Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008160.1 Hibiscus syriacus cultivar Beakdansim tig00110729_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: 1466564
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:1002261 original size:23 final size:23
Alignment explanation
Indices: 1002230--1002302 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1002220 ATAGGTAAAA
*
1002230 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1002253 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1002276 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1002299 ATAT
1 ATAT
1002303 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1002957 original size:183 final size:183
Alignment explanation
Indices: 1002682--1003357 Score: 1248
Period size: 183 Copynumber: 3.7 Consensus size: 183
1002672 GCAATGCTAT
*
1002682 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
* *
1002747 GTGTCGGTACTTTATGTCTAGATTGGAAGAAAAATGTGTCGATA-CATTGTCAAAAAGTGTCGAC
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-TAAAAAAGTGTCGAC
1002811 ATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 ATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
1002865 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
*
1002930 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTGTCAAAAAGTGTCGAC
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-TAAAAAAGTGTCGAC
1002994 ATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 ATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
1003048 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1003113 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
* *
1003178 TTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
131 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
*
1003231 CGGCATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
*
1003296 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTTGATACCATTTAAAAAAGTGTCG
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
1003358 GTAATTTTAA
Statistics
Matches: 485, Mismatches: 7, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
183 481 0.99
184 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (183 bp):
CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:1005848 original size:25 final size:25
Alignment explanation
Indices: 1005820--1005884 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
1005810 TTATCATTAA
1005820 ATTTAGGTATATACAATAACTACAT
1 ATTTAGGTATATACAATAACTACAT
*
1005845 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATATACAATAACTACAT
1005870 ATTTAGGTATATACA
1 ATTTAGGTATATACA
1005885 TCTTTTGAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (25 bp):
ATTTAGGTATATACAATAACTACAT
Found at i:1006261 original size:23 final size:23
Alignment explanation
Indices: 1006230--1006302 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1006220 ATAGGTAAAA
*
1006230 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
1006253 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1006276 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1006299 ATAT
1 ATAT
1006303 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1006327 original size:46 final size:45
Alignment explanation
Indices: 1006230--1006327 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
1006220 ATAGGTAAAA
* * *
1006230 ATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATATCTATCCTTT
* *
1006276 ATATAATGTAATAGGTAGTGGTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TATCTATCCTTT
*
1006322 TTATAA
1 ATATAA
1006328 AAGTGTCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATATCTATCCTTT
Found at i:1006692 original size:23 final size:23
Alignment explanation
Indices: 1006661--1006733 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1006651 ATAGGTAAAA
*
1006661 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* **
1006684 ATATAATGTAATAGGTATCATTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1006707 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1006730 ATAT
1 ATAT
1006734 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1006838 original size:431 final size:431
Alignment explanation
Indices: 1006028--1007330 Score: 2405
Period size: 431 Copynumber: 3.0 Consensus size: 431
1006018 GTTAATGTTG
*
1006028 TTAAATT-TAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
1 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
1006092 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
*
1006157 AAATTACATAACTTTAAACA-AAGTATCGATCCTTTTTAT-AAAAGTATGAACACTTTCAATATA
131 AAATTACATAACTTTAAA-AGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
*
1006220 ATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGT
195 ATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGT
1006285 AATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACT
260 AATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACT
*
1006350 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
325 GTGGAAAATATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
*
1006415 GCGTCTAATGATTTCTTTTTTACGTTACGATATATATTATTA
390 GCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
*
1006457 TTAAATTAAAAATTCTAAATATTATTTTATCAAATATCAAAACAATCAAATAATTTTTTGTGTAA
1 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
*
1006522 ATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
* *
1006587 AAATCACATAACTTTAAAAGAAGTATCGATTCTTTTTATAAAAAGTATGGACACTTTCAATATAA
131 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
*
1006652 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCATTTATATAATGTA
196 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
1006717 ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
261 ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
1006782 TGGAAAATATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
326 TGGAAAATATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
*
1006847 CATCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
* * *
1006888 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCCAAACAATCAAATATTTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
1006953 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
1007018 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
131 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
* *
1007083 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGATAGCGTTTATATAATGTA
196 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
* * *
1007148 ATATGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCAATACTTTTTTCACTG
261 ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
1007213 TGGAAAATATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
326 TGGAAAATATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
1007278 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
1007319 TTAAATTAAAAA
1 TTAAATTAAAAA
1007331 CAATAAACAT
Statistics
Matches: 846, Mismatches: 25, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
429 8 0.01
430 154 0.18
431 684 0.81
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (431 bp):
TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
TGGAAAATATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
Found at i:1007123 original size:23 final size:23
Alignment explanation
Indices: 1007092--1007164 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1007082 ATAGGTAAAA
*
1007092 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1007115 ATATAATGTAATAGATAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1007138 ATATAATGTAATATGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1007161 ATAT
1 ATAT
1007165 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1007168 original size:21 final size:21
Alignment explanation
Indices: 1007092--1007173 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 21
1007082 ATAGGTAAAA
1007092 ATATGATGTAATAGGTAGCGCTT
1 ATAT-ATGTAATA-GTAGCGCTT
*
1007115 ATATAATGTAATAGATAGCGTTT
1 ATAT-ATGTAATAG-TAGCGCTT
*
1007138 ATATAATGTAATATGTAGTGCTT
1 ATAT-ATGTAATA-GTAGCGCTT
1007161 ATAT-TGTAA-AGTA
1 ATATATGTAATAGTA
1007174 TCTATCCTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.06
20 1 0.02
21 5 0.09
22 1 0.02
23 42 0.79
24 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
ATATATGTAATAGTAGCGCTT
Found at i:1007670 original size:23 final size:23
Alignment explanation
Indices: 1007641--1007688 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1007631 AAATAGGTAA
*
1007641 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAGTATATT
*
1007664 ATATAAGCGCTACCTAGTATGTT
1 ATATAAGCGCTACCTAGTATATT
1007687 AT
1 AT
1007689 TGTATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAGTATATT
Found at i:1007925 original size:20 final size:20
Alignment explanation
Indices: 1007897--1007935 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1007887 TTTTATATTT
* *
1007897 TAAATTTTTTTAAATTTATG
1 TAAAATTTTATAAATTTATG
1007917 TAAAATTTTATAAATTTAT
1 TAAAATTTTATAAATTTAT
1007936 TTTCTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TAAAATTTTATAAATTTATG
Found at i:1011036 original size:56 final size:56
Alignment explanation
Indices: 1010970--1011075 Score: 167
Period size: 56 Copynumber: 1.9 Consensus size: 56
1010960 TATCCTACGA
* * * *
1010970 TCTCTGTAGCTCGGACCTTAGAACTCTATGAATAACAACTATTCTTTTAATTATAG
1 TCTCTGTAGCTAGGACCTTAGAACTCTAGGAATAACAACCATTCCTTTAATTATAG
*
1011026 TCTCTTTAGCTAGGACCTTAGAACTCTAGGAATAACAACCATTCCTTTAA
1 TCTCTGTAGCTAGGACCTTAGAACTCTAGGAATAACAACCATTCCTTTAA
1011076 CCACTTAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (56 bp):
TCTCTGTAGCTAGGACCTTAGAACTCTAGGAATAACAACCATTCCTTTAATTATAG
Found at i:1011664 original size:19 final size:19
Alignment explanation
Indices: 1011630--1011693 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
1011620 TATGGTTTTC
1011630 TATTATTTATTTTATTATTAT
1 TATTA-TTA-TTTATTATTAT
1011651 TATTATTATTTATTATTAT
1 TATTATTATTTATTATTAT
* *
1011670 TAATATTATTT-TATAGTAT
1 TATTATTATTTAT-TATTAT
1011689 TATTA
1 TATTA
1011694 ATAAAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 1 0.03
19 30 0.77
20 3 0.08
21 5 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TATTATTATTTATTATTAT
Found at i:1011669 original size:22 final size:22
Alignment explanation
Indices: 1011630--1011696 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
1011620 TATGGTTTTC
*
1011630 TATTATTTATTTTATTATTATTAT
1 TATTATTTA--TTATTATTAATAT
1011654 TATTATTTATTATTATTAATAT
1 TATTATTTATTATTATTAATAT
*
1011676 TATT-TTATAGTATTATTAATA
1 TATTATT-TATTATTATTAATA
1011697 AAATATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.05
22 29 0.73
24 9 0.22
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (22 bp):
TATTATTTATTATTATTAATAT
Found at i:1011705 original size:22 final size:22
Alignment explanation
Indices: 1011664--1011705 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1011654 TATTATTTAT
** *
1011664 TATTATTAATATTATTTTATAG
1 TATTATTAATAAAATATTATAG
1011686 TATTATTAATAAAATATTAT
1 TATTATTAATAAAATATTAT
1011706 TTACAAACAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTATTAATAAAATATTATAG
Found at i:1011706 original size:3 final size:3
Alignment explanation
Indices: 1011630--1011693 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
1011620 TATGGTTTTC
*
1011630 TAT TATT TAT T-T TAT TAT TAT TAT TAT TATT TAT TAT TAT TAA TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
1011676 TAT T-T TA- TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1011694 ATAAAATATT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.11
3 41 0.77
4 6 0.11
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1013694 original size:28 final size:27
Alignment explanation
Indices: 1013663--1013716 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
1013653 TAATTCTTTC
*
1013663 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
*
1013691 TTTTCATAATATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
1013717 TTATTAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:1013724 original size:24 final size:22
Alignment explanation
Indices: 1013685--1013739 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
1013675 TTATATATAC
1013685 TTATTATTTTCATAATATTTATA
1 TTATTATTTTCATAATATTT-TA
*
1013708 TATATTATTTT-ATTAATGTTTTA
1 T-TATTATTTTCA-TAATATTTTA
1013731 TT-TTATTTT
1 TTATTATTTT
1013740 TCAAGTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 7 0.24
22 1 0.03
23 5 0.17
24 16 0.55
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTATTTTCATAATATTTTA
Found at i:1017021 original size:15 final size:15
Alignment explanation
Indices: 1017001--1017032 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1016991 ATCAATACCT
*
1017001 TTTTGCATACATTCA
1 TTTTGCACACATTCA
1017016 TTTTGCACACATTCA
1 TTTTGCACACATTCA
1017031 TT
1 TT
1017033 ATTCATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCACACATTCA
Found at i:1024950 original size:64 final size:64
Alignment explanation
Indices: 1024882--1025102 Score: 227
Period size: 64 Copynumber: 3.5 Consensus size: 64
1024872 TTGAAGGTGT
* **
1024882 ATCGATGCATTGGTAGTGCATCGATGCACTC-TTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAGGTAGTGCATCGATGCA-TCACATTAATAAT-AAAACATCGAATGCAATTCATG
1024945 C
64 C
* * **
1024946 ATCGATGCATAAGTAGTGCATCGATGCATCACATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCACATTAATAATAAAACATCGAATGCAATTCATGC
* ** * * ** *
1025010 ATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCACATTAATAATAAAACATCGAATGCAATTCATGC
1025074 A-CAGATGCATCA-GTAGTGCATCGATGCAT
1 ATC-GATGCAT-AGGTAGTGCATCGATGCAT
1025103 ACCTTCATTA
Statistics
Matches: 133, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
63 4 0.03
64 124 0.93
65 5 0.04
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCACATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:1025422 original size:24 final size:24
Alignment explanation
Indices: 1025395--1025467 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
1025385 GCATGCATAA
*
1025395 GATATAT-ATATGTTCATGTGATAT
1 GATATATGATATG-ACATGTGATAT
*
1025419 GATATGTGATATGACATGTGATAT
1 GATATATGATATGACATGTGATAT
* *
1025443 GAGAACATGATATGA-A-GTGATAT
1 GA-TATATGATATGACATGTGATAT
1025466 GA
1 GA
1025468 GATACATGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
23 9 0.21
24 19 0.45
25 14 0.33
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (24 bp):
GATATATGATATGACATGTGATAT
Found at i:1025427 original size:12 final size:12
Alignment explanation
Indices: 1025409--1025444 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1025399 TATATATGTT
1025409 CATGTGATATGA
1 CATGTGATATGA
*
1025421 TATGTGATATGA
1 CATGTGATATGA
1025433 CATGTGATATGA
1 CATGTGATATGA
1025445 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:1025466 original size:23 final size:26
Alignment explanation
Indices: 1025409--1025477 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
1025399 TATATATGTT
**
1025409 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
1025433 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
1025458 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
1025478 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:1025605 original size:15 final size:15
Alignment explanation
Indices: 1025587--1025616 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1025577 CAAGGGTATA
1025587 ATAGTCCTTCGGGAT
1 ATAGTCCTTCGGGAT
1025602 ATAGTCCTTCGGGAT
1 ATAGTCCTTCGGGAT
1025617 GTAGGGGTCC
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:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (15 bp):
ATAGTCCTTCGGGAT
Found at i:1026576 original size:21 final size:19
Alignment explanation
Indices: 1026542--1026588 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
1026532 TCCAAGATTA
1026542 TCTTTTTTGAAATTCAATT
1 TCTTTTTTGAAATTCAATT
1026561 TCTTTTGTTCGAAATTCAATT
1 TCTTTT-TT-GAAATTCAATT
*
1026582 TATTTTT
1 TCTTTTT
1026589 CACATAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 16 0.64
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (19 bp):
TCTTTTTTGAAATTCAATT
Found at i:1027982 original size:235 final size:234
Alignment explanation
Indices: 1027705--1028439 Score: 1070
Period size: 235 Copynumber: 3.2 Consensus size: 234
1027695 TTGAAGGTAG
1027705 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAACCTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAACCTTGTTT
1027770 AACCTTTTGTTTGAATTCATTACTCAATGGATCAACTTTTCCAGAGAAA-TTCGTAATGAGAAGA
66 AACCTTTTGTTTGAATTCATTACTCAATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGA
* * ** *
1027834 ATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCT
131 ATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTTGAATCT
*
1027899 ATCACAGAAGGAGATAGATCAACATCAACTTTTCCAGAGAA
196 ATCACA-AAAGAGATAGATC-ACATCAACTTTTCCAGAGAA
1027940 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAACCTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAACCTTGTTT
1028005 AACCTTTTGTTTGAATTCATTACTCAATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGA
66 AACCTTTTGTTTGAATTCATTACTCAATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGA
* * * *
1028070 ACTCATCTGAAGAAGGAATAAGAAGTTTATAATGAGAAGAACTTGTTTAACCTTTTGTTTGAAT-
131 ATTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTTGAATC
* ** *
1028134 TCATTAC---TCA-AT-G----GATCAACTTTTCCAGAGAA
195 T-ATCACAAAAGAGATAGATCACATCAACTTTTCCAGAGAA
* *
1028166 AGCTCGTAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA-CTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA-AACCTTGTT
1028230 TAACCTTTTGTTTGAATTCATTACTCAAT-GATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAG
65 TAACCTTTTGTTTGAATTCATTACTCAATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAG
* *
1028294 AATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA-CGTTTGTTTGATTC
130 AATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTTGAATC
* * * *
1028358 TATCACATAAAGAGATAGATCAGTATCAGCATTTCCAGA-AGG
195 TATCACA-AAAGAGATAGATCA-CATCAACTTTTCCAGAGA-A
* *
1028400 AGTTCATAATGAGAATAACTCATCTGAAGAA-GAATAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1028440 TTTGTTCAAC
Statistics
Matches: 451, Mismatches: 32, Indels: 36
0.87 0.06 0.07
Matches are distributed among these distances:
223 15 0.03
224 36 0.08
225 46 0.10
226 106 0.24
227 3 0.01
228 2 0.00
229 1 0.00
231 1 0.00
232 2 0.00
233 10 0.02
234 41 0.09
235 114 0.25
236 26 0.06
237 48 0.11
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (234 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAACCTTGTTT
AACCTTTTGTTTGAATTCATTACTCAATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGA
ATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTTGAATCT
ATCACAAAAGAGATAGATCACATCAACTTTTCCAGAGAA
Found at i:1028049 original size:113 final size:113
Alignment explanation
Indices: 1027922--1028354 Score: 766
Period size: 113 Copynumber: 3.9 Consensus size: 113
1027912 ATAGATCAAC
*
1027922 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1027987 AATGAGAA-AACCTTGTTTAACCTTTTGTTTGAATTCATTACTCAATGG
66 AATGAGAAGAA-CTTGTTTAACCTTTTGTTTGAATTCATTACTCAATGG
* *
1028035 ATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTTAT
1 ATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1028100 AATGAGAAGAACTTGTTTAACCTTTTGTTTGAATTCATTACTCAATGG
66 AATGAGAAGAACTTGTTTAACCTTTTGTTTGAATTCATTACTCAATGG
*
1028148 ATCAACTTTTCCAGAGAAAGCTCGTAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1028213 AATGAGAAGAACTTGTTTAACCTTTTGTTTGAATTCATTACTCAAT-G
66 AATGAGAAGAACTTGTTTAACCTTTTGTTTGAATTCATTACTCAATGG
* *
1028260 ATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAATTTATCTGAAG-AGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
1028324 AATGAGAAGAACTTGTTTAA-CGTTTGTTTGA
66 AATGAGAAGAACTTGTTTAACCTTTTGTTTGA
1028355 TTCTATCACA
Statistics
Matches: 309, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
110 10 0.03
111 37 0.12
112 45 0.15
113 215 0.70
114 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (113 bp):
ATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTTAACCTTTTGTTTGAATTCATTACTCAATGG
Found at i:1028700 original size:3 final size:3
Alignment explanation
Indices: 1028683--1028768 Score: 117
Period size: 3 Copynumber: 29.3 Consensus size: 3
1028673 ATGGTTTTTC
1028683 TAT TATT TAT T-T TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1028727 TAT TAT TAT TAT TAT TAT T-T ATAT TAT TAT TA- AAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT T
1028769 TACAAACAGG
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
2 6 0.08
3 65 0.87
4 4 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1029214 original size:15 final size:15
Alignment explanation
Indices: 1029194--1029222 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1029184 CAAGGACGGG
1029194 GAACCAAACAACAAT
1 GAACCAAACAACAAT
1029209 GAACCAAACAACAA
1 GAACCAAACAACAA
1029223 CAAAACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.28, G:0.07, T:0.03
Consensus pattern (15 bp):
GAACCAAACAACAAT
Found at i:1030125 original size:18 final size:19
Alignment explanation
Indices: 1030090--1030149 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
1030080 ATATGTTTAT
*
1030090 TATTA-ATATATTTAAA-A
1 TATTATATATATATAAATA
1030107 TATTAT-TATTATTATAAATA
1 TATTATATA-TA-TATAAATA
1030127 TA-TATATATATATAAATAA
1 TATTATATATATATAAAT-A
1030146 TATT
1 TATT
1030150 TATTTATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
17 7 0.20
18 9 0.26
19 13 0.37
20 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTATATATATATAAATA
Found at i:1031078 original size:36 final size:37
Alignment explanation
Indices: 1031011--1031080 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
1031001 CCCGGCCCGA
*
1031011 CCCGAATATCACACTTAAAAAAACCCGACCTGACTCG
1 CCCGAATATCACACTTAAAAAAACCCAACCTGACTCG
1031048 CCCGAATATCACACTT-AAAAAACCCAACCTGAC
1 CCCGAATATCACACTTAAAAAAACCCAACCTGAC
1031081 CCGAACAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 16 0.50
37 16 0.50
ACGTcount: A:0.40, C:0.36, G:0.09, T:0.16
Consensus pattern (37 bp):
CCCGAATATCACACTTAAAAAAACCCAACCTGACTCG
Found at i:1032100 original size:21 final size:21
Alignment explanation
Indices: 1032057--1032110 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1032047 TAATATATTA
* *
1032057 TTAAATT-AAAACTTGAATAT
1 TTAAATTAAAAATTTAAATAT
*
1032077 TTAAATTAAAAATTTAAATTT
1 TTAAATTAAAAATTTAAATAT
1032098 TTATAA-TAAAAAT
1 TTA-AATTAAAAAT
1032111 AAAAGCGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.24
21 20 0.69
22 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAAATTAAAAATTTAAATAT
Found at i:1033621 original size:29 final size:29
Alignment explanation
Indices: 1033581--1033658 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
1033571 CGGTGACTGG
* *
1033581 TATATTT-ACGATTTAACACCGGTCAGAT
1 TATATTTCCCGATCTAACACCGGTCAGAT
1033609 TATATTTCCCGATCTAACACCGGTCAGAT
1 TATATTTCCCGATCTAACACCGGTCAGAT
1033638 TATATTTCCCGATCTAACACC
1 TATATTTCCCGATCTAACACC
1033659 CGTAGCAGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.15
29 40 0.85
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (29 bp):
TATATTTCCCGATCTAACACCGGTCAGAT
Found at i:1034023 original size:17 final size:18
Alignment explanation
Indices: 1033987--1034027 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1033977 ATATTATGTA
*
1033987 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
1034005 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
1034022 TTTACT
1 TTTACT
1034028 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:1036288 original size:26 final size:24
Alignment explanation
Indices: 1036217--1036288 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
1036207 TTATATTTGT
1036217 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
1036242 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
1036264 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
1036289 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:1039798 original size:51 final size:51
Alignment explanation
Indices: 1039692--1039789 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
1039682 TAGCGTGGAT
* **
1039692 CAGGGGGTGTGCTATACCCACGTGTAAGCCATGTCAGCATATAGCGCGGTA
1 CAGGGGGTGCGCTATACCCACGTGTAAGCCAAATCAGCATATAGCGCGGTA
**
1039743 CAGGGGGTGCGCTATACCCCACGTG-GCGCCAAATCAGCATATAGCGC
1 CAGGGGGTGCGCTATA-CCCACGTGTAAGCCAAATCAGCATATAGCGC
1039790 AGGGCAGGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 33 0.80
52 8 0.20
ACGTcount: A:0.23, C:0.28, G:0.31, T:0.18
Consensus pattern (51 bp):
CAGGGGGTGCGCTATACCCACGTGTAAGCCAAATCAGCATATAGCGCGGTA
Found at i:1040115 original size:22 final size:22
Alignment explanation
Indices: 1040084--1040138 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
1040074 AAAGCTTCGA
1040084 TCGAA-TGGATTTGACTCGAGC
1 TCGAACTGGATTTGACTCGAGC
1040105 TCGAACTGGATTTGACTCGAGC
1 TCGAACTGGATTTGACTCGAGC
*
1040127 TCGAACTAGATT
1 TCGAACTGGATT
1040139 CGAATTCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (22 bp):
TCGAACTGGATTTGACTCGAGC
Found at i:1040607 original size:3 final size:3
Alignment explanation
Indices: 1040599--1040627 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1040589 TCTATTTTCC
1040599 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1040628 AAGAGGGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1042214 original size:15 final size:15
Alignment explanation
Indices: 1042172--1042215 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1042162 TAACGTCTCT
1042172 AATAACAGCGACTCC
1 AATAACAGCGACTCC
* * *
1042187 ATTAATAGTGACTCC
1 AATAACAGCGACTCC
1042202 AATAACAGCGACTC
1 AATAACAGCGACTC
1042216 TGGTAATAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (15 bp):
AATAACAGCGACTCC
Found at i:1043064 original size:2 final size:2
Alignment explanation
Indices: 1043057--1043082 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1043047 ATCCATTAAC
1043057 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1043083 TCTGCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1045399 original size:16 final size:17
Alignment explanation
Indices: 1045380--1045421 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1045370 AGGAAAATGA
1045380 GAAGGAAAGAAT-AAAT
1 GAAGGAAAGAATAAAAT
* *
1045396 GAAGAAAATAATAAAAT
1 GAAGGAAAGAATAAAAT
1045413 GAAGAGAAA
1 GAAG-GAAA
1045422 TATAACTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 10 0.48
17 8 0.38
18 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (17 bp):
GAAGGAAAGAATAAAAT
Found at i:1048784 original size:19 final size:19
Alignment explanation
Indices: 1048760--1048797 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1048750 TCACATCATC
1048760 TTTATTTAAATTCAAAATA
1 TTTATTTAAATTCAAAATA
1048779 TTTATTTAAATTCAAAATA
1 TTTATTTAAATTCAAAATA
1048798 AAAGATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTATTTAAATTCAAAATA
Found at i:1048824 original size:14 final size:15
Alignment explanation
Indices: 1048793--1048828 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1048783 TTTAAATTCA
*
1048793 AAATAAAAGATAATT
1 AAATAAAAGATAAAT
1048808 AAATAAAA-ATAAAT
1 AAATAAAAGATAAAT
1048822 AAATAAA
1 AAATAAA
1048829 TAAGAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
AAATAAAAGATAAAT
Found at i:1056339 original size:27 final size:27
Alignment explanation
Indices: 1056301--1056361 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
1056291 TAGATCTAAG
1056301 GCTAGACAGTCTGGGTTGGTTTATGCT
1 GCTAGACAGTCTGGGTTGGTTTATGCT
1056328 GCTAGACAGTCTGGGTTGGTTTATGCT
1 GCTAGACAGTCTGGGTTGGTTTATGCT
1056355 GCTAGAC
1 GCTAGAC
1056362 GTCGACATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.16, C:0.16, G:0.33, T:0.34
Consensus pattern (27 bp):
GCTAGACAGTCTGGGTTGGTTTATGCT
Found at i:1057940 original size:28 final size:29
Alignment explanation
Indices: 1057873--1057944 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
1057863 GAATACCGTT
* *
1057873 TATATGATATCTGATTTATTGTACATTTC
1 TATATGATTTCTGATTTACTGTACATTTC
*
1057902 TGATATGATTTCTGATTT-CTGTA-TTTATC
1 T-ATATGATTTCTGATTTACTGTACATT-TC
1057931 TATATGATTTCTGA
1 TATATGATTTCTGA
1057945 GTCTGGAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 15 0.39
29 8 0.21
30 15 0.39
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (29 bp):
TATATGATTTCTGATTTACTGTACATTTC
Found at i:1058554 original size:2 final size:2
Alignment explanation
Indices: 1058547--1058577 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1058537 TACATTTTTC
1058547 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 T
1058578 TGTATGAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1059189 original size:3 final size:3
Alignment explanation
Indices: 1059181--1059224 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1059171 TTTATTTGAT
1059181 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1059225 CATCTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1066379 original size:17 final size:17
Alignment explanation
Indices: 1066359--1066392 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1066349 AATTCAAAAT
* *
1066359 AATAGATAATTAAATAA
1 AATAAATAAATAAATAA
1066376 AATAAATAAATAAATAA
1 AATAAATAAATAAATAA
1066393 GGAAAGATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AATAAATAAATAAATAA
Found at i:1066921 original size:18 final size:18
Alignment explanation
Indices: 1066894--1066939 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1066884 CCCAAGGAGG
*
1066894 AGGAGAAGAAGCATCCGA
1 AGGAGAAGAAGAATCCGA
* *
1066912 AGGAGCAGAAGAATCTGA
1 AGGAGAAGAAGAATCCGA
1066930 AGGAGAAGAA
1 AGGAGAAGAA
1066940 CAATTGGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.11, G:0.35, T:0.07
Consensus pattern (18 bp):
AGGAGAAGAAGAATCCGA
Found at i:1066924 original size:24 final size:24
Alignment explanation
Indices: 1066877--1066924 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1066867 GGAAGGCGAG
* *
1066877 GAAGCATCCCAAGGAGGAGGAGAA
1 GAAGCATCCCAAGGAGCAGAAGAA
*
1066901 GAAGCATCCGAAGGAGCAGAAGAA
1 GAAGCATCCCAAGGAGCAGAAGAA
1066925 TCTGAAGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.44, C:0.17, G:0.35, T:0.04
Consensus pattern (24 bp):
GAAGCATCCCAAGGAGCAGAAGAA
Found at i:1072113 original size:39 final size:39
Alignment explanation
Indices: 1072070--1072144 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
1072060 AAGACCTTAC
* * *
1072070 CGTAGACTCCTCTGCTTTGTGATAAGGGTAAGTCCTATT
1 CGTAGACTCCTATGCTTTATGATAAGAGTAAGTCCTATT
* * *
1072109 CGTAGGCTCCTATGCTTTATGCTCAGAGTAAGTCCT
1 CGTAGACTCCTATGCTTTATGATAAGAGTAAGTCCT
1072145 TACCGCAGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (39 bp):
CGTAGACTCCTATGCTTTATGATAAGAGTAAGTCCTATT
Found at i:1072581 original size:2 final size:2
Alignment explanation
Indices: 1072576--1072620 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1072566 TATATATATA
*
1072576 TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1072618 TG T
1 TG T
1072621 TTATTGTATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1074581 original size:29 final size:30
Alignment explanation
Indices: 1074549--1074609 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
1074539 TTAAAATTTT
* *
1074549 TTCGAGGACTAAATTAAAA-TTTAATTAAA
1 TTCGAGGACCAAAGTAAAATTTTAATTAAA
* *
1074578 TTCGATGACCAAAGTAAAATTTTGATTAAA
1 TTCGAGGACCAAAGTAAAATTTTAATTAAA
1074608 TT
1 TT
1074610 TGATTCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (30 bp):
TTCGAGGACCAAAGTAAAATTTTAATTAAA
Found at i:1076001 original size:39 final size:39
Alignment explanation
Indices: 1075953--1076027 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
1075943 CATACTGCAT
1075953 GCTCATCTGCTTTGTGCTAAGGGTAAGTCCTTACCGTAG
1 GCTCATCTGCTTTGTGCTAAGGGTAAGTCCTTACCGTAG
* * *
1075992 GCTCCTCTGCTTTGTGCTCAGGGTAAGTTCTTACCG
1 GCTCATCTGCTTTGTGCTAAGGGTAAGTCCTTACCG
1076028 CAAGTCCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (39 bp):
GCTCATCTGCTTTGTGCTAAGGGTAAGTCCTTACCGTAG
Found at i:1076077 original size:12 final size:12
Alignment explanation
Indices: 1076060--1076091 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1076050 AAGGCCTTAT
1076060 TGGGTGTACATG
1 TGGGTGTACATG
1076072 TGGGTGTACATG
1 TGGGTGTACATG
1076084 TGGGTGTA
1 TGGGTGTA
1076092 TGGTTCTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.06, G:0.44, T:0.34
Consensus pattern (12 bp):
TGGGTGTACATG
Found at i:1078289 original size:39 final size:39
Alignment explanation
Indices: 1078213--1078289 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
1078203 ACCTTATTGC
*
1078213 AGGCTCATCTGCTTTGTGCTAAAGGTAAATCCTTACCGT
1 AGGCTCATCTGCTTTGTGCTAAAGGTAAATCCATACCGT
* * * *
1078252 AGGCTCCTCTGCTTTGTGCTCAAGGTAAGTGCATACCG
1 AGGCTCATCTGCTTTGTGCTAAAGGTAAATCCATACCG
1078290 CAAGTTCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (39 bp):
AGGCTCATCTGCTTTGTGCTAAAGGTAAATCCATACCGT
Found at i:1081977 original size:4 final size:4
Alignment explanation
Indices: 1081949--1081995 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
1081939 TTTGAATTCA
* *
1081949 AAAT -AAT ATAT AATT AAAT -AA- AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1081994 AA
1 AA
1081996 GAAAAGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 7 0.19
4 29 0.81
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:1081979 original size:18 final size:18
Alignment explanation
Indices: 1081948--1081988 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 18
1081938 ATTTGAATTC
1081948 AAAATAATATATAATTAAATA
1 AAAATAA-ATA-AA-TAAATA
1081969 AAAATAAATAAATAAATA
1 AAAATAAATAAATAAATA
1081987 AA
1 AA
1081989 TAAATAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 2 0.10
20 3 0.15
21 7 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATAAATAAATAAATA
Found at i:1081983 original size:22 final size:21
Alignment explanation
Indices: 1081948--1081992 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1081938 ATTTGAATTC
* *
1081948 AAAATAATATATAATTAAATA
1 AAAATAATAAATAAATAAATA
1081969 AAAATAAATAAATAAATAAATA
1 AAAAT-AATAAATAAATAAATA
1081991 AA
1 AA
1081993 TAAGAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATAATAAATAAATAAATA
Found at i:1082507 original size:24 final size:24
Alignment explanation
Indices: 1082477--1082524 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1082467 GGAAGGCGAG
* *
1082477 GAAGCATCTCAAGGAGGAGAAGAA
1 GAAGCATCCCAAGGAGCAGAAGAA
1082501 GAAGCATCCCAAGGAGCAGAAGAA
1 GAAGCATCCCAAGGAGCAGAAGAA
1082525 TCTGAAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.17, G:0.31, T:0.06
Consensus pattern (24 bp):
GAAGCATCCCAAGGAGCAGAAGAA
Found at i:1087816 original size:39 final size:39
Alignment explanation
Indices: 1087756--1087855 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 39
1087746 TCTATGAGTT
* * *
1087756 GTAAGACCTTACCTCAGGCTCCTCTGCTTCGTGCTAAGG
1 GTAAGTCCTTACCGCAAGCTCCTCTGCTTCGTGCTAAGG
* * *
1087795 GTAAGTCCTTGCCGCAAGCTCCTCTGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAAGCTCCTCTGCTTCGTGCTAAGG
1087834 GTAAGTCCTTACCGCAAG-TCCT
1 GTAAGTCCTTACCGCAAGCTCCT
1087856 TATGCTATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 4 0.07
39 50 0.93
ACGTcount: A:0.17, C:0.31, G:0.23, T:0.29
Consensus pattern (39 bp):
GTAAGTCCTTACCGCAAGCTCCTCTGCTTCGTGCTAAGG
Found at i:1091571 original size:39 final size:39
Alignment explanation
Indices: 1091512--1091599 Score: 122
Period size: 39 Copynumber: 2.3 Consensus size: 39
1091502 ACTTGTAAGA
*
1091512 CCTTACTGCAGGCTCATCTGCTTTGTGCTAAAGGTAAAT
1 CCTTACCGCAGGCTCATCTGCTTTGTGCTAAAGGTAAAT
* * * **
1091551 CCTTACCGCAGGCTCCTCTGCTTTGTGCTCAGGGTATGT
1 CCTTACCGCAGGCTCATCTGCTTTGTGCTAAAGGTAAAT
1091590 CCTTACCGCA
1 CCTTACCGCA
1091600 AGTCCTTATG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.32
Consensus pattern (39 bp):
CCTTACCGCAGGCTCATCTGCTTTGTGCTAAAGGTAAAT
Found at i:1092005 original size:2 final size:2
Alignment explanation
Indices: 1092000--1092028 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1091990 ACATTTTTCT
1092000 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 T
1092029 CGTATGAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1095812 original size:23 final size:24
Alignment explanation
Indices: 1095769--1095815 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1095759 GGAAGGCGAG
*
1095769 GAAGCATCTCAAGGAGGAGAAGAA
1 GAAGCATCTCAAGGAGCAGAAGAA
1095793 GAAGCATC-CAAGGAGCAGAAGAA
1 GAAGCATCTCAAGGAGCAGAAGAA
1095816 TCTGAAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.47, C:0.15, G:0.32, T:0.06
Consensus pattern (24 bp):
GAAGCATCTCAAGGAGCAGAAGAA
Found at i:1099736 original size:30 final size:29
Alignment explanation
Indices: 1099668--1099736 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 29
1099658 TTCGAGGACT
1099668 AAATTGAAATTTTAATTAAATTTGATGACC
1 AAATTGAAATTTTAATTAAATTTGAT-ACC
*
1099698 AAAGTGAAATTTTAATTAAATTTGGAT-CC
1 AAATTGAAATTTTAATTAAATTT-GATACC
1099727 AAATTTGAAA
1 AAA-TTGAAA
1099737 AGAACTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 5 0.14
30 27 0.77
31 3 0.09
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.38
Consensus pattern (29 bp):
AAATTGAAATTTTAATTAAATTTGATACC
Found at i:1100220 original size:17 final size:17
Alignment explanation
Indices: 1100198--1100231 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1100188 GGGTCGACCT
1100198 GACCTGACCCATTGTCC
1 GACCTGACCCATTGTCC
*
1100215 GACCTGACCCGTTGTCC
1 GACCTGACCCATTGTCC
1100232 AACCCGAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.41, G:0.21, T:0.24
Consensus pattern (17 bp):
GACCTGACCCATTGTCC
Found at i:1103458 original size:30 final size:30
Alignment explanation
Indices: 1103422--1103483 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
1103412 CCTAAATTTT
* * *
1103422 TTCGAAGACTAAATTGAAATTTTAATTAAA
1 TTCGAAGACCAAAGTGAAAATTTAATTAAA
*
1103452 TTCGAAGACCAAAGTGAAAATTTGATTAAA
1 TTCGAAGACCAAAGTGAAAATTTAATTAAA
1103482 TT
1 TT
1103484 TGATTCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (30 bp):
TTCGAAGACCAAAGTGAAAATTTAATTAAA
Found at i:1104859 original size:38 final size:39
Alignment explanation
Indices: 1104798--1104871 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 39
1104788 CATACTGCAT
1104798 GCTCCTCTGCTTTGTGCTAAGGGTAAGTCCTTACCGTAG
1 GCTCCTCTGCTTTGTGCTAAGGGTAAGTCCTTACCGTAG
*
1104837 GCTCCTCTG-TTTGTGCTCAGGGTAAGTCCTTACCG
1 GCTCCTCTGCTTTGTGCTAAGGGTAAGTCCTTACCG
1104872 CAAGTCCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 25 0.74
39 9 0.26
ACGTcount: A:0.14, C:0.27, G:0.26, T:0.34
Consensus pattern (39 bp):
GCTCCTCTGCTTTGTGCTAAGGGTAAGTCCTTACCGTAG
Found at i:1105284 original size:2 final size:2
Alignment explanation
Indices: 1105277--1105314 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1105267 CAGTTTTCTG
1105277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1105315 CTTATGAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1112674 original size:15 final size:15
Alignment explanation
Indices: 1112642--1112689 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1112632 TCAGATCATA
*
1112642 ATTTGGATATATGAT
1 ATTTGGATATATGTT
* *
1112657 ATTTGAATATATTTT
1 ATTTGGATATATGTT
*
1112672 ATTCGGATATATGTT
1 ATTTGGATATATGTT
1112687 ATT
1 ATT
1112690 CAGATCTGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (15 bp):
ATTTGGATATATGTT
Found at i:1119631 original size:20 final size:20
Alignment explanation
Indices: 1119606--1119645 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1119596 TTTTGGTGCA
1119606 GAGGGAATCGATCCCCCCTT
1 GAGGGAATCGATCCCCCCTT
*
1119626 GAGGGAATCGATTCCCCCTT
1 GAGGGAATCGATCCCCCCTT
1119646 TGAAGGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (20 bp):
GAGGGAATCGATCCCCCCTT
Found at i:1119660 original size:23 final size:21
Alignment explanation
Indices: 1119606--1119667 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
1119596 TTTTGGTGCA
1119606 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAATCGATTCCCCCCTT
*
1119626 GAGGGAATCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCTT
*
1119647 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAATCGATTCCCCCC
1119668 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.31
21 9 0.25
22 1 0.03
23 15 0.42
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCTT
Found at i:1128029 original size:26 final size:26
Alignment explanation
Indices: 1127997--1128050 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1127987 ATTTAGTGTG
*
1127997 TATGGTGGGCACGACCTTATATGTAT
1 TATGGTGGACACGACCTTATATGTAT
* *
1128023 TATGGTGGACGCGACCTTATGTGTAT
1 TATGGTGGACACGACCTTATATGTAT
1128049 TA
1 TA
1128051 GCACTTTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TATGGTGGACACGACCTTATATGTAT
Found at i:1129590 original size:12 final size:12
Alignment explanation
Indices: 1129572--1129614 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1129562 AGATGATGAT
1129572 GAAGAAGACGAA
1 GAAGAAGACGAA
* *
1129584 GACGAAGACGAT
1 GAAGAAGACGAA
*
1129596 GAAGAAGAAGAA
1 GAAGAAGACGAA
*
1129608 GAGGAAG
1 GAAGAAG
1129615 CTGTAATTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.53, C:0.07, G:0.37, T:0.02
Consensus pattern (12 bp):
GAAGAAGACGAA
Found at i:1132545 original size:16 final size:16
Alignment explanation
Indices: 1132524--1132558 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1132514 AATATTGGCT
*
1132524 TAAGGATAATTTAAAC
1 TAAGGATAATGTAAAC
1132540 TAAGGATAATGTAAAC
1 TAAGGATAATGTAAAC
1132556 TAA
1 TAA
1132559 TTAGATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (16 bp):
TAAGGATAATGTAAAC
Found at i:1134507 original size:27 final size:27
Alignment explanation
Indices: 1134465--1134532 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1134455 GTGTAGGAAT
*
1134465 TATAGAG--ATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1134490 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1134517 TATAGAGATATGATTT
1 TATAGAGATATGATTT
1134533 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1138263 original size:27 final size:27
Alignment explanation
Indices: 1138221--1138288 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1138211 GTGTAGGAAT
1138221 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1138246 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1138273 TATAGAGATATGATTT
1 TATAGAGATATGATTT
1138289 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1140906 original size:108 final size:108
Alignment explanation
Indices: 1140791--1141000 Score: 305
Period size: 108 Copynumber: 1.9 Consensus size: 108
1140781 ATATACACAT
* * * * *
1140791 TTTGCAGACGTAATTGGTCGAAGTTGAATTTTTAAAAAAG-GACAATATTCCTTTTTCATTATTA
1 TTTGCAGACGTAACTAGCCGAAGTTAAATTTTT-AAAAAGTAACAATATTCCTTTTTCATTATTA
* * *
1140855 AGATCATTTAATGATTTTTTTATAATATAGAAATTAAAGTTTAC
65 ACATCACTCAATGATTTTTTTATAATATAGAAATTAAAGTTTAC
* *
1140899 TTTGCAGACGTAACTAGCCGAAGTTAAATTTTTAAAAAGTAATAATATTTCTTTTTCATTATTAA
1 TTTGCAGACGTAACTAGCCGAAGTTAAATTTTTAAAAAGTAACAATATTCCTTTTTCATTATTAA
*
1140964 CATCACTCAATGATTTTTTTATAATATAGATATTAAA
66 CATCACTCAATGATTTTTTTATAATATAGAAATTAAA
1141001 ATGAACTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
107 6 0.07
108 84 0.93
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (108 bp):
TTTGCAGACGTAACTAGCCGAAGTTAAATTTTTAAAAAGTAACAATATTCCTTTTTCATTATTAA
CATCACTCAATGATTTTTTTATAATATAGAAATTAAAGTTTAC
Found at i:1146926 original size:6 final size:6
Alignment explanation
Indices: 1146916--1147064 Score: 235
Period size: 6 Copynumber: 24.8 Consensus size: 6
1146906 GAATGACAAG
* * * * *
1146916 CACATG CACATT CACATG CACATT CACATG CACATG CACATT CACATG
1 CACATT CACATT CACATT CACATT CACATT CACATT CACATT CACATT
* *
1146964 CACATT CACATT CACATG CACATT CACATG CACATT CACATT CACATT
1 CACATT CACATT CACATT CACATT CACATT CACATT CACATT CACATT
1147012 CACATT CACATT CACATT CACATT CACATT CACATT CACATT CACATT
1 CACATT CACATT CACATT CACATT CACATT CACATT CACATT CACATT
1147060 CACAT
1 CACAT
1147065 GCATCACTGG
Statistics
Matches: 132, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 132 1.00
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.28
Consensus pattern (6 bp):
CACATT
Found at i:1147755 original size:17 final size:18
Alignment explanation
Indices: 1147733--1147766 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1147723 TTGAGACTAA
*
1147733 AATAAAATA-AAATTAAG
1 AATAAAAGAGAAATTAAG
1147750 AATAAAAGAGAAATTAA
1 AATAAAAGAGAAATTAA
1147767 AAGGACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AATAAAAGAGAAATTAAG
Found at i:1148746 original size:12 final size:12
Alignment explanation
Indices: 1148729--1148762 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1148719 TTGGTGATTT
1148729 AATAAGAAGAAG
1 AATAAGAAGAAG
*
1148741 AATAAGTAGAAG
1 AATAAGAAGAAG
*
1148753 AAGAAGAAGA
1 AATAAGAAGA
1148763 GGGGGTCACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (12 bp):
AATAAGAAGAAG
Found at i:1154093 original size:17 final size:17
Alignment explanation
Indices: 1154071--1154106 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1154061 TAAAAAGTTT
1154071 AAACATAATTTTAAAAC
1 AAACATAATTTTAAAAC
1154088 AAACATAATTTTAAAAC
1 AAACATAATTTTAAAAC
1154105 AA
1 AA
1154107 TGCATCCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (17 bp):
AAACATAATTTTAAAAC
Found at i:1155721 original size:2 final size:2
Alignment explanation
Indices: 1155716--1155740 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1155706 ATATATATAT
1155716 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1155741 TACTAATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1158026 original size:17 final size:18
Alignment explanation
Indices: 1158006--1158039 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1157996 AAGAAAATAT
1158006 AATAA-ATAAGTAAAAAC
1 AATAACATAAGTAAAAAC
1158023 AATAACATAAGTAAAAA
1 AATAACATAAGTAAAAA
1158040 TAAATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (18 bp):
AATAACATAAGTAAAAAC
Found at i:1159667 original size:3 final size:3
Alignment explanation
Indices: 1159659--1159697 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1159649 ACCTGTATAT
*
1159659 TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1159698 AAAAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1159677 original size:9 final size:9
Alignment explanation
Indices: 1159663--1159727 Score: 64
Period size: 9 Copynumber: 7.6 Consensus size: 9
1159653 GTATATTAAT
1159663 AATAATAAA
1 AATAATAAA
*
1159672 AATAATAAT
1 AATAATAAA
*
1159681 AATAATAAT
1 AATAATAAA
1159690 AATAATAAA
1 AATAATAAA
1159699 AA-AATAAA
1 AATAATAAA
*
1159707 TA-AATAAA
1 AATAATAAA
*
1159715 TA-AATAAA
1 AATAATAAA
*
1159723 TATAA
1 AATAA
1159728 AAGACCTGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
8 23 0.44
9 29 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AATAATAAA
Found at i:1159708 original size:12 final size:12
Alignment explanation
Indices: 1159666--1159722 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 12
1159656 TATTAATAAT
1159666 AATAAAAATAAT-
1 AATAAAAA-AATA
*
1159678 AATAATAATAATAA
1 AATAA-AAAAAT-A
1159692 TAATAAAAAAATA
1 -AATAAAAAAATA
*
1159705 AATAAATAAATA
1 AATAAAAAAATA
1159717 AATAAA
1 AATAAA
1159723 TATAAAAGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 25 0.66
13 3 0.08
14 5 0.13
15 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AATAAAAAAATA
Found at i:1159708 original size:15 final size:14
Alignment explanation
Indices: 1159659--1159721 Score: 72
Period size: 15 Copynumber: 4.2 Consensus size: 14
1159649 ACCTGTATAT
1159659 TAATAATAATAAAAA
1 TAATAATAA-AAAAA
*
1159674 TAATAATAATAATAA
1 TAATAATAA-AAAAA
1159689 TAATAATAAAAAAA
1 TAATAATAAAAAAA
*
1159703 TAAATAAATAAATAAA
1 T-AAT-AATAAAAAAA
1159719 TAA
1 TAA
1159722 ATATAAAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
14 5 0.12
15 28 0.65
16 10 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
TAATAATAAAAAAA
Found at i:1159709 original size:4 final size:4
Alignment explanation
Indices: 1159693--1159724 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1159683 TAATAATAAT
*
1159693 AATA AAAA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA
1159725 TAAAAGACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:1160148 original size:141 final size:137
Alignment explanation
Indices: 1159926--1160226 Score: 371
Period size: 141 Copynumber: 2.2 Consensus size: 137
1159916 GAAACACGTT
* * **
1159926 TCCTACGTGATGAGGAAATCTGG---TCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTG
1 TCCTACGTGATGAGGAAGTCTGGTCATCAAGGGATGACACGGCTCATACACGATGAAGAACTCTG
*
1159988 GTCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTGATGAGGACGGATGATTAT-CTAAGGTT
66 GCCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTGATGAGGACGGATGATTATCCTAAGGTT
1160052 GACACGGC
131 GACAC-GC
* * *
1160060 TCCTACGTGATGAGGAAGTCTGGTCATCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
1 TCCTACGTGATGAGGAAGTCTGGTCATC-AA-GG--GATGACACGGCTCATACACGATGAAGAAC
* * * *
1160125 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
62 TCTGGCCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTGATGAGGACGGATGATTATCCTAA
* *
1160190 TGTTGACACTC
127 GGTTGACACGC
1160201 TCCTACGTG-TCGAGG-AGATCTGGTCA
1 TCCTACGTGAT-GAGGAAG-TCTGGTCA
1160227 GTTGATGTTG
Statistics
Matches: 143, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
134 22 0.15
137 2 0.01
138 2 0.01
139 2 0.01
140 3 0.02
141 100 0.70
142 12 0.08
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (137 bp):
TCCTACGTGATGAGGAAGTCTGGTCATCAAGGGATGACACGGCTCATACACGATGAAGAACTCTG
GCCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTGATGAGGACGGATGATTATCCTAAGGTT
GACACGC
Found at i:1161203 original size:24 final size:23
Alignment explanation
Indices: 1161176--1161226 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 23
1161166 TCTTTTTCTT
1161176 TTTTTTTGATTGATTTTTTT-TTGA
1 TTTTTTTGATT--TTTTTTTATTGA
1161200 TTTTTTTGATTTTTTTTTGATTGA
1 TTTTTTTGATTTTTTTTT-ATTGA
1161224 TTT
1 TTT
1161227 AAGTGTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.28
24 18 0.72
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (23 bp):
TTTTTTTGATTTTTTTTTATTGA
Found at i:1161205 original size:9 final size:9
Alignment explanation
Indices: 1161191--1161215 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1161181 TTGATTGATT
1161191 TTTTTTTGA
1 TTTTTTTGA
1161200 TTTTTTTGA
1 TTTTTTTGA
1161209 TTTTTTT
1 TTTTTTT
1161216 TTGATTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:1172800 original size:17 final size:16
Alignment explanation
Indices: 1172773--1172804 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1172763 AAGAAAATAT
1172773 AATAAATAAGTAAAAC
1 AATAAATAAGTAAAAC
1172789 AATAACATAAGTAAAA
1 AATAA-ATAAGTAAAA
1172805 ATAAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (16 bp):
AATAAATAAGTAAAAC
Found at i:1174435 original size:3 final size:3
Alignment explanation
Indices: 1174427--1174474 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
1174417 ACCTGTATAT
*
1174427 TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA -AA -AA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1174472 TAA
1 TAA
1174475 AAAATAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 6 0.15
3 35 0.85
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:1174477 original size:6 final size:6
Alignment explanation
Indices: 1174428--1174494 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
1174418 CCTGTATATT
* * * *
1174428 AATAAT AATAAA AATAAT AATAAT AATAAT AATAAA AA-ATAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATA-AA AATAAA
* *
1174476 AA-ATA AATAAA TATAAA AA
1 AATAAA AATAAA AATAAA AA
1174495 CCCGGACAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 5 0.10
6 45 0.88
7 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
AATAAA
Found at i:1174482 original size:12 final size:13
Alignment explanation
Indices: 1174428--1174481 Score: 78
Period size: 12 Copynumber: 4.4 Consensus size: 13
1174418 CCTGTATATT
1174428 AATAATAAT-AAA
1 AATAATAATAAAA
*
1174440 AATAATAAT-AAT
1 AATAATAATAAAA
1174452 AATAATAATAAAA
1 AATAATAATAAAA
1174465 AATAA-AATAAAA
1 AATAATAATAAAA
1174477 AATAA
1 AATAA
1174482 ATAAATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
12 32 0.82
13 7 0.18
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAATAATAAAA
Found at i:1174487 original size:15 final size:15
Alignment explanation
Indices: 1174449--1174494 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
1174439 AAATAATAAT
*
1174449 AATAATAATAATAAAA
1 AATAA-AATAAAAAAA
1174465 AATAAAATAAAAAATA
1 AATAAAATAAAAAA-A
1174481 AATAAATATAAAAA
1 AATAAA-ATAAAAA
1174495 CCCGGACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.30
16 12 0.44
17 7 0.26
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AATAAAATAAAAAAA
Found at i:1174935 original size:18 final size:17
Alignment explanation
Indices: 1174910--1174945 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1174900 TATATGCTAT
1174910 ATATATTGATAAATATA
1 ATATATTGATAAATATA
*
1174927 ATATGATTGATTAATATA
1 ATAT-ATTGATAAATATA
1174945 A
1 A
1174946 AAAAATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (17 bp):
ATATATTGATAAATATA
Found at i:1180992 original size:20 final size:20
Alignment explanation
Indices: 1180967--1181006 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1180957 TTGCTGCTAC
1180967 ATCTACGACTACAAGAACAA
1 ATCTACGACTACAAGAACAA
1180987 ATCTACGACTACAAGAACAA
1 ATCTACGACTACAAGAACAA
1181007 TTAAGAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.25, G:0.10, T:0.15
Consensus pattern (20 bp):
ATCTACGACTACAAGAACAA
Found at i:1182540 original size:20 final size:20
Alignment explanation
Indices: 1182503--1182541 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1182493 TGTATTTACT
*
1182503 AAAAAAATTTATATATTATA
1 AAAAAAATTTATAAATTATA
1182523 AAAAAAACTTTA-AAATTAT
1 AAAAAAA-TTTATAAATTAT
1182542 TTAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAAATTTATAAATTATA
Found at i:1190622 original size:999 final size:998
Alignment explanation
Indices: 1188687--1190686 Score: 3840
Period size: 999 Copynumber: 2.0 Consensus size: 998
1188677 CCTTCAGTTG
1188687 GGTATTTCAACAACTTTATCAGGATGGCATGATTCGACAAGATCCTAAGCTAAAGACCAGTGAGG
1 GGTATTTCAACAACTTTATCAGGATGGCATGATTCGACAAGATCCTAAGCTAAAGACCAGTGAGG
1188752 GTGGACAATATTACGAATATCACCAAGAAGAAGGGCATGAAATTCAGCTTTGCCCTGAATTCAGG
66 GTGGACAATATTACGAATATCACCAAGAAGAAGGGCATGAAATTCAGCTTTGCCCTGAATTCAGG
1188817 GGGTTACTACAAAGAATGATGAATAATAAGGAGGTAGAGTTCTTTGAGGAGGATAAGGAAAAAAG
131 GGGTTACTACAAAGAATGATGAATAATAAGGAGGTAGAGTTCTTTGAGGAGGATAAGGAAAAAAG
1188882 AGGAGAAGATGTCTTTACAACAGAAAATTCTGAGCCCGTTCACAGAACAAACAAACCAGTGGTCA
196 AGGAGAAGATGTCTTTACAACAGAAAATTCTGAGCCCGTTCACAGAACAAACAAACCAGTGGTCA
*
1188947 TCATTGTGAAACCATCAGCAATGAATTCTGGGTCGTCAATGCCAAAAGTTGTAATCACATCTCCT
261 TCATTGTGAAACCATCAGCAATGAATTCTGGGTCGTCAATGCCAAAAGTTGTAATCACAGCTCCT
*
1189012 TCACCATTTTCGTTTAAAGATACCCGCAAGGTGCCTTGGAACTACACTGCCAATGTTTCATTGAT
326 TCACCATTTTCGTTTAAAGATACCCGCAAGGTACCTTGGAACTACACTGCCAATGTTTCATTGAT
1189077 AAAGGAATCTGGCTCGCTAGAGAAAATAAAGGTAGTTGAAGATGAAACACCAAGAGACAACTTGA
391 AAAGGAATCTGGCTCGCTAGAGAAAATAAAGGTAGTTGAAGATGAAACACCAAGAGACAACTTGA
*
1189142 ATATTGAAATAGTGAGTGAAGTCGGGAACTTCACAAGAAGTGGGAGGTGTTATTATCCCGAGATG
456 ATATTGAAATAGCGAGTGAAGTCGGGAACTTCACAAGAAGTGGGAGGTGTTATTATCCCGAGATG
*
1189207 TCAAAAGAAATGGAAAAAGTGAAGGCAAAAGGAAAACCTGTGGTGGTACCGCAAAAGATATTTGA
521 TCAAAAGAAATGGAAAAAGTGAAGGCAAAAGGAAAAACTGTGGTGGTACCGCAAAAGATATTTGA
1189272 TGATGAACTCCCACCAATGATCAATGAGCCGGTAACAAAAATGCAAGCTCAAGAATTCTTGAAGT
586 TGATGAACTCCCACCAATGATCAATGAGCCGGTAACAAAAATGCAAGCTCAAGAATTCTTGAAGT
1189337 TTTTAAAACATAGTGAGTATAGTGTAGTTGAGTAGCTACACAAGCAACAAGCACGGATTTCAATT
651 TTTTAAAACATAGTGAGTATAGTGTAGTTGAGTAGCTACACAAGCAACAAGCACGGATTTCAATT
1189402 CTAGATTTGTTAATGAATTCAGAAGTACACCGGAATGCTTTGTTAGTAGTACTCAATCAAACATT
716 CTAGATTTGTTAATGAATTCAGAAGTACACCGGAATGCTTTGTTAGTAGTACTCAATCAAACATT
1189467 TGTGCCTAAAGATATATCAGTGAACAAGTTGGATCGAATTGTAGGGCACATAGCTGCTGATAACT
781 TGTGCCTAAAGATATATCAGTGAACAAGTTGGATCGAATTGTAGGGCACATAGCTGCTGATAACT
*
1189532 ACATAACTTTCACTGATGATGAAATTCCAGATAGTGGAATGGGATCAGTAAAAGCCCTCAATATC
846 ACATAACTTTCACTGATGATGAAATTCCAGATAGTGGAATGGGATCAGTAAAAGCCCACAATATC
1189597 ACAACTCATTGCCATGGTCATGTCTTACCAGGGGTTTTGATTGACAATGGGTCTGCACTAAATGT
911 ACAACTCATTGCCATGGTCATGTCTTACCAGGGGTTTTGATTGACAATGGGTCTGCACTAAATGT
* *
1189662 TATGCCTGTGGCCATGTTACGAA
976 TATGCCTATGGCCACGTTACGAA
1189685 GGTATTTCAACAACTTTATCAGGATGGCATGATTCGACAAGATCCTAAGCTAAAGACCAGTGAGG
1 GGTATTTCAACAACTTTATCAGGATGGCATGATTCGACAAGATCCTAAGCTAAAGACCAGTGAGG
*
1189750 GTGGACAATATTACGAATATCACCAAGAAGAAGGGCATGAAATTCAGCTTTGCCCTGAATTCATG
66 GTGGACAATATTACGAATATCACCAAGAAGAAGGGCATGAAATTCAGCTTTGCCCTGAATTCAGG
1189815 GGGTTACTACAAAGAATGATGAATAATAAGGAGGTAGAGTTCTTTGAGGAGGATAAGGAAAAAAA
131 GGGTTACTACAAAGAATGATGAATAATAAGGAGGTAGAGTTCTTTGAGGAGGATAAGG-AAAAAA
1189880 GAGGAGAAGATGTCTTTACAACAGAAAATTCTGAGCCCGTTCACAGAACAAACAAACCAGTGGTC
195 GAGGAGAAGATGTCTTTACAACAGAAAATTCTGAGCCCGTTCACAGAACAAACAAACCAGTGGTC
1189945 ATCATTGTGAAACCATCAGCAATGAATTCTGGGTCGTCAATGCCAAAAGTTGTAATCACAGCTCC
260 ATCATTGTGAAACCATCAGCAATGAATTCTGGGTCGTCAATGCCAAAAGTTGTAATCACAGCTCC
*
1190010 TTCACCATTTTCGTTTAAAGATACCCGCAAGTTACCTTGGAACTACACTGCCAATGTTTCATTGA
325 TTCACCATTTTCGTTTAAAGATACCCGCAAGGTACCTTGGAACTACACTGCCAATGTTTCATTGA
*
1190075 TAAAGGAATCTGGCTCGCTAGAGAAAATAAAGGTAGTTGAAGATGAAGCACCAAGAGACAACTTG
390 TAAAGGAATCTGGCTCGCTAGAGAAAATAAAGGTAGTTGAAGATGAAACACCAAGAGACAACTTG
1190140 -ATGATTGAAATAGCGAGTGAAGTCGGGAACTTCACAAGAAGTGGGAGGTGTTATTATCCCGAGA
455 AAT-ATTGAAATAGCGAGTGAAGTCGGGAACTTCACAAGAAGTGGGAGGTGTTATTATCCCGAGA
1190204 TGTCAAAAGAAATGGAAAAAGTGAAGGCAAAAGGAAAAACTGTGGTGGTACCGCAAAAGATATTT
519 TGTCAAAAGAAATGGAAAAAGTGAAGGCAAAAGGAAAAACTGTGGTGGTACCGCAAAAGATATTT
1190269 GATGATGAACTCCCACCAATGATCAATGAGCCGGTAACAAAAATGCAAGCTCAAGAATTCTTGAA
584 GATGATGAACTCCCACCAATGATCAATGAGCCGGTAACAAAAATGCAAGCTCAAGAATTCTTGAA
* *
1190334 GTTTTTAAAACATAGTGAGTATAGTGTAGTTGAGTAGCTACATAAGCAACAAGCACGGATTTCGA
649 GTTTTTAAAACATAGTGAGTATAGTGTAGTTGAGTAGCTACACAAGCAACAAGCACGGATTTCAA
*
1190399 TTCTGGATTTGTTAATGAATTCAGAAGTACACCGGAATGCTTTGTTAGTAGTACTCAATCAAACA
714 TTCTAGATTTGTTAATGAATTCAGAAGTACACCGGAATGCTTTGTTAGTAGTACTCAATCAAACA
1190464 TTTGTGCCTAAAGATATATCAGTGAACAAGTTGGATCGAATTGTAGGGCACATAGCTGCTGATAA
779 TTTGTGCCTAAAGATATATCAGTGAACAAGTTGGATCGAATTGTAGGGCACATAGCTGCTGATAA
1190529 CTACATAACTTTCACTGATGATGAAATTCCAGATAGTGGAATGGGATCAGTAAAAGCCCACAATA
844 CTACATAACTTTCACTGATGATGAAATTCCAGATAGTGGAATGGGATCAGTAAAAGCCCACAATA
* *
1190594 TCACAACTCATTGTCATGGTCATGTCTTACCAGGGGTTTTGATTGACAATGGGTCTGCACTCAAT
909 TCACAACTCATTGCCATGGTCATGTCTTACCAGGGGTTTTGATTGACAATGGGTCTGCACTAAAT
1190659 GTTATGCCTATGGCCACGTTACGAA
974 GTTATGCCTATGGCCACGTTACGAA
1190684 GGT
1 GGT
1190687 TATCGGTGGA
Statistics
Matches: 985, Mismatches: 15, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
998 189 0.19
999 796 0.81
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (998 bp):
GGTATTTCAACAACTTTATCAGGATGGCATGATTCGACAAGATCCTAAGCTAAAGACCAGTGAGG
GTGGACAATATTACGAATATCACCAAGAAGAAGGGCATGAAATTCAGCTTTGCCCTGAATTCAGG
GGGTTACTACAAAGAATGATGAATAATAAGGAGGTAGAGTTCTTTGAGGAGGATAAGGAAAAAAG
AGGAGAAGATGTCTTTACAACAGAAAATTCTGAGCCCGTTCACAGAACAAACAAACCAGTGGTCA
TCATTGTGAAACCATCAGCAATGAATTCTGGGTCGTCAATGCCAAAAGTTGTAATCACAGCTCCT
TCACCATTTTCGTTTAAAGATACCCGCAAGGTACCTTGGAACTACACTGCCAATGTTTCATTGAT
AAAGGAATCTGGCTCGCTAGAGAAAATAAAGGTAGTTGAAGATGAAACACCAAGAGACAACTTGA
ATATTGAAATAGCGAGTGAAGTCGGGAACTTCACAAGAAGTGGGAGGTGTTATTATCCCGAGATG
TCAAAAGAAATGGAAAAAGTGAAGGCAAAAGGAAAAACTGTGGTGGTACCGCAAAAGATATTTGA
TGATGAACTCCCACCAATGATCAATGAGCCGGTAACAAAAATGCAAGCTCAAGAATTCTTGAAGT
TTTTAAAACATAGTGAGTATAGTGTAGTTGAGTAGCTACACAAGCAACAAGCACGGATTTCAATT
CTAGATTTGTTAATGAATTCAGAAGTACACCGGAATGCTTTGTTAGTAGTACTCAATCAAACATT
TGTGCCTAAAGATATATCAGTGAACAAGTTGGATCGAATTGTAGGGCACATAGCTGCTGATAACT
ACATAACTTTCACTGATGATGAAATTCCAGATAGTGGAATGGGATCAGTAAAAGCCCACAATATC
ACAACTCATTGCCATGGTCATGTCTTACCAGGGGTTTTGATTGACAATGGGTCTGCACTAAATGT
TATGCCTATGGCCACGTTACGAA
Found at i:1199229 original size:20 final size:20
Alignment explanation
Indices: 1199183--1199247 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
1199173 ACTATGCTTG
1199183 AAGAAAAAAATGGAAAAAAT
1 AAGAAAAAAATGGAAAAAAT
*
1199203 AAAAAAAAAAT-GAAAGAAA-
1 AAGAAAAAAATGGAAA-AAAT
*
1199222 AAGGAAAAAAAT-AAAAAAAT
1 AA-GAAAAAAATGGAAAAAAT
1199242 GAAGAA
1 -AAGAA
1199248 GGAGGGTTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 9 0.24
20 27 0.71
21 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (20 bp):
AAGAAAAAAATGGAAAAAAT
Found at i:1200531 original size:2 final size:2
Alignment explanation
Indices: 1200524--1200575 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
1200514 TTGGGATTTA
1200524 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1200562 -T AT -T AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT A
1200576 AAATGTTTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
1 7 0.16
2 36 0.84
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:1200541 original size:12 final size:11
Alignment explanation
Indices: 1200524--1200575 Score: 62
Period size: 10 Copynumber: 5.3 Consensus size: 11
1200514 TTGGGATTTA
1200524 ATATA-TATAT
1 ATATATTATAT
1200534 ATATA-TATAT
1 ATATATTATAT
1200544 ATATATTAT-T
1 ATATATTATAT
1200554 AT-TATTAT-T
1 ATATATTATAT
1200563 AT-TATTATAT
1 ATATATTATAT
1200573 ATA
1 ATA
1200576 AAATGTTTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
9 15 0.38
10 21 0.54
11 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATATTATAT
Found at i:1201897 original size:2 final size:2
Alignment explanation
Indices: 1201890--1201920 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1201880 AGTCATGTTA
1201890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1201921 ACATTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1211164 original size:154 final size:153
Alignment explanation
Indices: 1210839--1211259 Score: 565
Period size: 154 Copynumber: 2.7 Consensus size: 153
1210829 TTTGGTAAAA
* * *
1210839 AAAAAAGAACTTAAAATAAATGACAAATTGAAGGAATAAGGAGATTATGAAAAACTGAAGGACTA
1 AAAAAAG-ACTTAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTA
* * * *
1210904 AATTGAAAAATAAAAAATTTGTAACCAAAAAGAGAAATTGAAAGTACACATGTATTCTACTATGG
65 AATTGAAAAATAAAAAA-AT-T-ATCAAAAAGAGAAATTGAAAGTACAAATGCATTCTACTATGG
** * *
1210969 TTTAGGAGCATGTGGCTCACATTTGGT
127 TTTAGGAGCATGTAACTCAAATTTGCT
* * * *
1210996 AAAAAAGGATTTAAAATAAATAATGAATTGAAGAAATAAGGATATTAT-AAAAATTTGAAGGACT
1 AAAAAA-GACTTAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAA-TTGAAGGACT
*
1211060 AAATTGAAAAATAAAAAAATTATCAAAAAGAGGAATTGAAAGTACAAATGCATTCTACTATGGTT
64 AAATTGAAAAATAAAAAAATTATCAAAAAGAGAAATTGAAAGTACAAATGCATTCTACTATGGTT
1211125 TAGGAGCATGTAACTCAAATTTGCT
129 TAGGAGCATGTAACTCAAATTTGCT
*
1211150 AAAAATAGACTTAAAATAAATGACGAATGGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTA
1 AAAAA-AGACTTAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTA
* ** *
1211215 AATTAAAAAATAAAAATTTGTTATCAAAGAGAGAAATTGAAAGTA
65 AATTGAAAAATAAAAA--AATTATCAAAAAGAGAAATTGAAAGTA
1211260 AACATGTATT
Statistics
Matches: 232, Mismatches: 26, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
154 128 0.55
155 7 0.03
156 29 0.12
157 67 0.29
158 1 0.00
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (153 bp):
AAAAAAGACTTAAAATAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTAA
ATTGAAAAATAAAAAAATTATCAAAAAGAGAAATTGAAAGTACAAATGCATTCTACTATGGTTTA
GGAGCATGTAACTCAAATTTGCT
Found at i:1212090 original size:2 final size:2
Alignment explanation
Indices: 1212083--1212119 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1212073 GCTTTAAGAG
1212083 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1212120 ATTTATGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1218784 original size:2 final size:2
Alignment explanation
Indices: 1218777--1218824 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1218767 ACATATACGA
1218777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1218819 AT AT AT
1 AT AT AT
1218825 GCATAAAAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1220628 original size:3 final size:3
Alignment explanation
Indices: 1220620--1220742 Score: 183
Period size: 3 Copynumber: 41.0 Consensus size: 3
1220610 TAAACAAAAT
* * * * * * *
1220620 TAA TAA TAA TAA TAA TAA TAA CAA TAA CAA CAA CAA CAA CAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1220668 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1220716 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1220743 GTATAATACT
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 116 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:1221228 original size:46 final size:46
Alignment explanation
Indices: 1221169--1221460 Score: 243
Period size: 46 Copynumber: 6.6 Consensus size: 46
1221159 CTTTAGGAAA
* *
1221169 TGATAACATGGTTCCTACGTGATGAGGATGACTGGTTATCTAGGGG
1 TGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGG
* * *
1221215 TGATAACACGGTTCCTACGAGATGAGGATGGCTGGTTATCTAGGGG
1 TGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGG
* * * *
1221261 T-AGTAACACGGTTCCTATGTGATGAGGACAACTGATTATCT-GGAG
1 TGA-TAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGG
* * *
1221306 T--TGACACGGTTCCTACATGATGAGGA-AATCTGG---TCTA---G
1 TGATAACACGGTTCCTACGTGATGAGGACGA-CTGGTTATCTAGGGG
* * * ** ** *
1221344 TGATGACACAGTTCCTACGTGATGAGGACGGCAAGCCATCTAAGGG
1 TGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGG
* * *
1221390 TGATAACACGGTTCCTACGTGATGAGAACGAATGGTTATCTA-GGA
1 TGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGG
* *
1221435 T--TGACACGGCTCCTACGTGATGAGGA
1 TGATAACACGGTTCCTACGTGATGAGGA
1221461 GATCAGGTCA
Statistics
Matches: 201, Mismatches: 33, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
38 2 0.01
40 28 0.14
42 2 0.01
43 51 0.25
45 8 0.04
46 110 0.55
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (46 bp):
TGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGG
Found at i:1221414 original size:129 final size:129
Alignment explanation
Indices: 1221214--1221481 Score: 335
Period size: 129 Copynumber: 2.1 Consensus size: 129
1221204 TTATCTAGGG
* * * ** ** * *
1221214 GTGATAACACGGTTCCTACGAGATGAGGATGGCTGGTTATCTAGGGGTAGTAACACGGTTCCTAT
1 GTGATGACACAGTTCCTACGAGATGAGGACGGCAAGCCATCTAAGGGTAGTAACACGGTTCCTAC
* * * *
1221279 GTGATGAGGAC-AACTGATTATCT-GGAGTTGACACGGTTCCTACATGATGAGGAAATCTGGTCT
66 GTGATGAGAACGAA-TGATTATCTAGGA-TTGACACGGCTCCTACATGATGAGGAAATCAGGTCA
1221342 A
129 A
*
1221343 GTGATGACACAGTTCCTACGTGATGAGGACGGCAAGCCATCTAAGGGT-GATAACACGGTTCCTA
1 GTGATGACACAGTTCCTACGAGATGAGGACGGCAAGCCATCTAAGGGTAG-TAACACGGTTCCTA
* * *
1221407 CGTGATGAGAACGAATGGTTATCTAGGATTGACACGGCTCCTACGTGATGAGGAGATCAGGTCAA
65 CGTGATGAGAACGAATGATTATCTAGGATTGACACGGCTCCTACATGATGAGGAAATCAGGTCAA
1221472 GTGATGACAC
1 GTGATGACAC
1221482 TGCCCATCTG
Statistics
Matches: 119, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
128 1 0.01
129 113 0.95
130 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (129 bp):
GTGATGACACAGTTCCTACGAGATGAGGACGGCAAGCCATCTAAGGGTAGTAACACGGTTCCTAC
GTGATGAGAACGAATGATTATCTAGGATTGACACGGCTCCTACATGATGAGGAAATCAGGTCAA
Found at i:1221817 original size:38 final size:37
Alignment explanation
Indices: 1221745--1221817 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 37
1221735 GATTTTTTTA
* *
1221745 TGTCTCAAATGAGAAAAAATTTGTTTTGAAAGAAAAT
1 TGTCTCAAACGAGAAAAAATTTGTTTTCAAAGAAAAT
* *
1221782 TGTCTCAAACGAGACAACATTT-TGTTTCAAGAGAAA
1 TGTCTCAAACGAGAAAAAATTTGT-TTTCAA-AGAAA
1221818 CAACATCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 1 0.03
37 24 0.80
38 5 0.17
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (37 bp):
TGTCTCAAACGAGAAAAAATTTGTTTTCAAAGAAAAT
Found at i:1221939 original size:32 final size:32
Alignment explanation
Indices: 1221898--1221972 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
1221888 TTCACATCAG
*
1221898 AATGTTGAATCCCCAAAGATGCCCCAATATTC
1 AATGTTGAATCCCCAAAGATGCCCCAACATTC
* *
1221930 AATGTTGAATCTCCAAAGATGCCTCAACATTC
1 AATGTTGAATCCCCAAAGATGCCCCAACATTC
* *
1221962 ACTATTGAATC
1 AATGTTGAATC
1221973 TTTAAATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (32 bp):
AATGTTGAATCCCCAAAGATGCCCCAACATTC
Found at i:1223009 original size:15 final size:14
Alignment explanation
Indices: 1222976--1223027 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
1222966 CTTCTTGTCC
* *
1222976 CTTTTCCTTTGTTT
1 CTTTTCTTTTGCTT
*
1222990 ATTTTCTATTTGCTT
1 CTTTTCT-TTTGCTT
*
1223005 CTTTTCTTTTTCTT
1 CTTTTCTTTTGCTT
1223019 CTTCTTCTT
1 CTT-TTCTT
1223028 CAAGTGTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 14 0.45
15 17 0.55
ACGTcount: A:0.04, C:0.21, G:0.04, T:0.71
Consensus pattern (14 bp):
CTTTTCTTTTGCTT
Found at i:1227124 original size:21 final size:20
Alignment explanation
Indices: 1227100--1227139 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1227090 TAAAAATGAA
*
1227100 ATGCAGATGCAAAATGCAAAT
1 ATGCAAATGC-AAATGCAAAT
*
1227121 ATGCAAATGCATATGCAAA
1 ATGCAAATGCAAATGCAAA
1227140 AATATTGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.20
Consensus pattern (20 bp):
ATGCAAATGCAAATGCAAAT
Found at i:1227142 original size:14 final size:13
Alignment explanation
Indices: 1227098--1227140 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1227088 CTTAAAAATG
*
1227098 AAATGCAGATGCA
1 AAATGCATATGCA
1227111 AAATGCAAATATGC-
1 AAATGC--ATATGCA
1227125 AAATGCATATGCA
1 AAATGCATATGCA
1227138 AAA
1 AAA
1227141 ATATTGATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.23
13 9 0.35
14 6 0.23
15 5 0.19
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (13 bp):
AAATGCATATGCA
Found at i:1229428 original size:32 final size:31
Alignment explanation
Indices: 1229374--1229463 Score: 119
Period size: 32 Copynumber: 2.9 Consensus size: 31
1229364 AATGATGAAA
* *
1229374 AATG-ACACAATCAAAAGAAAATAAATAGGTT
1 AATGTACACAAACAAAAGGAAATAAATA-GTT
*
1229405 AATGTACATAAACAAAAGGAAATAAATTAGTT
1 AATGTACACAAACAAAAGGAAATAAA-TAGTT
*
1229437 AATGTACACAAACAAAAGGAAAGAAAT
1 AATGTACACAAACAAAAGGAAATAAAT
1229464 CATTTAATAC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
31 5 0.10
32 45 0.87
33 2 0.04
ACGTcount: A:0.59, C:0.09, G:0.13, T:0.19
Consensus pattern (31 bp):
AATGTACACAAACAAAAGGAAATAAATAGTT
Found at i:1232570 original size:3 final size:3
Alignment explanation
Indices: 1232562--1232640 Score: 126
Period size: 3 Copynumber: 26.3 Consensus size: 3
1232552 TAAACAAAAT
1232562 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1232609 TAA TAA TAA TAA TAA TAAA TAA GT-A TAA TAA T
1 TAA TAA TAA TAA TAA T-AA TAA -TAA TAA TAA T
1232641 TTAAGTCCGA
Statistics
Matches: 72, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 3 0.04
3 65 0.90
4 4 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1240353 original size:35 final size:35
Alignment explanation
Indices: 1240307--1240376 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1240297 AAAAACTTAG
1240307 TAAAATCTAACCATACCTGTACCCAACACCCACAC
1 TAAAATCTAACCATACCTGTACCCAACACCCACAC
1240342 TAAAATCTAACCATACCTGTACCCAACACCCACAC
1 TAAAATCTAACCATACCTGTACCCAACACCCACAC
1240377 CCACACCCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.40, G:0.03, T:0.17
Consensus pattern (35 bp):
TAAAATCTAACCATACCTGTACCCAACACCCACAC
Found at i:1243053 original size:9 final size:9
Alignment explanation
Indices: 1243039--1243080 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
1243029 TTTTCAACTA
1243039 AAAAAATAT
1 AAAAAATAT
1243048 AAAAAATAT
1 AAAAAATAT
**
1243057 CTAAAATAT
1 AAAAAATAT
1243066 ATAAAAATAT
1 A-AAAAATAT
1243076 AAAAA
1 AAAAA
1243081 TTTTAGGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAAATAT
Done.