Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008259.1 Hibiscus syriacus cultivar Beakdansim tig00110912_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: 2373650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:771851 original size:15 final size:15
Alignment explanation
Indices: 771818--771848 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
771808 ATATTTTAAT
771818 AATAATATTAACATA
1 AATAATATTAACATA
771833 AATAATATTAA-ATA
1 AATAATATTAACATA
771847 AA
1 AA
771849 ATATTCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAATATTAACATA
Found at i:772229 original size:21 final size:21
Alignment explanation
Indices: 772189--772229 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
772179 AATACATAAT
* *
772189 AGTACCGATACTGCTCAAGAC
1 AGTACCAATACTACTCAAGAC
*
772210 AGTACCAATACTACTTAAGA
1 AGTACCAATACTACTCAAGA
772230 GGTTTGACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (21 bp):
AGTACCAATACTACTCAAGAC
Found at i:785560 original size:3 final size:3
Alignment explanation
Indices: 785554--785582 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
785544 ATCACCGAAC
785554 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
785583 TCTGATTTAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:786782 original size:2 final size:2
Alignment explanation
Indices: 786775--786833 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
786765 GGGTGTGATA
786775 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
786817 AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC A
786834 AAATCATCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:808130 original size:6 final size:6
Alignment explanation
Indices: 808119--808175 Score: 71
Period size: 6 Copynumber: 9.3 Consensus size: 6
808109 TATGCCTAAG
* *
808119 AAAGAA AAAGAA AAAGAA GAAA-AA GAAGAA AAAGAA AAAGAA AAAAAGA
1 AAAGAA AAAGAA AAAGAA -AAAGAA AAAGAA AAAGAA AAAGAA AAAGA-A
808168 AAAGAA AA
1 AAAGAA AA
808176 GGAGGGTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
5 2 0.05
6 34 0.77
7 8 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:808140 original size:9 final size:9
Alignment explanation
Indices: 808116--808154 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
808106 TATTATGCCT
*
808116 AAGAAAGAAA
1 AAGAAA-AAG
808126 AAGAAAAAG
1 AAGAAAAAG
808135 AAGAAAAAG
1 AAGAAAAAG
808144 AAGAAAAAG
1 AAGAAAAAG
808153 AA
1 AA
808155 AAAGAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 22 0.79
10 6 0.21
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:808140 original size:15 final size:14
Alignment explanation
Indices: 808119--808175 Score: 89
Period size: 15 Copynumber: 4.0 Consensus size: 14
808109 TATGCCTAAG
808119 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
808133 AGAAGAAAAAGAAGAA
1 A-AAGAAAAAGAA-AA
808149 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
808163 AAAG-AAAAGAAAA
1 AAAGAAAAAGAAAA
808176 GGAGGGTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.22
14 7 0.17
15 22 0.54
16 3 0.07
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAGAAAA
Found at i:808165 original size:9 final size:9
Alignment explanation
Indices: 808116--808176 Score: 59
Period size: 9 Copynumber: 6.3 Consensus size: 9
808106 TATTATGCCT
808116 AAGAAAGAAA
1 AAGAAA-AAA
*
808126 AAGAAAAAG
1 AAGAAAAAA
*
808135 AAGAAAAAG
1 AAGAAAAAA
808144 AAGAAAAAGA
1 AAGAAAAA-A
*
808154 AAAAGAAAAA
1 AAGA-AAAAA
808164 AAGAAAAGAA
1 AAGAAAA-AA
808174 AAG
1 AAG
808177 GAGGGTTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
9 22 0.50
10 18 0.41
11 4 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:808175 original size:24 final size:25
Alignment explanation
Indices: 808119--808176 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
808109 TATGCCTAAG
808119 AAAGAAAAAGAAAAAGAAGAAAAAGA
1 AAAG-AAAAGAAAAAGAAGAAAAAGA
*
808145 AGA-AAAAGAAAAAGAA-AAAAAGA
1 AAAGAAAAGAAAAAGAAGAAAAAGA
808168 AAAGAAAAG
1 AAAGAAAAG
808177 GAGGGTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 9 0.31
24 18 0.62
26 2 0.07
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (25 bp):
AAAGAAAAGAAAAAGAAGAAAAAGA
Found at i:809727 original size:138 final size:140
Alignment explanation
Indices: 809198--809788 Score: 690
Period size: 140 Copynumber: 4.2 Consensus size: 140
809188 ACCAATCAAT
* * *
809198 ATTTCAAATGGAGGGTTCATAATGAGAAGAACTCATCCGAT-GAGGGAGAAGAAGTTAATAATAA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTTATAATAA
* * * * **
809262 AAAGAACTTGTTCAACCTTTTCTCGATTCATCACATATGGAGTTAAATCAGTGACATCTCACTTG
66 GAAGAACTTGTTCAACCTTTGCTCGATTCATCACATATGGAGTTGAATCAGCGACGCCTCACTTG
*
809327 AGGGATTAAA
131 AGGGATTAAC
* * * *
809337 ATTTCCAATGGAGAGTTAATTATGAGAAGAACTCATCCGATAGAGAGAAAAGAAGTTCT-TAATA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTT-TATAATA
* * * * * *
809401 AGAAGAACTTGTTTAACATTTGCTCGATTCATCGCATATGGAGTTGGATCAGCAACGCCTTACTT
65 AGAAGAACTTGTTCAACCTTTGCTCGATTCATCACATATGGAGTTGAATCAGCGACGCCTCACTT
*
809466 GAGGGATTGAC
130 GAGGGATTAAC
* * * **
809477 ATTTCCAATTGAGAGTTCACAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATGG
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTTATAATAA
* * * * *
809542 GAACAACTTGTTCAACCTTTTCTCGATTCATCACATATGGAGTTGAATCAGCGATGCCTAACGTG
66 GAAGAACTTGTTCAACCTTTGCTCGATTCATCACATATGGAGTTGAATCAGCGACGCCTCACTTG
809607 AAGGG-TTAAC
131 -AGGGATTAAC
* * *
809617 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-CGA-GGAGAAGTAGTTTATAATGA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTTATAATAA
* * * * ** * * *
809680 GAATAACTTATTAAACCTTAGCTCGATTCATCGTATTTGGAGTTGAATCAGCGATGCCTCAC-TC
66 GAAGAACTTGTTCAACCTTTGCTCGATTCATCACATATGGAGTTGAATCAGCGACGCCTCACTTG
* *
809744 AAGGATCAAC
131 AGGGATTAAC
* * *
809754 ATTTTCAGTAGAGAGTTCATAATGAGAAGAACTCA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCA
809789 CAGCTTGAAT
Statistics
Matches: 385, Mismatches: 62, Indels: 12
0.84 0.14 0.03
Matches are distributed among these distances:
136 3 0.01
137 37 0.10
138 70 0.18
139 39 0.10
140 232 0.60
141 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (140 bp):
ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTTATAATAA
GAAGAACTTGTTCAACCTTTGCTCGATTCATCACATATGGAGTTGAATCAGCGACGCCTCACTTG
AGGGATTAAC
Found at i:809933 original size:14 final size:15
Alignment explanation
Indices: 809909--809966 Score: 64
Period size: 14 Copynumber: 3.8 Consensus size: 15
809899 TCTACCTATA
*
809909 TATTATCATTAATAT
1 TATTATTATTAATAT
*
809924 TATTATATTATAAATAT
1 TA-T-TATTATTAATAT
*
809941 TA-TATTATAAATAT
1 TATTATTATTAATAT
809955 TATTATTATTAA
1 TATTATTATTAA
809967 ACCAAAAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 14 0.38
15 10 0.27
16 1 0.03
17 12 0.32
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATTATTAATAT
Found at i:809960 original size:12 final size:14
Alignment explanation
Indices: 809924--809963 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
809914 TCATTAATAT
809924 TATTATATTATAAA
1 TATTATATTATAAA
809938 TATTATATTATAAA
1 TATTATATTATAAA
809952 TATTATTATTAT
1 TATTA-TATTAT
809964 TAAACCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTATATTATAAA
Found at i:810032 original size:23 final size:23
Alignment explanation
Indices: 810001--810051 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
809991 CCTCAAGCCC
* *
810001 AACCCAACCCAGAACCTAACCAT
1 AACCCAACCCAGAACCCAACCAG
* *
810024 AACCTAACCCAGAGCCCAACCAG
1 AACCCAACCCAGAACCCAACCAG
810047 AACCC
1 AACCC
810052 GACCTGGAGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.45, G:0.08, T:0.06
Consensus pattern (23 bp):
AACCCAACCCAGAACCCAACCAG
Found at i:810328 original size:2 final size:2
Alignment explanation
Indices: 810321--810351 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
810311 GTTTCAAGGT
810321 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
810352 TTAATTTCGA
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:810468 original size:35 final size:35
Alignment explanation
Indices: 810374--810468 Score: 90
Period size: 35 Copynumber: 2.7 Consensus size: 35
810364 AATAAATTTT
* *
810374 TATTTTCTTTTTAGTTTCGAATATCAATAAAAAGGAAA
1 TATTTTC-TTTTAGTTTCGAA-A-AAATAAAAAGAAAA
*
810412 GA-TTT-TTTTAGTTTTCG-AAAAATAACAAA-AAAA
1 TATTTTCTTTTAG-TTTCGAAAAAATAA-AAAGAAAA
810445 TATTTTCTTTTAGTTTCGAAAAAA
1 TATTTTCTTTTAGTTTCGAAAAAA
810469 CGGTAAACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
33 9 0.19
34 12 0.25
35 18 0.38
36 5 0.10
37 3 0.06
38 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.42
Consensus pattern (35 bp):
TATTTTCTTTTAGTTTCGAAAAAATAAAAAGAAAA
Found at i:819176 original size:131 final size:130
Alignment explanation
Indices: 818910--819265 Score: 390
Period size: 131 Copynumber: 2.7 Consensus size: 130
818900 CTTAATAGGG
* * * * * * *
818910 AAAATAGTAATATCTTTTCATTTCGGTTGAAGCAATAAATGACTACTTCAAGGCATGAGAGGTCA
1 AAAATAATGATATCTATTCATTTCGATTGGAGTAATAAATGACTACTTTAAGGCATGAGAGGTCA
* * * * ** * * *
818975 TTCATTTCGATTGGAAATAATTATATATTACCGTTTTCTTTCGAATCAATATTTATTTTTAAGAC
66 TTTATTCCAATTGGAAATAATTAGATATTACCGTTTTCACTCAAATCAATATTGAATTTTAAGAC
* * * *
819040 AAAATAATGATTTCTATTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGATAGGTCA
1 AAAATAATGATATCTATTCATTTCGATTGGAGTAATAAATGACTACTTTAAGGCATGAGAGGTCA
* * * *
819105 TTTATTCCCAATTGGAAATCATTAGATGTTATCGTTTTCACTCAAATCAATGTTGAATTTTAAGA
66 TTTATT-CCAATTGGAAATAATTAGATATTACCGTTTTCACTCAAATCAATATTGAATTTTAAGA
819170 C
130 C
* * * * * *
819171 GAAATAATGATATCTCTTCATTTTGATTAGAGTAATAAATGACTACTTTAAGGTATGAGATGTCA
1 AAAATAATGATATCTATTCATTTCGATTGGAGTAATAAATGACTACTTTAAGGCATGAGAGGTCA
* * *
819236 TTTATTGTCGATTGG-AATAATTAGTTATTA
66 TTTATT-CCAATTGGAAATAATTAGATATTA
819266 TCATTTTCTC
Statistics
Matches: 185, Mismatches: 40, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
130 71 0.38
131 114 0.62
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (130 bp):
AAAATAATGATATCTATTCATTTCGATTGGAGTAATAAATGACTACTTTAAGGCATGAGAGGTCA
TTTATTCCAATTGGAAATAATTAGATATTACCGTTTTCACTCAAATCAATATTGAATTTTAAGAC
Found at i:828079 original size:14 final size:15
Alignment explanation
Indices: 828051--828079 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
828041 AATTTTAAGA
828051 TTTTGAAACTTACTC
1 TTTTGAAACTTACTC
828066 TTTTGAAA-TTACTC
1 TTTTGAAACTTACTC
828080 CCCCTTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (15 bp):
TTTTGAAACTTACTC
Found at i:834284 original size:20 final size:20
Alignment explanation
Indices: 834242--834284 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
834232 TTGTTTTAAT
* *
834242 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
834262 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
834282 TTT
1 TTT
834285 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:839560 original size:8 final size:7
Alignment explanation
Indices: 839547--839606 Score: 50
Period size: 7 Copynumber: 7.9 Consensus size: 7
839537 AAGTGAAGAA
839547 AAAAAATG
1 AAAAAA-G
839555 AAAAAATG
1 AAAAAA-G
839563 ATGAAAAAG
1 A--AAAAAG
839572 AAAAGAA-
1 AAAA-AAG
839579 AAAAAAG
1 AAAAAAG
839586 AAAAAAG
1 AAAAAAG
*
839593 AGGAAAAG
1 A-AAAAAG
839601 AAAAAA
1 AAAAAA
839607 AAGATAGAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
6 2 0.04
7 19 0.42
8 17 0.38
9 2 0.04
10 5 0.11
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:839567 original size:31 final size:29
Alignment explanation
Indices: 839532--839608 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 29
839522 CACTTGAAGA
**
839532 ATGAAAAGTGAAGAAAAAAAATGAAAAAATG
1 ATGAAAAGAAAAGAAAAAAAA-GAAAAAA-G
839563 ATGAAAAAGAAAAGAAAAAAAAGAAAAAAG
1 ATG-AAAAGAAAAGAAAAAAAAGAAAAAAG
*
839593 AGGAAAAGAAAA-AAAA
1 ATGAAAAGAAAAGAAAA
839609 GATAGAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.10
29 9 0.21
30 3 0.07
31 10 0.24
32 16 0.38
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.06
Consensus pattern (29 bp):
ATGAAAAGAAAAGAAAAAAAAGAAAAAAG
Found at i:839583 original size:24 final size:23
Alignment explanation
Indices: 839555--839625 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
839545 AAAAAAAATG
*
839555 AAAAAATGATGAAAAAGAAAAGA
1 AAAAAAAGATGAAAAAGAAAAGA
*
839578 AAAAAAAGA-AAAAAGAGGAAAAGA
1 AAAAAAAGATGAAAA-A-GAAAAGA
*
839602 AAAAAAAGATAGAATAAATAAAAG
1 AAAAAAAGAT-GAA-AAAGAAAAG
839626 GGGGTTTAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 4 0.10
23 9 0.23
24 16 0.41
25 5 0.13
26 3 0.08
27 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (23 bp):
AAAAAAAGATGAAAAAGAAAAGA
Found at i:841146 original size:131 final size:130
Alignment explanation
Indices: 840859--841292 Score: 485
Period size: 133 Copynumber: 3.3 Consensus size: 130
840849 GAAAATCAAA
* *
840859 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATTAATGTATTCAGATATGATTTTCCCT-A
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATTAATGT-CTCAGATCTGATTTTCCCTGA
* * * * *
840923 GAGAAACAACGGAATAAATCCCCTCTTTCCAGATTTGATATTCCCTAAGTTACAATAGAACCAGT
65 -AGAAGCAACGGAACAAAT-CCCTCTTTCCAGATTTGATATTCCCTGAG-TACAATAAAACAAGT
*
840988 CTAA
127 CTAC
* * * * *
840992 CTCGATTTAATCTTCCCTAAAGAACAGTGAAATGAATTAATGTCCCCAGATCTGATTTTCCTTGA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATTAATGT-CTCAGATCTGATTTTCCCTGA
* * *
841057 AGAAGCAGCGGAACAAATCCC-CTTTCCAGATTTCATATTCCCTGAGTAGCAATAAAACGAGTCT
65 AGAAGCAACGGAACAAATCCCTCTTTCCAGATTTGATATTCCCTGAGTA-CAATAAAACAAGTCT
841121 AC
129 AC
* ** * **
841123 CTCGATTCAATCTTCCCTTAAGAATTGTGGAATGAATCAACATCTCATGATCTGATTTTCCCTGA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATTAATGTCTCA-GATCTGATTTTCCCTGA
* * * * * *
841188 AGAAGCAACGAAACAGATCCTCTCTTTCCAGATTTGATCTTCCTTGAGTAACAGTGAAACAAGTC
65 AGAAGCAACGGAACAAATCC-CTCTTTCCAGATTTGATATTCCCTGAGT-ACAATAAAACAAGTC
*
841253 TGC
128 TAC
* * *
841256 CTTGAATCAATCTTCCCTGAATAACAGTGGAATGAAT
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAAT
841293 CAACGTTTCC
Statistics
Matches: 253, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
130 5 0.02
131 105 0.42
132 4 0.02
133 137 0.54
134 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (130 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATTAATGTCTCAGATCTGATTTTCCCTGAA
GAAGCAACGGAACAAATCCCTCTTTCCAGATTTGATATTCCCTGAGTACAATAAAACAAGTCTAC
Found at i:841488 original size:3 final size:3
Alignment explanation
Indices: 841482--841511 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
841472 TATCTTCTTC
841482 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
841512 TTAATTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:841828 original size:81 final size:81
Alignment explanation
Indices: 841725--841880 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 81
841715 GGGTTTTGGA
*
841725 TGAAACCCCAAAGCCACAACCTCTGAGACCGAATC-ATCTGGACCCATCCAAAGGTCAAGATCAA
1 TGAAACCCCAAAGCCACAACCTCTGAGACCGAA-CGATATGGACCCATCCAAAGGTCAAGATCAA
841789 GCCAAACAAATTTTTGC
65 GCCAAACAAATTTTTGC
* * * * * * *
841806 TGAAACCCTAGAGCCACGACCTCTGAGACTGCACGATATGGACCCATCCAAATGTCGAGATCAAG
1 TGAAACCCCAAAGCCACAACCTCTGAGACCGAACGATATGGACCCATCCAAAGGTCAAGATCAAG
*
841871 CCAATCAAAT
66 CCAAACAAAT
841881 CTTCCACCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
80 1 0.02
81 64 0.98
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (81 bp):
TGAAACCCCAAAGCCACAACCTCTGAGACCGAACGATATGGACCCATCCAAAGGTCAAGATCAAG
CCAAACAAATTTTTGC
Found at i:843102 original size:62 final size:61
Alignment explanation
Indices: 842967--843103 Score: 140
Period size: 62 Copynumber: 2.2 Consensus size: 61
842957 ATTAAAAATG
* *
842967 TTCATTTTAGTCACTTTTACACTTTATTTTGTTTTGATTTTTGACATGATGATTTGTTTAT
1 TTCATTTTAGTCACTTTTACACTTTATTTTATTTTAATTTTTGACATGATGATTTGTTTAT
* *
843028 TT-ATATTATAGTC-CTATTTACA-TGTTGTTTTATTTTAATTTTTG-CATGATG-CTTGCATGT
1 TTCAT-TT-TAGTCACT-TTTACACT-TTATTTTATTTTAATTTTTGACATGATGATTTG--T-T
843088 TAT
59 TAT
843091 TTCATTTTAGTCA
1 TTCATTTTAGTCA
843104 TTAATTAGTT
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
60 5 0.08
61 14 0.22
62 34 0.54
63 8 0.13
64 2 0.03
ACGTcount: A:0.21, C:0.10, G:0.12, T:0.57
Consensus pattern (61 bp):
TTCATTTTAGTCACTTTTACACTTTATTTTATTTTAATTTTTGACATGATGATTTGTTTAT
Found at i:843712 original size:131 final size:130
Alignment explanation
Indices: 843467--843830 Score: 430
Period size: 131 Copynumber: 2.8 Consensus size: 130
843457 TTAATATGAA
* * * *
843467 AAATAGTAATATCTTTTCATTT-TAGTTGAAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCA
1 AAATAGTGATATCTCTTCATTTCGA-TTGAAGTAATAAATGACT-CTTTAAGGCATGAGAGGTCA
* * * **
843531 TTCATTCTCGATTGGAAATAAATAGATATTACCGTTTTCTTTCGAATCAATATTG-ATTTTCAAG
64 TTTATTCTCGACTGGAAATAAATAGATATTACCATTTTCACTCGAATCAATATTGAATTTT-AAG
843595 ACG
128 ACG
*
843598 AAATAGTGATATCTCTTCATTTCGATTGAAGTAATAAATGACTACTTTAAGGCATAAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGAAGTAATAAATGACT-CTTTAAGGCATGAGAGGTCAT
* * * * * * * *
843663 TTATTTTCGGCTGGAAATCATTAGGTATTATCATTTTCACTCGATTCAATGTTGAATTTTAAGAC
65 TTATTCTCGACTGGAAATAAATAGATATTACCATTTTCACTCGAATCAATATTGAATTTTAAGAC
843728 G
130 G
* * * *
843729 AAATAGTGATATCGCTTCATTTCGATT-AGAGTAATAAATGACTGTTTAAGTCATGAGAAGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGA-AGTAATAAATGACTCTTTAAGGCATGAGAGGTCAT
* *
843793 TTATTCTCGATTGGAAAT-AATGAGATACTACCATTTTC
65 TTATTCTCGACTGGAAATAAAT-AGATATTACCATTTTC
843831 TCTCTTAGAA
Statistics
Matches: 198, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
129 2 0.01
130 46 0.23
131 144 0.73
132 6 0.03
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (130 bp):
AAATAGTGATATCTCTTCATTTCGATTGAAGTAATAAATGACTCTTTAAGGCATGAGAGGTCATT
TATTCTCGACTGGAAATAAATAGATATTACCATTTTCACTCGAATCAATATTGAATTTTAAGACG
Found at i:844504 original size:60 final size:61
Alignment explanation
Indices: 844432--844568 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 61
844422 TGTTTAAGGT
* * * *
844432 AAAG-TACAAAAATGGTCCCC-CGGCTATAGGTTACTGCTTTGTTGAGTCTCCT-GATTATTA
1 AAAGTTAC-AAAATGGTCCCCTCGACTATAAGATACTGCTTTGTTGAGT-TCCTCGACTATTA
* ** *
844492 AAAGTTACAAAATGG-CCCCTTGACTATAAGATGTTGCTTTGTTGAGTTCCTCGGCTATTA
1 AAAGTTACAAAATGGTCCCCTCGACTATAAGATACTGCTTTGTTGAGTTCCTCGACTATTA
*
844552 AAAGTTAAAAAATGGTC
1 AAAGTTACAAAATGGTC
844569 GACTATTCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 8 0.12
60 52 0.81
61 4 0.06
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (61 bp):
AAAGTTACAAAATGGTCCCCTCGACTATAAGATACTGCTTTGTTGAGTTCCTCGACTATTA
Found at i:848162 original size:18 final size:17
Alignment explanation
Indices: 848141--848174 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
848131 GCTAAATTTG
*
848141 GTATTGATACTCAAGGGA
1 GTATCGATACT-AAGGGA
848159 GTATCGATACTAAGGG
1 GTATCGATACTAAGGG
848175 TATTTTAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (17 bp):
GTATCGATACTAAGGGA
Found at i:850907 original size:26 final size:26
Alignment explanation
Indices: 850878--850927 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
850868 GTCTTCAGAA
850878 AAAGTCAACGGGTCAA-GGTCAAATTC
1 AAAGTCAA-GGGTCAATGGTCAAATTC
*
850904 AAAGTCAATGGTCAATGGTCAAAT
1 AAAGTCAAGGGTCAATGGTCAAAT
850928 GGGATGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (26 bp):
AAAGTCAAGGGTCAATGGTCAAATTC
Found at i:856350 original size:3 final size:3
Alignment explanation
Indices: 856342--856414 Score: 76
Period size: 3 Copynumber: 24.3 Consensus size: 3
856332 TCATCCCGAC
* * * * * *
856342 ATT ATT ATT ATT ATT ATC ATT AAT ATT ATT ATT GTT GTT GTC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
856390 ATT ATT ATT ATT ATT ACTT -TT ATT A
1 ATT ATT ATT ATT ATT A-TT ATT ATT A
856415 ATTTGTGCAG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.93
4 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:872462 original size:14 final size:14
Alignment explanation
Indices: 872443--872476 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
872433 GATAGAACTT
872443 ATTAAAAAAATAAA
1 ATTAAAAAAATAAA
* *
872457 ATTAAAGAAATATA
1 ATTAAAAAAATAAA
872471 ATTAAA
1 ATTAAA
872477 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
ATTAAAAAAATAAA
Found at i:872565 original size:39 final size:38
Alignment explanation
Indices: 872522--872620 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 38
872512 ATTGATAGAG
* * * *
872522 TGAAATAATTTAATAAATTAATATTTTAGAATTTTATGA
1 TGAAATAATATAAGAAATTAA-AATTTAGAATATTATGA
* *
872561 TGAAATAGTATAAGAAATTAAAATTTAGAATATTATGG
1 TGAAATAATATAAGAAATTAAAATTTAGAATATTATGA
**
872599 TGAAATAA-ATTGGAAATTAAAA
1 TGAAATAATATAAGAAATTAAAA
872621 ATAAAAATCT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 12 0.24
38 21 0.41
39 18 0.35
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (38 bp):
TGAAATAATATAAGAAATTAAAATTTAGAATATTATGA
Found at i:873194 original size:26 final size:26
Alignment explanation
Indices: 873154--873203 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
873144 AAAAATTATG
*
873154 ATTATGTATCATTTGATCAAAAATGT
1 ATTATATATCATTTGATCAAAAATGT
* *
873180 ATTATATATCGTTTGATCACAAAT
1 ATTATATATCATTTGATCAAAAAT
873204 TAGTCAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (26 bp):
ATTATATATCATTTGATCAAAAATGT
Found at i:874658 original size:7 final size:7
Alignment explanation
Indices: 874640--874669 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
874630 GATACTAGCG
874640 TTATATTT
1 TTATA-TT
874648 TTATATT
1 TTATATT
874655 TTATATT
1 TTATATT
874662 TTATATT
1 TTATATT
874669 T
1 T
874670 CATTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATATT
Found at i:886672 original size:5 final size:6
Alignment explanation
Indices: 886659--886685 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
886649 TTTAATTTAA
886659 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
886686 GCAGGAACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:893501 original size:22 final size:22
Alignment explanation
Indices: 893473--893515 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
893463 AGTTTTATTA
893473 AAGTTTTCT-CTTTTTACTTTTC
1 AAGTTTTCTCCTTTTT-CTTTTC
*
893495 AAGTTTTTTCCTTTTTCTTTT
1 AAGTTTTCTCCTTTTTCTTTT
893516 ATTTTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (22 bp):
AAGTTTTCTCCTTTTTCTTTTC
Found at i:895302 original size:31 final size:33
Alignment explanation
Indices: 895201--895326 Score: 94
Period size: 31 Copynumber: 4.1 Consensus size: 33
895191 TGTACGTAGG
*
895201 TAAATTAA-TTTATATTA--TTATT-T-TTGTT
1 TAAATTAAGTTTAGATTATTTTATTGTATTGTT
*
895229 TAAATTTAG-TTAGATTATTTT-TTGTATTGATT
1 TAAATTAAGTTTAGATTATTTTATTGTATTG-TT
*
895261 T--GTTATAGTTTA-ATT-TTTTATTGTATTGTT
1 TAAATTA-AGTTTAGATTATTTTATTGTATTGTT
* * * *
895291 TAAATTAAGTTTAGTTTGTTTTATTTTTTTGTT
1 TAAATTAAGTTTAGATTATTTTATTGTATTGTT
895324 TAA
1 TAA
895327 TTTTTTTACT
Statistics
Matches: 77, Mismatches: 8, Indels: 21
0.73 0.08 0.20
Matches are distributed among these distances:
28 14 0.18
29 2 0.03
30 12 0.16
31 22 0.29
32 11 0.14
33 16 0.21
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.63
Consensus pattern (33 bp):
TAAATTAAGTTTAGATTATTTTATTGTATTGTT
Found at i:895333 original size:21 final size:22
Alignment explanation
Indices: 895299--895347 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
895289 TTTAAATTAA
* * *
895299 GTTTAGTTTGTTTTATTTTTTT
1 GTTTAATTTGTTTTACTTTATT
895321 GTTTAATTT-TTTTACTTTATT
1 GTTTAATTTGTTTTACTTTATT
895342 GTTTAA
1 GTTTAA
895348 ATTAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.71
Consensus pattern (22 bp):
GTTTAATTTGTTTTACTTTATT
Found at i:895370 original size:11 final size:10
Alignment explanation
Indices: 895348--895388 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
895338 TATTGTTTAA
*
895348 ATTAATTTAT
1 ATTAAATTAT
895358 ATTAAACTTAT
1 ATTAAA-TTAT
895369 ATTAAATTAT
1 ATTAAATTAT
*
895379 ATTAAGTTAT
1 ATTAAATTAT
895389 TGTTTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (10 bp):
ATTAAATTAT
Found at i:897789 original size:27 final size:27
Alignment explanation
Indices: 897759--897825 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
897749 GAGTTTACTA
* * **
897759 ACATTAATTCAAATGTAGATATTTATC
1 ACATTCATTCAAATATAGATATCCATC
*
897786 ACATTCATTAAAATATAGATATCCATC
1 ACATTCATTCAAATATAGATATCCATC
897813 ACATTCATTCAAA
1 ACATTCATTCAAA
897826 AAAATATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.36
Consensus pattern (27 bp):
ACATTCATTCAAATATAGATATCCATC
Found at i:901845 original size:45 final size:45
Alignment explanation
Indices: 901786--902070 Score: 376
Period size: 45 Copynumber: 6.4 Consensus size: 45
901776 GAATACCATG
*
901786 AGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* * * *
901831 AGTGGTACCATTTATGCCGATATTGCACTGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* *
901876 AGTGACACCTTTTAT-CCGATAATGCACCGTTATGCATTTTTATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* * **
901920 TGTGGCACATTTTATGTTGATAATGCACCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* *
901965 TGTTGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* * * * * *
902010 TGTTGCACCTTTTATGCTGATAATTCACCGTTATACATTTTCGTTT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTC-ATT
902056 A-TGGCACCTTTTATG
1 AGTGGCACCTTTTATG
902071 TCTATTCATA
Statistics
Matches: 211, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
44 38 0.18
45 171 0.81
46 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (45 bp):
AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
Found at i:902093 original size:134 final size:133
Alignment explanation
Indices: 901788--902071 Score: 345
Period size: 134 Copynumber: 2.1 Consensus size: 133
901778 ATACCATGAG
* * ** *
901788 TGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATTAGTGGTACCATTTATGCCGATA
1 TGGCACATTTTATGTTGATAATGCA-CGTTAAACATTTTCATTAGTGGCACCATTTATGCCGATA
* * * *
901853 TTGCACTGTTATGCATTTTCATTAGTGACACCTTTTATCCGATAATGCACCGTTATGCATTTTTA
65 ATGCACCGTTATGCATTTTCATTAGTGACACCTTTTATCCGATAATGCACCGTTATACATTTTCA
*
901918 TTTG
130 TTTA
** * * *
901922 TGGCACATTTTATGTTGATAATGCACCGTTATGCATTTTCATTTGTTGCACCTTTTATGCCGATA
1 TGGCACATTTTATGTTGATAATGCA-CGTTAAACATTTTCATTAGTGGCACCATTTATGCCGATA
* * *
901987 ATGCACCGTTATGCATTTTCATTTGTTG-CACCTTTTATGCTGATAATTCACCGTTATACATTTT
65 ATGCACCGTTATGCATTTTCATTAG-TGACACCTTTTAT-CCGATAATGCACCGTTATACATTTT
*
902051 CGTTTA
128 CATTTA
*
902057 TGGCACCTTTTATGT
1 TGGCACATTTTATGT
902072 CTATTCATAG
Statistics
Matches: 132, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
134 91 0.69
135 41 0.31
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.43
Consensus pattern (133 bp):
TGGCACATTTTATGTTGATAATGCACGTTAAACATTTTCATTAGTGGCACCATTTATGCCGATAA
TGCACCGTTATGCATTTTCATTAGTGACACCTTTTATCCGATAATGCACCGTTATACATTTTCAT
TTA
Found at i:908294 original size:22 final size:22
Alignment explanation
Indices: 908265--908316 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
908255 ACATGTATGT
908265 GAAGTTGGTTTGCAAGG-CAT-A
1 GAAGTTGGTTTGC-AGGCCATGA
908286 GTAAGTTGGTTTGCAGGCCATGA
1 G-AAGTTGGTTTGCAGGCCATGA
908309 GAAGTTGG
1 GAAGTTGG
908317 AATTCTTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.14
22 22 0.79
23 2 0.07
ACGTcount: A:0.25, C:0.10, G:0.37, T:0.29
Consensus pattern (22 bp):
GAAGTTGGTTTGCAGGCCATGA
Found at i:908401 original size:41 final size:41
Alignment explanation
Indices: 908356--908457 Score: 145
Period size: 40 Copynumber: 2.5 Consensus size: 41
908346 AGGCATGTAA
* *
908356 AAAGCATGGAGAT-TTCACCAGGCTATGTTGAAGACTCATGG
1 AAAGCATGAAG-TCTTCACCAGGCCATGTTGAAGACTCATGG
* *
908397 AAAGCATGAAGTCATCACCA-GCCATGTTGAAGACTCGTGG
1 AAAGCATGAAGTCTTCACCAGGCCATGTTGAAGACTCATGG
908437 AAAGCATGAAGTCTTCACCAG
1 AAAGCATGAAGTCTTCACCAG
908458 CTCACTATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 38 0.70
41 16 0.30
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (41 bp):
AAAGCATGAAGTCTTCACCAGGCCATGTTGAAGACTCATGG
Found at i:908481 original size:41 final size:40
Alignment explanation
Indices: 908370--908482 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 40
908360 CATGGAGATT
* * * *
908370 TCACCAGGCTATGTTGAAGACTCATGGAAAGCATGAAGTCA
1 TCACCA-GCCATGATGAAGACTCGTAGAAAGCATGAAGTCA
* * *
908411 TCACCAGCCATGTTGAAGACTCGTGGAAAGCATGAAGTCT
1 TCACCAGCCATGATGAAGACTCGTAGAAAGCATGAAGTCA
908451 TCACCAGCTCACT-ATGAAGACGT-GTAGAAAGC
1 TCACCAGC-CA-TGATGAAGAC-TCGTAGAAAGC
908483 GTTGAGTCTT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
40 39 0.61
41 23 0.36
42 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (40 bp):
TCACCAGCCATGATGAAGACTCGTAGAAAGCATGAAGTCA
Found at i:909933 original size:29 final size:28
Alignment explanation
Indices: 909856--909934 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
909846 CAATGTTAAA
* *
909856 ATAATATATTCAATTATATTATAATAATAT
1 ATAATA-ATT-AATTATATTTTAAAAATAT
* *
909886 ATGAT-ATTATATTCTTATTTTAAAAATAT
1 ATAATAATTA-ATT-ATATTTTAAAAATAT
909915 ATAATAAATTAATTATATTT
1 ATAAT-AATTAATTATATTT
909935 ATTAATGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
27 1 0.03
28 6 0.15
29 21 0.54
30 7 0.18
31 4 0.10
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (28 bp):
ATAATAATTAATTATATTTTAAAAATAT
Found at i:910246 original size:23 final size:23
Alignment explanation
Indices: 910203--910250 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
910193 TTTTCCAATG
*
910203 TTATAATAATATATTTAATTATA
1 TTATAATAATATATATAATTATA
910226 TTATAATAATATATGAT-ATTATA
1 TTATAATAATATAT-ATAATTATA
910249 TT
1 TT
910251 CTTATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATAATAATATATATAATTATA
Found at i:910826 original size:367 final size:366
Alignment explanation
Indices: 909577--911037 Score: 2445
Period size: 367 Copynumber: 4.0 Consensus size: 366
909567 GTATCTTTGG
*
909577 TTATTAATGGTTTTGACCCCGATAAATGGAACGATC-GTGGTGGTGTTCTTGACCGAGAAAGGTA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGA-CGGTGGTGGTGTTCTTGACCGAGAAAGGTA
*
909641 ACATTTTGAATTATTTTTCTCTCA-ATTCTAAATCATTACGGTTTGGTTTTCCTTAAGTTATTTT
65 ACATTTTGAATTATTTTTCTCT-AGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTT
* *
909705 TTGAATTTTTCACTTTAAAACATAATTACTCAAAATAATATTATTTATATATTTAATACCAATAT
129 TCGAATTTTTCACTTTAAAGCATAATTACTCAAAATAATATTATTTATATATTTAATACCAATAT
*
909770 ATTATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAGTAT
194 ATTATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATAT
*
909835 ATAATATTTTCCAATGTTAAAATAATATATTCAATTATATTATAATAATATATGATATTATATTC
259 ATAATATTTTCCAATGTTATAATAATATATTCAATTATATTATAATAATATATGATATTATATTC
*
909900 TTATTTTAA-AA-ATAT-AT--A--A-T--AAATTAATTATAT
324 TTATTTTAACAATATATAATAAATTATTAAAAAATAATTATAT
* * *
909933 TTATTAATGGTTTTGACCTCGACAAATGGAACGACAGTAGTGGTGTTCTTGACCGAGAAAGGTAA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
*
909998 CATTTTGAATTATTTTTCTCTCGATTCTAAATCATTACGGTTTGA-TTTCCTTAAGTTATTTTTC
66 CATTTTGAATTATTTTTCTCTAGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTTC
*
910062 AAATTTTTCACTTTAAAGCATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATA-
131 GAATTTTTCACTTTAAAGCATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATAT
* *
910126 -A-TATATTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAT
196 TATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAT
*
910189 AATATTTTCCAATGTTATAATAATATATTTAATTATATTATAATAATATATGATATTATATTCTT
261 AATATTTTCCAATGTTATAATAATATATTCAATTATATTATAATAATATATGATATTATATTCTT
910254 ATTTTAACAATATATAATAAATTATTAAAAAAATTAATTATAT
326 ATTTTAACAATATATAATAAATTATT-AAAAAA-TAATTATAT
910297 TTATTAACT-GTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGT-
1 TTATTAA-TGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTA
* *
910360 ACAATTTTGAATTATTTTTCTCTCGATTCTAAATCATTATGGTTTGATTTTCCTTAAGTTATTTT
65 AC-ATTTTGAATTATTTTTCTCTAGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTT
* **
910425 TTGAATTTTTCACTTTAAATAATAATTACTCAAAATAATATTATTTATATATTTAATACCAATAT
129 TCGAATTTTTCACTTTAAAGCATAATTACTCAAAATAATATTATTTATATATTTAATACCAATAT
910490 ATTATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATAT
194 ATTATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATAT
* *
910555 ATAATATTTTCCAATGTTATAATAATATATTCAATTATATTGTAATAATATATGATATTGTATTC
259 ATAATATTTTCCAATGTTATAATAATATATTCAATTATATTATAATAATATATGATATTATATTC
* *
910620 TTATTTTAACAATATATAATAAACTCTTAAAAAAATAATTATAT
324 TTATTTTAACAATATATAATAAATTATT-AAAAAATAATTATAT
910664 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
1 TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
* * * *
910729 CATTTTGAATTATTTTTCTCTAGAATCAAAATCATTATGGTGTGATTTTCCTTAAGTTATTTTTC
66 CATTTTGAATTATTTTTCTCTAGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTTC
* *
910794 GAATTTTTCATTTTAAAGCATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATAG
131 GAATTTTTCACTTTAAAGCATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATAT
*
910859 TATTTTAGTATTATTTTAATAAATTAATTACTAAGATATAATTTTTAATCATTTTAATAATATAT
196 TATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAT
*
910924 AATATTTTCCAATGTTATAATAATATATTAAATTATATTATAATAATATATGATATTATATTCTT
261 AATATTTTCCAATGTTATAATAATATATTCAATTATATTATAATAATATATGATATTATATTCTT
910989 ATTTTAACAATATATAATAAATTATTAAAAAATAATTATAT
326 ATTTTAACAATATATAATAAATTATTAAAAAATAATTATAT
911030 TTATTAAT
1 TTATTAAT
911038 TTCATAAAAT
Statistics
Matches: 1039, Mismatches: 44, Indels: 34
0.93 0.04 0.03
Matches are distributed among these distances:
352 129 0.12
353 3 0.00
354 4 0.00
355 83 0.08
356 102 0.10
357 1 0.00
359 1 0.00
360 1 0.00
363 5 0.00
364 110 0.11
365 80 0.08
366 24 0.02
367 341 0.33
368 155 0.15
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (366 bp):
TTATTAATGGTTTTGACCCCGACAAATGGAACGACGGTGGTGGTGTTCTTGACCGAGAAAGGTAA
CATTTTGAATTATTTTTCTCTAGATTCTAAATCATTACGGTTTGATTTTCCTTAAGTTATTTTTC
GAATTTTTCACTTTAAAGCATAATTACTCAAAATAATATTATTTATATATTTAATACCAATATAT
TATTTTAGTATTATTTTAATAAATTAATTATTAAGATATAATTTTTAATCATTTTAATAATATAT
AATATTTTCCAATGTTATAATAATATATTCAATTATATTATAATAATATATGATATTATATTCTT
ATTTTAACAATATATAATAAATTATTAAAAAATAATTATAT
Found at i:910964 original size:23 final size:23
Alignment explanation
Indices: 910938--910985 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
910928 TTTTCCAATG
*
910938 TTATAATAATATATTAAATTATA
1 TTATAATAATATATGAAATTATA
*
910961 TTATAATAATATATGATATTATA
1 TTATAATAATATATGAAATTATA
910984 TT
1 TT
910986 CTTATTTTAA
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:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTATAATAATATATGAAATTATA
Found at i:920777 original size:18 final size:18
Alignment explanation
Indices: 920754--920793 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
920744 TCGTTTACAA
920754 TTTTTGAATTTTTGTATT
1 TTTTTGAATTTTTGTATT
** *
920772 TTTTTGGCTTTTTTTATT
1 TTTTTGAATTTTTGTATT
920790 TTTT
1 TTTT
920794 CTGTTTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.78
Consensus pattern (18 bp):
TTTTTGAATTTTTGTATT
Found at i:935173 original size:12 final size:11
Alignment explanation
Indices: 935154--935187 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
935144 TTATCATGTT
935154 TAAAAATAAAA
1 TAAAAATAAAA
*
935165 GTTAAAATAAAA
1 -TAAAAATAAAA
935177 TAAAAATAAAA
1 TAAAAATAAAA
935188 ACTTGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:935188 original size:24 final size:24
Alignment explanation
Indices: 935154--935206 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
935144 TTATCATGTT
* *
935154 TAAAAATAAAAGTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAAGAAAA
935177 TAAAAATAAAAACTTGAAAAGAAAA
1 TAAAAAT-AAAACTTGAAAAGAAAA
*
935202 GAAAA
1 TAAAA
935207 GAAAGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.28
24 6 0.24
25 12 0.48
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.17
Consensus pattern (24 bp):
TAAAAATAAAACTTGAAAAGAAAA
Found at i:939892 original size:21 final size:21
Alignment explanation
Indices: 939868--939991 Score: 169
Period size: 21 Copynumber: 5.7 Consensus size: 21
939858 AAAGTGTCAT
939868 AGTACACAAAGTACTACTCCA
1 AGTACACAAAGTACTACTCCA
939889 AGTACACAAAGTACT-CTTTCCA
1 AGTACACAAAGTACTAC--TCCA
*
939911 TAGTACACAAAGTACTACTCTA
1 -AGTACACAAAGTACTACTCCA
* *
939933 AGTACACAAAGTACCATTACCA
1 AGTACACAAAGTACTACT-CCA
939955 TAGTACACAAAGTACTACTCCA
1 -AGTACACAAAGTACTACTCCA
939977 AGTACACAAAGTACT
1 AGTACACAAAGTACT
939992 TTTCTGAAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.01
21 46 0.51
22 12 0.13
23 31 0.34
24 1 0.01
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.23
Consensus pattern (21 bp):
AGTACACAAAGTACTACTCCA
Found at i:939915 original size:44 final size:44
Alignment explanation
Indices: 939865--939995 Score: 221
Period size: 44 Copynumber: 3.0 Consensus size: 44
939855 CACAAAGTGT
939865 CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTTC
1 CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTTC
* *
939909 CATAGTACACAAAGTACTACTCTAAGTACACAAAGTAC-CATTAC
1 CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTC-TTTC
939953 CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACT-TTTC
1 CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTTC
939996 TGAAAAATAC
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
43 4 0.05
44 77 0.95
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.24
Consensus pattern (44 bp):
CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTTC
Found at i:941536 original size:21 final size:22
Alignment explanation
Indices: 941512--941556 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
941502 AATAGCAATC
941512 TTCATG-AAATTT-TCCTTTAAT
1 TTCATGTAAATTTAT-CTTTAAT
*
941533 TTCATGTTAATTTATCTTTAAT
1 TTCATGTAAATTTATCTTTAAT
941555 TT
1 TT
941557 AAGATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 14 0.67
23 1 0.05
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.58
Consensus pattern (22 bp):
TTCATGTAAATTTATCTTTAAT
Found at i:956312 original size:15 final size:15
Alignment explanation
Indices: 956277--956314 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
956267 AACTAATTCG
956277 GGACTAAAATATAAA
1 GGACTAAAATATAAA
**
956292 TAACTAAAATATAAA
1 GGACTAAAATATAAA
956307 GGACTAAA
1 GGACTAAA
956315 TAGGTTATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.21
Consensus pattern (15 bp):
GGACTAAAATATAAA
Found at i:960806 original size:21 final size:20
Alignment explanation
Indices: 960782--960884 Score: 134
Period size: 21 Copynumber: 4.8 Consensus size: 20
960772 AAAGTGCCAT
*
960782 AGTACACAAAGTATTACTCCA
1 AGTACACAAAGTACT-CTCCA
960803 AGTACACAAAGTACTACTCCA
1 AGTACACAAAGTACT-CTCCA
960824 AGTACACAAAGTACTCTTACCA
1 AGTACACAAAGTACTC-T-CCA
*
960846 TCGTACACAAAGTACTTCTCCA
1 -AGTACACAAAGTAC-TCTCCA
960868 AGTACACAAAGTACTCT
1 AGTACACAAAGTACTCT
960885 TACGAAAATA
Statistics
Matches: 75, Mismatches: 3, Indels: 9
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.05
21 49 0.65
22 6 0.08
23 14 0.19
24 2 0.03
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (20 bp):
AGTACACAAAGTACTCTCCA
Found at i:960860 original size:44 final size:44
Alignment explanation
Indices: 960804--960887 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
960794 ATTACTCCAA
960804 GTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTACCATC
1 GTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTACCATC
*
960848 GTACACAAAGTACTTCTCCAAGTACACAAAGTACTCTTAC
1 GTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTAC
960888 GAAAATACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.24
Consensus pattern (44 bp):
GTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTACCATC
Found at i:960986 original size:17 final size:17
Alignment explanation
Indices: 960961--960997 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
960951 ATACATAATG
*
960961 CTAATGTACACAAAGTA
1 CTAAAGTACACAAAGTA
960978 CTAAAGTACACAAAGTA
1 CTAAAGTACACAAAGTA
960995 CTA
1 CTA
960998 CTACAATACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.22
Consensus pattern (17 bp):
CTAAAGTACACAAAGTA
Found at i:969284 original size:13 final size:13
Alignment explanation
Indices: 969266--969314 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
969256 CTTAGAATGT
969266 TTAAAAATAAAAC
1 TTAAAAATAAAAC
969279 TT-AAAATAAAA-
1 TTAAAAATAAAAC
969290 -TAAAAATGAAAAC
1 TTAAAAAT-AAAAC
* *
969303 TTGAAAAGAAAA
1 TTAAAAATAAAA
969315 AAGAAAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 5 0.17
12 13 0.43
13 6 0.20
14 5 0.17
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:969301 original size:24 final size:24
Alignment explanation
Indices: 969267--969314 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
969257 TTAGAATGTT
*
969267 TAAAAATAAAACTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAAGAAAA
969290 TAAAAATGAAAACTTGAAAAGAAAA
1 TAAAAAT-AAAACTTGAAAAGAAAA
969315 AAGAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (24 bp):
TAAAAATAAAACTTGAAAAGAAAA
Found at i:972197 original size:15 final size:15
Alignment explanation
Indices: 972177--972212 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
972167 TGAAAGTAAG
972177 ATCAAAGAATTGCAA
1 ATCAAAGAATTGCAA
*
972192 ATCAAAGAATTGTAA
1 ATCAAAGAATTGCAA
972207 ATCAAA
1 ATCAAA
972213 ATTAATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (15 bp):
ATCAAAGAATTGCAA
Found at i:975990 original size:23 final size:23
Alignment explanation
Indices: 975958--976020 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
975948 TTAGTGCAGT
* *
975958 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
*
975981 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
976004 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
976021 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.17
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCTTGAAG
Found at i:976028 original size:21 final size:21
Alignment explanation
Indices: 975979--976061 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
975969 CCCCCCTTGA
*
975979 AGGGGAACCGATTCCCCCTTTGA-
1 AGGGGAACCGATTCCCCC---CAC
976002 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTCCCCCCAC
* *
976023 AGGGGAATCGATTACCCCCAC
1 AGGGGAACCGATTCCCCCCAC
* *
976044 AGGGGAATCGATACCCCC
1 AGGGGAACCGATTCCCCC
976062 TGAGGGTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 35 0.65
23 18 0.33
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATTCCCCCCAC
Found at i:981858 original size:2 final size:2
Alignment explanation
Indices: 981851--981877 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
981841 TGATAGCTAC
981851 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
981878 AGAAGAACCA
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:984532 original size:4 final size:4
Alignment explanation
Indices: 984523--984559 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
984513 CATTCTTCAA
*
984523 ATAC ATAC ATAC ATAC AT-- ATAT ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
984560 TATATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:984546 original size:2 final size:2
Alignment explanation
Indices: 984539--984622 Score: 134
Period size: 2 Copynumber: 42.5 Consensus size: 2
984529 ACATACATAC
* * *
984539 AT AT AT AT AC AT AC AT AC 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
984581 AT AT AT AT AT AT AT AT AT AT AT A- 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
984622 A
1 A
984623 GTTAAAATCC
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:992790 original size:14 final size:14
Alignment explanation
Indices: 992771--992799 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
992761 ACTGATTGAA
992771 GCAGTATCGATACT
1 GCAGTATCGATACT
992785 GCAGTATCGATACT
1 GCAGTATCGATACT
992799 G
1 G
992800 ATGTGAGGTA
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:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (14 bp):
GCAGTATCGATACT
Found at i:993338 original size:28 final size:28
Alignment explanation
Indices: 993298--993354 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
993288 ATGTTATTAG
*
993298 TATGTTAATATATTCTACGTGAAAATGT
1 TATGTAAATATATTCTACGTGAAAATGT
* *
993326 TATGTAAATATATTCTATGTGAATATGT
1 TATGTAAATATATTCTACGTGAAAATGT
993354 T
1 T
993355 CTATGTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (28 bp):
TATGTAAATATATTCTACGTGAAAATGT
Found at i:993350 original size:15 final size:15
Alignment explanation
Indices: 993298--993380 Score: 82
Period size: 15 Copynumber: 5.7 Consensus size: 15
993288 ATGTTATTAG
*
993298 TATGTTAATATATTC
1 TATGTGAATATATTC
*
993313 TACGTGAA-A-ATGT-
1 TATGTGAATATAT-TC
*
993326 TATGTAAATATATTC
1 TATGTGAATATATTC
*
993341 TATGTGAATATGTTC
1 TATGTGAATATATTC
* *
993356 TATGTGAATGTAGTC
1 TATGTGAATATATTC
993371 TATGTGAATA
1 TATGTGAATA
993381 AAAGATACTT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
13 8 0.15
14 4 0.07
15 42 0.78
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (15 bp):
TATGTGAATATATTC
Found at i:996980 original size:15 final size:15
Alignment explanation
Indices: 996956--996990 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
996946 TTATTAGTAT
*
996956 GTGAATATGTTCTAC
1 GTGAAAATGTTCTAC
*
996971 GTGAAAATGTTCTAT
1 GTGAAAATGTTCTAC
996986 GTGAA
1 GTGAA
996991 TGTAGTCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (15 bp):
GTGAAAATGTTCTAC
Found at i:997164 original size:24 final size:24
Alignment explanation
Indices: 997135--997192 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
997125 CAGGACAAAA
* *
997135 CTACGTGGCACTTCAGTGCATATT
1 CTACGTGGCACTCCAGTGCAAATT
* *
997159 CTACGTGGAACTCCGGTGCAAATT
1 CTACGTGGCACTCCAGTGCAAATT
*
997183 CTACGCGGCA
1 CTACGTGGCA
997193 GTTTCGACTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (24 bp):
CTACGTGGCACTCCAGTGCAAATT
Found at i:997321 original size:13 final size:13
Alignment explanation
Indices: 997303--997329 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
997293 TTTTTCATAT
997303 ATAATGTTTCTTG
1 ATAATGTTTCTTG
997316 ATAATGTTTCTTG
1 ATAATGTTTCTTG
997329 A
1 A
997330 AAATATATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (13 bp):
ATAATGTTTCTTG
Found at i:998293 original size:22 final size:22
Alignment explanation
Indices: 998260--998312 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
998250 TGTATTAGTA
998260 TGGTT-AAAAATTAATTTTTAT
1 TGGTTAAAAAATTAATTTTTAT
998281 TGGTTAAAAAATTAATTTTTAT
1 TGGTTAAAAAATTAATTTTTAT
*
998303 TGTTTAAAAA
1 TGGTTAAAAA
998313 TCTCGAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
TGGTTAAAAAATTAATTTTTAT
Found at i:1001008 original size:19 final size:19
Alignment explanation
Indices: 1000981--1001033 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1000971 ATTTAAATGA
*
1000981 ATAAATAAAATAATATCAT
1 ATAATTAAAATAATATCAT
*
1001000 ATAATTAAAA-AATCATTAT
1 ATAATTAAAATAAT-ATCAT
*
1001019 AT-ATTTAAATAATAT
1 ATAATTAAAATAATAT
1001034 AGCACTCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAATTAAAATAATATCAT
Found at i:1007643 original size:32 final size:30
Alignment explanation
Indices: 1007607--1007682 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
1007597 TCCAATCAAG
1007607 AACAAAAAAGAAAAGAAGCAAAAAAGGAA-AAA
1 AACAAAAAAGAAAAG-AG-AAAAAA-GAACAAA
*
1007639 AACAAAGAAA-AAAAGAGAAACAAGAACAAA
1 AACAAA-AAAGAAAAGAGAAAAAAGAACAAA
1007669 AATC-AAAAAGAAAA
1 AA-CAAAAAAGAAAA
1007683 AGGGACAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
29 6 0.15
30 16 0.41
31 3 0.08
32 11 0.28
33 3 0.08
ACGTcount: A:0.78, C:0.08, G:0.13, T:0.01
Consensus pattern (30 bp):
AACAAAAAAGAAAAGAGAAAAAAGAACAAA
Found at i:1007652 original size:21 final size:24
Alignment explanation
Indices: 1007626--1007668 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
1007616 GAAAAGAAGC
1007626 AAAAAAG-GAAA-AA-AACAAAGA
1 AAAAAAGAGAAACAAGAACAAAGA
1007647 AAAAAAGAGAAACAAGAACAAA
1 AAAAAAGAGAAACAAGAACAAA
1007669 AATCAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 2 0.11
24 6 0.32
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (24 bp):
AAAAAAGAGAAACAAGAACAAAGA
Found at i:1007669 original size:29 final size:28
Alignment explanation
Indices: 1007603--1007670 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
1007593 AAGATCCAAT
*
1007603 CAAGAAC-AAAAAAGAAAAGAAGCAAAA
1 CAAGAACAAAAAAAGAAAAAAAGCAAAA
*
1007630 -AAGGAAAAAAACAAAGAAAAAAAG-AGAAA
1 CAA-GAACAAAA-AAAGAAAAAAAGCA-AAA
1007659 CAAGAACAAAAA
1 CAAGAACAAAAA
1007671 TCAAAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
26 2 0.06
27 3 0.09
28 5 0.15
29 21 0.64
30 2 0.06
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (28 bp):
CAAGAACAAAAAAAGAAAAAAAGCAAAA
Found at i:1008058 original size:175 final size:169
Alignment explanation
Indices: 1007716--1008061 Score: 552
Period size: 175 Copynumber: 2.0 Consensus size: 169
1007706 ATTCCCTAAA
*
1007716 AAATGGCACATTAAGCTTCAAACTATGAGATTGATCAAGCACATAATCACCGAATCACTGAATCA
1 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAG-ACATAATCACCGAATCACTGAATCA
1007781 CTTCACTCGAAGATCATAGAGCATCAAGAGAGAGAAACATTTTGAGCAGGATTGAAGACATCATA
65 CTTCACTCGAAGATCATAGAGCATCAAGAGAGAG-AACATTTTGAGCAGGATTGAAGACATCATA
1007846 ATGAATTGATCCTTGGTTCAACACCCTAAAACACTTGTTTG
129 ATGAATTGATCCTTGGTTCAACACCCTAAAACACTTGTTTG
1007887 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAG-CATAATCATTCCCGAATCACTGAAT
1 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGACATAATCA---CCGAATCACTGAAT
*
1007951 CACTTCACTCGAAGATCATAGAGCATCAAGAGAGAG-ACATTTTGAGCAGGACATGATTGAAGGC
63 CACTTCACTCGAAGATCATAGAGCATCAAGAGAGAGAACATTTTGAGCA-G----GATTGAAGAC
* *
1008015 ATCATAATGAATTGATCCTTGGTTTAACACCCTGAAACACTTGTTTG
123 ATCATAATGAATTGATCCTTGGTTCAACACCCTAAAACACTTGTTTG
1008062 GGCCTATTTA
Statistics
Matches: 163, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
169 8 0.05
170 12 0.07
171 39 0.24
172 50 0.31
175 54 0.33
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (169 bp):
AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGACATAATCACCGAATCACTGAATCAC
TTCACTCGAAGATCATAGAGCATCAAGAGAGAGAACATTTTGAGCAGGATTGAAGACATCATAAT
GAATTGATCCTTGGTTCAACACCCTAAAACACTTGTTTG
Found at i:1009667 original size:106 final size:106
Alignment explanation
Indices: 1009543--1009848 Score: 490
Period size: 106 Copynumber: 2.9 Consensus size: 106
1009533 GTGCCACTTG
* * * *
1009543 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTTTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
1009608 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCC
*
1009649 AGACAACGCAAGTTCAACTTCACGAA-AAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATT
1 AGACAACGCAAGTTCAACTTCAC-AACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATT
1009713 TCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCC
* *
1009755 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
* *
1009820 TAGAGCCAAGTTCAACTTCAC-GACGAAAG
66 CAGAGCCAATTTCAACTTCACAG-CGAAAG
1009849 GACCGCTGGT
Statistics
Matches: 186, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
105 2 0.01
106 182 0.98
107 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCC
Found at i:1009857 original size:169 final size:169
Alignment explanation
Indices: 1009657--1010007 Score: 562
Period size: 169 Copynumber: 2.1 Consensus size: 169
1009647 CCAGACAACG
*
1009657 CAAGTTCAACTTCACGAAAAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGAAAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
1009722 ATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
66 ATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1009787 ACCGCTGGTTGCCAACAAACAAC-TTCTCAATTTTAGAGC
131 ACCGCTGGTTGCCAACAAACAACTTTC-CAATTTCAGAGC
* * *
1009826 CAAGTTCAACTTCACGACGAAA-GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
1 CAAGTTCAACTTCACGA-AAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
* * *
1009890 AATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGG
65 AATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
1009955 GACCGCTGGTTGTCAATAAACAACTTTCCAATTTCAGAGC
130 GACCGCTGGTTGCCAACAAACAACTTTCCAATTTCAGAGC
*
1009995 CAATTTCAACTTC
1 CAAGTTCAACTTC
1010008 TCAGCGAAGG
Statistics
Matches: 168, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
169 162 0.96
170 6 0.04
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (169 bp):
CAAGTTCAACTTCACGAAAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGCCAACAAACAACTTTCCAATTTCAGAGC
Found at i:1009870 original size:63 final size:63
Alignment explanation
Indices: 1009763--1009903 Score: 219
Period size: 63 Copynumber: 2.2 Consensus size: 63
1009753 CCAGACAACG
* * *
1009763 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCCAACAAACAACTTCTCAATTTTAGAGC
1 CAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGCCAACAAACAACTTCCCAATTTCAGAGC
* * *
1009826 CAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGC
1 CAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGCCAACAAACAACTTCCCAATTTCAGAGC
*
1009889 CAATTTCAACTTCAC
1 CAAGTTCAACTTCAC
1009904 AGCGTAGGAT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (63 bp):
CAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGCCAACAAACAACTTCCCAATTTCAGAGC
Found at i:1009901 original size:275 final size:275
Alignment explanation
Indices: 1009551--1010080 Score: 857
Period size: 275 Copynumber: 1.9 Consensus size: 275
1009541 TGAGACAACA
* * *
1009551 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTTTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAAGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
1009616 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAAAAGGG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAAAAGGG
1009681 ACCGCTGGTTGTCAACAAACAAC-TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGAT
131 ACCGCTGGTTGTCAACAAACAACTTTC-CAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGAT
* *
1009745 ATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCCAACAAACAA
195 ATTGGAC-CCAAGACAACGCAAGCTCAACTTCACGACGAAGGGACCGCTGATTGCCAACAAACAA
1009809 CTTCTCAATTTTAGAGC
259 CTTCTCAATTTTAGAGC
* * *
1009826 CAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAAGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * **
1009891 ATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAAAAGGG
* * * *
1009956 ACCGCTGGTTGTCAATAAACAACTTTCCAATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATC
131 ACCGCTGGTTGTCAACAAACAACTTTCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATA
* *
1010021 TTGGACCCAAGACAACGCAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGCCAACAAA
196 TTGGACCCAAGACAACGCAAGCTCAACTTCACGACGAAGGGACCGCTGATTGCCAACAAA
1010081 ATTTCATTCA
Statistics
Matches: 234, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
274 2 0.01
275 229 0.98
276 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (275 bp):
CAAGTTCAACTTCACAACGAAAGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAAAAGGG
ACCGCTGGTTGTCAACAAACAACTTTCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATA
TTGGACCCAAGACAACGCAAGCTCAACTTCACGACGAAGGGACCGCTGATTGCCAACAAACAACT
TCTCAATTTTAGAGC
Found at i:1010013 original size:106 final size:106
Alignment explanation
Indices: 1009826--1010235 Score: 523
Period size: 106 Copynumber: 3.9 Consensus size: 106
1009816 ATTTTAGAGC
*
1009826 CAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
*
1009891 ATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
*
1009932 CAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTT-CCAATTTCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCCCAATTTCAGAGCC
* * *
1009996 AATTTCAACTTCTCAGCGAAGGATCTTGGACCCAAGACAACG
65 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
* * * * * * *
1010038 CAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGCCAA-CAA-AATTT--C-A-TTCAGAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
* *
1010097 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
* * * ** *
1010138 CAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAATAATTTCCCGGTTCCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
* *
1010202 AATTTCAACTTCAC-GACGGAGGATATTAGACTCA
65 AATTTCAACTTCACAG-CGAAGGATATTGGACTCA
1010236 GAACAATGCT
Statistics
Matches: 263, Mismatches: 32, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
99 1 0.00
100 76 0.29
101 3 0.01
102 6 0.02
103 3 0.01
104 3 0.01
105 3 0.01
106 165 0.63
107 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
Found at i:1011018 original size:37 final size:37
Alignment explanation
Indices: 1010965--1011069 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
1010955 CCTTTTCGTC
*
1010965 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1011002 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1011039 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1011070 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1011584 original size:19 final size:20
Alignment explanation
Indices: 1011565--1011626 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
1011555 TCTATACATA
*
1011565 TATTTTTTATTTATTTATAT
1 TATTTTTTATTTATTTATAC
*
1011585 TCATTTGTTATTT-TTTAATAC
1 T-ATTTTTTATTTATTT-ATAC
*
1011606 TATATTTATTATTTATATATA
1 TAT-TTT-TTATTTATTTATA
1011627 TATATATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 6 0.18
21 16 0.48
22 9 0.27
23 2 0.06
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTTTTTATTTATTTATAC
Found at i:1011628 original size:19 final size:19
Alignment explanation
Indices: 1011540--1011634 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 19
1011530 TTTTTTACAC
*
1011540 TATATAT-TA-TTATTATC
1 TATATATATATTTATTATT
* *
1011557 TATACATATATTTTTTATT
1 TATATATATATTTATTATT
* *
1011576 TATTTATATTCATTTGTTATTT
1 TATATATA-T-ATTTATTA-TT
*
1011598 TTTAATACTATATTTATTATT
1 TAT-ATA-TATATTTATTATT
*
1011619 TATATATATATATATT
1 TATATATATATTTATT
1011635 TTTTTTAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
17 6 0.10
18 2 0.03
19 21 0.35
20 4 0.07
21 11 0.18
22 11 0.18
23 3 0.05
24 2 0.03
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (19 bp):
TATATATATATTTATTATT
Found at i:1011646 original size:19 final size:19
Alignment explanation
Indices: 1011595--1011646 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
1011585 TCATTTGTTA
*
1011595 TTTTTTAATACTATATTTATT
1 TTTTTTAA-A-TATATATATT
* * *
1011616 ATTTATATATATATATATT
1 TTTTTTAAATATATATATT
1011635 TTTTTTAAATAT
1 TTTTTTAAATAT
1011647 TTTACTTATA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 18 0.75
20 1 0.04
21 5 0.21
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTAAATATATATATT
Found at i:1011856 original size:18 final size:19
Alignment explanation
Indices: 1011830--1011865 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1011820 GTTTTTGATT
*
1011830 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
1011848 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
1011866 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:1011952 original size:16 final size:16
Alignment explanation
Indices: 1011931--1011971 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1011921 ATTTCATTTA
*
1011931 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
1011947 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
1011962 TATT-TTTATT
1 T-TTATTTATT
1011972 CTTCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:1011989 original size:25 final size:24
Alignment explanation
Indices: 1011922--1011990 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 24
1011912 TATATTAATA
*
1011922 TTTCATTTATTTATTTATTTTTCCT
1 TTTCATTT-TTTATTTATTTTTCAT
*
1011947 TTT-ATTTTTTTTACTTATTTTT-AT
1 TTTCA--TTTTTTATTTATTTTTCAT
1011971 TCTTCATTTTTTCATTTATT
1 T-TTCATTTTTT-ATTTATT
1011991 CATTTTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
24 9 0.25
25 23 0.64
26 4 0.11
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTCATTTTTTATTTATTTTTCAT
Found at i:1012916 original size:19 final size:19
Alignment explanation
Indices: 1012887--1012930 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1012877 AGCGCGGTAT
*
1012887 AAGGTGCGCGCCTTCCTGTA
1 AAGG-GCGCGCCTTCCTGCA
1012907 AAGGGCGCGCCTTCCTGCA
1 AAGGGCGCGCCTTCCTGCA
1012926 AAGGG
1 AAGGG
1012931 GGTTAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.18, C:0.30, G:0.34, T:0.18
Consensus pattern (19 bp):
AAGGGCGCGCCTTCCTGCA
Found at i:1027056 original size:36 final size:36
Alignment explanation
Indices: 1026980--1027074 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
1026970 TTCAATCAGG
* * *
1026980 CCTTCAGAAAAGAGTAGTGAAGCGATACAAATATAG
1 CCTTCACAAAAGAGTAGTGAAGCGATACAAATACAA
* ** * * * *
1027016 CCTTCGCGGATGAGTAGTGAAGCGATGCACATCCAA
1 CCTTCACAAAAGAGTAGTGAAGCGATACAAATACAA
1027052 CCTTCACAAAAGAGTAGTGAAGC
1 CCTTCACAAAAGAGTAGTGAAGC
1027075 AGTAACATAT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (36 bp):
CCTTCACAAAAGAGTAGTGAAGCGATACAAATACAA
Found at i:1030433 original size:21 final size:21
Alignment explanation
Indices: 1030396--1030455 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1030386 TATAATGAAT
*
1030396 GGTCAAATT-AAAGAATTAAAA
1 GGTCAATTTGAAA-AATTAAAA
* *
1030417 GGTCAATTTGAAAAATTGAAT
1 GGTCAATTTGAAAAATTAAAA
*
1030438 GGCCAATTTGAAAAATTA
1 GGTCAATTTGAAAAATTA
1030456 TTTCAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (21 bp):
GGTCAATTTGAAAAATTAAAA
Found at i:1031120 original size:17 final size:20
Alignment explanation
Indices: 1031093--1031138 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 20
1031083 ATTTTAATGC
*
1031093 AGTAAAAATGTTT-TCATG-
1 AGTATAAATGTTTGTCATGT
1031111 AGT-TAAATGTTTGTCATGT
1 AGTATAAATGTTTGTCATGT
1031130 AGTATAAAT
1 AGTATAAAT
1031139 ATGAATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 3 0.12
20 5 0.21
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (20 bp):
AGTATAAATGTTTGTCATGT
Found at i:1038787 original size:25 final size:24
Alignment explanation
Indices: 1038754--1038802 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1038744 TTAAATTTAG
1038754 TTTTAATTAA-AATATAATTATTAAT
1 TTTTAATTAACAA-AT-ATTATTAAT
*
1038779 TTTTTATTAACAAATATTATTAAT
1 TTTTAATTAACAAATATTATTAAT
1038803 ATAAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 11 0.50
26 2 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTAATTAACAAATATTATTAAT
Found at i:1040103 original size:31 final size:31
Alignment explanation
Indices: 1040068--1040129 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1040058 TAATTATTAC
1040068 TTCAAATATTAAATCCAT-AACAATCAGTTCG
1 TTCAAATATTAAATCCATAAAC-ATCAGTTCG
*
1040099 TTCAAATTTTAAATCCATAAACATCAGTTCG
1 TTCAAATATTAAATCCATAAACATCAGTTCG
1040130 GGTATGACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.34
Consensus pattern (31 bp):
TTCAAATATTAAATCCATAAACATCAGTTCG
Found at i:1043140 original size:21 final size:21
Alignment explanation
Indices: 1043091--1043146 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1043081 ATCATGTGAA
* *
1043091 ATATGTCTCGAATGACCTATGT
1 ATATGTCCCGAA-GACCTATAT
* *
1043113 ATTTGTCCCGAAGACCTCTAT
1 ATATGTCCCGAAGACCTATAT
1043134 ATATGTCCCGAAG
1 ATATGTCCCGAAG
1043147 GACCGCGTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (21 bp):
ATATGTCCCGAAGACCTATAT
Found at i:1045253 original size:8 final size:8
Alignment explanation
Indices: 1045240--1045273 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1045230 TTAATCCCTT
*
1045240 TTTATTTC
1 TTTATTCC
1045248 TTTATTCC
1 TTTATTCC
*
1045256 ATTATTCC
1 TTTATTCC
1045264 TTTATTCC
1 TTTATTCC
1045272 TT
1 TT
1045274 CAAAGTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTATTCC
Found at i:1046986 original size:21 final size:21
Alignment explanation
Indices: 1046949--1047017 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
1046939 TGTGTATTGA
1046949 TACAGTGTATCGATGCACTGC
1 TACAGTGTATCGATGCACTGC
* * *
1046970 TATAGTTTATTGATGCACTGC
1 TACAGTGTATCGATGCACTGC
*
1046991 TACAGTGTATCAATGCACTGC
1 TACAGTGTATCGATGCACTGC
1047012 TACAGT
1 TACAGT
1047018 AATCTGAGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
TACAGTGTATCGATGCACTGC
Found at i:1047889 original size:22 final size:21
Alignment explanation
Indices: 1047864--1047923 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
1047854 GGCATGTGAA
*
1047864 ATTTGTCTCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTAT-T
* * *
1047886 ATTTGTCCCAAATGACCTCTT
1 ATTTGTCCCGAAGGACCTATT
*
1047907 ATATGTCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
1047924 GCGGAGACCC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (21 bp):
ATTTGTCCCGAAGGACCTATT
Found at i:1047923 original size:21 final size:22
Alignment explanation
Indices: 1047867--1047923 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
1047857 ATGTGAAATT
* *
1047867 TGTCTCGAAGGACCTATGTATT
1 TGTCCCGAAGGACCTATGTATA
* * *
1047889 TGTCCCAAATGACCTCT-TATA
1 TGTCCCGAAGGACCTATGTATA
1047910 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
1047924 GCGGAGACCC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:1056081 original size:13 final size:13
Alignment explanation
Indices: 1056063--1056087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1056053 AATCAAAAAC
1056063 ATCAAATTTAGAA
1 ATCAAATTTAGAA
1056076 ATCAAATTTAGA
1 ATCAAATTTAGA
1056088 TTTTTGATTT
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
ATCAAATTTAGAA
Found at i:1056529 original size:23 final size:22
Alignment explanation
Indices: 1056499--1056580 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
1056489 TGCATGCCTT
*
1056499 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAAG
* * *
1056521 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAAG
*
1056543 GTGTATCGATGCACATTCAAAG
1 GTGCATCGATGCACATTCAAAG
1056565 AGATGCATCGATGCAC
1 -G-TGCATCGATGCAC
1056581 TGTTAAGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 4 0.08
23 17 0.35
24 12 0.25
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAAG
Found at i:1058905 original size:21 final size:20
Alignment explanation
Indices: 1058884--1058954 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
1058874 GTTGTGGTTA
1058884 AAATAAAAAAAATAAGAATT
1 AAATAAAAAAAATAAGAATT
* *
1058904 AAATAAAAGAAAAAAATAATT
1 AAATAAAA-AAAATAAGAATT
* *
1058925 AAATAAACAAATTAAAGAGATT
1 AAATAAAAAAAAT-AAGA-ATT
1058947 AAGATAAA
1 AA-ATAAA
1058955 GAGAAACTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 11 0.27
21 20 0.49
22 5 0.12
23 5 0.12
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (20 bp):
AAATAAAAAAAATAAGAATT
Found at i:1059615 original size:19 final size:19
Alignment explanation
Indices: 1059559--1059621 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1059549 CTATTTAAAC
**
1059559 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
1059579 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
1059599 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
1059618 TAAA
1 TAAA
1059622 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1059649 original size:64 final size:68
Alignment explanation
Indices: 1059524--1059721 Score: 208
Period size: 64 Copynumber: 2.8 Consensus size: 68
1059514 TAAAACATCT
* ** *
1059524 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC--CTA-AAAAAT-AATATAAT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAATAAT
*
1059584 ATTC
65 ATCC
1059588 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC------AAAGATAAAA-ATAAA
1059653 AATAATATCC
59 AATAATATCC
* *
1059663 TAAAACTTAATTAAAATACTAAAAGCCTATTTAAACTAAAATACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAA-CCTATTTAAACTAAAATACAAAGATAAAA-ATAA
1059722 TGTTTAAAAT
Statistics
Matches: 114, Mismatches: 7, Indels: 20
0.81 0.05 0.14
Matches are distributed among these distances:
63 5 0.04
64 36 0.32
70 15 0.13
72 1 0.01
73 4 0.04
74 2 0.02
75 32 0.28
76 19 0.17
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAATAATA
TCC
Found at i:1059666 original size:75 final size:76
Alignment explanation
Indices: 1059579--1059743 Score: 244
Period size: 76 Copynumber: 2.2 Consensus size: 76
1059569 AAAAAATAAT
*
1059579 ATAATATTCTAAATCCTAATTAAAATACTAAAA-CCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAGCCTATTTAAACTAAAATACAAAGATAAA-AT
1059643 AAAAT-ATAAAA
65 AAAATGATAAAA
* *
1059654 ATAATATCCTAAAACTTAATTAAAATACTAAAAGCCTATTTAAACTAAAATACAAAGATAAAATA
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAGCCTATTTAAACTAAAATACAAAGATAAAATA
* * *
1059719 TAATGTTTAAA
66 AAATGATAAAA
*
1059730 ATATTATCCTAAAT
1 ATAATATCCTAAAT
1059744 TTGAGTTTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 36 0.45
76 44 0.55
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAATCCTAATTAAAATACTAAAAGCCTATTTAAACTAAAATACAAAGATAAAATA
AAATGATAAAA
Found at i:1067122 original size:21 final size:20
Alignment explanation
Indices: 1067090--1067137 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
1067080 GTTATGGTTA
*
1067090 AAATAAAAAAAATAAGAATT
1 AAATAAAAAAAAAAAGAATT
*
1067110 AAATAAAAGAAAAAAATAATT
1 AAATAAAA-AAAAAAAGAATT
1067131 AAATAAA
1 AAATAAA
1067138 CAAATTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (20 bp):
AAATAAAAAAAAAAAGAATT
Found at i:1067654 original size:21 final size:21
Alignment explanation
Indices: 1067630--1067688 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1067620 AGCCTTCAAA
1067630 ATCTTAAAAAC-AAGTTAAAAC
1 ATCTTAAAAACTAA-TTAAAAC
**
1067651 ATCTTAAATCCTAATTAAAAC
1 ATCTTAAAAACTAATTAAAAC
*
1067672 A-CTT-AAAACTATTTAAA
1 ATCTTAAAAACTAATTAAA
1067689 CTAAAATACC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 10 0.31
20 3 0.09
21 17 0.53
22 2 0.06
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.31
Consensus pattern (21 bp):
ATCTTAAAAACTAATTAAAAC
Found at i:1067746 original size:19 final size:19
Alignment explanation
Indices: 1067690--1067752 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1067680 CTATTTAAAC
**
1067690 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
1067710 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
1067730 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
1067749 TAAA
1 TAAA
1067753 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1067791 original size:75 final size:76
Alignment explanation
Indices: 1067710--1067874 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 76
1067700 AAAAAATAAT
* * *
1067710 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAACATAAA-AT
1067774 AAAATA-TAAAA
65 AAAATATTAAAA
* *
1067785 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAACATAAAATA
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAACATAAAATA
* *
1067850 TAATATTTAAA
66 AAATATTAAAA
*
1067861 ATATTATCCTAAAT
1 ATAATATCCTAAAT
1067875 TTGAGTTTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 33 0.42
76 46 0.58
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAACATAAAATA
AAATATTAAAA
Found at i:1072553 original size:19 final size:20
Alignment explanation
Indices: 1072503--1072553 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1072493 GAAACCCCTT
* *
1072503 TGAAAATATATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
1072523 TGAAAATGCATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1072542 TGAAGATACATG
1 TGAAAATACATG
1072554 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1079973 original size:31 final size:31
Alignment explanation
Indices: 1079884--1079979 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
1079874 CATGTAGAAC
* *
1079884 ATGTATGTATGTATAATATATGCATTGTATAT
1 ATGTATGTATGTATAATGTATGCA-TGTATGT
* * *
1079916 ATG-ATGCATGTAGATTGTA-GAACATGTATGT
1 ATGTATGTATGTATAATGTATG--CATGTATGT
*
1079947 ATGTGTGTATGTATAATGTATGCATGTATGT
1 ATGTATGTATGTATAATGTATGCATGTATGT
1079978 AT
1 AT
1079980 ACAGATAGAC
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 1 0.02
31 32 0.63
32 17 0.33
33 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (31 bp):
ATGTATGTATGTATAATGTATGCATGTATGT
Found at i:1080331 original size:20 final size:20
Alignment explanation
Indices: 1080237--1080603 Score: 424
Period size: 20 Copynumber: 18.4 Consensus size: 20
1080227 CGATTTCCAT
* ** *
1080237 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1080257 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1080277 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1080297 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1080317 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1080337 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1080357 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1080377 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1080397 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
1080417 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1080437 AATCGCAATG-G-ATCCGTA
1 AATCGCAACGCGTATCCGTA
1080455 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1080475 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
*
1080495 AATCGCAACGCTTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1080515 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1080535 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1080555 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1080575 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1080595 AATCACAAC
1 AATCGCAAC
1080604 ACTTAAATTT
Statistics
Matches: 301, Mismatches: 34, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
18 16 0.05
19 6 0.02
20 275 0.91
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:1081062 original size:26 final size:27
Alignment explanation
Indices: 1081024--1081075 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
1081014 AGAAAGTAAC
* *
1081024 TTTATTAATCTAATAATTATAATTAAA
1 TTTATTAACCTAAGAATTATAATTAAA
*
1081051 TTTATT-ACCTAAGGATTATAATTAA
1 TTTATTAACCTAAGAATTATAATTAA
1081076 TAATTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (27 bp):
TTTATTAACCTAAGAATTATAATTAAA
Found at i:1082290 original size:136 final size:137
Alignment explanation
Indices: 1082083--1082939 Score: 790
Period size: 136 Copynumber: 6.3 Consensus size: 137
1082073 TAAATCGAAA
** * * * *
1082083 ATTAAAATGGAACCTCTAGCATAAAGGCGAGGACCAAATTAAAGATTCACCT-AATTTAAGGACT
1 ATTAAAATGGAACCTCGGGCATAAATGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAGGACT
* * * * *
1082147 AAAGTGAAATGAATCTAAAAT-AGAGTTTCTAATTATTAATCCTAACCAATTTTAACAAACTATT
66 -AAGTGAAATAAAACTAAAATGA-AGTCTCTAA-TATTAATCCTAACCAATTTTAACAAATTATC
1082211 GGATCAAATG
128 GGATCAAATG
* * * *
1082221 ATTCAAATGGAACCTC-GGCATAAATGCGA-GACCAAATTAAAAATTTTGCTAAATTAAAGGAAT
1 ATTAAAATGGAACCTCGGGCATAAATGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAGGACT
* * * * * * *
1082284 AAGTGAAATCAAACTTGAAATGGAGGCTCTGATATTAATCATAACCAATTTTAGCAAATTATCGG
66 AAGTGAAATAAAAC-TAAAATGAAGTCTCTAATATTAATCCTAACCAATTTTAACAAATTATCGG
* *
1082349 ATCGAATA
130 ATCAAATG
*** * *
1082357 ATTAAAATGGAACCTCATACATAAA-GCGAGGACCAAATTAAAAATTCACCTAATTTAAA-GACT
1 ATTAAAATGGAACCTCGGGCATAAATGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAGGACT
*
1082420 AAAGTGAAATTAAAGCTAAAATGAAGTCTCT-A-ATTAATCCTAACCAATTTTAAACAAATTATC
66 -AAGTGAAA-TAAAACTAAAATGAAGTCTCTAATATTAATCCTAACCAATTTT-AACAAATTATC
*
1082483 -AATCAAATG
128 GGATCAAATG
* * *
1082492 ATTTAAAATGGAACCTCGAGCATAAATGTGAGGA-C-AATT-AAAATTCTTTCTAAATTAAAGGA
1 A-TTAAAATGGAACCTCGGGCATAAATGCGAGGACCAAATTAAAAATTC-TCCTAAATTAAAGGA
* *
1082554 CTAAGTTGCAATTAAAACTAAAATGAATGT-TCTAATATT-AT-CTAAACAATTTTAACAAA-TA
64 CTAAG-TG-AAATAAAACTAAAATGAA-GTCTCTAATATTAATCCTAACCAATTTTAACAAATTA
* *
1082615 T-TGATCGAATG
126 TCGGATCAAATG
* * *
1082626 ATTAAAAAGGAACCTCGGGCATAAATG-TAGGATCAAATTAAAAA-TCTCCT-AA--AAAGGACT
1 ATTAAAATGGAACCTCGGGCATAAATGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAGGACT
* * * * *
1082686 AAGGTGAATTAAATCTAAAATGAACG-CTCTAATATTAATCTTAACGAA-TTTAACAAATTATCA
66 AA-GTGAAATAAAACTAAAATGAA-GTCTCTAATATTAATCCTAACCAATTTTAACAAATTATCG
* * *
1082749 TATCGATTG
129 GATCAAATG
* ** * * * * **
1082758 ATTGAAATAAAAACTCGGGCATAAATGCAAGGACCAAATTAAAAATTCTCTTAAATTATAGGGTT
1 ATTAAAATGGAACCTCGGGCATAAATGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAGGACT
* * * * * * * *
1082823 AAGGTGAAATTAACCTGAAATGTAGGCTCTAATATTAATCCTAACAAATTTCAACAAATTATCGA
66 AA-GTGAAATAAAACTAAAATGAAGTCTCTAATATTAATCCTAACCAATTTTAACAAATTATCGG
1082888 ATCAAATG
130 ATCAAATG
* * *
1082896 ATTAAAATGAAACCTCGGGAATAAATGTGAGGACCAAATTAAAA
1 ATTAAAATGGAACCTCGGGCATAAATGCGAGGACCAAATTAAAA
1082940 TTTCACTAAT
Statistics
Matches: 592, Mismatches: 93, Indels: 68
0.79 0.12 0.09
Matches are distributed among these distances:
129 27 0.05
130 23 0.04
131 9 0.02
132 35 0.06
133 43 0.07
134 29 0.05
135 53 0.09
136 154 0.26
137 140 0.24
138 79 0.13
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (137 bp):
ATTAAAATGGAACCTCGGGCATAAATGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAGGACT
AAGTGAAATAAAACTAAAATGAAGTCTCTAATATTAATCCTAACCAATTTTAACAAATTATCGGA
TCAAATG
Found at i:1082444 original size:17 final size:18
Alignment explanation
Indices: 1082411--1082444 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1082401 TTCACCTAAT
*
1082411 TTAAAGACTAAAGTGAAA
1 TTAAAGACTAAAATGAAA
1082429 TTAAAG-CTAAAATGAA
1 TTAAAGACTAAAATGAA
1082445 GTCTCTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (18 bp):
TTAAAGACTAAAATGAAA
Found at i:1085384 original size:117 final size:115
Alignment explanation
Indices: 1085146--1085385 Score: 281
Period size: 117 Copynumber: 2.1 Consensus size: 115
1085136 TTTTTCACCC
* *
1085146 CTTTGGAC-TAATTCTTCTCATTATGAACTCTCCATTGAAAATATTGCTCTACCTTTTGTGATGG
1 CTTTGGACGTAATTCTTCTCATTATGAACTCTCCATTGAAAATATTGATCTACCTTTTATGATGG
* * * *
1085210 ATTTGAACCAAGGTTGAACAAGTTTTCCTTATTATGAACTTCCTTTTCCT
66 ATTTGAACAAAGGTTGAACAAGTTTTCCTCATCATGAACTTCCTTCTCCT
* * * * *
1085260 CTCTGGACGT-ATTGTTGTCATTATGAACTCTCCATTGAAAATGTTGATCTACTTTATTCTATGA
1 CTTTGGACGTAATTCTTCTCATTATGAACTCTCCATTGAAAATATTGATCTAC-CT-TT-TATGA
* * *
1085324 TGG-TTTTAAGCAAAGGTTGAACAAGTTTTTCTCATCATGAACTT-CTTCTCTTT
63 TGGATTTGAA-CAAAGGTTGAACAAGTTTTCCTCATCATGAACTTCCTTCTC-CT
1085377 CTTTGGACG
1 CTTTGGACG
1085386 AGTTATCTCA
Statistics
Matches: 105, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
114 45 0.43
115 2 0.02
116 12 0.11
117 46 0.44
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (115 bp):
CTTTGGACGTAATTCTTCTCATTATGAACTCTCCATTGAAAATATTGATCTACCTTTTATGATGG
ATTTGAACAAAGGTTGAACAAGTTTTCCTCATCATGAACTTCCTTCTCCT
Found at i:1085970 original size:23 final size:23
Alignment explanation
Indices: 1085944--1085992 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1085934 GTTCTTGGTT
1085944 TAGTGTTGGTTGATTTAGGTGAG
1 TAGTGTTGGTTGATTTAGGTGAG
1085967 TAGTGTTGGTTGATTTAGGTGAG
1 TAGTGTTGGTTGATTTAGGTGAG
1085990 TAG
1 TAG
1085993 ATAAACCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.43
Consensus pattern (23 bp):
TAGTGTTGGTTGATTTAGGTGAG
Done.