Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003949.1 Hibiscus syriacus cultivar Beakdansim tig00008537_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: 268680
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:195126 original size:19 final size:22
Alignment explanation
Indices: 195102--195153 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
195092 ATGCAGAAAT
*
195102 AGTATCGATACCGTA-T-TAG-
1 AGTATCGATACCATAGTATAGA
*
195121 AGTATCGATATCATAGTATAGA
1 AGTATCGATACCATAGTATAGA
195143 AGTATCGATAC
1 AGTATCGATAC
195154 TAAGAGACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.48
20 1 0.04
21 3 0.11
22 10 0.37
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGA
Found at i:195173 original size:94 final size:94
Alignment explanation
Indices: 195050--195244 Score: 223
Period size: 94 Copynumber: 2.1 Consensus size: 94
195040 ACTAAGGTGG
* * *
195050 GTATCGATACTATGAGGAAGGTATTGATACCAT-GATTACAGAATGCAGAAATAGTATCGATACC
1 GTATCGATACTAAGAGGAAGATATCGATACCATAGA-TACAGAATGCAGAAATAGTATCGATACC
* * * *
195114 GTATTAGAGTATCGATATCATAGTATAGAA
65 GAAATAGAGTATCGATACCACAGTATAGAA
* * * * *
195144 GTATCGATACTAAGA-GACAGATATCGATACCATAGATCCATAATGTAGAAATGGTATCGATACT
1 GTATCGATACTAAGAGGA-AGATATCGATACCATAGATACAGAATGCAGAAATAGTATCGATACC
* * *
195208 GAAATGGAGTATCGGTACCACATTATAGAA
65 GAAATAGAGTATCGATACCACAGTATAGAA
195238 GTATCGA
1 GTATCGA
195245 ACCATGGTAG
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
93 2 0.02
94 80 0.95
95 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.27
Consensus pattern (94 bp):
GTATCGATACTAAGAGGAAGATATCGATACCATAGATACAGAATGCAGAAATAGTATCGATACCG
AAATAGAGTATCGATACCACAGTATAGAA
Found at i:195673 original size:55 final size:55
Alignment explanation
Indices: 195590--195759 Score: 279
Period size: 55 Copynumber: 3.1 Consensus size: 55
195580 TTACCGAATT
*
195590 GCACTATGTGTGC-AAACTAAGAAATTCATAATAAGTTTATGAATTACTGTATGG
1 GCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGG
*
195644 GCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGG
1 GCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGG
* * * *
195699 GCACTTTGTGTGCAAAACTAAGAAATTCATAGTAGGTTTATGAATTTTTGTATGG
1 GCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGG
195754 GCACTA
1 GCACTA
195760 AGAAATTCAT
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
54 13 0.12
55 94 0.88
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (55 bp):
GCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGG
Found at i:197394 original size:2 final size:2
Alignment explanation
Indices: 197383--197418 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
197373 AAAATATAAA
197383 AT AT -T 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 AT AT AT A
197419 ATCGGGGCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:199083 original size:21 final size:19
Alignment explanation
Indices: 199033--199081 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
199023 ATAATAAAAC
*
199033 TATATTCATACTCATAATA
1 TATATTCACACTCATAATA
199052 TATATTCACACTCATAATA
1 TATATTCACACTCATAATA
199071 TATATTCACAC
1 TATATTCACAC
199082 ACACACCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (19 bp):
TATATTCACACTCATAATA
Found at i:199713 original size:20 final size:20
Alignment explanation
Indices: 199676--199713 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
199666 ATGTCATTCA
* *
199676 TAAAATAATATTATAATATG
1 TAAAATAATATAAAAATATG
199696 TAAAATAATATAAAAATA
1 TAAAATAATATAAAAATA
199714 AATATTTTTT
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:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
TAAAATAATATAAAAATATG
Found at i:202785 original size:29 final size:27
Alignment explanation
Indices: 202752--202820 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
202742 ATATATGTTA
* *
202752 TTTTTTTATTTTTTAGTTTGTATCTTTAT
1 TTTTTTTATTTTTTACTTT-TACCTTT-T
*
202781 TTTTTTTCTTCTTTTACTTTTACCTTTT
1 TTTTTTTATT-TTTTACTTTTACCTTTT
202809 TATTTTTTATTT
1 T-TTTTTTATTT
202821 ATTTTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 3 0.09
29 23 0.68
30 8 0.24
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.77
Consensus pattern (27 bp):
TTTTTTTATTTTTTACTTTTACCTTTT
Found at i:202826 original size:30 final size:32
Alignment explanation
Indices: 202776--202836 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
202766 AGTTTGTATC
* *
202776 TTTATTTTTTTTCTTCTTTTACTTTT-ACCTT
1 TTTATTTTTTATCTTATTTTACTTTTCACCTT
*
202807 TTTATTTTTTAT-TTATTTTATTTTTCACCT
1 TTTATTTTTTATCTTATTTTACTTTTCACCT
202837 AGATTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (32 bp):
TTTATTTTTTATCTTATTTTACTTTTCACCTT
Found at i:203727 original size:4 final size:4
Alignment explanation
Indices: 203718--203744 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
203708 CAATGCATGT
203718 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
203745 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:209125 original size:165 final size:165
Alignment explanation
Indices: 208854--209802 Score: 1504
Period size: 165 Copynumber: 5.8 Consensus size: 165
208844 TTTAAGACAA
* * *** * * * *
208854 CATTTGCATCATAACTCAAGGATAGAAGGGTTATCTACC-AGCAAAGACCTTCGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
* * *
208918 GCTCAACTCCAAGGCACATCATTTCCAGTATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACT
66 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACT
*
208983 CTCGAGTTCGATTACACTAAGCTTCGAGGGCACAT
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * *
209018 CATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTTGGGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
209083 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACT
66 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACT
* **
209148 CTTGAGTTCGATTACACTCTTCTTCGAGGGCACAT
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* *
209183 CATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
*
209248 GCTCAGCTCCAAGGCACATCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACT
66 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACT
*
209313 CTCGAGTTCGATTACACTCAGCTTCGAGGGAACAT
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * *
209348 CATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTTTGGGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
* * * *
209413 GCTCATCTCCAAGGCACATTATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACT
66 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACT
* * *
209478 CTCGAGTTCGATTATACTCCGCTTTGAGGGCACAT
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
*
209513 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
*
209578 GCTCAGCTCCAAGGTACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACT
66 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACT
*
209643 CTCGAGTTCGATTACACTCAGCTTCGAGGTCACAT
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * *
209678 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAATCAAATACCTTTGGGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
* *
209743 GCTCAGCTCCAAGGCACATCATTTGTAGTATAGCTTAAGTCGATAAGGGCTATCTGCCAA
66 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
209803 CCGAAGACCT
Statistics
Matches: 731, Mismatches: 53, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
164 33 0.05
165 698 0.95
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (165 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACT
CTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
Found at i:211143 original size:2 final size:2
Alignment explanation
Indices: 211136--211180 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
211126 AACACTTTAT
211136 TA TA TA TA TA TA 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
211178 TA T
1 TA T
211181 TTCATTCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:212610 original size:17 final size:16
Alignment explanation
Indices: 212588--212622 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
212578 CAAAGAGGCT
212588 TTATATTTAATTTTATA
1 TTATATTTAATTTT-TA
*
212605 TTATATTTTATTTTTA
1 TTATATTTAATTTTTA
212621 TT
1 TT
212623 TTAATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATTTAATTTTTA
Found at i:212746 original size:20 final size:19
Alignment explanation
Indices: 212686--212747 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
212676 TAGATATTTA
*
212686 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
212705 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
212723 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
212743 ATTTT
1 ATTTT
212748 GATTTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:213254 original size:31 final size:31
Alignment explanation
Indices: 213212--213271 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
213202 TAGTTGTATG
* *
213212 AATTGTTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGTAAAACTAA
213243 AATTATTTAAATCTCAGTATTGTAAAACT
1 AATTATTTAAATCTCAGTATTGTAAAACT
213272 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGTAAAACTAA
Found at i:219063 original size:26 final size:25
Alignment explanation
Indices: 219028--219088 Score: 104
Period size: 26 Copynumber: 2.4 Consensus size: 25
219018 ATTTGTAGTA
*
219028 GAAAAATAATATTTATTATAATGAT
1 GAAAAATAATATTTATTATAATGAC
219053 GAAAAAATAATATTTATTATAATGAC
1 G-AAAAATAATATTTATTATAATGAC
219079 GAAAAATAAT
1 GAAAAATAAT
219089 GACAACATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 10 0.29
26 24 0.71
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (25 bp):
GAAAAATAATATTTATTATAATGAC
Found at i:219069 original size:23 final size:26
Alignment explanation
Indices: 219029--219088 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 26
219019 TTTGTAGTAG
*
219029 AAAAATAATATTTATTATAATGATGA-
1 AAAAATAATA-TTATTATAATAATGAC
*
219055 AAAAATAATA-T-TTATTATAATGAC
1 AAAAATAATATTATTATAATAATGAC
219079 GAAAAATAAT
1 -AAAAATAAT
219089 GACAACATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 10 0.33
24 1 0.03
25 9 0.30
26 10 0.33
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (26 bp):
AAAAATAATATTATTATAATAATGAC
Found at i:219417 original size:24 final size:25
Alignment explanation
Indices: 219370--219417 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
219360 GTAGAATTTT
*
219370 TTTATTTTAATGATAAAAAATAATA
1 TTTATTATAATGATAAAAAATAATA
*
219395 TTTATTATAATGA-CAAAAATAAT
1 TTTATTATAATGATAAAAAATAAT
219418 GGCACCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
TTTATTATAATGATAAAAAATAATA
Found at i:219652 original size:21 final size:21
Alignment explanation
Indices: 219623--219667 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
219613 AATATGTAAA
219623 TCGCATTGCGATTTTACAAAT
1 TCGCATTGCGATTTTACAAAT
* *
219644 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
219665 TCG
1 TCG
219668 TAACACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:220283 original size:19 final size:20
Alignment explanation
Indices: 220261--220326 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
220251 AAATCGCAAC
220261 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
220280 GCGATTTTCA-TTTCGCATT
1 GCGATTTTCAGTTTCGCGTT
* *
220299 ACGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
220319 GCGATTTT
1 GCGATTTT
220327 ATGTTTCAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
19 25 0.61
20 16 0.39
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:222010 original size:21 final size:21
Alignment explanation
Indices: 221986--222031 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
221976 GTTAGGGGAG
* *
221986 TTACGTGATGAGGTCAATGCT
1 TTACGTGAGGAGGTCAATACT
*
222007 TTACGTGAGGAGGTCGATACT
1 TTACGTGAGGAGGTCAATACT
222028 TTAC
1 TTAC
222032 ATGAAGACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:222093 original size:21 final size:21
Alignment explanation
Indices: 222052--222093 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
222042 TGGTGCATGG
*
222052 TGTGATGAGGTACGGTCTTTA
1 TGTGATGAGGTAAGGTCTTTA
*
222073 TGTGGTGAGGTAGAGGT-TTTA
1 TGTGATGAGGTA-AGGTCTTTA
222094 CGCGATGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.19, C:0.05, G:0.38, T:0.38
Consensus pattern (21 bp):
TGTGATGAGGTAAGGTCTTTA
Found at i:222443 original size:21 final size:21
Alignment explanation
Indices: 222415--222512 Score: 101
Period size: 21 Copynumber: 4.7 Consensus size: 21
222405 GATTCACCTG
222415 TCATCGTTCAAGAGGCCTCTCC
1 TCATCGTTCAAGAGGCC-CTCC
**
222437 T-ATCGTTCAAGAGGCCCTTA
1 TCATCGTTCAAGAGGCCCTCC
* * *
222457 TCATCCTTTAAGAGCCCCTCC
1 TCATCGTTCAAGAGGCCCTCC
* **
222478 -CACCGTTCAAGAGGCCCTTG
1 TCATCGTTCAAGAGGCCCTCC
222498 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
222513 TCTCTCCCAC
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
20 17 0.28
21 42 0.70
22 1 0.02
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.27
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCTCC
Found at i:222490 original size:41 final size:42
Alignment explanation
Indices: 222415--222532 Score: 139
Period size: 41 Copynumber: 2.8 Consensus size: 42
222405 GATTCACCTG
* * * *
222415 TCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCTTA
1 TCATCCTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCTTA
* *
222457 TCATCCTTTAAGA-GCCCCTCCCACCGTTCAAGAGGCCCTTG
1 TCATCCTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCTTA
* * * *
222498 TCATCGTTCAAGAGGTCTCTCCCACCGTTCGAGAG
1 TCATCCTTCAAGAGGCCCCTCCCACCGTTCAAGAG
222533 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 35 0.55
42 29 0.45
ACGTcount: A:0.20, C:0.34, G:0.19, T:0.26
Consensus pattern (42 bp):
TCATCCTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCTTA
Found at i:222526 original size:21 final size:20
Alignment explanation
Indices: 222419--222532 Score: 77
Period size: 21 Copynumber: 5.5 Consensus size: 20
222409 CACCTGTCAT
* *
222419 CGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCC-CTCCCAC
**
222440 CGTTCAAGAGGCCCTTATCATC
1 CGTTCAAGAGGCCC-TCCCA-C
* *
222462 C-TTTAAGAGCCCCTCCCAC
1 CGTTCAAGAGGCCCTCCCAC
** *
222481 CGTTCAAGAGGCCCTTGTCAT
1 CGTTCAAGAGGCCC-TCCCAC
*
222502 CGTTCAAGAGGTCTCTCCCAC
1 CGTTCAAGAGG-CCCTCCCAC
*
222523 CGTTCGAGAG
1 CGTTCAAGAG
222533 CCCGATTCAC
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
19 2 0.03
20 14 0.20
21 51 0.73
22 3 0.04
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.25
Consensus pattern (20 bp):
CGTTCAAGAGGCCCTCCCAC
Found at i:224280 original size:18 final size:18
Alignment explanation
Indices: 224257--224292 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
224247 AAGCCGGTTG
224257 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
224275 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
224293 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:226689 original size:24 final size:24
Alignment explanation
Indices: 226662--226707 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
226652 ATCATCAAAA
226662 TCCGAGTATTGACCAAGATCAATG
1 TCCGAGTATTGACCAAGATCAATG
*
226686 TCCGGGTATTGACCAAGATCAA
1 TCCGAGTATTGACCAAGATCAA
226708 ATTTCGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAATG
Found at i:227465 original size:16 final size:15
Alignment explanation
Indices: 227443--227481 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
227433 ATTTTTTTTT
227443 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
227459 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
227474 AAAAATTA
1 AAAAATTA
227482 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:227724 original size:61 final size:60
Alignment explanation
Indices: 227650--227771 Score: 174
Period size: 61 Copynumber: 2.0 Consensus size: 60
227640 TGTGAAATTA
227650 AAATTCGTGTTGCGAATTCGAAAATCGA-GTTGCGAATTCAGAAATCGAGTTGCAAATTTG
1 AAATTCGTGTTGCGAATTCGAAAATC-ACGTTGCGAATTCAGAAATCGAGTTGCAAATTTG
* * ** *
227710 AAATTCAGTGTTGCGAATTTGTAAATCACGTTGCGAATTTGGAAATCGCGTTGCAAATTTG
1 AAATTC-GTGTTGCGAATTCGAAAATCACGTTGCGAATTCAGAAATCGAGTTGCAAATTTG
227771 A
1 A
227772 CTTATGTGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
60 7 0.13
61 48 0.87
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (60 bp):
AAATTCGTGTTGCGAATTCGAAAATCACGTTGCGAATTCAGAAATCGAGTTGCAAATTTG
Found at i:227848 original size:20 final size:20
Alignment explanation
Indices: 227658--227859 Score: 119
Period size: 20 Copynumber: 10.0 Consensus size: 20
227648 TAAAATTCGT
* *
227658 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAAATCGC
* *
227678 GTTGCGAA-TTCAGAAATCGA
1 GTTGCGAATTTGA-AAATCGC
* * *
227698 GTTGCAAATTTGAAATTCAGT
1 GTTGCGAATTTGAAAATC-GC
* *
227719 GTTGCGAATTTGTAAATCAC
1 GTTGCGAATTTGAAAATCGC
*
227739 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGAAAATCGC
* ** *
227759 GTTGCAAATTTGACTTAT-GT
1 GTTGCGAATTTGA-AAATCGC
*
227779 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGA-A-AATCGC
* *
227799 GTTGCG-ATTT-ACATATTCAC
1 GTTGCGAATTTGA-A-AATCGC
* *
227819 ATTGCAAATTTGAAAATCGC
1 GTTGCGAATTTGAAAATCGC
227839 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAAATCGC
227860 AACGCGAATT
Statistics
Matches: 142, Mismatches: 31, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.01
19 7 0.05
20 97 0.68
21 35 0.25
22 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGC
Found at i:227866 original size:21 final size:21
Alignment explanation
Indices: 227825--227887 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
227815 TCACATTGCA
**
227825 AATTT-GAAAATCGCGTTGCG
1 AATTTGGAAAATCGCAATGCG
*
227845 AATTTGGAAAATCGCAACGCG
1 AATTTGGAAAATCGCAATGCG
* *
227866 AATTCGTAAAATCGCAATGCG
1 AATTTGGAAAATCGCAATGCG
227887 A
1 A
227888 TTTACATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 5 0.14
21 31 0.86
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTTGGAAAATCGCAATGCG
Found at i:231005 original size:3 final size:3
Alignment explanation
Indices: 230990--231027 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
230980 ATTAATTAAT
* *
230990 TAA TAA TAT TAA TAA TAA TGA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
231028 ATTATAACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:233332 original size:112 final size:103
Alignment explanation
Indices: 233196--233470 Score: 254
Period size: 103 Copynumber: 2.6 Consensus size: 103
233186 AAATATAAAT
* * *
233196 TAAACTTACCAATCCACTCGAATACAGTTTAATATATAAAATCAAACTAAATAGTCTAATTAATT
1 TAAACTTACCAAACCACTCAAATACAGTTTAATATATAAAATCAAAATAAATAGTCTAATTAA-T
* *
233261 TTATATTTA-CAATAAAAATCCTAAACCCTAAACAATA-AATTTTACAC
65 TTATA-TTACCAAT-AAAA----AAA---TAAAAAATATAATTTGA-AC
*** * *
233308 TAAACTTACCAAACCACTCAAATAC-GATTTAATCCCTAAAAT-AAAATTAATTAGTCTCA-TAA
1 TAAACTTACCAAACCACTCAAATACAG-TTTAATATATAAAATCAAAA-TAAATAGTCTAATTAA
233370 TTTATATTACTCAATAAAAAAATAAAAAATATAATTTGAAC
64 TTTATATTAC-CAATAAAAAAATAAAAAATATAATTTGAAC
* * ** *
233411 TAAACTTAACAAACTACTCAAATACAACTTAATATGTAAAATCAAAATAAATAGTCTAAT
1 TAAACTTACCAAACCACTCAAATACAGTTTAATATATAAAATCAAAATAAATAGTCTAAT
233471 AGTTATTATT
Statistics
Matches: 136, Mismatches: 19, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
103 54 0.40
104 10 0.07
106 3 0.02
109 3 0.02
110 10 0.07
111 11 0.08
112 45 0.33
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (103 bp):
TAAACTTACCAAACCACTCAAATACAGTTTAATATATAAAATCAAAATAAATAGTCTAATTAATT
TATATTACCAATAAAAAAATAAAAAATATAATTTGAAC
Found at i:233817 original size:25 final size:25
Alignment explanation
Indices: 233789--233841 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
233779 CCATGCATTG
* *
233789 CATTATTGGTGCACAATAATGGCAC
1 CATTATTAGTGCACAATAATGACAC
*
233814 CATTATTAGTGCCCAATAATGACAC
1 CATTATTAGTGCACAATAATGACAC
233839 CAT
1 CAT
233842 GATTCGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (25 bp):
CATTATTAGTGCACAATAATGACAC
Found at i:235766 original size:20 final size:20
Alignment explanation
Indices: 235743--235794 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
235733 AACGCGATCC
235743 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
235763 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
235783 CCAAAATCGCAA
1 CCAGAATCGCAA
235795 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:235892 original size:20 final size:20
Alignment explanation
Indices: 235869--236042 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
235859 GTGAATATGA
* *
235869 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
235889 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
235909 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
235929 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
235949 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
235969 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
235989 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
236009 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
236030 AAATCGCAACGCG
1 AAATCGCAACGCG
236043 ATATTTAAAG
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 113 0.86
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:235919 original size:60 final size:60
Alignment explanation
Indices: 235850--236040 Score: 247
Period size: 60 Copynumber: 3.2 Consensus size: 60
235840 GATTTTCCAT
* ** * *
235850 AATCGCAACGTGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGTGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* *** *
235910 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGTGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * **
235970 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGTGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
236031 AATCGCAACG
1 AATCGCAACG
236041 CGATATTTAA
Statistics
Matches: 110, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 81 0.74
61 29 0.26
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (60 bp):
AATCGCAACGTGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:236463 original size:33 final size:33
Alignment explanation
Indices: 236424--236494 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
236414 TTCACTTAGA
*
236424 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
236457 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
236490 TTTCA
1 TTTCA
236495 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:236634 original size:14 final size:14
Alignment explanation
Indices: 236615--236669 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
236605 AGAATGACTG
236615 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
236629 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
236648 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
236662 TCGCAACG
1 TCGCAACG
236670 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:236652 original size:33 final size:33
Alignment explanation
Indices: 236615--236685 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
236605 AGAATGACTG
**
236615 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
236648 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
236681 TCGCA
1 TCGCA
236686 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:236703 original size:19 final size:19
Alignment explanation
Indices: 236681--236778 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
236671 GAAACCAAAA
*
236681 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
236700 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
236714 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
236733 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
236747 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
236766 TCGCGTTGCGATT
1 TCGCGTTGCGATT
236779 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:236722 original size:14 final size:14
Alignment explanation
Indices: 236703--236792 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
236693 TTTCATTTCG
236703 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
236717 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
236736 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
236750 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
236767 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
236783 CGTTGCGATT
1 CGTTGCGATT
236793 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:236728 original size:33 final size:33
Alignment explanation
Indices: 236686--236800 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
236676 CAAAATCGCA
236686 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
236719 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
236752 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
236785 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
236801 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:238729 original size:185 final size:185
Alignment explanation
Indices: 238499--238970 Score: 926
Period size: 185 Copynumber: 2.6 Consensus size: 185
238489 TAGATTGCTT
*
238499 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
238564 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
238629 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
238684 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
238749 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
238814 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
238869 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
238934 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
238971 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 285 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:238813 original size:93 final size:93
Alignment explanation
Indices: 238499--238970 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
238489 TAGATTGCTT
*
238499 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
238564 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
238592 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
238656 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
238684 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
238749 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
238777 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
238841 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
238869 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
238934 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
238962 AGTAAATTT
1 AGTAAATTT
238971 ATCCATTCAA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.49
93 191 0.51
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:239054 original size:19 final size:19
Alignment explanation
Indices: 239014--239142 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
239004 TAGTTTACTT
* *
239014 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
239034 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
239053 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
239072 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
239086 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
239105 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
239119 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
239138 TCGCA
1 TCGCA
239143 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:239093 original size:33 final size:32
Alignment explanation
Indices: 239050--239142 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
239040 CGCGAAACCA
**
239050 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
239082 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
239115 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
239143 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:239140 original size:52 final size:52
Alignment explanation
Indices: 239014--239142 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
239004 TAGTTTACTT
**
239014 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
239066 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
239119 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
239143 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:239160 original size:19 final size:19
Alignment explanation
Indices: 239138--239272 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
239128 GAAACCAAAA
*
239138 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
239157 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
239173 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
239190 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
239206 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
239223 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
239242 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
239262 TCGTGTTGCGA
1 TCGCGTTGCGA
239273 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:239179 original size:14 final size:14
Alignment explanation
Indices: 239160--239216 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
239150 TTTCATTTCG
239160 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
239174 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
239191 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
239207 CGTTGCGATT
1 CGTTGCGATT
239217 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:239185 original size:33 final size:33
Alignment explanation
Indices: 239143--239235 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
239133 CAAAATCGCA
*
239143 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
239176 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
239209 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
239236 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:241197 original size:14 final size:14
Alignment explanation
Indices: 241178--241213 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
241168 ATTGTTTAAT
241178 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
241192 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
241206 TGATTTGT
1 TGATTTGT
241214 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:241336 original size:19 final size:19
Alignment explanation
Indices: 241320--241421 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
241310 AAAAATGACT
241320 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
241339 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
241358 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
241372 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
241391 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
241411 ATCGCAATGCG
1 ATCGCAATGCG
241422 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:241474 original size:19 final size:19
Alignment explanation
Indices: 241450--241742 Score: 383
Period size: 19 Copynumber: 16.4 Consensus size: 19
241440 GATTATCTCG
241450 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
241469 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
241488 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
241502 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
241521 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
241540 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
241559 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
241578 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
241597 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
241616 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
241630 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
241649 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
241668 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
241682 TTGCGATTTTTATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
241702 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
241716 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
241735 TTGCGATT
1 TTGCGATT
241743 GTATTTTTCG
Statistics
Matches: 243, Mismatches: 10, Indels: 42
0.82 0.03 0.14
Matches are distributed among these distances:
14 29 0.12
16 23 0.09
17 20 0.08
18 3 0.01
19 157 0.65
20 11 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:241490 original size:52 final size:52
Alignment explanation
Indices: 241428--241742 Score: 321
Period size: 52 Copynumber: 5.9 Consensus size: 52
241418 TGCGTTTATA
*
241428 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
241480 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
241532 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
241589 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
241641 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTT
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
241693 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
241743 GTATTTTTCG
Statistics
Matches: 240, Mismatches: 10, Indels: 25
0.87 0.04 0.09
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 4 0.02
52 128 0.53
53 18 0.08
54 6 0.03
55 8 0.03
57 62 0.26
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:244040 original size:12 final size:12
Alignment explanation
Indices: 244023--244047 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
244013 TCTTCGGGGA
244023 CTTTTTCTTCTT
1 CTTTTTCTTCTT
244035 CTTTTTCTTCTT
1 CTTTTTCTTCTT
244047 C
1 C
244048 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:244256 original size:24 final size:24
Alignment explanation
Indices: 244222--244268 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
244212 CTGAAACATC
244222 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
244246 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
244269 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:244979 original size:20 final size:20
Alignment explanation
Indices: 244951--245319 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
244941 AAATTTAAGT
* * * *
244951 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
244971 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
244991 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
245011 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
245031 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
245051 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
245071 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
245091 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
245111 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
245131 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
245151 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
245171 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
245191 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
245211 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
245231 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
245251 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
245271 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
245291 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
245311 GTTGCGATT
1 GTTGCGATT
245320 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:246108 original size:32 final size:33
Alignment explanation
Indices: 246054--246116 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
246044 TATGTTAGAT
** *
246054 AAAAAAATGAAAATAAATAGAATAAAGAAAATA
1 AAAAAAACCAAAATAAATAGAATAAAAAAAATA
246087 AAAAAAACCAAAATAAA-AGAATAAAAAAAA
1 AAAAAAACCAAAATAAATAGAATAAAAAAAA
246117 GAGTGAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.11
Consensus pattern (33 bp):
AAAAAAACCAAAATAAATAGAATAAAAAAAATA
Found at i:246205 original size:43 final size:43
Alignment explanation
Indices: 246124--246205 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
246114 AAAGAGTGAA
*
246124 GATAAAAATAAATACGATAATAAAAATAAAATGAAAAAAGAAT
1 GATAAAAATAAATACGATAATAAAAATAAAATAAAAAAAGAAT
* *
246167 GATAATAATATATAC-ATAATAAACAAGT-AAATAAAAAAA
1 GATAAAAATAAATACGATAATAAA-AA-TAAAATAAAAAAA
246206 TAAAAAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 8 0.24
43 25 0.74
44 1 0.03
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.21
Consensus pattern (43 bp):
GATAAAAATAAATACGATAATAAAAATAAAATAAAAAAAGAAT
Found at i:246599 original size:21 final size:21
Alignment explanation
Indices: 246575--246617 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
246565 AAAATGTTTT
*
246575 AAAAA-ATAATAATAAATTAAA
1 AAAAAGATAA-AATAAAATAAA
246596 AAAAAGATAAAATAAAATAAA
1 AAAAAGATAAAATAAAATAAA
246617 A
1 A
246618 CATATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (21 bp):
AAAAAGATAAAATAAAATAAA
Found at i:246605 original size:16 final size:17
Alignment explanation
Indices: 246577--246617 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
246567 AATGTTTTAA
* *
246577 AAAATAATA-ATAAATT
1 AAAATAAAAGATAAAAT
246593 AAAA-AAAAGATAAAAT
1 AAAATAAAAGATAAAAT
246609 AAAATAAAA
1 AAAATAAAA
246618 CATATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 14 0.67
17 4 0.19
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAATAAAAGATAAAAT
Found at i:246617 original size:19 final size:19
Alignment explanation
Indices: 246595--246634 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
246585 AATAAATTAA
246595 AAAAAAGATAAAATAAAAT
1 AAAAAAGATAAAATAAAAT
* * *
246614 AAAACATATAAAATATAAT
1 AAAAAAGATAAAATAAAAT
246633 AA
1 AA
246635 TAATAGTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (19 bp):
AAAAAAGATAAAATAAAAT
Found at i:246766 original size:22 final size:22
Alignment explanation
Indices: 246738--246784 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
246728 TAGCCTCGGG
246738 GTTCCGTAGATCTAAAAAGTTA
1 GTTCCGTAGATCTAAAAAGTTA
246760 GTTCCGTAGATCTAAAAAGTTA
1 GTTCCGTAGATCTAAAAAGTTA
246782 GTT
1 GTT
246785 TCGAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (22 bp):
GTTCCGTAGATCTAAAAAGTTA
Found at i:247077 original size:37 final size:37
Alignment explanation
Indices: 247023--247171 Score: 280
Period size: 37 Copynumber: 4.0 Consensus size: 37
247013 ATGCTTATGG
247023 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
247060 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
247097 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
247134 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
247171 A
1 A
247172 ACGTTATGTT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 109 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:248524 original size:110 final size:110
Alignment explanation
Indices: 248311--248825 Score: 825
Period size: 110 Copynumber: 4.7 Consensus size: 110
248301 TTGTGTCGCT
* * *
248311 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTAACTCTGAATGAAA-TGAGAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
248375 TGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
248420 TCGAGTCCAATATCATTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAGGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
248485 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
248530 TCGAGTCTAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAGTTGTATG
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG-AAAAGTTGTTTG
* * * * *
248595 TTAATAGTTAGTCGCCCATTCGCGGTGAAGTTGAGCTTGTGTTGTC
65 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
*
248641 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTATGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
248706 TGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* ** *
248751 TCAAGTCCAATATCCTTCGCTGTGAAAATGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
248816 TGACAGTCAG
66 TGACAGTCAG
248826 CTTGTCTCGA
Statistics
Matches: 374, Mismatches: 30, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
109 45 0.12
110 229 0.61
111 100 0.27
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:248707 original size:221 final size:221
Alignment explanation
Indices: 248311--248825 Score: 795
Period size: 221 Copynumber: 2.3 Consensus size: 221
248301 TTGTGTCGCT
* * *
248311 TCGAGT-TCAATATCCTTCGCTGTGAAGTTGAAATTAACTCTGAATGAAA-TG-AGAAGTTGTTT
1 TCGAGTCT-AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAGTTGTAT
* * *
248373 GTTGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTC
65 GTTAACAGTCAGTCGCCCATTCACGGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTC
* *
248438 ACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAGGTTGTTTGTTGACAGTCAGTCGCCCCT
130 ACTGTGAAGTTGAAATTGACTATGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCT
248503 TCGCTGTGAAGTTGAGCTTGTGTTGTC
195 TCGCTGTGAAGTTGAGCTTGTGTTGTC
*
248530 TCGAGTCTAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAGTTGTATG
1 TCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAGTTGTATG
* * * * *
248595 TTAATAGTTAGTCGCCCATTCGCGGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCG
66 TTAACAGTCAGTCGCCCATTCACGGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTCA
*
248660 CTGTGAAGTTGAAATTGACTATGAATGAAACTGAAAAGTTGTTTGTTGATAGTCAGTCGCCCCTT
131 CTGTGAAGTTGAAATTGACTATGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTT
248725 CGCTGTGAAGTTGAGCTTGTGTTGTC
196 CGCTGTGAAGTTGAGCTTGTGTTGTC
* * ** * *
248751 TCAAGTCCAATATCCTTCGCTGTGAAAATGAAATTGACTCTGAATGAAACTG-AAAAGTTATTTG
1 TCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAGTTGTATG
*
248815 TTGACAGTCAG
66 TTAACAGTCAG
248826 CTTGTCTCGA
Statistics
Matches: 268, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
219 45 0.17
220 21 0.08
221 202 0.75
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (221 bp):
TCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAGTTGTATG
TTAACAGTCAGTCGCCCATTCACGGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTCA
CTGTGAAGTTGAAATTGACTATGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTT
CGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:250160 original size:18 final size:18
Alignment explanation
Indices: 250137--250173 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
250127 CTGATGGACG
250137 GGATGAAATCTGAAGATA
1 GGATGAAATCTGAAGATA
250155 GGATGAAATCTGAAGATA
1 GGATGAAATCTGAAGATA
250173 G
1 G
250174 TCTCTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.30, T:0.22
Consensus pattern (18 bp):
GGATGAAATCTGAAGATA
Found at i:250547 original size:14 final size:13
Alignment explanation
Indices: 250530--250583 Score: 67
Period size: 12 Copynumber: 4.2 Consensus size: 13
250520 TTTGTTTTTG
*
250530 TTTCTCTTTTTTAT
1 TTTCTCTTTGTT-T
250544 TTTCTCTTTGTTT
1 TTTCTCTTTGTTT
250557 TTTC-CTTTGTTT
1 TTTCTCTTTGTTT
*
250569 TTTCACTTT-TTT
1 TTTCTCTTTGTTT
250581 TTT
1 TTT
250584 GTTCTGATTG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
12 18 0.47
13 9 0.24
14 11 0.29
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.78
Consensus pattern (13 bp):
TTTCTCTTTGTTT
Found at i:250558 original size:12 final size:12
Alignment explanation
Indices: 250513--250583 Score: 63
Period size: 12 Copynumber: 5.4 Consensus size: 12
250503 TTTTCTTCAC
250513 TTTTTCCTTTGTTT
1 TTTTTCCTTTG--T
*
250527 TTGTTTCTCTTTTT
1 TT-TTTC-CTTTGT
250541 TATTTTCTCTTTGT
1 T-TTTTC-CTTTGT
250555 TTTTTCCTTTGT
1 TTTTTCCTTTGT
250567 TTTTTCACTTT-T
1 TTTTTC-CTTTGT
250579 TTTTT
1 TTTTT
250584 GTTCTGATTG
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
12 18 0.35
13 9 0.18
14 15 0.29
15 5 0.10
16 4 0.08
ACGTcount: A:0.03, C:0.14, G:0.06, T:0.77
Consensus pattern (12 bp):
TTTTTCCTTTGT
Found at i:253807 original size:29 final size:29
Alignment explanation
Indices: 253746--253810 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
253736 ATAAACAAGT
*
253746 AAATAAAAAAATAAAAAGAAAATACAAAT
1 AAATAAAAAAATAAAAAGAAAATACAAAA
** *
253775 AAATAAAACAAATTTAAAGAAGATA-AAAA
1 AAATAAAA-AAATAAAAAGAAAATACAAAA
253804 AAATAAA
1 AAATAAA
253811 GATAAGGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (29 bp):
AAATAAAAAAATAAAAAGAAAATACAAAA
Found at i:254035 original size:2 final size:2
Alignment explanation
Indices: 254030--254067 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
254020 AGAAAAAATG
254030 TA TA TA TA 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
254068 ATAGTAATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:254216 original size:19 final size:20
Alignment explanation
Indices: 254177--254217 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
254167 AAAATGTTTT
* *
254177 AAAAAATAATAATAAATTAA
1 AAAAAATAATAACAAAATAA
254197 AAAAAATAA-AACAAAATAA
1 AAAAAATAATAACAAAATAA
254216 AA
1 AA
254218 CATATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAAAATAATAACAAAATAA
Found at i:254653 original size:37 final size:37
Alignment explanation
Indices: 254603--254710 Score: 189
Period size: 37 Copynumber: 2.9 Consensus size: 37
254593 TTATGGATCT
254603 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
*
254640 TATTTTTAGGAGTTTGAATCATGGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
**
254677 TATTTTTAGGAGTTTGAATTTTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
254711 ACGTTATGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
Found at i:259845 original size:11 final size:11
Alignment explanation
Indices: 259829--259853 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
259819 CTCACGTGAC
259829 ATAATATATAT
1 ATAATATATAT
259840 ATAATATATAT
1 ATAATATATAT
259851 ATA
1 ATA
259854 TTAAATATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATATATAT
Found at i:260666 original size:12 final size:12
Alignment explanation
Indices: 260625--260674 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
260615 AAATAATAAA
260625 AAATAAAAATAG
1 AAATAAAAATAG
*
260637 ACATATAAAAATAA
1 A-A-ATAAAAATAG
*
260651 AAATAAAAATTG
1 AAATAAAAATAG
*
260663 AAATAATAATAG
1 AAATAAAAATAG
260675 TTATATAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 19 0.61
13 2 0.06
14 10 0.32
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (12 bp):
AAATAAAAATAG
Found at i:261251 original size:134 final size:134
Alignment explanation
Indices: 260858--261431 Score: 794
Period size: 134 Copynumber: 4.3 Consensus size: 134
260848 CTGTTTCTGC
* * * * * * *
260858 AGGGTAGATCAGA-TCGAG-AAACGTTGATTCA-TTCCACTGTTTTTCATGGAAGATTGAATCAT
1 AGGGGAGATCAGACTCGAGAAAACTTTGATCCACTT-CACTATTCTTCAGGGAAGATTGAATCAA
* *
260920 AATCGATTTGCTTCACTGCTCTTCAGGAAGACTAAATCTGAAAGAAGAAGAATATGCTCCACTAC
65 AATCAATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTCCACTAC
260985 TCTTT
130 TCTTT
* * * *
260990 AAGGGAGATCAGACTCGAGAAAAATTTGATCCGCTTCACTGTTCTTCAGGAAGAAGATTGAATCA
1 AGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAGG--GAAGATTGAATCA
*
261055 AAATCAATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTA
64 AAATCAATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTCCACTA
261120 CTCTTT
129 CTCTTT
* * *
261126 AGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCAGTACTCTTCAGGGAAGATTGAATCAAA
1 AGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAGGGAAGATTGAATCAAA
* * * ** *
261191 ATCGATTTGCTTCACTACTCTTCAGGAAGACCAAATTTGAAAGAAGAAGAATATATTCCACCACT
66 ATCAATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTCCACTACT
261256 CTTT
131 CTTT
* * * *
261260 AGGAGAGACCAGACTCGAGAAAACTTTGATCCACTTTACTATTCTTCAGGGAAGATTGAATCAGA
1 AGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAGGGAAGATTGAATCAAA
* * *
261325 ATCAATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAAGAAGAAGAATGTTCTCCACTACT
66 ATCAATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTCCACTACT
261390 CTTT
131 CTTT
* * * *
261394 AGGGGATATCAGACTCAAGAAATCTTTGATCTACTTCA
1 AGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
261432 ATGCTCTTTA
Statistics
Matches: 389, Mismatches: 48, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
132 11 0.03
133 5 0.01
134 248 0.64
135 2 0.01
136 123 0.32
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (134 bp):
AGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAGGGAAGATTGAATCAAA
ATCAATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTCCACTACT
CTTT
Found at i:261470 original size:268 final size:269
Alignment explanation
Indices: 260907--261500 Score: 825
Period size: 268 Copynumber: 2.2 Consensus size: 269
260897 TTTTTCATGG
* * *
260907 AAGATTGAATCATAATCGATTTGCTTCACTGCTCTTCAGGAAGACTAAATCTGAAAGAAGAAGAA
1 AAGATTAAATCAAAATCGATTTGCTTCACTACTCTTCAGGAAGACTAAATCTGAAAGAAGAAGAA
* * * * *
260972 TATGCTCCACTACTCTTTAAGGGAGATCAGACTCGAGAAAAATTTGATCCGCTTCACTGTTCTTC
66 TATACTCCACCACTCTTTAAGGGAGACCAGACTCGAGAAAAATTTGATCCACTTCACTATTCTTC
*
261037 AGGAAGAAGATTGAATCAAAATCAATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAA
131 AGG-AGAAGATTGAATCAAAATCAATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAAGAA
* *
261102 GAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCAGTA
195 GAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAACTCAAGAAAACTTTGATCCACTTCAATA
* *
261167 CTCTTCAGGG
260 CTCTTCAAGA
* * *
261177 AAGATTGAATCAAAATCGATTTGCTTCACTACTCTTCAGGAAGACCAAATTTGAAAGAAGAAGAA
1 AAGATTAAATCAAAATCGATTTGCTTCACTACTCTTCAGGAAGACTAAATCTGAAAGAAGAAGAA
* * *
261242 TATATTCCACCACTCTTT-AGGAGAGACCAGACTCGAGAAAACTTTGATCCACTTTACTATTCTT
66 TATACTCCACCACTCTTTAAGG-GAGACCAGACTCGAGAAAAATTTGATCCACTTCACTATTCTT
*
261306 CAGG-GAAGATTGAATCAGAATCAATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAAGAA
130 CAGGAGAAGATTGAATCAAAATCAATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAAGAA
* * * * * * *
261370 GAAGAATGTTCTCCACTACTCTTTAGGGGATATCAGACTCAAGAAATCTTTGATCTACTTCAATG
195 GAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAACTCAAGAAAACTTTGATCCACTTCAATA
*
261435 CTCTTTAAGA
260 CTCTTCAAGA
** * * ** *
261445 AAGATTAAAT-TGAATGTGGTTTGCTTTGCTTCTCTTCAGGAAGACTAAATCTGAAA
1 AAGATTAAATCAAAAT-CGATTTGCTTCACTACTCTTCAGGAAGACTAAATCTGAAA
261501 ATCAAACATT
Statistics
Matches: 286, Mismatches: 36, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
267 3 0.01
268 163 0.57
269 3 0.01
270 117 0.41
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (269 bp):
AAGATTAAATCAAAATCGATTTGCTTCACTACTCTTCAGGAAGACTAAATCTGAAAGAAGAAGAA
TATACTCCACCACTCTTTAAGGGAGACCAGACTCGAGAAAAATTTGATCCACTTCACTATTCTTC
AGGAGAAGATTGAATCAAAATCAATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAAGAAG
AAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAACTCAAGAAAACTTTGATCCACTTCAATAC
TCTTCAAGA
Found at i:262281 original size:80 final size:77
Alignment explanation
Indices: 262148--262671 Score: 422
Period size: 80 Copynumber: 6.5 Consensus size: 77
262138 TACAATACTG
* * * *
262148 AAAGATTGAATTCTCTTCATGAGAAAGTCAAGAATGACAATGAAAGATTGAC-TCATCTTCACGA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-A--AAAGATTGACTTC-TCTTCACGA
*
262212 GGGAGTCAAGAATAAC
62 GGAAGTCAAGAATAAC
* *
262228 AAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAATATTGA---CTCTTCACGAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA---AAAGATTGACTTCTCTTCACGAG
*
262290 GGAGTCAAGAA-AGAC
63 GAAGTCAAGAATA-AC
* * * * *
262305 AATACCGAAATATTGACTTATCTTCATGAGAAAGTCAAGAATGACATTGAAAGATTGAC-TCTTT
1 AA-A--G----ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA---AAAGATTGACTTC-TC
*
262369 TTCACGAGGGAGTCAAGAATAAC
55 TTCACGAGGAAGTCAAGAATAAC
* * *
262392 AAAGATTGACTTTTCTTCACGAGG-AG-CTAAGAATAAC-AAAGATTGACATCTCTTCACGAAGA
1 AAAGATTGACTTCTCTTCACGAGGAAGTC-AAGAATAACAAAAGATTGACTTCTCTTCACGAGGA
*
262454 AGTCAAGAATGACATTG
65 AGTCAAGAAT-A-A--C
* * * * *
262471 AAAGATTGAATCCTCTTCACGAGGGAGTTAAGAATAAC-AAAGATTGACTTCTCTTCATGAGGAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAAGATTGACTTCTCTTCACGAGGAA
262535 GTCAAGAATAAC
66 GTCAAGAATAAC
* *
262547 TTTGAAAGATTGACTCCTCTTCACGAGGGAGTCAAGAATAAC-AAAGATTGACTTCTCTTCACGA
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAAGATTGACTTCTCTTCACGA
262611 GGAAGTCAAGAATAAC
62 GGAAGTCAAGAATAAC
* * * *
262627 ATTGAAATATTGACTCCTCTTCATGAGGGAGTCAAGAATAACAAA
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAA
262672 TTCATGAACA
Statistics
Matches: 383, Mismatches: 35, Indels: 51
0.82 0.07 0.11
Matches are distributed among these distances:
75 29 0.08
76 4 0.01
77 26 0.07
78 4 0.01
79 33 0.09
80 216 0.56
81 2 0.01
84 42 0.11
86 2 0.01
87 24 0.06
88 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (77 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAAGATTGACTTCTCTTCACGAGGAA
GTCAAGAATAAC
Found at i:262667 original size:42 final size:42
Alignment explanation
Indices: 262146--262669 Score: 492
Period size: 42 Copynumber: 13.0 Consensus size: 42
262136 ATTACAATAC
* * ** * *
262146 TGAAAGATTGAATTCTCTTCATGAGAAAGTCAAGAATGACAA
1 TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATAACAT
262188 TGAAAGATTGAC-TCATCTTCACGAGGGAGTCAAGAATAAC--
1 TGAAAGATTGACTTC-TCTTCACGAGGGAGTCAAGAATAACAT
* *
262228 --AAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAT
1 TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATAACAT
*
262268 TGAAATATTGA---CTCTTCACGAGGGAGTCAAGAA-AGACAAT
1 TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATA-AC-AT
* * * * ** *
262308 ACCGAAATATTGACTTATCTTCATGAGAAAGTCAAGAATGACAT
1 --TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATAACAT
*
262352 TGAAAGATTGAC-TCTTTTTCACGAGGGAGTCAAGAATAAC--
1 TGAAAGATTGACTTC-TCTTCACGAGGGAGTCAAGAATAACAT
*
262392 --AAAGATTGACTTTTCTTCACGA-GGAG-CTAAGAATAAC--
1 TGAAAGATTGACTTCTCTTCACGAGGGAGTC-AAGAATAACAT
* * * *
262429 --AAAGATTGACATCTCTTCACGAAGAAGTCAAGAATGACAT
1 TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATAACAT
* * *
262469 TGAAAGATTGAATCCTCTTCACGAGGGAGTTAAGAATAAC--
1 TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATAACAT
* * *
262509 --AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACTT
1 TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATAACAT
*
262549 TGAAAGATTGACTCCTCTTCACGAGGGAGTCAAGAATAAC--
1 TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATAACAT
*
262589 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAT
1 TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATAACAT
* * *
262629 TGAAATATTGACTCCTCTTCATGAGGGAGTCAAGAATAACA
1 TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATAACA
262670 AATTCATGAA
Statistics
Matches: 400, Mismatches: 51, Indels: 62
0.78 0.10 0.12
Matches are distributed among these distances:
36 1 0.00
37 33 0.08
38 132 0.33
39 27 0.07
40 2 0.00
41 3 0.01
42 180 0.45
44 2 0.00
45 20 0.05
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (42 bp):
TGAAAGATTGACTTCTCTTCACGAGGGAGTCAAGAATAACAT
Found at i:264443 original size:17 final size:16
Alignment explanation
Indices: 264423--264546 Score: 103
Period size: 17 Copynumber: 7.5 Consensus size: 16
264413 TCTTTTCCCC
264423 TTTTTCTTTTCTATCTT
1 TTTTTCTTTTCT-TCTT
264440 TTTTT-TTCTTCTTTCTT
1 TTTTTCTT-TTC-TTCTT
*
264457 TTTTTC-TTTCTTTTCT
1 TTTTTCTTTTCTTCT-T
*
264473 TTTTTCTTTCCTT-TT
1 TTTTTCTTTTCTTCTT
*
264488 CTTTT-TTTTCTTCTTT
1 TTTTTCTTTTCTTC-TT
264504 TTTTTCTTTTCTTTTCTT
1 TTTTTCTTTTC--TTCTT
* *
264522 TTTTCCTTTTTTCTCTT
1 TTTTTCTTTTCT-TCTT
264539 TTTTTCTT
1 TTTTTCTT
264547 CTCTCTCCTT
Statistics
Matches: 88, Mismatches: 8, Indels: 22
0.75 0.07 0.19
Matches are distributed among these distances:
14 6 0.07
15 8 0.09
16 20 0.23
17 39 0.44
18 12 0.14
19 3 0.03
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTCTTCTT
Found at i:264458 original size:12 final size:12
Alignment explanation
Indices: 264425--264548 Score: 101
Period size: 12 Copynumber: 10.1 Consensus size: 12
264415 TTTTCCCCTT
264425 TTTCTTTTCTATC
1 TTTCTTTTCT-TC
*
264438 TTTTTTTTTCTTC
1 -TTTCTTTTCTTC
*
264451 TTTCTTTTTTTC
1 TTTCTTTTCTTC
*
264463 TTTCTTTTCTTT
1 TTTCTTTTCTTC
*
264475 TTTCTTTCCTTTTC
1 TTTCTTT--TCTTC
*
264489 TTTTTTTTCTTC
1 TTTCTTTTCTTC
*
264501 TTTTTTTTC-T-
1 TTTCTTTTCTTC
*
264511 TTTCTTTTCTTT
1 TTTCTTTTCTTC
264523 TTTCCTTTT-TTC
1 TTT-CTTTTCTTC
*
264535 TCTTTTTTTCTTC
1 T-TTCTTTTCTTC
264548 T
1 T
264549 CTCTCCTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
10 8 0.09
11 2 0.02
12 50 0.55
13 13 0.14
14 18 0.20
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTCTTTTCTTC
Found at i:264474 original size:34 final size:32
Alignment explanation
Indices: 264423--264548 Score: 130
Period size: 34 Copynumber: 3.8 Consensus size: 32
264413 TCTTTTCCCC
*
264423 TTTTTCTTTTCTATCTTTTTTTTTCTTCTTTCTT
1 TTTTTCTTTT-TTTCTTTTTTTTTCTT-TTTCTT
*
264457 TTTTTCTTTCTTTTCTTTTTTCTTTCCTTTTCTTT
1 TTTTTCTTT-TTTTCTTTTTT-TTTCTTTTTC-TT
* *
264492 TTTTTCTTCTTTT-TTTTCTTTTC-TTTTCTT
1 TTTTTCTTTTTTTCTTTTTTTTTCTTTTTCTT
*
264522 TTTTCCTTTTTTCTCTTTTTTTCTTCT
1 TTTTTCTTTTTT-TCTTTTTTT-TTCT
264549 CTCTCCTTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
30 12 0.15
31 6 0.08
32 10 0.13
33 8 0.10
34 26 0.33
35 16 0.21
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (32 bp):
TTTTTCTTTTTTTCTTTTTTTTTCTTTTTCTT
Found at i:264511 original size:47 final size:47
Alignment explanation
Indices: 264439--264550 Score: 156
Period size: 47 Copynumber: 2.3 Consensus size: 47
264429 TTTTCTATCT
*
264439 TTTTTTTTCTTCTTTCTTTTTTTC-TTTCTTTTCTTTTTTCTTTCCTTTTC
1 TTTTTTTTCTTC--TCTTTTTTTCTTTTCTTTTCTTTTTTCCTT--TTTTC
264489 TTTTTTTTCTTCT-TTTTTTTCTTTTCTTTTCTTTTTTCCTTTTTTC
1 TTTTTTTTCTTCTCTTTTTTTCTTTTCTTTTCTTTTTTCCTTTTTTC
264535 TCTTTTTTTCTTCTCT
1 T-TTTTTTTCTTCTCT
264551 CTCCTTTTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
46 6 0.10
47 20 0.34
48 20 0.34
50 12 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (47 bp):
TTTTTTTTCTTCTCTTTTTTTCTTTTCTTTTCTTTTTTCCTTTTTTC
Found at i:264553 original size:17 final size:17
Alignment explanation
Indices: 264423--264573 Score: 91
Period size: 17 Copynumber: 8.9 Consensus size: 17
264413 TCTTTTCCCC
* *
264423 TTTTTCTTTTCTATCTT
1 TTTTTCTTCTCTCTCTT
*
264440 TTTTT-TTCTTCTTTCTT
1 TTTTTCTTC-TCTCTCTT
*
264457 TTTTTCTT-TCT-TTTCT
1 TTTTTCTTCTCTCTCT-T
*
264473 TTTTTCTT-TC-CTTTT
1 TTTTTCTTCTCTCTCTT
*
264488 CTTTTTTTTCT-TCT-TT
1 -TTTTTCTTCTCTCTCTT
* *
264504 TTTTTCTTTTCTTTTCTT
1 TTTTTCTTCTC-TCTCTT
* * *
264522 TTTTCCTTTTTTCTCTT
1 TTTTTCTTCTCTCTCTT
264539 TTTTTCTTCTCTCTCCTT
1 TTTTTCTTCTCTCT-CTT
*
264557 TTTATCTCTCTCTCTCT
1 TTTTTCT-TCTCTCTCT
264574 CTATATTTTT
Statistics
Matches: 108, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
15 11 0.10
16 28 0.26
17 38 0.35
18 24 0.22
19 7 0.06
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTTCTCTCTCTT
Found at i:264558 original size:35 final size:37
Alignment explanation
Indices: 264451--264559 Score: 104
Period size: 35 Copynumber: 3.1 Consensus size: 37
264441 TTTTTTCTTC
* * *
264451 TTTCTTTTTTTCTTTCTTTTCTTT-TT-TCTTTCCTTT
1 TTTCCTTTTTTC-TTCTTTTTTTTCTTCTCTCTCCTTT
* * *
264487 TCTT--TTTTTTCTTCTTTTTTTTCTTTTCTTTTCTTT
1 T-TTCCTTTTTTCTTCTTTTTTTTCTTCTCTCTCCTTT
264523 TTTCCTTTTTTC-TC-TTTTTTTCTTCTCTCTCCTTT
1 TTTCCTTTTTTCTTCTTTTTTTTCTTCTCTCTCCTTT
264558 TT
1 TT
264560 ATCTCTCTCT
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
34 10 0.16
35 31 0.49
36 13 0.21
37 9 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (37 bp):
TTTCCTTTTTTCTTCTTTTTTTTCTTCTCTCTCCTTT
Found at i:264559 original size:65 final size:64
Alignment explanation
Indices: 264429--264559 Score: 153
Period size: 65 Copynumber: 2.0 Consensus size: 64
264419 CCCCTTTTTC
* * *
264429 TTTTCTATCTTTTTTTTTCTTCTTTCTTTTTTTCTTTCTTTTCTTTTTTCTTTCCTTTTCTTTT
1 TTTTCTATCTTTTTTTTTCTTCTTTCTTTTTTCCTTTCTTTTCTTTTTTCTTTCCTTCTCCTTT
*
264493 TTTTCT-TCTTTTTTTTCTTTTCTTTTCTTTTTTCCTTT-TTTCTCTTTTTT-TCTT-CTCTCTC
1 TTTTCTATCTTTTTTTT-TCTTC-TTTCTTTTTTCCTTTCTTT-TCTTTTTTCT-TTCCT-TCTC
264554 CTTT
61 CTTT
264558 TT
1 TT
264560 ATCTCTCTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
63 10 0.17
64 16 0.28
65 32 0.55
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.79
Consensus pattern (64 bp):
TTTTCTATCTTTTTTTTTCTTCTTTCTTTTTTCCTTTCTTTTCTTTTTTCTTTCCTTCTCCTTT
Found at i:266030 original size:14 final size:14
Alignment explanation
Indices: 266007--266045 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
265997 ACATGTTAAG
266007 ATGCAATGTATATT
1 ATGCAATGTATATT
*
266021 ATGTAATGTATATT
1 ATGCAATGTATATT
266035 ATGCAATGTAT
1 ATGCAATGTAT
266046 GAGTATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (14 bp):
ATGCAATGTATATT
Found at i:266042 original size:28 final size:31
Alignment explanation
Indices: 266007--266071 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
265997 ACATGTTAAG
*
266007 ATGCAATGTAT-A-T-TATGT-AATGTATATT
1 ATGCAATGTATGAGTATATGTGAATGTACA-T
266035 ATGCAATGTATGAGTATATGTGAATGTACAT
1 ATGCAATGTATGAGTATATGTGAATGTACAT
266066 ATGCAA
1 ATGCAA
266072 AAATGCATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 11 0.34
29 1 0.03
30 1 0.03
31 12 0.38
32 7 0.22
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.38
Consensus pattern (31 bp):
ATGCAATGTATGAGTATATGTGAATGTACAT
Done.