Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006981.1 Hibiscus syriacus cultivar Beakdansim tig00017984_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: 188633
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:156577 original size:40 final size:40
Alignment explanation
Indices: 156522--157052 Score: 708
Period size: 40 Copynumber: 13.3 Consensus size: 40
156512 AATACGGAAT
*
156522 ATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
* * *
156562 ATTTTATCTCACTCAAAATTG-TTTTCCTTGAAACATAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
** *
156601 ATTTTATCTCATTCAAGATTGTTTTTCCTCGAAACAGAA-
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
* *
156640 ATTTTATCTCACTCAAGATTGTTTTTCCTCGAAACAGAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
*
156680 ATTTTATCTCGCTCAAGATTGTTTTTCCTCGAAACAGAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
**
156720 ATTTTATCTCGCAAAAGATTGTTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
** * * *
156760 ATTTTATCTCATTCAATATTATTTTTCGTTGAAACAGAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
156800 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
156840 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAAACAGAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTG-AAACAGAAG
* * * * *
156881 ATTTTATCTCACTAAATATTGTTTTCCCTTGAAACATAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
** * *
156921 ATTTTATCTCGCTTGAGATTATTTTTCCTCGAAACAGAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
** * *
156961 ATTTTATCTCGCTTGAGATTGTTTTTCCTAGAAACAAAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
** * * * *
157001 ATTTTATCTCGCTTGAGATAG-TTTCCCTCGAAACAAAAG
1 ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
157040 ATTTTATCTCGCT
1 ATTTTATCTCGCT
157053 TGAGATAGTT
Statistics
Matches: 446, Mismatches: 42, Indels: 7
0.90 0.08 0.01
Matches are distributed among these distances:
39 103 0.23
40 307 0.69
41 36 0.08
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.40
Consensus pattern (40 bp):
ATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAG
Found at i:156690 original size:20 final size:20
Alignment explanation
Indices: 156667--156769 Score: 65
Period size: 20 Copynumber: 5.2 Consensus size: 20
156657 ATTGTTTTTC
156667 CTCGAAACAGAAGATTTTAT
1 CTCGAAACAGAAGATTTTAT
** *
156687 CTCG---CTCAAGATTGTTTTT
1 CTCGAAACAGAAGA-T-TTTAT
156706 CCTCGAAACAGAAGATTTTAT
1 -CTCGAAACAGAAGATTTTAT
*
156727 CTCGCAAA-AGATTG-TTTT-T
1 CTCG-AAACAGA-AGATTTTAT
*
156746 CCTTGAAACAGAAGATTTTAT
1 -CTCGAAACAGAAGATTTTAT
156767 CTC
1 CTC
156770 ATTCAATATT
Statistics
Matches: 61, Mismatches: 10, Indels: 24
0.64 0.11 0.25
Matches are distributed among these distances:
17 5 0.08
18 1 0.02
19 9 0.15
20 31 0.51
21 9 0.15
22 1 0.02
23 5 0.08
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (20 bp):
CTCGAAACAGAAGATTTTAT
Found at i:156944 original size:20 final size:20
Alignment explanation
Indices: 156921--156985 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
156911 GAAACATAAG
156921 ATTTTATCTCGCTTGAGATT
1 ATTTTATCTCGCTTGAGATT
**** **
156941 ATTTT-TCCTCGAAACAGAAG
1 ATTTTAT-CTCGCTTGAGATT
156961 ATTTTATCTCGCTTGAGATT
1 ATTTTATCTCGCTTGAGATT
*
156981 GTTTT
1 ATTTT
156986 TCCTAGAAAC
Statistics
Matches: 30, Mismatches: 13, Indels: 4
0.64 0.28 0.09
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTTTATCTCGCTTGAGATT
Found at i:157177 original size:37 final size:37
Alignment explanation
Indices: 157115--157219 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
157105 CCTTTTCGTC
* *
157115 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * * *
157152 TTGCTAGGATTTAAACTCTTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * *
157189 CTATTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
157220 CCACAAGCAT
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:157806 original size:23 final size:22
Alignment explanation
Indices: 157753--157797 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
157743 TTTCTTTGCG
157753 TTTTATTATTACTATTATATTTA
1 TTTTATT-TTACTATTATATTTA
157776 TTATTATTTTACTATTATATTT
1 TT-TTATTTTACTATTATATTT
157798 TCCTTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATTTTACTATTATATTTA
Found at i:157811 original size:23 final size:23
Alignment explanation
Indices: 157755--157851 Score: 68
Period size: 23 Copynumber: 4.3 Consensus size: 23
157745 TCTTTGCGTT
157755 TTATTA-T-TACTATTATATTTA
1 TTATTATTCTACTATTATATTTA
*
157776 TTATTATTTTACTATTATATTT-
1 TTATTATTCTACTATTATATTTA
157798 TCCT-TTATTCTACTTATTTATATTATA
1 T--TATTATTCTAC-TA-TTATATT-TA
157825 TGTA-TATT-T--T-TTATATTTA
1 T-TATTATTCTACTATTATATTTA
157844 TTATTATT
1 TTATTATT
157852 ATATTTTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 22
0.73 0.02 0.25
Matches are distributed among these distances:
18 2 0.03
19 7 0.11
20 7 0.11
21 6 0.09
22 3 0.05
23 21 0.33
24 3 0.05
25 8 0.12
26 6 0.09
27 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (23 bp):
TTATTATTCTACTATTATATTTA
Found at i:157853 original size:15 final size:15
Alignment explanation
Indices: 157755--157857 Score: 58
Period size: 15 Copynumber: 6.9 Consensus size: 15
157745 TCTTTGCGTT
157755 TTATTATTACTATTATA
1 TTATTATTA-TATT-TA
157772 TTTATTATTAT-TTTA
1 -TTATTATTATATTTA
* *
157787 CTATTA-TAT-TTTC
1 TTATTATTATATTTA
* * *
157800 CT-TTATTCTACTTA
1 TTATTATTATATTTA
157814 TT-TATATTATATGTATA
1 TTAT-TATTATAT-T-TA
157831 TT-TT-TTATATTTA
1 TTATTATTATATTTA
157844 TTATTATTATATTT
1 TTATTATTATATTT
157858 TTTTACTTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
12 3 0.04
13 14 0.20
14 12 0.17
15 22 0.31
16 4 0.06
17 6 0.09
18 9 0.13
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (15 bp):
TTATTATTATATTTA
Found at i:157900 original size:12 final size:11
Alignment explanation
Indices: 157878--157918 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
157868 TCTTTCTTTT
157878 TATTATTCTTG
1 TATTATTCTTG
157889 TATTATTACTTG
1 TATTATT-CTTG
* *
157901 TATTATTTTTA
1 TATTATTCTTG
157912 TATTATT
1 TATTATT
157919 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:157934 original size:2 final size:2
Alignment explanation
Indices: 157927--157969 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
157917 TTTATTTTGT
157927 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
157969 T
1 T
157970 GCGTATGTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:158166 original size:18 final size:18
Alignment explanation
Indices: 158132--158166 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
158122 ATTATTGTTG
*
158132 TTATATATACATTTATTA
1 TTATATATACATATATTA
*
158150 TTATATATATATATATT
1 TTATATATACATATATT
158167 CTACACAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATATATACATATATTA
Found at i:160243 original size:21 final size:21
Alignment explanation
Indices: 160217--160258 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
160207 CCAGAATGGG
*
160217 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
160238 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
160259 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:160395 original size:21 final size:20
Alignment explanation
Indices: 160361--160437 Score: 69
Period size: 20 Copynumber: 4.1 Consensus size: 20
160351 GCTTTAGACA
160361 GGGGGGAATC-GTACCCCCTG
1 GGGGGGAATCTGTA-CCCCTG
*
160381 GGGGGGTATCTGTA-CCC--
1 GGGGGGAATCTGTACCCCTG
*
160398 ---GGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTA-CCCCTG
160416 GGGGGGAATCTGTACCCCTG
1 GGGGGGAATCTGTACCCCTG
160436 GG
1 GG
160438 CAATCTTGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
19 3 0.06
20 17 0.36
21 13 0.28
ACGTcount: A:0.13, C:0.27, G:0.39, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCTG
Found at i:160403 original size:14 final size:14
Alignment explanation
Indices: 160384--160411 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
160374 CCCCCTGGGG
160384 GGGTATCTGTACCC
1 GGGTATCTGTACCC
160398 GGGTATCTGTACCC
1 GGGTATCTGTACCC
160412 CCTGGGGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (14 bp):
GGGTATCTGTACCC
Found at i:163357 original size:34 final size:32
Alignment explanation
Indices: 163304--163373 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
163294 ACCTTACAAC
*
163304 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
163336 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
163370 TCCC
1 TCCC
163374 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:163682 original size:21 final size:21
Alignment explanation
Indices: 163656--163697 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
163646 CCAGAATGGG
*
163656 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
163677 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
163698 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:163815 original size:21 final size:21
Alignment explanation
Indices: 163781--163859 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
163771 CTTTAGACAT
*
163781 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
*
163802 GGGGGTATCTGTA--CCC---
1 GGGGGAATCTGTACCCCCTGG
*
163818 -GGGGTATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
163838 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
163859 G
1 G
163860 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 31 0.63
ACGTcount: A:0.13, C:0.28, G:0.39, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:163821 original size:15 final size:15
Alignment explanation
Indices: 163803--163832 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
163793 ACCCCCTGGG
163803 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
163818 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
163833 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:163838 original size:36 final size:36
Alignment explanation
Indices: 163782--163853 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
163772 TTTAGACATG
*
163782 GGGGAATCGGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
* *
163818 GGGGTATCTGTACCCCCTGGGGGGGAATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
163854 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.21
Consensus pattern (36 bp):
GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
Found at i:166581 original size:22 final size:22
Alignment explanation
Indices: 166515--166582 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
166505 CGTCAAACAG
166515 TTGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
*
166537 ATGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
166559 TTGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
166581 TT
1 TT
166583 AACCAAACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (22 bp):
TTGAGCATCAAATGCCAAACCT
Found at i:167610 original size:106 final size:106
Alignment explanation
Indices: 167399--168667 Score: 1781
Period size: 106 Copynumber: 12.0 Consensus size: 106
167389 ATATCGTGCC
* * * * * *
167399 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
167463 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
167504 ACTCCAGACAACGCAAGTTCCACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
167569 AATTTCATATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** *
167610 ACTCCAGACAACATAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCC
*
167674 CAATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
167716 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
167781 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
167822 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
167887 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
167928 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCC
* * * *
167992 CAATTTTAGAGCCAATTTTAACTTCATAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
168034 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
168099 AATTTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
168140 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTCGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
168205 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
168246 ACTCTAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
168311 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
168352 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * * *
168417 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGAATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * **
168458 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAAGAGG-CGGCTGATTGTCAA-AAA-AAAAT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG-GGACCGCTGGTTGTCAATAAACAATTTC
* *
168518 -C-A-TTCAGAGTCAATTTTAACTTCACAGCGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
168558 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
168623 AGTTCCAGAGCCAATTTCAATTTCACGAAG-G-AGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCAC--AGCGAAGGATATTGG
168664 ACTC
1 ACTC
168668 AGAACAATGC
Statistics
Matches: 1050, Mismatches: 97, Indels: 33
0.89 0.08 0.03
Matches are distributed among these distances:
99 2 0.00
100 73 0.07
101 5 0.00
102 4 0.00
104 4 0.00
105 55 0.05
106 897 0.85
107 8 0.01
108 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:169460 original size:37 final size:37
Alignment explanation
Indices: 169398--169502 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
169388 CCTTTTCGTC
* *
169398 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * * *
169435 TTGCTAGGATTTAAACTCTTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * *
169472 CTATTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
169503 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:170083 original size:24 final size:23
Alignment explanation
Indices: 170056--170165 Score: 97
Period size: 24 Copynumber: 4.9 Consensus size: 23
170046 CTTTGCGTTT
170056 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTA-TA
*
170080 TTATTTTTACTATTATATTT-TCA
1 TTATTATTACTATTATATTTAT-A
*
170103 TT-TTATT-CTACT-TATTTATA
1 TTATTATTACTATTATATTTATA
* *
170123 TTATATATGTA-TATTTTTTTTATA
1 TTAT-TAT-TACTATTATATTTATA
*
170147 TT-TTATTATTATTATATTT
1 TTATTATTACTATTATATTT
170166 TTTACTTTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
20 8 0.11
21 8 0.11
22 19 0.27
23 8 0.11
24 28 0.39
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATTATTACTATTATATTTATA
Found at i:170207 original size:12 final size:11
Alignment explanation
Indices: 170185--170225 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
170175 TCTTTCTTTT
170185 TATTATTCTTG
1 TATTATTCTTG
170196 TATTATTACTTG
1 TATTATT-CTTG
* *
170208 TATTATTTTTA
1 TATTATTCTTG
170219 TATTATT
1 TATTATT
170226 TTTTGTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:170226 original size:11 final size:11
Alignment explanation
Indices: 170181--170228 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
170171 TTTCTCTTTC
170181 TTTT-TATTAT
1 TTTTGTATTAT
*
170191 TCTTGTATTAT
1 TTTTGTATTAT
*
170202 TACTTGTATTAT
1 T-TTTGTATTAT
*
170214 TTTTATATTAT
1 TTTTGTATTAT
170225 TTTT
1 TTTT
170229 TGTTATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 3 0.09
11 19 0.58
12 11 0.33
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (11 bp):
TTTTGTATTAT
Found at i:170231 original size:23 final size:23
Alignment explanation
Indices: 170181--170231 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
170171 TTTCTCTTTC
*
170181 TTTT-TATTATTCTTGTATTATT
1 TTTTGTATTATTCTTATATTATT
** *
170203 ACTTGTATTATTTTTATATTATT
1 TTTTGTATTATTCTTATATTATT
170226 TTTTGT
1 TTTTGT
170232 TATATATATA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTTGTATTATTCTTATATTATT
Found at i:170795 original size:22 final size:21
Alignment explanation
Indices: 170760--170834 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 21
170750 TTATTCGTAC
170760 TTTGTTATTA-TTATTTTGTTTA
1 TTTGTT-TTATTTATTTT-TTTA
170782 TTTGTTTTATTTATTTTCTTT-
1 TTTGTTTTATTTATTTT-TTTA
* *
170803 TTCTTTTTTATATATATTTTATTA
1 TT-TGTTTTAT-T-TATTTTTTTA
170827 TTTGTTTT
1 TTTGTTTT
170835 TTACTTACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 5 0.11
22 23 0.52
23 8 0.18
24 8 0.18
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTGTTTTATTTATTTTTTTA
Found at i:170846 original size:26 final size:25
Alignment explanation
Indices: 170786--170855 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
170776 TGTTTATTTG
* *
170786 TTTTAT-T-TATTTTCTT-TTTCTT
1 TTTTATATATATTTTATTATTTGTT
170808 TTTTATATATATTTTATTATTTGTT
1 TTTTATATATATTTTATTATTTGTT
170833 TTTTACT-TACTATTTTA-TATTTG
1 TTTTA-TATA-TATTTTATTATTTG
170856 CTTTCTTCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 6 0.15
23 1 0.02
24 8 0.20
25 18 0.44
26 8 0.20
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.73
Consensus pattern (25 bp):
TTTTATATATATTTTATTATTTGTT
Found at i:171365 original size:28 final size:28
Alignment explanation
Indices: 171310--171366 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
171300 TTTGTCTCCC
* * *
171310 TTGAGATAGTTTCTCTTGAAACACAATT
1 TTGAGATAGTTTCCCTTGAAAAAAAATT
171338 TTGAGA-ACGTTTCCCTTGAAAAAAAATT
1 TTGAGATA-GTTTCCCTTGAAAAAAAATT
171366 T
1 T
171367 ATCTCTCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (28 bp):
TTGAGATAGTTTCCCTTGAAAAAAAATT
Found at i:171386 original size:36 final size:37
Alignment explanation
Indices: 171338--171492 Score: 118
Period size: 37 Copynumber: 4.2 Consensus size: 37
171328 AAACACAATT
*
171338 TTGAGA-ACGTTTCCCTTGAAA-AAAAATTTATCTCTC
1 TTGAGACA-GTTTCCCTTGAAACAAAAATTTATCTCAC
* ** * *
171374 TTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCCC
1 TTGAGACAGTTTCCCTTGAAACAAAAATTTATCTCAC
* ** * * * **
171411 TTAAGATGGTTTCTCTTAAAAC-CAAATTCGTCTCAC
1 TTGAGACAGTTTCCCTTGAAACAAAAATTTATCTCAC
*
171447 TTGAGACAGCTTTCCCTTGAAACAAGAAATTGAATCTCAC
1 TTGAGACAG-TTTCCCTTGAAACAA-AAATT-TATCTCAC
171487 TTGAGA
1 TTGAGA
171493 TGGTTTTTCT
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
36 33 0.36
37 41 0.45
39 5 0.05
40 12 0.13
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAAATTTATCTCAC
Found at i:171505 original size:76 final size:73
Alignment explanation
Indices: 171368--171508 Score: 176
Period size: 76 Copynumber: 1.9 Consensus size: 73
171358 AAAAAATTTA
* * ** *
171368 TCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCCCTTAAGATGGTTTCTCTTAAAAC
1 TCTCACTTGAGACAGTTTCCCTTGAAACAAAGAATTGTCTCACTTAAGATGGTTTCTCTTAAAAC
171433 CAAATTCG
66 CAAATTCG
* *
171441 TCTCACTTGAGACAGCTTTCCCTTGAAAC-AAGAAATTGAATCTCACTTGAGATGGTTTTTCTTA
1 TCTCACTTGAGACAG-TTTCCCTTGAAACAAAG-AATTG--TCTCACTTAAGATGGTTTCTCTTA
171505 AAAC
62 AAAC
171509 TTACTTATTC
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
73 17 0.30
74 15 0.26
76 25 0.44
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (73 bp):
TCTCACTTGAGACAGTTTCCCTTGAAACAAAGAATTGTCTCACTTAAGATGGTTTCTCTTAAAAC
CAAATTCG
Found at i:172183 original size:91 final size:92
Alignment explanation
Indices: 172064--172238 Score: 289
Period size: 91 Copynumber: 1.9 Consensus size: 92
172054 AAAGAGATGG
*
172064 ATCAACATTTCCAATAGAGAGTTAATAATGAGAAGAACTCATCC-AACGAGGAAGAAGAAGTTCA
1 ATCAACATTTCCAATAGAGAGTTAATAATGAGAAGAACTCATCCGAAAGAGGAAGAAGAAGTTCA
172128 TAATGAGAAGAACTTGTTCAACTTTGC
66 TAATGAGAAGAACTTGTTCAACTTTGC
* * * *
172155 ATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAATAGAGAGTTAATAATGAGAAGAACTCATCCGAAAGAGGAAGAAGAAGTTCA
*
172220 TAATGAGAAGAGCTTGTTC
66 TAATGAGAAGAACTTGTTC
172239 GACCTATCAC
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 41 0.53
92 36 0.47
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (92 bp):
ATCAACATTTCCAATAGAGAGTTAATAATGAGAAGAACTCATCCGAAAGAGGAAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACTTTGC
Found at i:172440 original size:332 final size:331
Alignment explanation
Indices: 171823--172479 Score: 1000
Period size: 332 Copynumber: 2.0 Consensus size: 331
171813 AGATAAACAG
*
171823 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACATAGGGAGAAAAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAAAAGTTCA
* * *
171888 TAATGAGAAGAGCTTGTTTGACCTATCACTCAATTCACGGCATTTTGAATCAGTGACACCTCACT
66 TAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCACGACATTTCGAATCAGTGACACCTCACT
* * * *
171953 TAAGGGATTGACATTTTCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAGAGGAGAAAGTTTAT
131 TAAGGGATTGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCAT
*
172018 AATGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTCCAATAGAG
196 AATGAGAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGATGGATCAACATTTCCAATAGAG
*
172083 AGTTAATAATGAGAAGAACTCATCCA-ACGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
261 AGTTAATAATGAGAAGAACTCATCCACAAGA-G-AGAAGAAGTTCATAATGAGAAGAACTTGTTC
172147 AACTTTGC
324 AACTTTGC
* *
172155 ATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAA-AGAGGGAGAAGAAGTTC
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AACAGAGGGAGAAAAAGTTC
* * ** *
172219 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACTACATTTCGAATCAGTGATGCCTC-G
65 ATAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCACGACATTTCGAATCAGTGACACCTCAC
*
172283 TTAGAGGGATTGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTC
130 TTA-AGGGATTGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTC
* * * *
172348 ATAATGAGAAGAACTTGTTCCTTTCAAGTCCACCACAGAAATAGGT-GACTCAACATTTTCAGT-
194 ATAATGAGAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGATGGA-TCAACATTTCCAATA
* * *
172411 GAAGAGTTCATAATGAGTAGAATTCATCCACAAGAGAGAAGAAGTTCATAATGAGAAGAACTTGT
258 G-AGAGTTAATAATGAGAAGAACTCATCCACAAGAGAGAAGAAGTTCATAATGAGAAGAACTTGT
172476 TCAA
322 TCAA
172480 TCCAACGACG
Statistics
Matches: 295, Mismatches: 25, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
331 39 0.13
332 251 0.85
333 5 0.02
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (331 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAAAAGTTCA
TAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCACGACATTTCGAATCAGTGACACCTCACT
TAAGGGATTGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCAT
AATGAGAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGATGGATCAACATTTCCAATAGAG
AGTTAATAATGAGAAGAACTCATCCACAAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CTTTGC
Found at i:172624 original size:3 final size:3
Alignment explanation
Indices: 172616--172724 Score: 159
Period size: 3 Copynumber: 36.7 Consensus size: 3
172606 TATATTATAT
* * *
172616 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
172661 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
172709 TTA TTA TCA TT- TTA TT
1 TTA TTA TTA TTA TTA TT
172725 TATATTTTAT
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
2 4 0.04
3 91 0.94
4 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:173228 original size:15 final size:16
Alignment explanation
Indices: 173210--173253 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
173200 TAAAATCATC
173210 TTTTTAA-AAAAATAA
1 TTTTTAAGAAAAATAA
*
173225 -TTTTAAGAAAAATCA
1 TTTTTAAGAAAAATAA
173240 TTTTTAAGACAAAA
1 TTTTTAAGA-AAAA
173254 GCTGGTCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.24
15 7 0.28
16 8 0.32
17 4 0.16
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (16 bp):
TTTTTAAGAAAAATAA
Found at i:174068 original size:2 final size:2
Alignment explanation
Indices: 174024--174050 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
174014 AAATTAATTT
174024 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
174051 TCAAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:175122 original size:14 final size:15
Alignment explanation
Indices: 175090--175121 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
175080 AAGAACCATG
175090 TTTTCCTTTCGTGCT
1 TTTTCCTTTCGTGCT
175105 TTTTCCTTT-G-GCT
1 TTTTCCTTTCGTGCT
175118 TTTT
1 TTTT
175122 TGCTTGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.00, C:0.22, G:0.12, T:0.66
Consensus pattern (15 bp):
TTTTCCTTTCGTGCT
Found at i:176436 original size:136 final size:136
Alignment explanation
Indices: 176087--176437 Score: 475
Period size: 136 Copynumber: 2.6 Consensus size: 136
176077 GACTTGAAAG
* **
176087 GAACAAGTTCTTCTCATTATGAAC--TTTCT-CCT-T-TAAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * * ** *
176147 CT--TTTAGAAATGGC-AATCCCTCTAACGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTG
66 CTCCATTGGAAAT-GCTGATCCCTCAAACGAGGCGTCACTGATTCGAAATACCATGAATCGAGTG
*
176209 ATAGGTT
130 ATAGGTC
* *
176216 AAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * *
176281 CTCCATAGGAAATACTGATCCCTCAAACGAGGTGTCACTGATTCGAAATACCATGAATCGAGTGA
66 CTCCATTGGAAATGCTGATCCCTCAAACGAGGCGTCACTGATTCGAAATACCATGAATCGAGTGA
176346 TAGGTC
131 TAGGTC
*
176352 GAACAAGCTCTTCTCATTATGAACTTTTTATCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
*
176417 CTCCATTGGAAATGTTGATCC
66 CTCCATTGGAAATGCTGATCC
176438 ATCTCTTTCT
Statistics
Matches: 192, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
129 22 0.11
131 4 0.02
132 3 0.02
133 1 0.01
134 27 0.14
135 1 0.01
136 134 0.70
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATGCTGATCCCTCAAACGAGGCGTCACTGATTCGAAATACCATGAATCGAGTGA
TAGGTC
Found at i:177333 original size:8 final size:7
Alignment explanation
Indices: 177296--177390 Score: 63
Period size: 7 Copynumber: 13.1 Consensus size: 7
177286 CAAACCCTCA
177296 TTTTTCT
1 TTTTTCT
* *
177303 CTTTTCA
1 TTTTTCT
177310 TTTTT-T
1 TTTTTCT
*
177316 TATTTCT
1 TTTTTCT
177323 TTTTTCATTT
1 TTTTTC---T
177333 TTTTTCT
1 TTTTTCT
177340 TTTTTC-
1 TTTTTCT
177346 TTTTTCAT
1 TTTTTC-T
177354 TTTTTCATT
1 TTTTTC--T
177363 TTTTTCT
1 TTTTTCT
177370 TTTTAT-T
1 TTTT-TCT
*
177377 TGTTT-T
1 TTTTTCT
177383 TTTTTCT
1 TTTTTCT
177390 T
1 T
177391 CAAGCATAGT
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
6 16 0.23
7 33 0.47
8 7 0.10
9 7 0.10
10 7 0.10
ACGTcount: A:0.06, C:0.12, G:0.01, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:177344 original size:30 final size:28
Alignment explanation
Indices: 177304--177388 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 28
177294 CATTTTTCTC
*
177304 TTTTCATTTTTTTATTTCTTTTTTCATTTT
1 TTTTC-TTTTTTTTTTTCTTTTTTCA-TTT
177334 TTTTCTTTTTTCTTTTTCATTTTTTCATTT
1 TTTTCTTTTTT-TTTTTC-TTTTTTCATTT
177364 TTTTCTTTTTATTTGTTT-TTTTTTC
1 TTTTCTTTTT-TTT-TTTCTTTTTTC
177389 TTCAAGCATA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
29 13 0.26
30 25 0.50
31 12 0.24
ACGTcount: A:0.07, C:0.11, G:0.01, T:0.81
Consensus pattern (28 bp):
TTTTCTTTTTTTTTTTCTTTTTTCATTT
Found at i:177351 original size:50 final size:50
Alignment explanation
Indices: 177296--177390 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
177286 CAAACCCTCA
*
177296 TTTTTC-TCTTTTCATTTTTTTATTTCTTTTTTCATTTTTTTTCTTTTTTC
1 TTTTTCATCTTTTCATTTTTTTATTT-TTATTTCATTTTTTTTCTTTTTTC
* * **
177346 TTTTTCATTTTTTCATTTTTTTCTTTTTATTTGTTTTTTTTTCTT
1 TTTTTCATCTTTTCATTTTTTTATTTTTATTTCATTTTTTTTCTT
177391 CAAGCATAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 22 0.56
51 17 0.44
ACGTcount: A:0.06, C:0.12, G:0.01, T:0.81
Consensus pattern (50 bp):
TTTTTCATCTTTTCATTTTTTTATTTTTATTTCATTTTTTTTCTTTTTTC
Found at i:177384 original size:17 final size:17
Alignment explanation
Indices: 177312--177384 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 17
177302 TCTTTTCATT
177312 TTTTTATTTCTTTTTTC
1 TTTTTATTTCTTTTTTC
177329 ATTTTT-TTTCTTTTTTC
1 -TTTTTATTTCTTTTTTC
177346 TTTTTCATTTTTTCATTTTTTTC
1 TTTTT-A---TTTC--TTTTTTC
*
177369 TTTTTATTTGTTTTTT
1 TTTTTATTTCTTTTTT
177385 TTTCTTCAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 15
0.75 0.02 0.24
Matches are distributed among these distances:
16 5 0.11
17 17 0.36
18 5 0.11
19 3 0.06
21 4 0.09
22 1 0.02
23 12 0.26
ACGTcount: A:0.07, C:0.10, G:0.01, T:0.82
Consensus pattern (17 bp):
TTTTTATTTCTTTTTTC
Done.