGCCTGAAGGTCTTGTACATGGCCCGAAGGACTTATCATCTTGCT-TGAAAGACTGAGAGATA
* * * * *
50918 ACCCAAAGGATTTAATAATCATGCTCGAAAGATTTACTGATGACCCGAAAGATTTACCAATTTTG
1 ACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTG
* * * *
50983 GAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTCATTTTGTA
66 GAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTAAAAATTTCATTTTCTG
* *
51048 AAAATACTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTAAATTATCACATGAAAACATC
131 AAAATACTAAATGA-AAACTTTGAAAATCGCTTTCTCA-TTTTCAAATTATCACATGAAAGCATC
* * * * * *
51113 TTGCCTAAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATG
194 TTGCCTGAAGGTCTTGTACATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTGAGAGATA
* * *
51176 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTAACAATTTTG
1 ACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTG
*** * *** * * * * * * * ** *
51241 GGCTTA-TTGAC-CCCT-TGTAA-TTAGGCCCAA---CTTGGGCTT-GTTGT---AATGGGCATG
66 GAAATAGTTTACTAGGTAAGAAACTTTGG--AAATCGCTT--TCTTACTTTTAAAAAT-TTCATT
** * * * * * ** *** ** *
51295 TAATAAAAAATAATAATTATTAATAA-TAATAATTATAAT-AATAAAT-ATTAACAAAATAT-AC
126 TTCT-GAAAATACTAA--ATGAA-AACT--T--TGAAAATCGCTTTCTCATTTTCAAATTATCAC
** * *** * * * * * * * * ** *
51356 GGGCGAAA-AAGAGTGCCT-AATGCTACCCT-T-CTTTGCCC--ATG-CTTGTGTTAACAAGAAT
183 --ATGAAAGCATCTTGCCTGAA-GGT--CTTGTACATGGCCCGAAGGAC-T-TATCATCTTG-CT
* * *
51414 AGGGAAAAGA-T-A-AAAAA
240 --TG-AAAGACTGAGAGATA
** * ** * * * *
51431 AGACAACATTTTTTTTCTGG-TTTTATCCTGATGTTGACTC-AAATGAGTCTGACAGATGACCCA
1 ACCCAA-A----------GGATTTAAT-C--ATCATG-CTCGAAA-GA--CTTACTGATGGCCCG
* ** ** * * *
51494 AAGGATTTAATTATCATACTCGAAAGA-CTTACTTATGGCCTGAAGAACTTACCAATTTTGGAAA
48 AAGGACTT-ACCA--ATTTTGGAAATAGTTTAC-TA-GG--T-AAGAA---A-C---TTTGGAAA
** * ** * * *
51558 T-ATTTTACTAGGTAAAAAACTTTGGAAATCGCTTTTACTTTTC-AAAAATTTCATTTTTCTGAA
98 TCGCTTT-CT---T-----ACTTT-TAAA--AATTTCA-TTTTCTGAAAA--T-A-----CTAAA
** * *
51621 AATACTAAATGAAAACTTTGAAAATCACTTTCTCATTTTCAAATTATCACATGAAAGAATCTTG-
142 TG---------AAAACTTTGAAAATCGCTTTCTCATTTTCAAATTATCACATGAAAGCATCTTGC
* * ** * * *
51685 CTCGAAGGTCTTATAGATATCCCGAAGGACTTATCATCTTTCTTGAAAGACTGACAGATG
198 CT-GAAGGTCTTGTACATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTGAGAGATA
* *
51745 A-CCAGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACCAATTTT
1 ACCCA-AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTT
* * * *
51809 GGAAATAGTTTACTTGGTAAGAAACTTTGGAAATTGCTTTCATACTTTTCAACAATTTCATTTTC
65 GGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTT-AAAAATTTCATTTTC
**
51874 TGAAAATACTAAATGATAAACTTTGAAAATTACTTTCTCATTTTCAAATTATCACATGAAAGCAT
129 TGAAAATACTAAATGA-AAACTTTGAAAATCGCTTTCTCATTTTCAAATTATCACATGAAAGCAT
* * * * * * * *
51939 CTTGCCCGAAGGTTTTATAGATGGCCCGAAGGACTTACCATCTTGCTCGGAAGGCTGAGAGATA
193 CTTGCCTGAAGGTCTTGTACATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTGAGAGATA
* * * * *
52003 ACCCAAAGGATTTAATAATCATGCTCGAAAGATTTACTGATGACCCAAAGGATTTACCAATTTTG
1 ACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTG
* * *
52068 GAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTTCATTTTGTG
66 GAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTAAAAATTTCATTTTCTG
* *
52133 AAAATACTAAATGAGAAACTTTGAAAATCGTTTTCTCATTTTTTAAATTATCACATGAAAGCATC
131 AAAATACTAAATGA-AAACTTTGAAAATCGCTTTCTCA-TTTTCAAATTATCACATGAAAGCATC
* * ** * * * * * * *
52198 TTGCAC-AAAAGAATTATAGATGACCCGAAGGACTTATCATCATGCTCGAAAGACTGACAGATG
194 TTGC-CTGAAGGTCTTGTACATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTGAGAGATA
* * *
52261 ACCCGAAGGATTTAATCATCATGCTTGAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTTG
1 ACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTG
* * * *
52326 GAAATAGTTTACTAGGTTAGAAACTTTGGAAATCACTTTTTTACTTTTCAAAATTTTCATTTTCT
66 GAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTT-AAAAATTTCATTTTCT
* *
52391 GAAAATTACTAAATGTGAAACTTTGAAAATCGCTTTCTTATTTTTCAAATTATCA
130 GAAAA-TACTAAATG-AAAACTTTGAAAATCGCTTTCTCA-TTTTCAAATTATCA
52446 TAAAGACAAC
Statistics
Matches: 2122, Mismatches: 490, Indels: 553
0.67 0.15 0.17
Matches are distributed among these distances:
251 6 0.00
252 9 0.00
253 29 0.01
254 31 0.01
255 58 0.03
256 29 0.01
257 195 0.09
258 960 0.45
259 33 0.02
260 45 0.02
261 1 0.00
262 2 0.00
263 1 0.00
264 1 0.00
265 6 0.00
266 41 0.02
267 1 0.00
268 7 0.00
269 13 0.01
270 7 0.00
271 20 0.01
272 22 0.01
273 8 0.00
274 21 0.01
275 13 0.01
276 7 0.00
277 5 0.00
279 9 0.00
280 2 0.00
281 3 0.00
282 2 0.00
283 1 0.00
284 12 0.01
285 23 0.01
286 57 0.03
287 123 0.06
288 9 0.00
289 8 0.00
290 7 0.00
291 7 0.00
292 2 0.00
294 6 0.00
295 10 0.00
296 4 0.00
297 6 0.00
298 28 0.01
299 4 0.00
300 8 0.00
301 28 0.01
302 1 0.00
303 12 0.01
304 19 0.01
305 2 0.00
306 2 0.00
307 7 0.00
309 2 0.00
311 5 0.00
312 9 0.00
313 14 0.01
314 28 0.01
315 24 0.01
316 24 0.01
317 15 0.01
318 14 0.01
319 6 0.00
320 5 0.00
322 3 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (256 bp):
ACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTG
GAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTAAAAATTTCATTTTCTG
AAAATACTAAATGAAAACTTTGAAAATCGCTTTCTCATTTTCAAATTATCACATGAAAGCATCTT
GCCTGAAGGTCTTGTACATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTGAGAGATA
Found at i:50112 original size:42 final size:42
Alignment explanation
Indices: 50047--50143 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
50037 TTATAGATGG
*
50047 CCCGAAGGACTT-ATCATCTTGCTCGAAAGACTGACAGATAA
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTGACAGATAA
* * * **
50088 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTGACAGATAA
50130 CCCGAAGGACTTAA
1 CCCGAAGGACTTAA
50144 CAATTTTGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 11 0.23
42 37 0.77
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (42 bp):
CCCGAAGGACTTAATCATCATGCTCGAAAGACTGACAGATAA
Found at i:50252 original size:16 final size:16
Alignment explanation
Indices: 50214--50249 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
50204 TGTAAAAAAA
50214 AATAATAATTATTAAT
1 AATAATAATTATTAAT
50230 AATAATAATTA-TAAT
1 AATAATAATTATTAAT
50245 AATAA
1 AATAA
50250 ATATTAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAATTATTAAT
Found at i:51204 original size:42 final size:42
Alignment explanation
Indices: 51130--51232 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 42
51120 AAGGTCTTAT
*
51130 AGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGACTGAC
1 AGATGGCCCGAAGGACTTAATCATCATGCTCGAAAGACTGAC
* * *
51171 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTTAATCATCATGCTCGAAAGACTGAC
* *
51213 TGATGGCCCAAAGGACTTAA
1 AGATGGCCCGAAGGACTTAA
51233 CAATTTTGGG
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 16 0.30
42 37 0.70
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (42 bp):
AGATGGCCCGAAGGACTTAATCATCATGCTCGAAAGACTGAC
Found at i:51341 original size:16 final size:16
Alignment explanation
Indices: 51303--51338 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
51293 TGTAATAAAA
51303 AATAATAATTATTAAT
1 AATAATAATTATTAAT
51319 AATAATAATTA-TAAT
1 AATAATAATTATTAAT
51334 AATAA
1 AATAA
51339 ATATTAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAATTATTAAT
Found at i:52291 original size:42 final size:42
Alignment explanation
Indices: 52214--52316 Score: 147
Period size: 42 Copynumber: 2.5 Consensus size: 42
52204 AAAAGAATTA
52214 TAGATGACCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
1 TAGATGACCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
* * *
52256 -AGATGACCCGAAGGATTTAATCATCATGCTTGAAAGACTTAC
1 TAGATGACCCGAAGGACTT-ATCATCATGCTCGAAAGACTGAC
*
52298 TA-ATGGCCCGAAGGACTTA
1 TAGATGACCCGAAGGACTTA
52317 CCAATTTTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 18 0.33
42 35 0.65
43 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
TAGATGACCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
Found at i:56697 original size:20 final size:20
Alignment explanation
Indices: 56651--56703 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
56641 GGTGTCAAAG
* * *
56651 TGTATCCATACACCCTGTAG
1 TGTATCCATGCACCCTGCAA
* *
56671 TGCATCCATGCACTCTGCAA
1 TGTATCCATGCACCCTGCAA
56691 TGTATCCATGCAC
1 TGTATCCATGCAC
56704 AGTGTATCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCCATGCACCCTGCAA
Found at i:56807 original size:15 final size:16
Alignment explanation
Indices: 56768--56816 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 16
56758 CAATGCGATT
56768 AGTGTACCGATGCACCCCG
1 AGTGTACCGATGCA---CG
56787 AGTGTACCGATGCAC-
1 AGTGTACCGATGCACG
*
56802 AGTGTATCGATGCAC
1 AGTGTACCGATGCAC
56817 CCTGGCTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 14 0.48
16 1 0.03
19 14 0.48
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (16 bp):
AGTGTACCGATGCACG
Found at i:59934 original size:21 final size:18
Alignment explanation
Indices: 59891--59947 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
59881 CAACAATTGG
59891 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
59909 TAACAATTGATATCATTTTGT
1 TAACAATTGATATC--TTT-T
*
59930 TAACAATTGGTAT-TTTT
1 TAACAATTGATATCTTTT
59947 T
1 T
59948 TCATTAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 2 0.06
18 17 0.49
20 3 0.09
21 13 0.37
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:59948 original size:21 final size:21
Alignment explanation
Indices: 59891--59938 Score: 75
Period size: 18 Copynumber: 2.4 Consensus size: 21
59881 CAACAATTGG
59891 TAACAATTGATATC--TTT-T
1 TAACAATTGATATCATTTTGT
59909 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
59930 TAACAATTG
1 TAACAATTG
59939 GTATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.52
20 3 0.11
21 10 0.37
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.46
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:60222 original size:20 final size:20
Alignment explanation
Indices: 60171--60224 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
60161 AGGGTGTCGA
*
60171 AGTGTATCCATACACCCTGC
1 AGTGTATCCATGCACCCTGC
* *
60191 AGTGCATCCATGCACTCTGC
1 AGTGTATCCATGCACCCTGC
60211 AGTGTATCCATGCA
1 AGTGTATCCATGCA
60225 TAGTATATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (20 bp):
AGTGTATCCATGCACCCTGC
Found at i:60330 original size:15 final size:15
Alignment explanation
Indices: 60310--60345 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
60300 TGCAATCCCG
60310 AGTGTACCGATGCAC
1 AGTGTACCGATGCAC
*
60325 AGTGTATCGATGCAC
1 AGTGTACCGATGCAC
*
60340 ACTGTA
1 AGTGTA
60346 GTGTATCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (15 bp):
AGTGTACCGATGCAC
Found at i:60763 original size:34 final size:33
Alignment explanation
Indices: 60724--60794 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
60714 TTTTGTAAAG
*
60724 GGGAAAGGTTCTAGCTAAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAAGCCCGTG-AAAAACTA
* * *
60758 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
60791 GGGA
1 GGGA
60795 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
Found at i:72073 original size:67 final size:67
Alignment explanation
Indices: 71963--72126 Score: 204
Period size: 67 Copynumber: 2.4 Consensus size: 67
71953 GAGTAGATTG
* * * * * *
71963 TTTGTCTCCCTTGAGACAGTTTCTCTTTAAACATTAACATTTGATATTGTTTCTCTCGAAATAAA
1 TTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTATTTCTCTCGAAACAAA
72028 GT
66 GT
* * * *
72030 TTTGTTTCGCTTGAGACAGTTTCTCTTGAAATATAAACCTTTGAGATTATTTCTCTCGAAGCAAA
1 TTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTATTTCTCTCGAAACAAA
72095 GT
66 GT
* *
72097 TTCT-TCTCGCTTGAGACATTTTCCCTTGAA
1 TT-TGTCTCGCTTGAGACAGTTTCTCTTGAA
72127 GCCCAAATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
67 82 0.99
68 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (67 bp):
TTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTATTTCTCTCGAAACAAA
GT
Found at i:72257 original size:14 final size:14
Alignment explanation
Indices: 72240--72266 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
72230 CGCAAATTTC
72240 GAAACAAAATTTTT
1 GAAACAAAATTTTT
72254 GAAACAAAATTTT
1 GAAACAAAATTTT
72267 ATCTCACCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (14 bp):
GAAACAAAATTTTT
Found at i:72266 original size:13 final size:13
Alignment explanation
Indices: 72233--72266 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
72223 CTTGAAACGC
*
72233 AAATTTCGAAACA
1 AAATTTTGAAACA
72246 AAATTTTTGAAACA
1 AAA-TTTTGAAACA
72260 AAATTTT
1 AAATTTT
72267 ATCTCACCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (13 bp):
AAATTTTGAAACA
Done.