Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_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: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 16
Found at i:2885597 original size:80 final size:80
Alignment explanation
Indices: 2885511--2885666 Score: 203
Period size: 83 Copynumber: 1.9 Consensus size: 80
2885501 TAAATAAAAG
* * *
2885511 TTTAATATTTTAAA-TTTAAA-AGA-TATTTTCTGTTTAAA-TTTAGATATTAAAAGATATTTAG
1 TTTAATATTTTAAATTTTAAATAGATTATTATATGTTTAAATTTTA-ATATTAAAAG-T-TTTAC
*
2885572 TTGGAGTAAAACTCTCAAT
63 TTGAAGT-AAACTCTCAAT
*
2885591 TTTAATATTTTAAATTTTAAATATATTATTATATGTTTAAATTTTAATATTAAAAGTTTTACTTG
1 TTTAATATTTTAAATTTTAAATAGATTATTATATGTTTAAATTTTAATATTAAAAGTTTTACTTG
2885656 AAGTAAACTCT
66 AAGTAAACTCT
2885667 ATCGAAACTA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
80 21 0.31
81 16 0.24
82 3 0.04
83 23 0.34
84 4 0.06
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (80 bp):
TTTAATATTTTAAATTTTAAATAGATTATTATATGTTTAAATTTTAATATTAAAAGTTTTACTTG
AAGTAAACTCTCAAT
Found at i:2885649 original size:21 final size:21
Alignment explanation
Indices: 2885588--2885649 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
2885578 TAAAACTCTC
* *
2885588 AATTTTAATATTTTAAATTTTA
1 AATTTTAATA-TTAAAAGTTTA
* * * *
2885610 AA-TATATTATTATATGTTTA
1 AATTTTAATATTAAAAGTTTA
2885630 AATTTTAATATTAAAAGTTT
1 AATTTTAATATTAAAAGTTT
2885650 TACTTGAAGT
Statistics
Matches: 29, Mismatches: 10, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
20 9 0.31
21 18 0.62
22 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
AATTTTAATATTAAAAGTTTA
Found at i:2892638 original size:32 final size:32
Alignment explanation
Indices: 2892579--2892660 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 32
2892569 ACTGTATCTG
* * *
2892579 CTATGCATTATCTAAAGGTGATACTAACACTC
1 CTATGCATTATCTGAATGTCATACTAACACTC
* * *
2892611 CTATGCATTATCTGAATGTCATGCTAACTCTG
1 CTATGCATTATCTGAATGTCATACTAACACTC
* *
2892643 ATGTGCATTATCTGAATG
1 CTATGCATTATCTGAATG
2892661 CAATATTGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (32 bp):
CTATGCATTATCTGAATGTCATACTAACACTC
Found at i:2892673 original size:32 final size:32
Alignment explanation
Indices: 2892579--2892702 Score: 90
Period size: 32 Copynumber: 3.9 Consensus size: 32
2892569 ACTGTATCTG
* * ** * * *
2892579 CTATGCATTATCTAAAGGTGATACTAACACTC
1 CTATGCATTATCTGAATGCAATATTAACTCTA
**
2892611 CTATGCATTATCTGAATGTC-ATGCTAACTCTGA
1 CTATGCATTATCTGAATG-CAATATTAACTCT-A
* *
2892644 -TGTGCATTATCTGAATGCAATATTGACTCTA
1 CTATGCATTATCTGAATGCAATATTAACTCTA
* * *
2892675 CTATCCTTTATTTGAATGCAATATTAAC
1 CTATGCATTATCTGAATGCAATATTAAC
2892703 ACTGTTGTGA
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
31 2 0.03
32 71 0.97
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (32 bp):
CTATGCATTATCTGAATGCAATATTAACTCTA
Found at i:2893820 original size:20 final size:20
Alignment explanation
Indices: 2893797--2893834 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2893787 ACGAAAGTGG
2893797 GTAGTATCAATACTCTAGTT
1 GTAGTATCAATACTCTAGTT
*
2893817 GTAGTATCGATACTCTAG
1 GTAGTATCAATACTCTAG
2893835 GTTCAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (20 bp):
GTAGTATCAATACTCTAGTT
Found at i:2893850 original size:21 final size:20
Alignment explanation
Indices: 2893799--2893855 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2893789 GAAAGTGGGT
**
2893799 AGTATCAATACTCTAGTTGT
1 AGTATCAATACTCTAGTTCA
*
2893819 AGTATCGATACTCTAGGTTCA
1 AGTATCAATACTCTA-GTTCA
*
2893840 ATTATCAATACCTCTA
1 AGTATCAATA-CTCTA
2893856 TGAGTATCGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 14 0.47
21 11 0.37
22 5 0.17
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
AGTATCAATACTCTAGTTCA
Found at i:2901971 original size:21 final size:22
Alignment explanation
Indices: 2901945--2901995 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
2901935 AGGGAATCGA
2901945 TCCCCCCTTG-AGGGAACCAAT
1 TCCCCCCTTGAAGGGAACCAAT
* *
2901966 TCCCCCTTTGAAAGGGAACCGAT
1 TCCCCCCTTG-AAGGGAACCAAT
2901989 TCCCCCC
1 TCCCCCC
2901996 ACAGGGGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
23 16 0.64
ACGTcount: A:0.22, C:0.41, G:0.18, T:0.20
Consensus pattern (22 bp):
TCCCCCCTTGAAGGGAACCAAT
Found at i:2906111 original size:31 final size:31
Alignment explanation
Indices: 2906076--2906153 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
2906066 TTCAATGTCC
*
2906076 AAGTGACCAAAACTTAATAAAACAATAATAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
*
2906107 AAGTGACGAAAACTTAATAAAACAATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
*
2906138 AAGCGACCAAAACTTA
1 AAGTGACCAAAACTTA
2906154 TCCTTCTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:2916425 original size:25 final size:25
Alignment explanation
Indices: 2916387--2916482 Score: 147
Period size: 25 Copynumber: 3.8 Consensus size: 25
2916377 ATTAAGGGGC
*
2916387 AACATTTTTCAAAATTCTTTCATTA
1 AACATTTTTCAAAATTCTTTCATCA
*
2916412 AACATTTTTTAAAATTCTTTCATCA
1 AACATTTTTCAAAATTCTTTCATCA
*
2916437 AACATTTTTCAAAAATTCTTTTATCA
1 AACATTTTTC-AAAATTCTTTCATCA
2916463 AACATTTTTCAAAACTTCTT
1 AACATTTTTCAAAA-TTCTT
2916483 CATTTATTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
25 36 0.55
26 29 0.45
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (25 bp):
AACATTTTTCAAAATTCTTTCATCA
Found at i:2916445 original size:26 final size:25
Alignment explanation
Indices: 2916387--2916482 Score: 129
Period size: 26 Copynumber: 3.8 Consensus size: 25
2916377 ATTAAGGGGC
* *
2916387 AACATTTTTCAAAATTCTTTCATTA
1 AACATTTTTAAAAATTCTTTCATCA
*
2916412 AACATTTTTTAAAATTCTTTCATCA
1 AACATTTTTAAAAATTCTTTCATCA
*
2916437 AACATTTTTCAAAAATTCTTTTATCA
1 AACATTTTT-AAAAATTCTTTCATCA
*
2916463 AACATTTTTCAAAACTTCTT
1 AACATTTTT-AAAAATTCTT
2916483 CATTTATTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 32 0.49
26 33 0.51
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (25 bp):
AACATTTTTAAAAATTCTTTCATCA
Found at i:2916864 original size:12 final size:12
Alignment explanation
Indices: 2916849--2916881 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2916839 ACTCTCTCTC
*
2916849 TCTTCTTCATCT
1 TCTTCTTCATAT
2916861 TCTTCTTCATAT
1 TCTTCTTCATAT
2916873 TCTTCTTCA
1 TCTTCTTCA
2916882 ACTCTCTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.30, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTTCTTCATAT
Found at i:2919184 original size:101 final size:101
Alignment explanation
Indices: 2919006--2919258 Score: 327
Period size: 101 Copynumber: 2.5 Consensus size: 101
2918996 TCTATTTTTG
* * * *
2919006 AGAAA-TCATTTT-GT-TTTCTTAAGACTGTTTCCCTAAAAACCTCAACAAGATTGTCTCATACA
1 AGAAATTCATTTTGGTCTTTCTCAAGACTGTTTCCCTAGAAACCTCAACATGACTGTCTCATACA
* *
2919068 GAGAAGTCAACTAGTCCTTCTTAGGATTGTTTCTCT
66 GAGAAGTCAACTAGTCCTTCTTAAGATCGTTTCTCT
* * *
2919104 AGAAATTCATTTTGGTCTTTCTCAAGA-TCGTTTCCCTAGAAACCTTAACCTGACTGTCTCATGC
1 AGAAATTCATTTTGGTCTTTCTCAAGACT-GTTTCCCTAGAAACCTCAACATGACTGTCTCATAC
2919168 AGA-AGAGTCAACTAGTCCTTCTTAAGATCGTTTCTCT
65 AGAGA-AGTCAACTAGTCCTTCTTAAGATCGTTTCTCT
* ** * *
2919205 AAAAATTTGTTTTGGTCTTTCTCAAGACTATTTCCCTAGAAACCTCAACTTGAC
1 AGAAATTCATTTTGGTCTTTCTCAAGACTGTTTCCCTAGAAACCTCAACATGAC
2919259 CTTATCATGT
Statistics
Matches: 134, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
98 5 0.04
99 7 0.05
100 4 0.03
101 117 0.87
102 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (101 bp):
AGAAATTCATTTTGGTCTTTCTCAAGACTGTTTCCCTAGAAACCTCAACATGACTGTCTCATACA
GAGAAGTCAACTAGTCCTTCTTAAGATCGTTTCTCT
Found at i:2919428 original size:38 final size:38
Alignment explanation
Indices: 2919386--2919488 Score: 109
Period size: 38 Copynumber: 2.7 Consensus size: 38
2919376 CATTCTTGAT
*
2919386 CTTCTTAAGATTGTTTCTCTAGAGACCTCAAT-TTAGTC
1 CTTCTTAAGATTGTTTCTCTAGAAACCTC-ATCTTAGTC
* * * *
2919424 CTTCTTAATATTATTTCCCTAGAAACCTCATCTTTGTC
1 CTTCTTAAGATTGTTTCTCTAGAAACCTCATCTTAGTC
* * * *
2919462 TTTCATAAGACTGTTTCTCTAAAAACC
1 CTTCTTAAGATTGTTTCTCTAGAAACC
2919489 AACTTTGTCT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
37 2 0.04
38 50 0.96
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (38 bp):
CTTCTTAAGATTGTTTCTCTAGAAACCTCATCTTAGTC
Found at i:2920100 original size:3 final size:3
Alignment explanation
Indices: 2920092--2920179 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
2920082 TGTCAAGGGC
2920092 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
2920140 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2920180 CCTTTATTGC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2923634 original size:19 final size:20
Alignment explanation
Indices: 2923595--2923634 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2923585 AAACACTGTC
2923595 TTTCAAACAATAAACCTTTT
1 TTTCAAACAATAAACCTTTT
2923615 TTTCAAACAATAAA-CTTTT
1 TTTCAAACAATAAACCTTTT
2923634 T
1 T
2923635 CGCTGTTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTCAAACAATAAACCTTTT
Found at i:2927827 original size:21 final size:23
Alignment explanation
Indices: 2927801--2927846 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
2927791 AAAAAAATAA
2927801 TATATTAAATT-TT-TTATCTTT
1 TATATTAAATTATTGTTATCTTT
*
2927822 TATATTAAATTATTGTTGTCTTT
1 TATATTAAATTATTGTTATCTTT
2927845 TA
1 TA
2927847 AAAAAGTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 2 0.09
23 9 0.41
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (23 bp):
TATATTAAATTATTGTTATCTTT
Found at i:2929640 original size:3 final size:3
Alignment explanation
Indices: 2929621--2929681 Score: 59
Period size: 3 Copynumber: 19.3 Consensus size: 3
2929611 TCGGGTCTTA
* * * *
2929621 TAT TTT TAT TTT TAT TAT TAA AATT TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT
2929668 TAT TAT TAT ATAT T
1 TAT TAT TAT -TAT T
2929682 TTTTCATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 40 0.83
4 8 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2929682 original size:32 final size:32
Alignment explanation
Indices: 2929621--2929682 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2929611 TCGGGTCTTA
* * *
2929621 TATTTTTATTTTTATTATTAAAATTTATTTAT
1 TATTATTATTATTATTATTAAAATATATTTAT
**
2929653 TATTATTATTATTATTATTATTATATATTT
1 TATTATTATTATTATTATTAAAATATATTT
2929683 TTTCATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (32 bp):
TATTATTATTATTATTATTAAAATATATTTAT
Found at i:2930881 original size:20 final size:21
Alignment explanation
Indices: 2930856--2930911 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
2930846 CTTTAATTAG
* *
2930856 AATTTTCTTTTTTTTC-TTTT
1 AATTTTATTTTATTTCATTTT
2930876 AATTTTATTTTATTTCATTTT
1 AATTTTATTTTATTTCATTTT
* *
2930897 CATTATTAATTTATT
1 AATT-TTATTTTATT
2930912 AGCCCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 14 0.47
21 7 0.23
22 9 0.30
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (21 bp):
AATTTTATTTTATTTCATTTT
Found at i:2932136 original size:15 final size:15
Alignment explanation
Indices: 2932116--2932145 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2932106 AAGGAAAAAA
2932116 TTAACTAATTCAATT
1 TTAACTAATTCAATT
*
2932131 TTAACTAGTTCAATT
1 TTAACTAATTCAATT
2932146 CAAACGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAACTAATTCAATT
Found at i:2937411 original size:24 final size:24
Alignment explanation
Indices: 2937382--2937429 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2937372 TAGAAGTTCG
2937382 ATTGAAGCCTAAAATTGGAGCTCA
1 ATTGAAGCCTAAAATTGGAGCTCA
*
2937406 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTGGAGCTCA
2937430 CTTTGTGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTGGAGCTCA
Found at i:2938682 original size:20 final size:20
Alignment explanation
Indices: 2938609--2938801 Score: 230
Period size: 20 Copynumber: 9.6 Consensus size: 20
2938599 GATTTTCCAG
* **
2938609 AATCGCAACGCGAATATG-A
1 AATCGCAACGCGTATCCGTA
* *
2938628 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2938648 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2938668 AATCGCAACGTGTATCTGTA
1 AATCGCAACGCGTATCCGTA
2938688 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2938708 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2938728 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2938748 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
2938769 AATCGCAAACGCGTATCCGTA
1 AATCGC-AACGCGTATCCGTA
2938790 AATCGCAACGCG
1 AATCGCAACGCG
2938802 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
18 1 0.01
19 12 0.08
20 109 0.73
21 18 0.12
22 9 0.06
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2939208 original size:14 final size:14
Alignment explanation
Indices: 2939189--2939245 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2939179 TTTCATTTCG
2939189 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2939203 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
2939222 CGTTGCTATTCTCT
1 CGTTGCGATTCTCT
2939236 CGTTGCGATT
1 CGTTGCGATT
2939246 TTCAAGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.25, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2939218 original size:33 final size:33
Alignment explanation
Indices: 2939179--2939249 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
2939169 TTCACTTAGA
2939179 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
*
2939212 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
2939245 TTTCA
1 TTTCA
2939250 AGTTAGTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.10, C:0.24, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
Found at i:2939227 original size:19 final size:18
Alignment explanation
Indices: 2939177--2939227 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 18
2939167 ATTTCACTTA
2939177 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
*
2939195 GA-TTC---TCTCGTTGC
1 GATTTCATTTCGCGTTGC
2939209 GATTTTCATTTCGCGTTGC
1 GA-TTTCATTTCGCGTTGC
2939228 TATTCTCTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
14 10 0.38
16 3 0.12
17 3 0.12
18 2 0.08
19 8 0.31
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.45
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:2939442 original size:19 final size:19
Alignment explanation
Indices: 2939420--2939548 Score: 80
Period size: 19 Copynumber: 7.1 Consensus size: 19
2939410 GAAACCAAAA
*
2939420 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2939439 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2939453 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2939472 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2939486 TCTCGTTGCGATTTTTCATT
1 TCGCGTTGCGA-TTTTCATT
* ***
2939506 ACTCTCGTTGCGACAGTCATT
1 --TCGCGTTGCGATTTTCATT
*
2939527 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2939547 TC
1 TC
2939549 ACCAAAGACA
Statistics
Matches: 87, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
14 20 0.23
16 3 0.03
17 9 0.10
19 22 0.25
20 17 0.20
21 5 0.06
22 11 0.13
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2939461 original size:14 final size:14
Alignment explanation
Indices: 2939442--2939498 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2939432 TTTCATTTCG
2939442 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2939456 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2939475 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2939489 CGTTGCGATT
1 CGTTGCGATT
2939499 TTTCATTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2939467 original size:33 final size:33
Alignment explanation
Indices: 2939425--2939548 Score: 158
Period size: 33 Copynumber: 3.5 Consensus size: 33
2939415 CAAAATCGCA
2939425 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2939458 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2939491 TTGCGATTTTTCATTACTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGA-TTTTCATT--TCGCGTT--G-C-G--ATTCTCTCG
2939533 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2939549 ACCAAAGACA
Statistics
Matches: 81, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
33 39 0.48
34 8 0.10
36 6 0.07
38 1 0.01
39 3 0.04
40 1 0.01
41 8 0.10
42 15 0.19
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2939513 original size:22 final size:20
Alignment explanation
Indices: 2939449--2939546 Score: 93
Period size: 20 Copynumber: 5.2 Consensus size: 20
2939439 TCGCGTTGCG
2939449 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2939469 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
2939482 ATTCTCTCGTTGCGATTTTTC
1 ATTCTCTCGTTGCGA-TTTTC
***
2939503 ATTACTCTCGTTGCGACAGTC
1 ATT-CTCTCGTTGCGATTTTC
2939524 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
2939544 ATT
1 ATT
2939547 TCACCAAAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
13 3 0.05
14 9 0.15
19 9 0.15
20 20 0.33
21 8 0.13
22 12 0.20
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2940140 original size:20 final size:20
Alignment explanation
Indices: 2940115--2940158 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2940105 CCCTCTAATC
2940115 TTTGCCTTCACAACTTTTGA
1 TTTGCCTTCACAACTTTTGA
2940135 TTTGCCTTCACAACTTTTGA
1 TTTGCCTTCACAACTTTTGA
2940155 TTTG
1 TTTG
2940159 TCTTAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (20 bp):
TTTGCCTTCACAACTTTTGA
Found at i:2940167 original size:20 final size:20
Alignment explanation
Indices: 2940115--2940167 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2940105 CCCTCTAATC
*
2940115 TTTGCCTTCACAACTTTTGA
1 TTTGCCTTAACAACTTTTGA
*
2940135 TTTGCCTTCACAACTTTTGA
1 TTTGCCTTAACAACTTTTGA
*
2940155 TTTGTCTTAACAA
1 TTTGCCTTAACAA
2940168 AATATCCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (20 bp):
TTTGCCTTAACAACTTTTGA
Found at i:2940483 original size:2 final size:2
Alignment explanation
Indices: 2940478--2940504 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2940468 ATTTAAAATA
2940478 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 A
2940505 AATTTAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2942236 original size:21 final size:20
Alignment explanation
Indices: 2942212--2942275 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
2942202 GAAGCAATCT
2942212 AAAATAGTTAAAAATAAAAAA
1 AAAATA-TTAAAAATAAAAAA
* * *
2942233 AAAATATTATAAACAAATAA
1 AAAATATTAAAAATAAAAAA
**
2942253 AAAATAATTAAATTTAAAAAA
1 AAAAT-ATTAAAAATAAAAAA
2942274 AA
1 AA
2942276 TTGAATAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATATTAAAAATAAAAAA
Found at i:2942254 original size:20 final size:21
Alignment explanation
Indices: 2942212--2942264 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
2942202 GAAGCAATCT
*
2942212 AAAATAGTTAAAAATAAAAAA
1 AAAATAGTTAAAAACAAAAAA
* *
2942233 AAAATA-TTATAAACAAATAA
1 AAAATAGTTAAAAACAAAAAA
*
2942253 AAAATAATTAAA
1 AAAATAGTTAAA
2942265 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAATAGTTAAAAACAAAAAA
Found at i:2942487 original size:14 final size:14
Alignment explanation
Indices: 2942468--2942496 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2942458 TGGTAAAGAA
2942468 AGGCCAAAATCGTC
1 AGGCCAAAATCGTC
2942482 AGGCCAAAATCGTC
1 AGGCCAAAATCGTC
2942496 A
1 A
2942497 AGCCTCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.14
Consensus pattern (14 bp):
AGGCCAAAATCGTC
Found at i:2943993 original size:32 final size:32
Alignment explanation
Indices: 2943956--2944026 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
2943946 TTTTCGGCAT
*
2943956 AACCTTATATTAGTTAATTATATTTTAGACTC
1 AACCTTATATTAGTTAATTATATTTTAAACTC
2943988 AACCTTATATTAGTTAATTATATTTTAAACTC
1 AACCTTATATTAGTTAATTATATTTTAAACTC
*
2944020 ATCCTTA
1 AACCTTA
2944027 CATGATAGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.46
Consensus pattern (32 bp):
AACCTTATATTAGTTAATTATATTTTAAACTC
Found at i:2946265 original size:14 final size:14
Alignment explanation
Indices: 2946246--2946272 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2946236 ACTTTTTTTT
2946246 TAAATATAATATTA
1 TAAATATAATATTA
2946260 TAAATATAATATT
1 TAAATATAATATT
2946273 TCATAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAATATAATATTA
Found at i:2946428 original size:14 final size:14
Alignment explanation
Indices: 2946409--2946440 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2946399 ATAGAAACTT
2946409 GAATAACTTGACAC
1 GAATAACTTGACAC
*
2946423 GAATAACTTGACTC
1 GAATAACTTGACAC
2946437 GAAT
1 GAAT
2946441 TTCTTAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (14 bp):
GAATAACTTGACAC
Found at i:2946651 original size:4 final size:4
Alignment explanation
Indices: 2946642--2946668 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2946632 AAAATAACAA
2946642 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
2946669 TCATTCTAAA
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:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2946679 original size:52 final size:52
Alignment explanation
Indices: 2946617--2946718 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
2946607 TATCTTATAA
* **
2946617 TCATTCTAAAATGTTAAAATAACAATATGTATGTATGTATGTATGTATGTAT
1 TCATTCTAAAATGTTAAAATAACAATATATATAAATGTATGTATGTATGTAT
2946669 TCATTCTAAAATGTTAAAATAACAATATATATAAATGTATGTATGTATGT
1 TCATTCTAAAATGTTAAAATAACAATATATATAAATGTATGTATGTATGT
2946719 GTGTATGTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (52 bp):
TCATTCTAAAATGTTAAAATAACAATATATATAAATGTATGTATGTATGTAT
Found at i:2947388 original size:10 final size:11
Alignment explanation
Indices: 2947372--2947400 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2947362 TAAAAGAATA
2947372 AAATTTAATTT
1 AAATTTAATTT
2947383 -AATTTAATTT
1 AAATTTAATTT
2947393 AAATTTAA
1 AAATTTAA
2947401 ACTGACATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:2949277 original size:12 final size:12
Alignment explanation
Indices: 2949256--2949284 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2949246 ATTTTAATTC
2949256 ATACTTTTTTTT
1 ATACTTTTTTTT
2949268 -TACTTTTTTTT
1 ATACTTTTTTTT
2949279 ATACTT
1 ATACTT
2949285 ATGAGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (12 bp):
ATACTTTTTTTT
Found at i:2949837 original size:27 final size:27
Alignment explanation
Indices: 2949786--2949838 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2949776 ATATATGTAT
* *
2949786 AAGTCTGGTTTCTAAACTTTTTAAAAA
1 AAGTCTGGTTTCTAAACTCTATAAAAA
2949813 AAGTCTGGTTTCTAATA-TCTATAAAA
1 AAGTCTGGTTTCTAA-ACTCTATAAAA
2949839 GTAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (27 bp):
AAGTCTGGTTTCTAAACTCTATAAAAA
Found at i:2953560 original size:2 final size:2
Alignment explanation
Indices: 2953553--2953587 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2953543 GAATAAATAG
2953553 TA TA TA TA 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 TA TA TA TA T
2953588 GTTTAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2953984 original size:31 final size:31
Alignment explanation
Indices: 2953941--2954004 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2953931 TAACAAGAGA
*
2953941 TGTCTAATGTTTTCT-TCGTTACAGTTTTAGG
1 TGTCTAATGTTTTCTCT-GTTACACTTTTAGG
2953972 TGTCTACA-GTTTTCTCTGTTACACTTTTAGG
1 TGTCTA-ATGTTTTCTCTGTTACACTTTTAGG
2954003 TG
1 TG
2954005 CATACCATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (31 bp):
TGTCTAATGTTTTCTCTGTTACACTTTTAGG
Found at i:2955855 original size:2 final size:2
Alignment explanation
Indices: 2955848--2955885 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2955838 TTTAATTATT
*
2955848 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2955886 GGATTCACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2956082 original size:13 final size:13
Alignment explanation
Indices: 2956066--2956090 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2956056 TTTAGAGTTT
2956066 GAGTTTTAGGGTA
1 GAGTTTTAGGGTA
2956079 GAGTTTTAGGGT
1 GAGTTTTAGGGT
2956091 TTGGAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (13 bp):
GAGTTTTAGGGTA
Found at i:2957513 original size:2 final size:2
Alignment explanation
Indices: 2957506--2957532 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2957496 AATTTTTCTT
2957506 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
2957533 CATTTCATCT
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:2959153 original size:28 final size:28
Alignment explanation
Indices: 2959092--2959142 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
2959082 CCCGTGTTCT
2959092 CCTTCTCCCCTCTCTCCTCCCTCCCCCA
1 CCTTCTCCCCTCTCTCCTCCCTCCCCCA
*
2959120 TCTTCT-CCCT-TCTCC-CCCTCCCC
1 CCTTCTCCCCTCTCTCCTCCCTCCCC
2959143 AGCAACCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 5 0.23
27 4 0.18
28 5 0.23
ACGTcount: A:0.02, C:0.67, G:0.00, T:0.31
Consensus pattern (28 bp):
CCTTCTCCCCTCTCTCCTCCCTCCCCCA
Found at i:2960996 original size:16 final size:18
Alignment explanation
Indices: 2960965--2960997 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2960955 GTAAAATGAA
2960965 TAAATAAATGATTTTGAT
1 TAAATAAATGATTTTGAT
2960983 TAAA-AAAT-ATTTTGA
1 TAAATAAATGATTTTGA
2960998 GAGTCGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
TAAATAAATGATTTTGAT
Found at i:2961674 original size:27 final size:28
Alignment explanation
Indices: 2961643--2961714 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
2961633 TGCCCTTTTC
2961643 TTAATATT-TAAAAATAAATAA-ATATCA
1 TTAATATTATAAAAATAAATAATATAT-A
*
2961670 TTAAT-TTATAAAATTAAATAATATATA
1 TTAATATTATAAAAATAAATAATATATA
* *
2961697 TTAATATAATAACAATAA
1 TTAATATTATAAAAATAA
2961715 TTAAACATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 2 0.05
27 23 0.61
28 13 0.34
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (28 bp):
TTAATATTATAAAAATAAATAATATATA
Found at i:2961729 original size:14 final size:14
Alignment explanation
Indices: 2961712--2961739 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2961702 ATAATAACAA
2961712 TAATTAAACATATT
1 TAATTAAACATATT
2961726 TAATTAAACATATT
1 TAATTAAACATATT
2961740 AAAATATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATTAAACATATT
Found at i:2961824 original size:26 final size:26
Alignment explanation
Indices: 2961788--2961838 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2961778 CTAAATATAA
*
2961788 AAAGTAATAAAACTT-GTAATTAAATG
1 AAAGTAATAAAA-TTAGTAACTAAATG
*
2961814 AAAGTATTAAAATTAGTAACTAAAT
1 AAAGTAATAAAATTAGTAACTAAAT
2961839 TATAACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (26 bp):
AAAGTAATAAAATTAGTAACTAAATG
Found at i:2962013 original size:15 final size:15
Alignment explanation
Indices: 2961993--2962025 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2961983 CATGCTGTTT
2961993 ATGATTAAAATAATA
1 ATGATTAAAATAATA
*
2962008 ATGATTAAAATCATA
1 ATGATTAAAATAATA
2962023 ATG
1 ATG
2962026 GCTAATTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (15 bp):
ATGATTAAAATAATA
Found at i:2962771 original size:21 final size:21
Alignment explanation
Indices: 2962745--2962799 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2962735 GGACGGTCTT
* *
2962745 CGGTGAGTCACCAAGTTATGG
1 CGGTGAGTCACCAAGCTATGA
2962766 CGGTGAGTCACCAAGCTATGA
1 CGGTGAGTCACCAAGCTATGA
*
2962787 CGGTGACTCACCA
1 CGGTGAGTCACCA
2962800 TAGAGCACTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (21 bp):
CGGTGAGTCACCAAGCTATGA
Found at i:2963848 original size:113 final size:112
Alignment explanation
Indices: 2963725--2964041 Score: 460
Period size: 113 Copynumber: 2.8 Consensus size: 112
2963715 AGAGTCATGC
*
2963725 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
*
2963790 ATGAACT-TTCTCTGGAAAAGTTGATCCAACGAGTGATGAATTCAAGCA
65 ATGAACTCTTC-CTGGAAAAGTTGATCCAACAAGTGATGAATTCAAGCA
* * * *
2963838 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGAGGAGTTATTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
2963903 ATGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGAATTCTAGCA
65 ATGAACTCTTCCTGGAAAAGTTGATCCAACAAGTGATGAATTCAAGCA
* *
2963951 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATCA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
2964016 TGAACTCTTCC-GGAAATA-TTGATCCA
66 TGAACTCTTCCTGGAAA-AGTTGATCCA
2964042 TTGAATTATG
Statistics
Matches: 181, Mismatches: 20, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
111 12 0.07
112 34 0.19
113 131 0.72
114 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (112 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTTCCTGGAAAAGTTGATCCAACAAGTGATGAATTCAAGCA
Found at i:2964434 original size:19 final size:21
Alignment explanation
Indices: 2964410--2964463 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2964400 AATAAAGCTT
2964410 TCATCTTT-AG-GAGAATTTA
1 TCATCTTTAAGAGAGAATTTA
2964429 TCATCTTTGAAGAGAGAATTTA
1 TCATCTTT-AAGAGAGAATTTA
*
2964451 TAATCTTTGAAGA
1 TCATCTTT-AAGA
2964464 ATGTAGATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 8 0.26
21 2 0.06
22 21 0.68
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (21 bp):
TCATCTTTAAGAGAGAATTTA
Found at i:2964448 original size:22 final size:22
Alignment explanation
Indices: 2964420--2964463 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2964410 TCATCTTTAG
*
2964420 GAGAATTTATCATCTTTGAAGA
1 GAGAATTTATAATCTTTGAAGA
2964442 GAGAATTTATAATCTTTGAAGA
1 GAGAATTTATAATCTTTGAAGA
2964464 ATGTAGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (22 bp):
GAGAATTTATAATCTTTGAAGA
Found at i:2965416 original size:75 final size:75
Alignment explanation
Indices: 2965287--2965462 Score: 230
Period size: 75 Copynumber: 2.3 Consensus size: 75
2965277 TCCACGTGAT
* * *
2965287 ATGGGCCTTCAGCATGCCCCAACATTTGATGATACAAGCGCTCAAAATACGTCAACATTCATT-A
1 ATGGGCTTTCAGCATGCCCCAACATTGGATGATACAAACGCTCAAAATACGTCAACATTC-TTGA
*
2965351 TTCTGATTGAA
65 TTCTAATTGAA
* * * *
2965362 ATGGGCTTTCAGCATGCCCCAACATTGGCTGATACAAATGTTCAAAATGA-GTCAATATTCTTGA
1 ATGGGCTTTCAGCATGCCCCAACATTGGATGATACAAACGCTCAAAAT-ACGTCAACATTCTTGA
2965426 TTCTAATTGAA
65 TTCTAATTGAA
* *
2965437 ATGGGCTTTCAGCTTGCTCCAACATT
1 ATGGGCTTTCAGCATGCCCCAACATT
2965463 TTCTTCTTGT
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
74 2 0.02
75 86 0.97
76 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (75 bp):
ATGGGCTTTCAGCATGCCCCAACATTGGATGATACAAACGCTCAAAATACGTCAACATTCTTGAT
TCTAATTGAA
Found at i:2970838 original size:8 final size:7
Alignment explanation
Indices: 2970825--2970888 Score: 53
Period size: 8 Copynumber: 9.0 Consensus size: 7
2970815 AAATATAATT
2970825 ATGCAAA
1 ATGCAAA
2970832 GATGC-AA
1 -ATGCAAA
2970839 ATGCAAAA
1 ATGC-AAA
2970847 ATG-AAA
1 ATGCAAA
*
2970853 ATGTAAAA
1 ATG-CAAA
*
2970861 ATGAAAAA
1 ATG-CAAA
2970869 ATGCAAA
1 ATGCAAA
2970876 ATGC-AA
1 ATGCAAA
2970882 ATGCAAA
1 ATGCAAA
2970889 TGTAAATATG
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
6 16 0.33
7 11 0.22
8 22 0.45
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.16
Consensus pattern (7 bp):
ATGCAAA
Found at i:2970844 original size:14 final size:14
Alignment explanation
Indices: 2970825--2970888 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
2970815 AAATATAATT
* *
2970825 ATGCAAAGATGCAA
1 ATGCAAAAATGAAA
2970839 ATGCAAAAATGAAA
1 ATGCAAAAATGAAA
*
2970853 ATGTAAAAATGAAAAA
1 ATGCAAAAATG--AAA
*
2970869 ATGC-AAAATGCAA
1 ATGCAAAAATGAAA
2970882 ATGCAAA
1 ATGCAAA
2970889 TGTAAATATG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
13 6 0.14
14 24 0.57
15 6 0.14
16 6 0.14
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.16
Consensus pattern (14 bp):
ATGCAAAAATGAAA
Found at i:2970854 original size:36 final size:36
Alignment explanation
Indices: 2970810--2970882 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
2970800 AAATAGTTTG
** * *
2970810 AAATAAAATATAATTATGCAAAGATGC-AAATGCAA
1 AAATAAAATATAAAAATGAAAAAATGCAAAATGCAA
*
2970845 AAATGAAAATGTAAAAATGAAAAAATGCAAAATGCAA
1 AAAT-AAAATATAAAAATGAAAAAATGCAAAATGCAA
2970882 A
1 A
2970883 TGCAAATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 4 0.13
36 18 0.58
37 9 0.29
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.19
Consensus pattern (36 bp):
AAATAAAATATAAAAATGAAAAAATGCAAAATGCAA
Found at i:2970988 original size:7 final size:7
Alignment explanation
Indices: 2970953--2970993 Score: 59
Period size: 6 Copynumber: 6.0 Consensus size: 7
2970943 ATAAAAGTAT
2970953 AAATGCA
1 AAATGCA
2970960 AAATG-A
1 AAATGCA
2970966 AAATGCA
1 AAATGCA
2970973 AAGATGCA
1 AA-ATGCA
2970981 AAATGC-
1 AAATGCA
2970987 AAATGCA
1 AAATGCA
2970994 TGTATGGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 12 0.39
7 12 0.39
8 7 0.23
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:2972504 original size:16 final size:15
Alignment explanation
Indices: 2972480--2972513 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2972470 AAATAAATAA
2972480 ATAAATAATAATGTAT
1 ATAAATAATAA-GTAT
*
2972496 ATAAGTAATAAGTAT
1 ATAAATAATAAGTAT
2972511 ATA
1 ATA
2972514 TAAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (15 bp):
ATAAATAATAAGTAT
Found at i:2973275 original size:2 final size:2
Alignment explanation
Indices: 2973268--2973300 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2973258 GATTAAAATA
2973268 AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2973301 AGTATGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2973301 original size:10 final size:11
Alignment explanation
Indices: 2973265--2973301 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 11
2973255 CATGATTAAA
2973265 ATAATATATAT
1 ATAATATATAT
2973276 ATATATATATAT
1 ATA-ATATATAT
2973288 ATAATAT-TAT
1 ATAATATATAT
2973298 ATAA
1 ATAA
2973302 GTATGATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.28
11 7 0.28
12 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATAATATATAT
Found at i:2973416 original size:27 final size:28
Alignment explanation
Indices: 2973375--2973436 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
2973365 TAATATTTAA
*
2973375 AAATAAATATCATTAAT-TTATAAAATT
1 AAATAAATATCATTAATATAATAAAATT
*
2973402 AAATAATATAT-ATTAATATAATAAAAAT
1 AAATAA-ATATCATTAATATAATAAAATT
*
2973430 AATTAAA
1 AAATAAA
2973437 CATATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AAATAAATATCATTAATATAATAAAATT
Found at i:2973446 original size:14 final size:14
Alignment explanation
Indices: 2973429--2973456 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2973419 ATAATAAAAA
2973429 TAATTAAACATATT
1 TAATTAAACATATT
2973443 TAATTAAACATATT
1 TAATTAAACATATT
2973457 AAAATATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATTAAACATATT
Found at i:2973534 original size:26 final size:26
Alignment explanation
Indices: 2973504--2973554 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2973494 CTAAATATAA
*
2973504 AAAGTAATAAAACTT-GTAATTAAATG
1 AAAGTAATAAAA-TTAGTAACTAAATG
*
2973530 AAAGTATTAAAATTAGTAACTAAAT
1 AAAGTAATAAAATTAGTAACTAAAT
2973555 TATAACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (26 bp):
AAAGTAATAAAATTAGTAACTAAATG
Found at i:2974380 original size:34 final size:34
Alignment explanation
Indices: 2974342--2974416 Score: 150
Period size: 34 Copynumber: 2.2 Consensus size: 34
2974332 TTCTGTTCTA
2974342 TTTGCTGCTTTGGTTGCTGTCGATGTTGTTCCCG
1 TTTGCTGCTTTGGTTGCTGTCGATGTTGTTCCCG
2974376 TTTGCTGCTTTGGTTGCTGTCGATGTTGTTCCCG
1 TTTGCTGCTTTGGTTGCTGTCGATGTTGTTCCCG
2974410 TTTGCTG
1 TTTGCTG
2974417 TTGGTTCTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.03, C:0.20, G:0.29, T:0.48
Consensus pattern (34 bp):
TTTGCTGCTTTGGTTGCTGTCGATGTTGTTCCCG
Found at i:2974984 original size:3 final size:3
Alignment explanation
Indices: 2974969--2975037 Score: 115
Period size: 3 Copynumber: 23.3 Consensus size: 3
2974959 GTTTGTATAT
2974969 ATA ATA A-A TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2975014 ATA ATA ATA ATA A-A ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
2975038 AAACGAATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 3 0.05
3 59 0.94
4 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2981417 original size:22 final size:22
Alignment explanation
Indices: 2981372--2981417 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2981362 CACCTCAAAA
* **
2981372 AATATTAAAATAATATATCTAG
1 AATATAAAAATAATATATAGAG
*
2981394 AATATAAAAATAATATCTAGAG
1 AATATAAAAATAATATATAGAG
2981416 AA
1 AA
2981418 CTCATCGCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (22 bp):
AATATAAAAATAATATATAGAG
Found at i:2984787 original size:160 final size:161
Alignment explanation
Indices: 2984522--2984842 Score: 635
Period size: 160 Copynumber: 2.0 Consensus size: 161
2984512 TGGATATCTT
2984522 CAACTTTGGGACCAAAAAAACACAAATAAAAAACCAATCTTGAGGAAACATAGGAACTCTGAACA
1 CAACTTTGGGACCAAAAAAACACAAATAAAAAACCAATCTTGAGGAAACATAGGAACTCTGAACA
2984587 ACAATGGTAAAAACCAGAATATTGTTGATGATGAGAAAACAGGCGCTAGGAACTACTGAAACAGG
66 ACAATGGTAAAAACCAGAATATTGTTGATGATGAGAAAACAGGCGCTAGGAACTACTGAAACAGG
2984652 AATATTGCTGACAAGATTGATAAATATTATG
131 AATATTGCTGACAAGATTGATAAATATTATG
2984683 CAACTTTGGGACCAAAAAAACACAAAT-AAAAACCAATCTTGAGGAAACATAGGAACTCTGAACA
1 CAACTTTGGGACCAAAAAAACACAAATAAAAAACCAATCTTGAGGAAACATAGGAACTCTGAACA
2984747 ACAATGGTAAAAACCAGAATATTGTTGATGATGAGAAAACAGGCGCTAGGAACTACTGAAACAGG
66 ACAATGGTAAAAACCAGAATATTGTTGATGATGAGAAAACAGGCGCTAGGAACTACTGAAACAGG
2984812 AATATTGCTGACAAGATTGATAAATATTATG
131 AATATTGCTGACAAGATTGATAAATATTATG
2984843 AAACAAAAAC
Statistics
Matches: 160, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
160 133 0.83
161 27 0.17
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.21
Consensus pattern (161 bp):
CAACTTTGGGACCAAAAAAACACAAATAAAAAACCAATCTTGAGGAAACATAGGAACTCTGAACA
ACAATGGTAAAAACCAGAATATTGTTGATGATGAGAAAACAGGCGCTAGGAACTACTGAAACAGG
AATATTGCTGACAAGATTGATAAATATTATG
Found at i:2989039 original size:20 final size:22
Alignment explanation
Indices: 2989014--2989053 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2989004 TGTTGTATAT
2989014 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
2989034 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
2989054 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:2989197 original size:20 final size:20
Alignment explanation
Indices: 2989172--2989238 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
2989162 TTCGTGCGTA
2989172 GATGCACAGCAGGATGCATC
1 GATGCACAGCAGGATGCATC
* *
2989192 GATGCACAGCAAGATGCATT
1 GATGCACAGCAGGATGCATC
*
2989212 GATGCACATCAGGATGCATC
1 GATGCACAGCAGGATGCATC
2989232 GATGCAC
1 GATGCAC
2989239 TAAGTGCATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (20 bp):
GATGCACAGCAGGATGCATC
Found at i:2990480 original size:44 final size:44
Alignment explanation
Indices: 2990432--2990691 Score: 349
Period size: 47 Copynumber: 5.8 Consensus size: 44
2990422 ACAATTAAAT
*
2990432 AATAAAAACATTAAGACACAAAATAAATAAAAAGTCCATAATTAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATT--A
* ** *
2990478 TAATAAAAACATTAAGAAACAAGATAAATAAAATCTCCATAACTAAA
1 -AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAA-T-TA
**
2990525 TAATAAAAACATTAAGAAACAAAATAAATAAAAAGTTTATAATTA
1 -AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
* *
2990570 AATAAAAACATTAAGAAACAAAATAAATAAAAAATTCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
*
2990614 AATAAAAACATTAAAAAAGCAAAATAAATAAAAAGTCCATAATTA
1 AATAAAAACATTAAGAAA-CAAAATAAATAAAAAGTCCATAATTA
* *
2990659 AATAAAAACATTAAGAAGCAAAATATATAAAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAA
2990692 CAAGTCTATC
Statistics
Matches: 191, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
44 73 0.38
45 41 0.21
46 1 0.01
47 75 0.39
48 1 0.01
ACGTcount: A:0.66, C:0.08, G:0.04, T:0.22
Consensus pattern (44 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
Found at i:2990540 original size:94 final size:90
Alignment explanation
Indices: 2990427--2990691 Score: 372
Period size: 89 Copynumber: 2.9 Consensus size: 90
2990417 TTTAAACAAT
*
2990427 TAAATAATAAAAACATTAAGACACAAAATAAATAAAAAGTCCATAATTAAATAATAAAAACATTA
1 TAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATT--A-AATAAAAACATTA
* **
2990492 AGAAACAAGATAAATAAAATCTCCATAA
63 AGAAACAAAATAAATAAAAAATCCATAA
**
2990520 CTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTTTATAATTAAATAAAAACATTAAG
1 -TAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTAAATAAAAACATTAAG
*
2990585 AAACAAAATAAATAAAAAATTCATAA
65 AAACAAAATAAATAAAAAATCCATAA
* *
2990611 T-TA-AATAAAAACATTAAAAAAGCAAAATAAATAAAAAGTCCATAATTAAATAAAAACATTAAG
1 TAAATAATAAAAACATTAAGAAA-CAAAATAAATAAAAAGTCCATAATTAAATAAAAACATTAAG
* *
2990674 AAGCAAAATATATAAAAA
65 AAACAAAATAAATAAAAA
2990692 CAAGTCTATC
Statistics
Matches: 157, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
88 17 0.11
89 56 0.36
90 1 0.01
91 37 0.24
92 1 0.01
94 45 0.29
ACGTcount: A:0.66, C:0.08, G:0.04, T:0.22
Consensus pattern (90 bp):
TAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTAAATAAAAACATTAAGA
AACAAAATAAATAAAAAATCCATAA
Found at i:2992809 original size:26 final size:26
Alignment explanation
Indices: 2992756--2992809 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
2992746 ATTAGTACAA
**
2992756 TAAAATATAATAAAATAATAAACTAT
1 TAAAATATAATAAAATAATAAAAAAT
* * *
2992782 TAAATTATTATAATATAATAAAAAAT
1 TAAAATATAATAAAATAATAAAAAAT
2992808 TA
1 TA
2992810 GCTTCGAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAAATATAATAAAATAATAAAAAAT
Found at i:2993725 original size:12 final size:14
Alignment explanation
Indices: 2993662--2993769 Score: 62
Period size: 14 Copynumber: 7.5 Consensus size: 14
2993652 TTAAAAAAAT
2993662 ATTA-ATTATTA-A
1 ATTATATTATTATA
2993674 ATTATATCTATTGATA
1 ATTATAT-TATT-ATA
* * *
2993690 ATTTTAATAATATA
1 ATTATATTATTATA
*
2993704 ATATATTTATTTTTATA
1 AT-TA--TATTATTATA
2993721 ATTATATTATTATA
1 ATTATATTATTATA
* *
2993735 ATATATAATATTACA
1 AT-TATATTATTATA
*
2993750 ATTTTATT-TTCATA
1 ATTATATTATT-ATA
2993764 A-TATAT
1 ATTATAT
2993770 AATAAATTAT
Statistics
Matches: 73, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
12 4 0.05
13 8 0.11
14 27 0.37
15 17 0.23
16 8 0.11
17 9 0.12
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.54
Consensus pattern (14 bp):
ATTATATTATTATA
Found at i:2993896 original size:20 final size:22
Alignment explanation
Indices: 2993871--2993914 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
2993861 ATAATATTCT
2993871 TATTTTAAT-ATATT-TTTTAA
1 TATTTTAATAATATTATTTTAA
2993891 TATTTTAATAATATTATTTTAA
1 TATTTTAATAATATTATTTTAA
2993913 TA
1 TA
2993915 AATAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
22 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTTAATAATATTATTTTAA
Found at i:2993924 original size:22 final size:22
Alignment explanation
Indices: 2993899--2993973 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 22
2993889 AATATTTTAA
2993899 TAATATTATTTTAATAAATAAT
1 TAATATTATTTTAATAAATAAT
*
2993921 TAATA-TA-ATTAAT-AATATAT
1 TAATATTATTTTAATAAATA-AT
* * * **
2993941 TATTCTCATTTTAATAAGCAAT
1 TAATATTATTTTAATAAATAAT
*
2993963 TAATATAATTT
1 TAATATTATTT
2993974 ATATTAATTT
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
19 4 0.10
20 10 0.26
21 3 0.08
22 20 0.51
23 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (22 bp):
TAATATTATTTTAATAAATAAT
Found at i:2993933 original size:42 final size:42
Alignment explanation
Indices: 2993887--2993979 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
2993877 AATATATTTT
* * *
2993887 TTAATATTTTAATAATATTATTTTAATAAATAATTAATATAA
1 TTAATATTATAATAATATCATTTTAATAAACAATTAATATAA
* * * * *
2993929 TTAATAATATATTATTCTCATTTTAATAAGCAATTAATATAA
1 TTAATATTATAATAATATCATTTTAATAAACAATTAATATAA
*
2993971 TTTATATTA
1 TTAATATTA
2993980 ATTTTATTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (42 bp):
TTAATATTATAATAATATCATTTTAATAAACAATTAATATAA
Found at i:3000366 original size:18 final size:17
Alignment explanation
Indices: 3000331--3000379 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
3000321 TTTAGTCCTC
* *
3000331 ATTTTAATTTAAATATA
1 ATTTAAATTTTAATATA
3000348 ATTTAAATTTTAATAATA
1 ATTTAAATTTTAAT-ATA
*
3000366 ATTTTAAATATTAA
1 A-TTTAAATTTTAA
3000380 AAATTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 12 0.44
18 4 0.15
19 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTTAATATA
Found at i:3007645 original size:20 final size:20
Alignment explanation
Indices: 3007620--3007657 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3007610 CATATGTTAA
3007620 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
3007640 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
3007658 TTAAAGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:3011838 original size:63 final size:62
Alignment explanation
Indices: 3011763--3011888 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 62
3011753 AAATATGATG
* *
3011763 AAAGTGAGTTATGAGAAGTGATAGGAACTATGTAAACATATGTAACATTATATGCTTAATAGA
1 AAAGTGAGTTATGAGAAGTGATAGGAACTAGGTAAAC-TATGTAACAGTATATGCTTAATAGA
3011826 AAAGTGAGTTATGAGAAGTGATAGGAACTAGGTAAACTATGTAACAGTATATGCTTAATAGA
1 AAAGTGAGTTATGAGAAGTGATAGGAACTAGGTAAACTATGTAACAGTATATGCTTAATAGA
3011888 A
1 A
3011889 GCATGAGTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
62 25 0.41
63 36 0.59
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (62 bp):
AAAGTGAGTTATGAGAAGTGATAGGAACTAGGTAAACTATGTAACAGTATATGCTTAATAGA
Found at i:3012817 original size:20 final size:20
Alignment explanation
Indices: 3012794--3012869 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
3012784 GAGGGATTAT
3012794 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
*
3012814 CAGTGTTCCTTCGAGG-C--A
1 CAGTGGTCCTTCG-GGACAAA
* * * *
3012832 TAGTGGTTCTTCGGAACAAT
1 CAGTGGTCCTTCGGGACAAA
3012852 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
3012870 TAGTGGTCAT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
17 1 0.02
18 12 0.28
20 28 0.65
21 2 0.05
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAA
Found at i:3012838 original size:38 final size:38
Alignment explanation
Indices: 3012795--3012885 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
3012785 AGGGATTATC
*
3012795 AGTGGTCCTTCGGGACAAACAGTGTTCCTTCGAGG-CAT
1 AGTGGTCCTTCGGGACAAACAGTGGTCCTTCG-GGACAT
* * *
3012833 AGTGGTTCTTCGGAACAATCAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACAT
*
3012871 AGTGGTCATTCGGGA
1 AGTGGTCCTTCGGGA
3012886 TAAATATTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 2 0.04
38 43 0.96
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACAT
Found at i:3012876 original size:18 final size:19
Alignment explanation
Indices: 3012795--3012885 Score: 89
Period size: 18 Copynumber: 4.8 Consensus size: 19
3012785 AGGGATTATC
*
3012795 AGTGGTCCTTCGGGACAAAC
1 AGTGGTCCTTCGGGAC-AAT
*
3012815 AGTGTTCCTTCGAGG-C-AT
1 AGTGGTCCTTCG-GGACAAT
* *
3012833 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGACAAT
3012852 CAGTGGTCCTTCGGGAC-AT
1 -AGTGGTCCTTCGGGACAAT
*
3012871 AGTGGTCATTCGGGA
1 AGTGGTCCTTCGGGA
3012886 TAAATATTCA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.02
18 26 0.44
19 4 0.07
20 26 0.44
21 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACAAT
Found at i:3013735 original size:9 final size:9
Alignment explanation
Indices: 3013723--3013753 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3013713 CACAAATTAT
3013723 AAAAAAGAA
1 AAAAAAGAA
3013732 AAAAAAGAA
1 AAAAAAGAA
*
3013741 AAAAGAGAA
1 AAAAAAGAA
3013750 AAAA
1 AAAA
3013754 GGAAGGAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:3013754 original size:9 final size:9
Alignment explanation
Indices: 3013723--3013754 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
3013713 CACAAATTAT
3013723 AAAAAAGA-
1 AAAAAAGAG
3013731 AAAAAA-AG
1 AAAAAAGAG
3013739 AAAAAAGAG
1 AAAAAAGAG
3013748 AAAAAAG
1 AAAAAAG
3013755 GAAGGAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.05
8 12 0.55
9 9 0.41
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:3021146 original size:86 final size:87
Alignment explanation
Indices: 3021001--3021173 Score: 339
Period size: 86 Copynumber: 2.0 Consensus size: 87
3020991 ATTGTACTAC
3021001 GATTAATCATAACGCCATTTAAGTTATCCAAATATGATCCAAATGAAACATCGATCGGATTTTAA
1 GATTAATCATAACGCCATTTAAGTTATCCAAATATGATCCAAATGAAACATCGATCGGATTTTAA
3021066 TCTCTAATGATTC-ATATTATT
66 TCTCTAATGATTCAATATTATT
3021087 GATTAATCATAACGCCATTTAAGTTATCCAAATATGATCCAAATGAAACATCGATCGGATTTTAA
1 GATTAATCATAACGCCATTTAAGTTATCCAAATATGATCCAAATGAAACATCGATCGGATTTTAA
3021152 TCTCTAATGATTCAATATTATT
66 TCTCTAATGATTCAATATTATT
3021174 ATACTACTAG
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 78 0.91
87 8 0.09
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (87 bp):
GATTAATCATAACGCCATTTAAGTTATCCAAATATGATCCAAATGAAACATCGATCGGATTTTAA
TCTCTAATGATTCAATATTATT
Found at i:3021586 original size:16 final size:17
Alignment explanation
Indices: 3021565--3021597 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3021555 ATTATCACTT
3021565 TTAA-TTTTTTTAAAGA
1 TTAATTTTTTTTAAAGA
3021581 TTAATTTTTTTTAAAGA
1 TTAATTTTTTTTAAAGA
3021598 AAAGAACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TTAATTTTTTTTAAAGA
Found at i:3021994 original size:23 final size:23
Alignment explanation
Indices: 3021963--3022007 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3021953 GAAAATGTTA
*
3021963 TATAAATTTTAAAAAAATAAAAT
1 TATAAATTTTAAAAAAAGAAAAT
* *
3021986 TATATATTTTTAAAAAAGAAAA
1 TATAAATTTTAAAAAAAGAAAA
3022008 CACATACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TATAAATTTTAAAAAAAGAAAAT
Found at i:3023832 original size:23 final size:23
Alignment explanation
Indices: 3023792--3023837 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
3023782 TCGTGACAAG
3023792 AAAAATATTCAAGAGCAAATAAAT
1 AAAAATATTCAAGAGCAAA-AAAT
3023816 AAAAAT-TTCCAAG-GCAAAAAAT
1 AAAAATATT-CAAGAGCAAAAAAT
3023838 TAATTGCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
23 7 0.33
24 10 0.48
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAAATATTCAAGAGCAAAAAAT
Found at i:3024758 original size:23 final size:23
Alignment explanation
Indices: 3024732--3024823 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
3024722 CACCACATCT
*
3024732 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
3024755 CGTAGAATTGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
3024778 CGTAGAATTGAACCGAAGTGTCA
1 CGTAGAAATGCACCGAAGTGCCA
*
3024801 CGTAAAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
3024824 TATAAAATGT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:3024847 original size:22 final size:22
Alignment explanation
Indices: 3024822--3024871 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3024812 ACCGAAGTGC
*
3024822 CATATA-AAATGTCCATAAGGAT
1 CATATAGAAAT-TCCATAAGAAT
*
3024844 CATATAGAAATTCCTTAAGAAT
1 CATATAGAAATTCCATAAGAAT
3024866 CATATA
1 CATATA
3024872 CATATTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (22 bp):
CATATAGAAATTCCATAAGAAT
Found at i:3024878 original size:22 final size:22
Alignment explanation
Indices: 3024822--3024878 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
3024812 ACCGAAGTGC
* *
3024822 CATATA-AAATGTCCATAAGGAT
1 CATATACAAAT-TCCTTAAGAAT
*
3024844 CATATAGAAATTCCTTAAGAAT
1 CATATACAAATTCCTTAAGAAT
*
3024866 CATATACATATTC
1 CATATACAAATTC
3024879 TAAGGACCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.32
Consensus pattern (22 bp):
CATATACAAATTCCTTAAGAAT
Found at i:3025873 original size:159 final size:163
Alignment explanation
Indices: 3025673--3025995 Score: 609
Period size: 159 Copynumber: 2.0 Consensus size: 163
3025663 CATTTCATTT
3025673 TATGGTCAATCTTATTTAGCTTATCTCAATTCTTATTAAATCATATAATTCTATTATACTAATTC
1 TATGGTCAATCTTATTTAGCTTATCTCAATTCTTATTAAATCATATAATTCTATTATACTAATTC
3025738 ATATAAATGATCACCTAACTACGTACTAACCCAATTCATGTTTCTATTGTTC-ATAAC-TTT-TA
66 ATATAAATGATCACCTAACTACGTACTAACCCAATTCATGTTTCTATTGTTCAATAACTTTTATA
3025800 CATGATTACCCAGTTCATATCGCTTCTCATAAA
131 CATGATTACCCAGTTCATATCGCTTCTCATAAA
3025833 TATGGTCAAT-TTATTTAGCTTATCTCAATTCTTATTAAATCATATAATTCTATTATACTAATTC
1 TATGGTCAATCTTATTTAGCTTATCTCAATTCTTATTAAATCATATAATTCTATTATACTAATTC
3025897 ATATAAATGATCACCTAACTACGTACTAACCCAATTCATGTTTCTATTGTTCATATAACTTTTAT
66 ATATAAATGATCACCTAACTACGTACTAACCCAATTCATGTTTCTATTGTTCA-ATAACTTTTAT
3025962 ACATGATTACCCAGTTCATATCGCTTCTCATAAA
130 ACATGATTACCCAGTTCATATCGCTTCTCATAAA
3025996 CTCACTTATA
Statistics
Matches: 159, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
159 106 0.67
160 10 0.06
161 5 0.03
162 3 0.02
163 35 0.22
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (163 bp):
TATGGTCAATCTTATTTAGCTTATCTCAATTCTTATTAAATCATATAATTCTATTATACTAATTC
ATATAAATGATCACCTAACTACGTACTAACCCAATTCATGTTTCTATTGTTCAATAACTTTTATA
CATGATTACCCAGTTCATATCGCTTCTCATAAA
Found at i:3029977 original size:29 final size:29
Alignment explanation
Indices: 3029944--3030000 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3029934 AGCATGCTAC
3029944 AAACT-TTGCTACCATAGTAGAAGAAGCTT
1 AAACTCTT-CTACCATAGTAGAAGAAGCTT
* *
3029973 AAACTCTTCTACTATAGTTGAAGAAGCT
1 AAACTCTTCTACCATAGTAGAAGAAGCT
3030001 ACAAGTGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (29 bp):
AAACTCTTCTACCATAGTAGAAGAAGCTT
Found at i:3037597 original size:60 final size:60
Alignment explanation
Indices: 3037530--3037650 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
3037520 GACACGTGAA
3037530 TATGCCTTGCCAGCAAGTTGATCCAGCATTTGAAAGTTGAACAGTGAAGGGAAGTGATCC
1 TATGCCTTGCCAGCAAGTTGATCCAGCATTTGAAAGTTGAACAGTGAAGGGAAGTGATCC
3037590 TATGCCTTGCCAGCAAGTTGATCCAGCATTTGAAAGTTGAACAGTGAAGGGAAGTGATCC
1 TATGCCTTGCCAGCAAGTTGATCCAGCATTTGAAAGTTGAACAGTGAAGGGAAGTGATCC
3037650 T
1 T
3037651 TCTTGGTGGC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (60 bp):
TATGCCTTGCCAGCAAGTTGATCCAGCATTTGAAAGTTGAACAGTGAAGGGAAGTGATCC
Found at i:3040784 original size:18 final size:19
Alignment explanation
Indices: 3040748--3040797 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
3040738 TAAGAAAAAT
* *
3040748 AAAAAGTAAAACTATATAA
1 AAAAAGTAAAAATAAATAA
3040767 AAAAAG-AAAAATAAATAA
1 AAAAAGTAAAAATAAATAA
*
3040785 GTAAAA-TAAAAAT
1 -AAAAAGTAAAAAT
3040798 GCTATGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (19 bp):
AAAAAGTAAAAATAAATAA
Found at i:3058670 original size:20 final size:20
Alignment explanation
Indices: 3058576--3058944 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
3058566 GATTTTCCAT
* ** *
3058576 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3058596 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3058616 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3058636 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
3058656 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
3058676 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3058696 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3058716 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3058736 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
3058756 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3058776 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3058796 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3058816 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
3058836 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3058856 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3058876 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3058896 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3058916 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3058936 AATCACAAC
1 AATCGCAAC
3058945 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3059665 original size:24 final size:24
Alignment explanation
Indices: 3059626--3059672 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3059616 AAATTTGGTC
3059626 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3059650 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3059673 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3059864 original size:12 final size:12
Alignment explanation
Indices: 3059847--3059871 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3059837 ATATAATCCT
3059847 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3059859 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3059871 G
1 G
3059872 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3062172 original size:19 final size:19
Alignment explanation
Indices: 3062150--3062441 Score: 383
Period size: 19 Copynumber: 16.4 Consensus size: 19
3062140 CGGAAAATAC
*
3062150 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3062169 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3062183 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3062203 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3062217 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3062236 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
3062254 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
3062268 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
3062287 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3062306 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3062325 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3062344 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3062363 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3062382 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
3062396 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3062415 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3062434 AATCGCAA
1 AATCGCAA
3062442 CGAGATAATC
Statistics
Matches: 244, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 38 0.16
15 2 0.01
16 17 0.07
17 8 0.03
18 11 0.05
19 155 0.64
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3062479 original size:52 final size:52
Alignment explanation
Indices: 3062150--3062463 Score: 321
Period size: 52 Copynumber: 5.9 Consensus size: 52
3062140 CGGAAAATAC
* *
3062150 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
*
3062203 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
* *
3062254 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
3062306 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
3062363 AATCGCAATGCGAAATGAAAATCGCAACGA-AAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA-AATCGCAATGCGAAATGAA
*
3062415 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
3062464 TATAAACGCA
Statistics
Matches: 240, Mismatches: 6, Indels: 31
0.87 0.02 0.11
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 50 0.21
52 80 0.33
53 28 0.12
54 4 0.02
55 3 0.01
57 64 0.27
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:3062579 original size:19 final size:19
Alignment explanation
Indices: 3062470--3062571 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3062460 AAATTATAAA
3062470 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3062489 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3062509 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3062525 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3062542 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3062561 CGCATTGCGAT
1 CGCATTGCGAT
3062572 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:3062697 original size:14 final size:14
Alignment explanation
Indices: 3062678--3062714 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3062668 CATCAATTAC
3062678 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3062692 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3062706 ACAAATCAA
1 ACAAATCAA
3062715 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3064690 original size:14 final size:14
Alignment explanation
Indices: 3064671--3064727 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3064661 GCGAAATGAA
*
3064671 AATCGCAACGACAG
1 AATCGCAACGAAAG
3064685 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
3064702 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3064718 AATCGCAACG
1 AATCGCAACG
3064728 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3064698 original size:33 final size:33
Alignment explanation
Indices: 3064652--3064744 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3064642 GCGAAACCAA
*
3064652 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3064685 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3064718 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3064745 TGCGATTTTG
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:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3064709 original size:19 final size:19
Alignment explanation
Indices: 3064615--3064749 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3064605 TAGTTTACTT
* *
3064615 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3064635 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3064654 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3064673 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3064687 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3064706 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3064720 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3064739 TCGCAATGCGA
1 TCGCAACGCGA
3064750 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3064767 original size:19 final size:19
Alignment explanation
Indices: 3064745--3064873 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3064735 AAAATCGCAA
3064745 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3064764 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3064778 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3064797 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3064811 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3064830 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3064849 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3064869 TGCGA
1 TGCGA
3064874 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3064787 original size:33 final size:33
Alignment explanation
Indices: 3064745--3064836 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3064735 AAAATCGCAA
3064745 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3064778 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3064811 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3064837 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3065208 original size:93 final size:93
Alignment explanation
Indices: 3064917--3065387 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
3064907 TTGAATGGAT
3064917 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3064982 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3065010 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3065074 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3065102 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3065167 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
3065195 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3065258 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3065286 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3065351 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3065379 AAATTTACT
1 AAATTTACT
3065388 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 3, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
91 88 0.24
92 96 0.26
93 188 0.51
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3065361 original size:184 final size:185
Alignment explanation
Indices: 3064917--3065387 Score: 917
Period size: 184 Copynumber: 2.6 Consensus size: 185
3064907 TTGAATGGAT
3064917 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3064982 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3065047 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
3065102 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3065167 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
3065232 TATA-TTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
3065286 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3065351 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
3065388 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
184 150 0.53
185 134 0.47
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3067130 original size:33 final size:33
Alignment explanation
Indices: 3067085--3067198 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
3067075 TCTTTTGGTT
3067085 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3067118 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3067151 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3067183 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3067199 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 31 0.41
33 45 0.59
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3067131 original size:19 final size:18
Alignment explanation
Indices: 3067092--3067203 Score: 95
Period size: 14 Copynumber: 6.8 Consensus size: 18
3067082 GTTGAAATGA
3067092 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
3067107 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
3067124 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
3067140 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
3067157 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
3067172 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
3067189 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
3067204 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 24
0.74 0.04 0.22
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 18 0.23
17 8 0.10
18 8 0.10
19 20 0.25
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:3067234 original size:14 final size:14
Alignment explanation
Indices: 3067215--3067269 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3067205 TTTGGTTTCG
3067215 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3067229 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3067248 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3067262 CGTTGCGA
1 CGTTGCGA
3067270 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3067247 original size:33 final size:33
Alignment explanation
Indices: 3067199--3067269 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3067189 AAAATCGCAA
**
3067199 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3067232 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3067265 TGCGA
1 TGCGA
3067270 CAGTCATTCT
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:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3067277 original size:33 final size:33
Alignment explanation
Indices: 3067210--3067291 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
3067200 GCGATTTTGG
***
3067210 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
3067243 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
3067276 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
3067292 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Done.