Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000857.1 Hibiscus syriacus cultivar Beakdansim tig00001660_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: 125406
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:4974 original size:2 final size:2
Alignment explanation
Indices: 4967--4997 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4957 TTATCTATGA
4967 AT 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 AT A
4998 AATGCCTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9371 original size:24 final size:23
Alignment explanation
Indices: 9344--9405 Score: 88
Period size: 24 Copynumber: 2.7 Consensus size: 23
9334 CGTATAAATT
9344 TGCACCGTAGTGCCACGTAGAATA
1 TGCACCGTAGTGCCACGTAGAA-A
* *
9368 TGCACCGAAGTGCCGCGTAGAAA
1 TGCACCGTAGTGCCACGTAGAAA
*
9391 TGCACCATAGTGCCA
1 TGCACCGTAGTGCCA
9406 TATAAGATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAA
Found at i:10790 original size:13 final size:13
Alignment explanation
Indices: 10755--10791 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
10745 GATGTCAAAT
**
10755 CAAATTCATCCTC
1 CAAATTCATTTTC
10768 CAAATTCATTTTC
1 CAAATTCATTTTC
10781 CAAATTCATTT
1 CAAATTCATTT
10792 AAACCTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (13 bp):
CAAATTCATTTTC
Found at i:12014 original size:32 final size:32
Alignment explanation
Indices: 11967--12028 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
11957 AATATACGGT
* *
11967 TAAAAAAAGGCGGTACC-GATTTTGTTATTGAC
1 TAAAAAAAAGCGGTACCAG-TTTTATTATTGAC
*
11999 TAAAAAAAAGTGGTACCAGTTTTATTATTG
1 TAAAAAAAAGCGGTACCAGTTTTATTATTG
12029 TGCATAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (32 bp):
TAAAAAAAAGCGGTACCAGTTTTATTATTGAC
Found at i:12954 original size:199 final size:198
Alignment explanation
Indices: 12616--13057 Score: 649
Period size: 199 Copynumber: 2.2 Consensus size: 198
12606 CACATATGTT
* *
12616 ACATCGAAACCGATAATTATAATATAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGA
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGA
*
12681 TTTTATGAGAGAATAGGTCAACATAATGTATCGACACAAATTTAAATGTGTCGATACATTTTGTC
66 TTTTATGAGAAAATAGGTCAACATAATGTATCGACACAAATTTAAATGTGTCGATACATTTTGTC
* *
12746 CAGAATGAATGCCAAACGAGGTGCACACATAAAGTGTCGATACATTTATTAAA-AGTATCGATCC
131 CAAAATGAATGCCAAACGAGGTGCACACACAAAGTGTCGATACATTTA--AAATAGTATCGATCC
12810 CAAAA
194 CAAAA
* *
12815 ACATCGAAACCGATAATTACAATGTAACAGGTAAATTTACAATGT-ACTCAGTATAAATATACCG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAAC-CAGTATAAATATACCG
* * *
12879 ATTTTATGAGAAAATAGGTCTACATAATGTATCGACAC-ATTTTAAGTTTGTGTCGATAC-TTTT
65 ATTTTATGAGAAAATAGGTCAACATAATGTATCGACACAAATTTAA--ATGTGTCGATACATTTT
* * * * *
12942 TTCCAAAATGAATGCCCAACGAGGTGCACGCACAAAGTGTTGATACATTTAAAATTGTATCGATC
128 GTCCAAAATGAATGCCAAACGAGGTGCACACACAAAGTGTCGATACATTTAAAATAGTATCGATC
13007 CCAAAA
193 CCAAAA
* * *
13013 ACATCAAAACCGATAATTATAATGTAATAGATAAATTTGCAATGT
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGT
13058 TTATTTTAAA
Statistics
Matches: 219, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
197 3 0.01
198 63 0.29
199 142 0.65
200 11 0.05
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (198 bp):
ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGA
TTTTATGAGAAAATAGGTCAACATAATGTATCGACACAAATTTAAATGTGTCGATACATTTTGTC
CAAAATGAATGCCAAACGAGGTGCACACACAAAGTGTCGATACATTTAAAATAGTATCGATCCCA
AAA
Found at i:13673 original size:21 final size:23
Alignment explanation
Indices: 13646--13695 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
13636 ACCTATTTTA
* *
13646 TTATATAAACGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
13669 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
13692 TTAT
1 TTAT
13696 TGTGATTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:13750 original size:23 final size:23
Alignment explanation
Indices: 13723--13766 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
13713 ATAGTAATTA
**
13723 ACCTATTTTATTATATAAGTGTT
1 ACCTATTACATTATATAAGTGTT
13746 ACCTATTACATTATATAAGTG
1 ACCTATTACATTATATAAGTG
13767 GTATCTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (23 bp):
ACCTATTACATTATATAAGTGTT
Found at i:13776 original size:87 final size:87
Alignment explanation
Indices: 13630--13859 Score: 336
Period size: 87 Copynumber: 2.7 Consensus size: 87
13620 ACAAATTAAA
* *
13630 TAATTAACCTATTTTATTATATAAACGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
*
13695 TTGTGATTGATAATGTTTATAG
66 TTGTGATTGATAATGTTTACAG
* * * * *
13717 TAATTAACCTATTTTATTATATAAGTGTTACCTATTACATTATATAAGTGGTATCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
* *
13782 TTGTGCTTGATAATGTTTCCAG
66 TTGTGATTGATAATGTTTACAG
** *
13804 TAATTAACCTA-TTTATTATATAAGCGCTACCTATTTTATTATATAAGCGTTACCTA
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTA
13860 TTTTATTATA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
86 38 0.30
87 88 0.70
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.44
Consensus pattern (87 bp):
TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
TTGTGATTGATAATGTTTACAG
Found at i:13782 original size:23 final size:23
Alignment explanation
Indices: 13732--13776 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13722 AACCTATTTT
* *
13732 ATTATATAAGTGTTACCTATTAC
1 ATTATATAAGTGGTACCTAATAC
*
13755 ATTATATAAGTGGTATCTAATA
1 ATTATATAAGTGGTACCTAATA
13777 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (23 bp):
ATTATATAAGTGGTACCTAATAC
Found at i:13845 original size:23 final size:23
Alignment explanation
Indices: 13810--13905 Score: 140
Period size: 23 Copynumber: 4.2 Consensus size: 23
13800 CCAGTAATTA
13810 ACCTA-TTTATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
*
13832 ACCTATTTTATTATATAAGCGTT
1 ACCTATTTTATTATATAAGCGCT
13855 ACCTATTTTATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
** * *
13878 ACCTATTACATTATATAAACGAT
1 ACCTATTTTATTATATAAGCGCT
13901 ACCTA
1 ACCTA
13906 ATATGTTATT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
22 5 0.07
23 62 0.93
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (23 bp):
ACCTATTTTATTATATAAGCGCT
Found at i:13876 original size:46 final size:45
Alignment explanation
Indices: 13810--14110 Score: 157
Period size: 46 Copynumber: 6.8 Consensus size: 45
13800 CCAGTAATTA
*
13810 ACCTA-TTTATTATATAAGCGCTACCTATTTTATTATATAAGCGTT
1 ACCTATTTTATTATATAAGCGCTACCTATTATATTATATAA-CGTT
* *
13855 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGAT
1 ACCTATTTTATTATATAAGCGCTACCTATTATATTATAT-AACGTT
* * * * * *** * * *
13901 ACCTAATATGTTAT-T--GTGTTTGATAATGT-TTCTAGTAA--TT
1 ACCTATTTTATTATATAAGCGCTACCTATTATATTATA-TAACGTT
* * * * *
13941 AACCTATTTTATCATATAAGTGATACCTATTACATTATATAAGCGGT
1 -ACCTATTTTATTATATAAGCGCTACCTATTATATTATATAA-CGTT
* * * * *
13988 ACCTAATATATTAT-T--GTGCT---TAATA-ATGTTTCAGTAA--TT
1 ACCTATTTTATTATATAAGCGCTACCTATTATAT-TAT-A-TAACGTT
* *
14027 AACCTATTTTATTATATAAGCGCTACCTATTTTATTATATAATCGCT
1 -ACCTATTTTATTATATAAGCGCTACCTATTATATTATATAA-CGTT
*
14074 ACCTATTTTATTATATAAGCGCTACCTAATATATTAT
1 ACCTATTTTATTATATAAGCGCTACCTATTATATTAT
14111 TGTGTTTAAT
Statistics
Matches: 186, Mismatches: 45, Indels: 49
0.66 0.16 0.17
Matches are distributed among these distances:
39 3 0.02
40 19 0.10
41 12 0.06
42 10 0.05
43 15 0.08
44 13 0.07
45 12 0.06
46 96 0.52
47 6 0.03
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (45 bp):
ACCTATTTTATTATATAAGCGCTACCTATTATATTATATAACGTT
Found at i:13980 original size:23 final size:23
Alignment explanation
Indices: 13954--14001 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
13944 CTATTTTATC
* *
13954 ATATAAGTGATACCTATTACATT
1 ATATAAGCGATACCTAATACATT
* *
13977 ATATAAGCGGTACCTAATATATT
1 ATATAAGCGATACCTAATACATT
14000 AT
1 AT
14002 TGTGCTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (23 bp):
ATATAAGCGATACCTAATACATT
Found at i:14002 original size:87 final size:86
Alignment explanation
Indices: 13855--14087 Score: 331
Period size: 87 Copynumber: 2.7 Consensus size: 86
13845 TATAAGCGTT
* *
13855 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGATACCTAATATGTTATTGTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGATACCTAATATATTATTGTGC
*
13920 TTGATAATGTTTCTAGTAATTA
66 TTAATAATGTTTC-AGTAATTA
* * * * *
13942 ACCTATTTTATCATATAAGTGATACCTATTACATTATATAAGCGGTACCTAATATATTATTGTGC
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGATACCTAATATATTATTGTGC
14007 TTAATAATGTTTCAGTAATTA
66 TTAATAATGTTTCAGTAATTA
** * * * *
14028 ACCTATTTTATTATATAAGCGCTACCTATTTTATTATATAATCGCTACCTATTTTATTAT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGATACCTAATATATTAT
14088 ATAAGCGCTA
Statistics
Matches: 129, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
86 59 0.46
87 70 0.54
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (86 bp):
ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGATACCTAATATATTATTGTGC
TTAATAATGTTTCAGTAATTA
Found at i:14016 original size:219 final size:219
Alignment explanation
Indices: 13636--14110 Score: 790
Period size: 219 Copynumber: 2.2 Consensus size: 219
13626 TAAATAATTA
* * * *
13636 ACCTATTTTATTATATAAACGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGA
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGATACCTAATATGTTATTGTGA
* * *
13701 TTGATAATGTTTATAGTAATTAACCTATTTTATTATATAAGTGTTACCTATTACATTATATAAGT
66 TTGATAATGTTTATAGTAATTAACCTATTTTATCATATAAGTGATACCTATTACATTATATAAGC
* * *
13766 GGTATCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACCTA-TTTATTATATAAGCG
131 GGTACCTAATATATTATTGTGCTTAATAATGTTT-CAGTAATTAACCTATTTTATTATATAAGCG
*
13830 CTACCTATTTTATTATATAAGCGTT
195 CTACCTATTTTATTATATAAGCGCT
*
13855 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGATACCTAATATGTTATTGTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGATACCTAATATGTTATTGTGA
*
13920 TTGATAATGTTTCTAGTAATTAACCTATTTTATCATATAAGTGATACCTATTACATTATATAAGC
66 TTGATAATGTTTATAGTAATTAACCTATTTTATCATATAAGTGATACCTATTACATTATATAAGC
13985 GGTACCTAATATATTATTGTGCTTAATAATGTTTCAGTAATTAACCTATTTTATTATATAAGCGC
131 GGTACCTAATATATTATTGTGCTTAATAATGTTTCAGTAATTAACCTATTTTATTATATAAGCGC
*
14050 TACCTATTTTATTATATAATCGCT
196 TACCTATTTTATTATATAAGCGCT
* *
14074 ACCTATTTTATTATATAAGCGCTACCTAATATATTAT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTAT
14111 TGTGTTTAAT
Statistics
Matches: 239, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
218 14 0.06
219 225 0.94
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (219 bp):
ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGATACCTAATATGTTATTGTGA
TTGATAATGTTTATAGTAATTAACCTATTTTATCATATAAGTGATACCTATTACATTATATAAGC
GGTACCTAATATATTATTGTGCTTAATAATGTTTCAGTAATTAACCTATTTTATTATATAAGCGC
TACCTATTTTATTATATAAGCGCT
Found at i:14034 original size:196 final size:197
Alignment explanation
Indices: 13832--14274 Score: 685
Period size: 196 Copynumber: 2.3 Consensus size: 197
13822 TATAAGCGCT
*
13832 ACCTATTTTATTATATAAGCGTTACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAA
1 ACCTATTTTATTATATAAGCGCTACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAA
* * * *
13897 CGATACCTAATATGTTATTGTGTTTGATAATGTTT-CTAGTAATTAACCTATTTTATCATATAAG
66 CGATACCTAATATATTATTGTGTTTAATAATGTTTACGA-TAATTAACATATTTTATCATATAAG
13961 TGATACCTATTACATTATATAAGCGGTACCTAATATATTATTGTGCTTAATAATGTTT-CAGTAA
130 TGATACCTATTACATTATATAAGCGGTACCTAATATATTATTGTGCTTAATAATGTTTCCAGTAA
14025 TTA
195 TTA
* ** *
14028 ACCTATTTTATTATATAAGCGCTACCTATTTTATTATATAATCGCTACCTATTTTATTATATAAG
1 ACCTATTTTATTATATAAGCGCTACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAA
* *
14093 CGCTACCTAATATATTATTGTGTTTAATAATGTTTACGATAATTAACATATTTTATTATATAAGT
66 CGATACCTAATATATTATTGTGTTTAATAATGTTTACGATAATTAACATATTTTATCATATAAGT
* * *
14158 GATATCTATTACATTATATAAGTGGTACCTAATATATTATTGTGCTTGATAATGTTTCCAGTAAT
131 GATACCTATTACATTATATAAGCGGTACCTAATATATTATTGTGCTTAATAATGTTTCCAGTAAT
14223 TA
196 TA
* ** * *
14225 A-CTATTTTATTATATAAGCGCTAGCTATTACATTATATAAGTGATACCTA
1 ACCTATTTTATTATATAAGCGCTACCTATTTTATTATATAAGCGCTACCTA
14275 ATATGTTATT
Statistics
Matches: 225, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
196 213 0.95
197 12 0.05
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (197 bp):
ACCTATTTTATTATATAAGCGCTACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAA
CGATACCTAATATATTATTGTGTTTAATAATGTTTACGATAATTAACATATTTTATCATATAAGT
GATACCTATTACATTATATAAGCGGTACCTAATATATTATTGTGCTTAATAATGTTTCCAGTAAT
TA
Found at i:14058 original size:23 final size:23
Alignment explanation
Indices: 14028--14110 Score: 139
Period size: 23 Copynumber: 3.6 Consensus size: 23
14018 TCAGTAATTA
14028 ACCTATTTTATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
*
14051 ACCTATTTTATTATATAATCGCT
1 ACCTATTTTATTATATAAGCGCT
14074 ACCTATTTTATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
* *
14097 ACCTAATATATTAT
1 ACCTATTTTATTAT
14111 TGTGTTTAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.45
Consensus pattern (23 bp):
ACCTATTTTATTATATAAGCGCT
Found at i:14154 original size:87 final size:86
Alignment explanation
Indices: 14053--14284 Score: 306
Period size: 87 Copynumber: 2.7 Consensus size: 86
14043 TAAGCGCTAC
** * * *
14053 CTATTTTATTATATAATCGCTACCTATTTTATTATATAAGCGCTACCTAATATATTATTGTGTTT
1 CTATTTTATTATATAATCGCTACCTATTACATTATATAAGTGATACCTAATATATTATTGTGCTT
*
14118 AATAATGTTTAC-GATAATTAA
66 AATAATGTTTCCAG-TAATTAA
* * *
14139 CATATTTTATTATATAAGT-GATATCTATTACATTATATAAGTGGTACCTAATATATTATTGTGC
1 C-TATTTTATTATATAA-TCGCTACCTATTACATTATATAAGTGATACCTAATATATTATTGTGC
*
14203 TTGATAATGTTTCCAGTAATTAA
64 TTAATAATGTTTCCAGTAATTAA
* * *
14226 CTATTTTATTATATAAGCGCTAGCTATTACATTATATAAGTGATACCTAATATGTTATT
1 CTATTTTATTATATAATCGCTACCTATTACATTATATAAGTGATACCTAATATATTATT
14285 ATACTTGGTA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
86 53 0.41
87 73 0.57
88 2 0.02
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (86 bp):
CTATTTTATTATATAATCGCTACCTATTACATTATATAAGTGATACCTAATATATTATTGTGCTT
AATAATGTTTCCAGTAATTAA
Found at i:14196 original size:23 final size:23
Alignment explanation
Indices: 14146--14197 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
14136 TAACATATTT
* *
14146 TATTATATAAGTGATATCTATTA
1 TATTATATAAGTGATACCTAATA
* *
14169 CATTATATAAGTGGTACCTAATA
1 TATTATATAAGTGATACCTAATA
14192 TATTAT
1 TATTAT
14198 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (23 bp):
TATTATATAAGTGATACCTAATA
Found at i:18282 original size:20 final size:22
Alignment explanation
Indices: 18254--18299 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
18244 CATTCAATGG
18254 ATTAATT-AATAAAAATATT-T
1 ATTAATTAAATAAAAATATTAT
* *
18274 ATTATTTAAATAAATATATTAT
1 ATTAATTAAATAAAAATATTAT
18296 ATTA
1 ATTA
18300 CATTTTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAATTAAATAAAAATATTAT
Found at i:21655 original size:3 final size:3
Alignment explanation
Indices: 21643--21683 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
21633 GTAATAAATT
*
21643 ATA A-A ATA ATA ATA ATA ATA ATA AT- ATA TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
21684 AATTAAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:22256 original size:117 final size:116
Alignment explanation
Indices: 22048--22423 Score: 576
Period size: 117 Copynumber: 3.2 Consensus size: 116
22038 TAAAATCTCA
** * * *
22048 TTTGAAAACATCCTGCACTGGAGGTCTTATGGATGGCCCTGAGATCTTATCATCTTGCACTGTAA
1 TTTGAAAACATCCTGCACTATAGGTCTTATGGATTGCCCTGAGGTCTTATCATCTTGCACTGTAG
* *
22113 GTCTTACAGATAACCCTGAGGTTTTAAATATCAAAAAGCTCCCGAAGGCTTT
66 GTCTTACAGATGACCCAGAGGTTTTAAATATCAAAAAGCTCCCGAAGGC-TT
* * *
22165 TTTGAACACATCCTGCACTACAGGTCTTATGGATTGCCCTGAGGTCTTATCATCTTGCATTGTAG
1 TTTGAAAACATCCTGCACTATAGGTCTTATGGATTGCCCTGAGGTCTTATCATCTTGCACTGTAG
* * *
22230 GTCTTACAGATGATCCAGAGGCTTTAAATATCAAAAAGCACCCGAAGGCTT
66 GTCTTACAGATGACCCAGAGGTTTTAAATATCAAAAAGCTCCCGAAGGCTT
* *
22281 TTTGAACACATCCTGCA-TGTAGGTCTTATGGA-TGCCCTGAGGTCTTATCATCTTGCACTGTAG
1 TTTGAAAACATCCTGCACTATAGGTCTTATGGATTGCCCTGAGGTCTTATCATCTTGCACTGTAG
* *
22344 GACTTACAGATGACCCATAGGTTTTAAATATCAAAAAGCTCCCGAAGGCTT
66 GTCTTACAGATGACCCAGAGGTTTTAAATATCAAAAAGCTCCCGAAGGCTT
22395 TTTGAAAACATCCTGCACTATAGGTCTTA
1 TTTGAAAACATCCTGCACTATAGGTCTTA
22424 CATATGTGGG
Statistics
Matches: 236, Mismatches: 22, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
114 92 0.39
115 23 0.10
116 19 0.08
117 102 0.43
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (116 bp):
TTTGAAAACATCCTGCACTATAGGTCTTATGGATTGCCCTGAGGTCTTATCATCTTGCACTGTAG
GTCTTACAGATGACCCAGAGGTTTTAAATATCAAAAAGCTCCCGAAGGCTT
Found at i:23127 original size:22 final size:22
Alignment explanation
Indices: 23102--23156 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
23092 AATAAAGTTT
*
23102 TCATTTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
*
23124 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
23146 TCATCTTTGAA
1 TCATCTTTGAA
23157 GAATGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:24619 original size:75 final size:75
Alignment explanation
Indices: 24491--24663 Score: 249
Period size: 75 Copynumber: 2.3 Consensus size: 75
24481 AGTATGAGTC
* * * *
24491 TTCAGCATGTCCCAATATTTGCTAATACAAACGTTCAAAATGCTTCAACATTCCTATTTCTGATT
1 TTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATGCTTCAACATTCCAATTTCTGATT
**
24556 GAAATGGGCT
66 GAAATAAGCT
* * *
24566 TTCAGCATGCCCCAACATTTGCTGATACGAACATTCAAAATG-TGTCAATATTCCAATTTCTGAT
1 TTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATGCT-TCAACATTCCAATTTCTGAT
24630 TGAAATAAGCT
65 TGAAATAAGCT
24641 TTCAGCATGCCCCAACATTTGCT
1 TTCAGCATGCCCCAACATTTGCT
24664 TCTTGTTGAT
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 1 0.01
75 87 0.99
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATGCTTCAACATTCCAATTTCTGATT
GAAATAAGCT
Found at i:29547 original size:7 final size:7
Alignment explanation
Indices: 29513--29548 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
29503 TAAAAGTACG
29513 AATGCAA
1 AATGCAA
29520 AATG-AA
1 AATGCAA
29526 AATGCAA
1 AATGCAA
29533 AGATGCAA
1 A-ATGCAA
29541 AATGCAA
1 AATGCAA
29548 A
1 A
29549 TGAATGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.22
7 14 0.52
8 7 0.26
ACGTcount: A:0.58, C:0.11, G:0.17, T:0.14
Consensus pattern (7 bp):
AATGCAA
Found at i:33244 original size:16 final size:18
Alignment explanation
Indices: 33213--33245 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
33203 TCTTTGTTTG
33213 TTGTTTCTGTTGGTTGCC
1 TTGTTTCTGTTGGTTGCC
33231 TTGTTTC-G-TGGTTGC
1 TTGTTTCTGTTGGTTGC
33246 TCCCGTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.00, C:0.15, G:0.30, T:0.55
Consensus pattern (18 bp):
TTGTTTCTGTTGGTTGCC
Found at i:33743 original size:3 final size:3
Alignment explanation
Indices: 33737--33788 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
33727 TTTATAAAAC
* * *
33737 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT ATT ATT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33784 AAT AA
1 AAT AA
33789 AAGTAAAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:47080 original size:37 final size:37
Alignment explanation
Indices: 46999--47084 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
46989 TTCACCCTAA
46999 ACCCGAACCCGACCCGAATATCACACTTAGAAAAACCC
1 ACCCG-ACCCGACCCGAATATCACACTTAGAAAAACCC
* * *
47037 AACCGACTCGACCCGAATATCACACTTA-AAAAATCCG
1 ACCCGACCCGACCCGAATATCACACTTAGAAAAA-CCC
47074 ACCCGACCCGA
1 ACCCGACCCGA
47085 ACAAAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 5 0.12
37 33 0.79
38 4 0.10
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (37 bp):
ACCCGACCCGACCCGAATATCACACTTAGAAAAACCC
Found at i:47192 original size:32 final size:33
Alignment explanation
Indices: 47156--47233 Score: 88
Period size: 38 Copynumber: 2.3 Consensus size: 33
47146 TTTTCACCCT
47156 AAACCCGACT-GACCCGAATATCACACTTAAAAA
1 AAACCCGACTCGACCCGAATATCACACTT-AAAA
*
47189 AACCCGACCCGACTCGACCCGAATATTACACTT-AAA
1 AA----ACCCGACTCGACCCGAATATCACACTTAAAA
47225 AAACCCGAC
1 AAACCCGAC
47234 CCGAACAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
32 7 0.18
33 2 0.05
36 5 0.13
37 8 0.21
38 17 0.44
ACGTcount: A:0.41, C:0.35, G:0.10, T:0.14
Consensus pattern (33 bp):
AAACCCGACTCGACCCGAATATCACACTTAAAA
Found at i:47226 original size:37 final size:37
Alignment explanation
Indices: 47158--47237 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
47148 TTCACCCTAA
47158 ACCCGACTGACCCGAATATCACACTTAAAAAAACCCG
1 ACCCGACTGACCCGAATATCACACTTAAAAAAACCCG
*
47195 ACCCGACTCGACCCGAATATTACACTT-AAAAAACCCG
1 ACCCGACT-GACCCGAATATCACACTTAAAAAAACCCG
47232 ACCCGA
1 ACCCGA
47238 ACAAAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 24 0.59
38 17 0.41
ACGTcount: A:0.39, C:0.36, G:0.11, T:0.14
Consensus pattern (37 bp):
ACCCGACTGACCCGAATATCACACTTAAAAAAACCCG
Found at i:47264 original size:158 final size:155
Alignment explanation
Indices: 46957--47274 Score: 493
Period size: 153 Copynumber: 2.1 Consensus size: 155
46947 TATAAGGTAA
* *
46957 AATTATATATTTTTTCGGTCGGTCCGGGTTTTTTCACCCTAAACCCGAACCCGACCCGAATATCA
1 AATTATATATATTTTCGGTCGGTCCGAGTTTTTTCACCCTAAACCCGAACCCGACCCGAATATCA
*
47022 CACTTAGAAAAACCCAACCGACTCGACCCGAATATCACACTTAAAAAATCCGACCCGACCCGAAC
66 CACTTAAAAAAACCCAACCGACTCGACCCGAATATCACACTTAAAAAA--C-ACCCGACCCGAAC
47087 AAAATAAAGTTTCATCCGACCCGACCCG
128 AAAATAAAGTTTCATCCGACCCGACCCG
* *
47115 AATTATATATATTTTCGGGTCGGTCCGATTTTTTTCACCCTAAACCCG-A-CTGACCCGAATATC
1 AATTATATATATTTTC-GGTCGGTCCGAGTTTTTTCACCCTAAACCCGAACCCGACCCGAATATC
* *
47178 ACACTTAAAAAAACCCGACCCGACTCGACCCGAATATTACACTT-AAAAA-ACCCGACCCGAACA
65 ACACTTAAAAAAACCC-AACCGACTCGACCCGAATATCACACTTAAAAAACACCCGACCCGAACA
47241 AAATAAAGTTTCATCCGACCCGACCCG
129 AAATAAAGTTTCATCCGACCCGACCCG
47268 AA-TATAT
1 AATTATAT
47275 GAATTAGAAA
Statistics
Matches: 151, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
152 5 0.03
153 43 0.28
157 33 0.22
158 41 0.27
159 29 0.19
ACGTcount: A:0.34, C:0.31, G:0.13, T:0.23
Consensus pattern (155 bp):
AATTATATATATTTTCGGTCGGTCCGAGTTTTTTCACCCTAAACCCGAACCCGACCCGAATATCA
CACTTAAAAAAACCCAACCGACTCGACCCGAATATCACACTTAAAAAACACCCGACCCGAACAAA
ATAAAGTTTCATCCGACCCGACCCG
Found at i:72963 original size:20 final size:22
Alignment explanation
Indices: 72917--72969 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
72907 AACTTGGTCA
72917 AAATTTT-AACGCAATTGATAT
1 AAATTTTAAACGCAATTGATAT
**
72938 TCATTTTAAAC-C-ATTGATAT
1 AAATTTTAAACGCAATTGATAT
72958 AAATTTTCAAAC
1 AAATTTT-AAAC
72970 AATTTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 13 0.50
21 10 0.38
22 3 0.12
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.40
Consensus pattern (22 bp):
AAATTTTAAACGCAATTGATAT
Found at i:76314 original size:20 final size:20
Alignment explanation
Indices: 76289--76371 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
76279 TTTTGGTGCA
*
76289 GAGGGAATCGATCCCCCCCT
1 GAGGGAACCGATCCCCCCCT
* *
76309 GAGGGAACCGATTCCCCCTT
1 GAGGGAACCGATCCCCCCCT
* *
76329 TAGGGGAACCGATTCCCCCCACA
1 GA-GGGAACCGA-TCCCCCC-CT
* *
76352 G-GGGAATCGATACCCCCCT
1 GAGGGAACCGATCCCCCCCT
76371 G
1 G
76372 GGGTTCTGTT
Statistics
Matches: 49, Mismatches: 11, Indels: 7
0.73 0.16 0.10
Matches are distributed among these distances:
19 2 0.04
20 24 0.49
21 17 0.35
22 6 0.12
ACGTcount: A:0.22, C:0.37, G:0.25, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCCT
Found at i:76326 original size:21 final size:21
Alignment explanation
Indices: 76289--76348 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
76279 TTTTGGTGCA
*
76289 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
*
76309 GAGGGAACCGATT-CCCCCTT
1 GAGGGAACCGATTCCCCCCCT
*
76329 TAGGGGAACCGATTCCCCCC
1 GA-GGGAACCGATTCCCCCC
76349 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.50
21 12 0.35
22 5 0.15
ACGTcount: A:0.20, C:0.38, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:76354 original size:21 final size:21
Alignment explanation
Indices: 76311--76369 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
76301 CCCCCCCTGA
***
76311 GGGAACCGATTCCCCCTTTAG
1 GGGAACCGATTCCCCCCACAG
76332 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
76353 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
76370 TGGGGTTCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.39, G:0.24, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:84761 original size:9 final size:9
Alignment explanation
Indices: 84749--84870 Score: 74
Period size: 9 Copynumber: 13.1 Consensus size: 9
84739 AAGAAGAAAT
84749 AAAAGAGAAA
1 AAAAGAG-AA
*
84759 AAAAAAGAAA
1 AAAAGAG-AA
84769 TAAAAGAGAA
1 -AAAAGAGAA
84779 AAAATGAGAA
1 AAAA-GAGAA
84789 AAAAG-GAA
1 AAAAGAGAA
*
84797 AAATGATGGAA
1 AAAAGA--GAA
*
84808 AAAACGAAAA
1 AAAA-GAGAA
84818 AAAAGAGAA
1 AAAAGAGAA
84827 AAAATG-GAA
1 AAAA-GAGAA
**
84836 AATGGA-AGA
1 AAAAGAGA-A
84845 AAAAGAG-A
1 AAAAGAGAA
*
84853 AAAA-TGAA
1 AAAAGAGAA
84861 AAAAGAGAA
1 AAAAGAGAA
84870 A
1 A
84871 TAAAAGGAGG
Statistics
Matches: 88, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
7 1 0.01
8 19 0.22
9 27 0.31
10 27 0.31
11 12 0.14
12 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (9 bp):
AAAAGAGAA
Found at i:84767 original size:10 final size:10
Alignment explanation
Indices: 84743--84830 Score: 76
Period size: 10 Copynumber: 8.8 Consensus size: 10
84733 CGCTTGAAGA
84743 AGAAATAAAAG
1 AGAAA-AAAAG
*
84754 AGAAAAAAAA
1 AGAAAAAAAG
84764 AGAAATAAAAG
1 AGAAA-AAAAG
*
84775 AGAAAAAATG
1 AGAAAAAAAG
84785 AG-AAAAAAG
1 AGAAAAAAAG
*
84794 -G-AAAAATG
1 AGAAAAAAAG
*
84802 ATGGAAAAAACG
1 A--GAAAAAAAG
84814 A-AAAAAAAG
1 AGAAAAAAAG
84823 AGAAAAAA
1 AGAAAAAA
84831 TGGAAAATGG
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
8 7 0.11
9 14 0.22
10 21 0.33
11 15 0.23
12 7 0.11
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:84789 original size:21 final size:21
Alignment explanation
Indices: 84742--84782 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
84732 TCGCTTGAAG
84742 AAGAAATAAAAGAGAAAAAAA
1 AAGAAATAAAAGAGAAAAAAA
84763 AAGAAATAAAAGAGAAAAAA
1 AAGAAATAAAAGAGAAAAAA
84783 TGAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (21 bp):
AAGAAATAAAAGAGAAAAAAA
Found at i:84808 original size:19 final size:17
Alignment explanation
Indices: 84778--84864 Score: 61
Period size: 19 Copynumber: 4.8 Consensus size: 17
84768 ATAAAAGAGA
*
84778 AAAAATGAGAAAAAAGG
1 AAAAATGAGAAAAAACG
84795 AAAAATGATGGAAAAAACG
1 AAAAATGA--GAAAAAACG
* *
84814 AAAAAAAAGAGAAAAAATG
1 --AAAAATGAGAAAAAACG
*
84833 GAAAATGGAAGAAAAAGA-G
1 AAAAAT-G-AGAAAAA-ACG
84852 AAAAATGA-AAAAA
1 AAAAATGAGAAAAA
84865 GAGAAATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
16 5 0.09
17 13 0.23
18 2 0.04
19 29 0.51
20 1 0.02
21 7 0.12
ACGTcount: A:0.71, C:0.01, G:0.21, T:0.07
Consensus pattern (17 bp):
AAAAATGAGAAAAAACG
Found at i:84809 original size:27 final size:29
Alignment explanation
Indices: 84778--84859 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
84768 ATAAAAGAGA
84778 AAAAATGAGAAAAAAG-GAAAAATGATGG
1 AAAAATGAGAAAAAAGAGAAAAATGATGG
* *
84806 AAAAAACGAAAAAAAAGAGAAAAA--ATGG
1 -AAAAATGAGAAAAAAGAGAAAAATGATGG
84834 -AAAATG-GAAGAAAAAGAGAAAAATGA
1 AAAAATGAG-A-AAAAAGAGAAAAATGA
84860 AAAAAGAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
26 6 0.14
27 13 0.30
28 4 0.09
29 15 0.34
30 6 0.14
ACGTcount: A:0.70, C:0.01, G:0.22, T:0.07
Consensus pattern (29 bp):
AAAAATGAGAAAAAAGAGAAAAATGATGG
Found at i:84847 original size:38 final size:36
Alignment explanation
Indices: 84770--84856 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 36
84760 AAAAAGAAAT
* *
84770 AAAAGAGAAAAAATGAGAAAAAAGGAAAAATGATGGAA
1 AAAAGA-AAAAAAAGAGAAAAAAGGAAAAATGA-AGAA
84808 AAAACGAAAAAAAAGAGAAAAAATGG-AAAATGGAAGAA
1 AAAA-GAAAAAAAAGAGAAAAAA-GGAAAAAT-GAAGAA
84846 AAAGAGAAAAA
1 AAA-AGAAAAA
84857 TGAAAAAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
38 36 0.84
39 7 0.16
ACGTcount: A:0.71, C:0.01, G:0.22, T:0.06
Consensus pattern (36 bp):
AAAAGAAAAAAAAGAGAAAAAAGGAAAAATGAAGAA
Found at i:86498 original size:55 final size:55
Alignment explanation
Indices: 86020--86482 Score: 538
Period size: 55 Copynumber: 8.6 Consensus size: 55
86010 ATTGAAGATG
* * * * * *
86020 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
* * * * *
86071 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
* * * * * *
86122 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
* * * * *
86173 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTC
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
* *
86228 GAGT-TCTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTATTT
1 GAGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
* *
86283 GAGTCTTATACTCCTTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTT
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
86338 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
* * **
86393 AAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTACTGAAGATTGTTC
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
* *
86448 GAGTCTTATACTCCATGAAAGAATAGGGAGCAGAC
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGAC
86483 CCGCCATTTG
Statistics
Matches: 384, Mismatches: 22, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
51 147 0.38
54 2 0.01
55 234 0.61
56 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (55 bp):
GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
Found at i:90886 original size:48 final size:48
Alignment explanation
Indices: 90830--90934 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
90820 AAATATTTTA
*
90830 TATGATTTCCGA-CTTGAATTATGTTCTGATA-CATTACCTGAATTCTGT
1 TATGATTTCCGATC-TGAATTATGTTCTGATATC-TAACCTGAATTCTGT
* * * *
90878 TATGATTTCTGATCTGGATTTTGTTCTGATATCTAATCTGAATTCTGT
1 TATGATTTCCGATCTGAATTATGTTCTGATATCTAACCTGAATTCTGT
*
90926 TTTGATTTC
1 TATGATTTC
90935 TGATATCTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 47 0.96
49 2 0.04
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (48 bp):
TATGATTTCCGATCTGAATTATGTTCTGATATCTAACCTGAATTCTGT
Found at i:90902 original size:24 final size:24
Alignment explanation
Indices: 90867--90938 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
90857 GATACATTAC
90867 CTGAATTCTGTTATGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * * * *
90891 CTGGATTTTGTTCTGATATCTAAT
1 CTGAATTCTGTTATGATTTCTGAT
*
90915 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
90939 ATCTCCGTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:91936 original size:14 final size:14
Alignment explanation
Indices: 91908--91944 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
91898 TAGCTGTTGA
91908 TTTCT-ATCATATT
1 TTTCTCATCATATT
*
91921 TTTCTCATCATTTT
1 TTTCTCATCATATT
91935 TTTCTC-TCAT
1 TTTCTCATCAT
91945 GGGTATTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTCTCATCATATT
Found at i:101151 original size:12 final size:12
Alignment explanation
Indices: 101134--101163 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
101124 TCTTGTAACC
101134 GGGTCTGGATCT
1 GGGTCTGGATCT
101146 GGGTCTGGATCT
1 GGGTCTGGATCT
101158 GGGTCT
1 GGGTCT
101164 TGGGCTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.17, G:0.43, T:0.33
Consensus pattern (12 bp):
GGGTCTGGATCT
Found at i:101279 original size:3 final size:3
Alignment explanation
Indices: 101271--101304 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
101261 TATGTAACAT
101271 TAA TAA TAA TAA TAA TAA TAA TATA TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA -TAA TA
101305 TTTATAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:109131 original size:24 final size:24
Alignment explanation
Indices: 109094--109149 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
109084 AATGTAAGTA
*
109094 ATTGGAA-TTTAAAAGGTCTGACT
1 ATTGGAAGATTAAAAGGTCTGACT
*
109117 GTTGGAAGATTAAAAGGTCTGACT
1 ATTGGAAGATTAAAAGGTCTGACT
109141 ATTGGAAGA
1 ATTGGAAGA
109150 AAATCGAGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (24 bp):
ATTGGAAGATTAAAAGGTCTGACT
Done.