Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold80
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: 1499392
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.28
Warning! 217494 characters in sequence are not A, C, G, or T
File 7 of 8
Found at i:1190634 original size:20 final size:19
Alignment explanation
Indices: 1190589--1190636 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1190579 ATCGATATAA
*
1190589 TGTATCGATACATGCTCAT
1 TGTATCGATACATACTCAT
*
1190608 TGGATCGATACATACTCAAT
1 TGTATCGATACATACTC-AT
1190628 TGTATCGAT
1 TGTATCGAT
1190637 GCATTAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATACTCAT
Found at i:1193684 original size:13 final size:13
Alignment explanation
Indices: 1193666--1193696 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1193656 ACATTTCTTC
1193666 ATGTATCGATACA
1 ATGTATCGATACA
1193679 ATGTATCGATACA
1 ATGTATCGATACA
*
1193692 TTGTA
1 ATGTA
1193697 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1193684 original size:33 final size:33
Alignment explanation
Indices: 1193646--1193712 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
1193636 ATTACAAGCT
1193646 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
1193679 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
1193712 A
1 A
1193713 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:1193765 original size:19 final size:19
Alignment explanation
Indices: 1193741--1193806 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
1193731 CTGCCAGTTT
1193741 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1193760 CATGTATCGAT---AT--A
1 CATGTATCGATACAATGAA
*
1193774 -ATGTATCGATACAAAGCAA
1 CATGTATCGATACAATG-AA
1193793 CATGTATCGATACA
1 CATGTATCGATACA
1193807 TCTGGGTGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
16 3 0.08
19 12 0.31
20 13 0.33
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1193783 original size:32 final size:33
Alignment explanation
Indices: 1193742--1193804 Score: 110
Period size: 32 Copynumber: 1.9 Consensus size: 33
1193732 TGCCAGTTTC
*
1193742 ATGTATCGATACAATG-AACATGTATCGATATA
1 ATGTATCGATACAAAGCAACATGTATCGATATA
1193774 ATGTATCGATACAAAGCAACATGTATCGATA
1 ATGTATCGATACAAAGCAACATGTATCGATA
1193805 CATCTGGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAACATGTATCGATATA
Found at i:1194419 original size:19 final size:20
Alignment explanation
Indices: 1194375--1194456 Score: 80
Period size: 21 Copynumber: 4.2 Consensus size: 20
1194365 TAAACGATTG
*
1194375 TCTCCTCCTTTATAAAAATTT
1 TCTCCCCCTTTATAAAAA-TT
*
1194396 TCTCCCCCTTTGTAAAAA-T
1 TCTCCCCCTTTATAAAAATT
**
1194415 TCTCCCCC-TTA-AACGATT
1 TCTCCCCCTTTATAAAAATT
*
1194433 ATCTCCTCCTTTATAAAAATT
1 -TCTCCCCCTTTATAAAAATT
1194454 TCT
1 TCT
1194457 TAAATTTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
17 3 0.06
18 3 0.06
19 16 0.33
20 6 0.12
21 21 0.43
ACGTcount: A:0.27, C:0.29, G:0.02, T:0.41
Consensus pattern (20 bp):
TCTCCCCCTTTATAAAAATT
Found at i:1196326 original size:13 final size:13
Alignment explanation
Indices: 1196308--1196332 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1196298 TAGTACCCAA
1196308 TGTATCGATACAT
1 TGTATCGATACAT
1196321 TGTATCGATACA
1 TGTATCGATACA
1196333 AGGAATATTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1223028 original size:56 final size:54
Alignment explanation
Indices: 1222810--1223078 Score: 257
Period size: 56 Copynumber: 4.9 Consensus size: 54
1222800 NNNNNNNNNN
* *
1222810 CCTGCTCTTTGAGGACTGAAA-GTGCCATCAACTTGTGTGGGCTTTAAGAGGTGT
1 CCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGGTGT
* ** *
1222864 CCTGCT-ATTGAGGGACTGGAAAAAATGCC-CCAA-TTGTGT-GGC-TTAAAGGTTT
1 CCTGCTCTTTG-GGGACT-G-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGTGT
1222916 CCTG-TCTTTGGGGACTGAAAAGGTTGCCACCAAAAAACTTGTGTGGGCTTTAAAAGGTTGT
1 CCTGCTCTTTGGGGACTG-AAAGG-TGCCACC----AACTTGTGTGGGCTTT-AAAGG-TGT
* *
1222977 CCTGCTCTTTGGGGACTGAAAGGTGCCACCACCTTGTGTGGGCTTTGAAAGG-GG
1 CCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGTGT
* *
1223031 CCTGCTTCTTTGGGGACTGAAAGGGGGCCACCACCTTGTGTGGGCTTT
1 CCTGC-TCTTTGGGGACTGAAA-GGTGCCACCAACTTGTGTGGGCTTT
1223079 GAAAAGAAAA
Statistics
Matches: 183, Mismatches: 13, Indels: 36
0.79 0.06 0.16
Matches are distributed among these distances:
50 5 0.03
51 11 0.06
52 14 0.08
53 7 0.04
54 20 0.11
55 23 0.13
56 52 0.28
57 10 0.05
58 3 0.02
59 2 0.01
60 12 0.07
61 11 0.06
62 13 0.07
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (54 bp):
CCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGTGT
Found at i:1223296 original size:62 final size:59
Alignment explanation
Indices: 1223142--1223705 Score: 339
Period size: 62 Copynumber: 9.2 Consensus size: 59
1223132 CAACTCGGGT
* * * *
1223142 GGCTTTAAAAGAAAAAGGCGTTCCGCTCTTTAAGGACTGAAAG-TGCCACCAACTTGTGT-
1 GGCTTTAAAAG-AAAAGGCATCCCGCTCTTTGAGGACTGAAGGTTGCC-CCAACTTGTGTG
*
1223201 GGCTTTAAAAGAAAAGGCGGTCCCGCTCTTTGAGGGACCTGAAGGTTGCCCCAACTTGTGTG
1 GGCTTTAAAAGAAAAGGC-ATCCCGCTCTTTGA-GGA-CTGAAGGTTGCCCCAACTTGTGTG
*
1223263 GGCTCTAAAAGAAAAGGCATTTTCCCG-TC-TTGAGGACTGAAGGTTTGTTCACCCAACTTGTGT
1 GGCTTTAAAAGAAAAGGCA---TCCCGCTCTTTGAGGACTGAAGG-TTG--C-CCCAACTTGTGT
1223326 G
59 G
*
1223327 GGCTTTAAAAGAAAAGGCATCCCGCTCTTTGA-GACTGAAGGTTGCCACAACTTGTGTG
1 GGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTTGCCCCAACTTGTGTG
** * ** *** *
1223385 TTCTTTTAAGAGAAAAGGGTGTCATACTC-TTGAGGACTGAAGGTTGCCACCACCTTGTGCTG
1 GGC-TTTAAAAGAAAA-GGCATCCCGCTCTTTGAGGACTGAAGGTTGCC-CCAACTTGTG-TG
* * * *
1223447 GGCTTT-AGAGAAATAAGCGTCCCGC-CTCTTGAGGACTTGAATGG-TGCCACCCAACTT-TTTG
1 GGCTTTAAAAGAAA-AGGCATCCCGCTCT-TTGAGGAC-TGAA-GGTTG-C-CCCAACTTGTGTG
* * * * * ** *
1223508 GGC-TTAAGAGAAACAAAGCGTTCTGCTCTTTGAGGACTAGAA-AATGCACCAACTTGTGTG
1 GGCTTTAAAAG-AA-AAGGCATCCCGCTCTTTGAGGACT-GAAGGTTGCCCCAACTTGTGTG
** * *
1223568 GGCTTTAAAAGGAAAAAAGGCGCCCCGCTCTTTGCGGACGGCAAGG-TGCCACCACACTTGCTGT
1 GGCTTTAAAA-G--AAAAGGCATCCCGCTCTTTGAGGACTG-AAGGTTGCC-CCA-ACTTG-TGT
1223632 G
59 G
* *** * * *
1223633 GGCTTTGAAATCCAAGGCCTCCCG-TCTCTTGAGGACTGGAAGGAAATGCACCAAACTTGTGTG
1 GGCTTTAAAAGAAAAGGCATCCCGCTCT-TTGAGGACT-GAAGG--TTGC-CCCAACTTGTGTG
1223696 GGC-TTAAAAG
1 GGCTTTAAAAG
1223706 GAAACCGGGC
Statistics
Matches: 407, Mismatches: 51, Indels: 91
0.74 0.09 0.17
Matches are distributed among these distances:
58 20 0.05
59 47 0.12
60 52 0.13
61 72 0.18
62 117 0.29
63 33 0.08
64 47 0.12
65 18 0.04
66 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (59 bp):
GGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTTGCCCCAACTTGTGTG
Found at i:1223327 original size:64 final size:60
Alignment explanation
Indices: 1223065--1223705 Score: 311
Period size: 62 Copynumber: 10.3 Consensus size: 60
1223055 GGGCCACCAC
* * *
1223065 CTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGGACCTGATGAACGGTGGGTGCC
1 CTTGTGTGGGCTTT-AAAAGAAAAGGCATCCCGCTCTTTGA-GGA-C---TGAA-GGT--TTGCC
1223130 ACCAA
57 -CCAA
* * * * * *
1223135 CTCGGGT-GGCTTTAAAAGAAAAAGGCGTTCCGCTCTTTAAGGACTGAAAG--TGCCACCAA
1 CTTGTGTGGGCTTTAAAAG-AAAAGGCATCCCGCTCTTTGAGGACTGAAGGTTTGCC-CCAA
*
1223194 CTTGTGT-GGCTTTAAAAGAAAAGGCGGTCCCGCTCTTTGAGGGACCTGAAGG-TTGCCCCAA
1 CTTGTGTGGGCTTTAAAAGAAAAGGC-ATCCCGCTCTTTGA-GGA-CTGAAGGTTTGCCCCAA
*
1223255 CTTGTGTGGGCTCTAAAAGAAAAGGCATTTTCCCG-TC-TTGAGGACTGAAGGTTTGTTCACCCA
1 CTTGTGTGGGCTTTAAAAGAAAAGGCA---TCCCGCTCTTTGAGGACTGAAGGTTTG--C-CCCA
1223318 A
60 A
*
1223319 CTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGA-GACTGAAGG-TTGCCACAA
1 CTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTTTGCCCCAA
** * ** *** *
1223377 CTTGTGTGTTCTTTTAAGAGAAAAGGGTGTCATACTC-TTGAGGACTGAAGG-TTGCCACCAC
1 CTTGTGTGGGC-TTTAAAAGAAAA-GGCATCCCGCTCTTTGAGGACTGAAGGTTTGCC-CCAA
* * *
1223438 CTTGTGCTGGGCTTT-AGAGAAATAAGCGTCCCGC-CTCTTGAGGACTTGAATGG--TGCCACCC
1 CTTGTG-TGGGCTTTAAAAGAAA-AGGCATCCCGCTCT-TTGAGGAC-TGAA-GGTTTG-C-CCC
1223499 AA
59 AA
* * * * * * ** *
1223501 CTT-TTTGGGC-TTAAGAGAAACAAAGCGTTCTGCTCTTTGAGGACTAGAA--AATGCACCAA
1 CTTGTGTGGGCTTTAAAAG-AA-AAGGCATCCCGCTCTTTGAGGACT-GAAGGTTTGCCCCAA
** * *
1223560 CTTGTGTGGGCTTTAAAAGGAAAAAAGGCGCCCCGCTCTTTGCGGACGGCAAGG--TGCCACCAC
1 CTTGTGTGGGCTTTAAAA-G--AAAAGGCATCCCGCTCTTTGAGGACTG-AAGGTTTGCC-CCA-
1223623 A
60 A
* *** * ** *
1223624 CTTGCTGTGGGCTTTGAAATCCAAGGCCTCCCG-TCTCTTGAGGACTGGAAGGAAATGCACCAAA
1 CTTG-TGTGGGCTTTAAAAGAAAAGGCATCCCGCTCT-TTGAGGACT-GAAGG-TTTGC-CCCAA
1223688 CTTGTGTGGGC-TTAAAAG
1 CTTGTGTGGGCTTTAAAAG
1223706 GAAACCGGGC
Statistics
Matches: 462, Mismatches: 59, Indels: 108
0.73 0.09 0.17
Matches are distributed among these distances:
58 20 0.04
59 61 0.13
60 52 0.11
61 72 0.16
62 117 0.25
63 34 0.07
64 51 0.11
65 18 0.04
66 1 0.00
67 1 0.00
68 8 0.02
69 22 0.05
70 5 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (60 bp):
CTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTTTGCCCCAA
Found at i:1223416 original size:122 final size:122
Alignment explanation
Indices: 1223057--1223636 Score: 339
Period size: 122 Copynumber: 4.7 Consensus size: 122
1223047 CTGAAAGGGG
* * *
1223057 GCCACCACCTTGTGTGGGCTTTGAAAAGAAAAAGC-ATCCTGCTCTTTGAGGGACCTGATGAACG
1 GCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGATCCCGCTCTTTGA-GGACC---TGAA-G
* * * * *
1223121 GTGGGTGCCACCAACTCGGGT-GGCTTTAAAAGAAAAAGGC-GT-TC-CGCTCTTTAAGGACTGA
60 GT---TGCCA-CAACTTGTGTGGGCTCTAAAAG-AAAAGGCATTATCACG-TC-TTGAGGACTGA
*
1223182 AAG-T
118 AGGTT
*
1223186 GCCACCAACTTGTGT-GGCTTTAAAAGAAAAGGCGGTCCCGCTCTTTGAGGGACCTGAAGGTTGC
1 GCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGATCCCGCTCTTTGA-GGACCTGAAGGTTGC
* * *
1223250 CCCAACTTGTGTGGGCTCTAAAAGAAAAGGCATTTTCCCGTCTTGAGGACTGAAGGTTT
65 CACAACTTGTGTGGGCTCTAAAAGAAAAGGCATTATCACGTCTTGAGGACTGAAGG-TT
*
1223309 GTTCACCCAACTTGTGTGGGCTTTAAAAGAAAAGGC-ATCCCGCTCTTTGA-GA-CTGAAGGTTG
1 G-CCA-CCAACTTGTGTGGGCTTTAAAAGAAAAGGCGATCCCGCTCTTTGAGGACCTGAAGGTTG
** * * *
1223371 CCACAACTTGTGTGTTCTTTTAAGAGAAAAGG-GTGTCAT-AC-TCTTGAGGACTGAAGGTT
64 CCACAACTTGTGTGGGC-TCTAAAAGAAAAGGCAT-T-ATCACGTCTTGAGGACTGAAGGTT
* * * *
1223430 GCCACCACCTTGTGCTGGGCTTT-AGAGAAATAAGCG-TCCCGC-CTCTTGAGGACTTGAATGG-
1 GCCACCAACTTGTG-TGGGCTTTAAAAGAAA-AGGCGATCCCGCTCT-TTGAGGACCTGAA-GGT
* * * * * * *
1223491 TGCCACCCAACTT-TTTGGGCT-TAAGAGAAACAAAGCGTTCT-GC-TCTTTGAGGACTAGAA-A
62 TGCCA--CAACTTGTGTGGGCTCTAAAAG-AA-AAGGCATTATCACGTC-TTGAGGACT-GAAGG
*
1223551 AT
121 TT
* * *
1223553 G-CACCAACTTGTGTGGGCTTTAAAAGGAAAAAAGGCG-CCCCGCTCTTTGCGGA-CGGCAAGG-
1 GCCACCAACTTGTGTGGGCTTTAAAA-G--AAAAGGCGATCCCGCTCTTTGAGGACCTG-AAGGT
1223614 TGCCACCACACTTGCTGTGGGCT
62 TGCCA-CA-ACTTG-TGTGGGCT
1223637 TTGAAATCCA
Statistics
Matches: 373, Mismatches: 42, Indels: 76
0.76 0.09 0.15
Matches are distributed among these distances:
119 17 0.05
120 38 0.10
121 46 0.12
122 77 0.21
123 54 0.14
124 34 0.09
125 40 0.11
126 18 0.05
127 11 0.03
128 24 0.06
129 14 0.04
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (122 bp):
GCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGATCCCGCTCTTTGAGGACCTGAAGGTTGCC
ACAACTTGTGTGGGCTCTAAAAGAAAAGGCATTATCACGTCTTGAGGACTGAAGGTT
Found at i:1223479 original size:183 final size:183
Alignment explanation
Indices: 1223142--1223583 Score: 419
Period size: 183 Copynumber: 2.4 Consensus size: 183
1223132 CAACTCGGGT
* *
1223142 GGCTTTAAAAGAAAAAGGCGTTCCGCTCTTTAAGGACTGAAAGTGCCACCAACTTGTGTGGCTTT
1 GGCTTTAAAAGAAAAAGGCATCCCGCTCTTTAAGGACTGAAAGTGCCACCAACTTGTGTGGCTTT
* *
1223207 AAAAGAAAAGGCGGTCCCGCTCTTTGAGGGACCTGAAGGTTGCCCCAACTTGTGTGGGCTCTAAA
66 AAAAGAAAAGGCGGTCACACTCTTTGAGGGACCTGAAGGTTGCCCCAACTTGTGTGGGCTCTAAA
* *
1223272 AGAAAAGGCATTTTCCCGTCTTGAGGACTGAAGGTTTGTTCACCCAACTTGTGTG
131 AGAAAAAGC--TGTCCCGTCTTGAGGACTGAAGGTTTGTTCACCCAACTTGTGTG
* * *
1223327 GGCTTTAAAAG-AAAAGGCATCCCGCTCTTTGA-GACTGAAGGTTGCCA-CAACTTGTGTGTTCT
1 GGCTTTAAAAGAAAAAGGCATCCCGCTCTTTAAGGACTGAAAG-TGCCACCAACTTGTGTG-GC-
* * *
1223389 TTTAAGAGAAAAGG-GTGTCATACTC-TTGA-GGA-CTGAAGGTTGCCACCACCTTGTGCTGGGC
63 TTTAAAAGAAAAGGCG-GTCACACTCTTTGAGGGACCTGAAGGTTGCC-CCAACTTGTG-TGGGC
* * * *
1223450 T-TTAGAGAAATAAGC-GTCCCGCCTCTTGAGGACTTGAATGG--TG-CCACCCAACTT-TTTG
125 TCTAAAAGAAA-AAGCTGTCCCG--TCTTGAGGAC-TGAA-GGTTTGTTCACCCAACTTGTGTG
* * * * * * *
1223508 GGC-TTAAGAGAAACAAAGCGTTCTGCTCTTTGAGGACTAGAAAATG-CACCAACTTGTGTGGGC
1 GGCTTTAAAAGAAA-AAGGCATCCCGCTCTTTAAGGACT-GAAAGTGCCACCAACTTGTGT-GGC
1223571 TTTAAAAGGAAAA
63 TTTAAAA-GAAAA
1223584 AAGGCGCCCC
Statistics
Matches: 214, Mismatches: 25, Indels: 38
0.77 0.09 0.14
Matches are distributed among these distances:
180 6 0.03
181 13 0.06
182 45 0.21
183 72 0.34
184 46 0.21
185 32 0.15
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (183 bp):
GGCTTTAAAAGAAAAAGGCATCCCGCTCTTTAAGGACTGAAAGTGCCACCAACTTGTGTGGCTTT
AAAAGAAAAGGCGGTCACACTCTTTGAGGGACCTGAAGGTTGCCCCAACTTGTGTGGGCTCTAAA
AGAAAAAGCTGTCCCGTCTTGAGGACTGAAGGTTTGTTCACCCAACTTGTGTG
Found at i:1237383 original size:52 final size:51
Alignment explanation
Indices: 1237320--1237657 Score: 167
Period size: 52 Copynumber: 6.4 Consensus size: 51
1237310 GAAATAACGA
*
1237320 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
** * ** * *
1237371 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCG
1 G-GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATCG
* * * *
1237423 GGATTGGAGTATCCCCCATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAATCGG
1 GG-TTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATC-G
*** * *
1237476 GGTTGGAGTATCCCC--TTG-GAAATAACGGGGTTGG-ATTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTATT-T-TTGGA-AATAAAATC-G
* *
1237531 GGTTGGAGTATCCCTGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATC-G
* ** * * * *
1237585 AGTTAAAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCG
*
1237635 GAGTTGGAATATCCCCGATTGTG
1 G-GTTGGAGTATCCCCGATTGTG
1237658 GAGAATTGAG
Statistics
Matches: 213, Mismatches: 45, Indels: 57
0.68 0.14 0.18
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 4 0.02
51 33 0.15
52 79 0.37
53 34 0.16
54 25 0.12
55 19 0.09
56 2 0.01
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
Found at i:1237507 original size:28 final size:27
Alignment explanation
Indices: 1237473--1237544 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
1237463 GCGATAAAAT
*
1237473 CGGGGTTGGAGTATCCCC-TTGGAAATAA
1 CGGGGTTGGAGTATCCCCGAT-G-AATAA
* *
1237501 CGGGGTTGGATTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATGAATAA
1237528 CGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
1237545 TGATTGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 20 0.51
28 18 0.46
29 1 0.03
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.26
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATGAATAA
Found at i:1237562 original size:212 final size:212
Alignment explanation
Indices: 1237256--1237659 Score: 582
Period size: 212 Copynumber: 1.9 Consensus size: 212
1237246 AGAAGAAAAA
* *
1237256 AAAATCGAGATTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCTGATGAAATAACGAG
1 AAAATCGAGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
* **
1237321 GTTGGAGTATCCTCGATTGTGAAAAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
66 GTTGGAGTATCCTCGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCAGAGTTAAAGTATCC
* *
1237385 CCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGG-GATTGGAGTATCCCCCATTGTGGAA
131 CCGATTAAA-GAAAATTAGCGTTTTGAAAATAAAACCGGAG-TTGGAATATCCCCCATTGTGGAA
1237449 AAATTAGTGTTTTAGCGAT
194 AAATTAGTGTTTTAGCGAT
* * * * * *
1237468 AAAATCGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGATTATCCCCGATG-ATTAACGGG
1 AAAATCGAGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
*
1237532 GTTGGAGTATCC-CTGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAGTTAAAGTAT
66 GTTGGAGTATCCTC-GATTGTGAA-AAATTGGTGATTTTTGGAAATAAAATCAGAGTTAAAGTAT
* * * *
1237596 CCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
129 CCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCCATTGTGGA
1237660 GAATTGAGAA
Statistics
Matches: 170, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
210 1 0.01
211 28 0.16
212 103 0.61
213 38 0.22
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (212 bp):
AAAATCGAGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
GTTGGAGTATCCTCGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCAGAGTTAAAGTATCC
CCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCCATTGTGGAAAA
ATTAGTGTTTTAGCGAT
Found at i:1240030 original size:13 final size:13
Alignment explanation
Indices: 1240012--1240071 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
1240002 ACAAAGATCC
1240012 ATGTATCGATACA
1 ATGTATCGATACA
1240025 ATGTATCGATACA
1 ATGTATCGATACA
1240038 CA-G-A---A-A-A
1 -ATGTATCGATACA
1240045 ATGTATCGATACA
1 ATGTATCGATACA
*
1240058 TTGTATCGATACA
1 ATGTATCGATACA
1240071 A
1 A
1240072 AACTTATGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
6 1 0.03
7 2 0.05
8 2 0.05
9 1 0.03
11 1 0.03
12 2 0.05
13 27 0.73
14 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1240033 original size:33 final size:33
Alignment explanation
Indices: 1239991--1240072 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1239981 AAAATTTCCA
***
1239991 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1240024 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1240057 ATTGTATCGATACAAA
1 AATGTATCGATACAAA
1240073 ACTTATGTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1240170 original size:21 final size:21
Alignment explanation
Indices: 1240146--1240203 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1240136 ACATTTGTAG
*
1240146 AATGTATTGATACATTCCACA
1 AATGTATCGATACATTCCACA
*
1240167 AATGTATCGATACATTCTACA
1 AATGTATCGATACATTCCACA
1240188 AATGTATCGATACATT
1 AATGTATCGATACATT
1240204 TGGATAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATTCCACA
Found at i:1241161 original size:13 final size:13
Alignment explanation
Indices: 1241143--1241168 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1241133 ATGTTCTTTA
1241143 TATCGATACATTG
1 TATCGATACATTG
1241156 TATCGATACATTG
1 TATCGATACATTG
1241169 GTTACTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:1241325 original size:22 final size:18
Alignment explanation
Indices: 1241285--1241333 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 18
1241275 TAATTCCTTT
1241285 TCAAAATTCATCTTTTTCATA
1 TCAAAA-TCATCTTTTTC--A
1241306 TCAAAATCATCTATTTTTCA
1 TCAAAATCATC--TTTTTCA
1241326 TCAAAATC
1 TCAAAATC
1241334 TTCATCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 14 0.54
21 6 0.23
22 6 0.23
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (18 bp):
TCAAAATCATCTTTTTCA
Found at i:1243100 original size:16 final size:16
Alignment explanation
Indices: 1243079--1243111 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1243069 GAAAAAAAAA
*
1243079 TTTAAAATAAGAATTT
1 TTTAAAATAAAAATTT
1243095 TTTAAAATAAAAATTT
1 TTTAAAATAAAAATTT
1243111 T
1 T
1243112 GCATTAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTTAAAATAAAAATTT
Found at i:1247406 original size:32 final size:33
Alignment explanation
Indices: 1247363--1247511 Score: 153
Period size: 36 Copynumber: 4.4 Consensus size: 33
1247353 TATCTTTCAT
* **
1247363 GGCTAATATAGAAACCTCCCTATC-TTTTCACG
1 GGCTAAGATAGAAACCTCCCTATCTTTTTCAAA
*
1247395 GGCTAAGATAGAACCTCTCTCCCTATCTTTTTCAAA
1 GGCTAAGATAGAA--AC-CTCCCTATCTTTTTCAAA
*
1247431 GGCTAAGATAGAAACCTCCCTATC-TTTTC-AC
1 GGCTAAGATAGAAACCTCCCTATCTTTTTCAAA
1247462 GAGCTAAGATAG-AACCTCTTTCCTTATCTTTTTCAAA
1 G-GCTAAGATAGAAACCTC---CC-TATCTTTTTCAAA
1247499 GGCTAAGATAGAA
1 GGCTAAGATAGAA
1247512 TCTCTCAATC
Statistics
Matches: 98, Mismatches: 7, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
31 8 0.08
32 27 0.28
33 9 0.09
34 4 0.04
35 13 0.13
36 34 0.35
37 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (33 bp):
GGCTAAGATAGAAACCTCCCTATCTTTTTCAAA
Found at i:1247435 original size:36 final size:35
Alignment explanation
Indices: 1247378--1247517 Score: 162
Period size: 36 Copynumber: 4.0 Consensus size: 35
1247368 ATATAGAAAC
**
1247378 CTCCCTATCTTTTCACGGGCTAAGATAGAACCTCT
1 CTCCCTATCTTTTCAAAGGCTAAGATAGAACCTCT
*
1247413 CTCCCTATCTTTTTCAAAGGCTAAGATAGAA--AC-
1 CTCCCTATC-TTTTCAAAGGCTAAGATAGAACCTCT
*
1247446 CTCCCTATCTTTTC-ACGAGCTAAGATAGAACCTCT
1 CTCCCTATCTTTTCAAAG-GCTAAGATAGAACCTCT
* * *
1247481 TTCCTTATCTTTTTCAAAGGCTAAGATAGAATCTCT
1 CTCCCTATC-TTTTCAAAGGCTAAGATAGAACCTCT
1247517 C
1 C
1247518 AATCACTTAG
Statistics
Matches: 88, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
31 2 0.02
32 17 0.19
33 9 0.10
34 2 0.02
35 16 0.18
36 40 0.45
37 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (35 bp):
CTCCCTATCTTTTCAAAGGCTAAGATAGAACCTCT
Found at i:1247443 original size:68 final size:68
Alignment explanation
Indices: 1247363--1247511 Score: 262
Period size: 68 Copynumber: 2.2 Consensus size: 68
1247353 TATCTTTCAT
* *
1247363 GGCTAATATAGAAACCTCCCTATCTTTTCACGGGCTAAGATAGAACCTCTCTCCCTATCTTTTTC
1 GGCTAAGATAGAAACCTCCCTATCTTTTCACGAGCTAAGATAGAACCTCTCTCCCTATCTTTTTC
1247428 AAA
66 AAA
* *
1247431 GGCTAAGATAGAAACCTCCCTATCTTTTCACGAGCTAAGATAGAACCTCTTTCCTTATCTTTTTC
1 GGCTAAGATAGAAACCTCCCTATCTTTTCACGAGCTAAGATAGAACCTCTCTCCCTATCTTTTTC
1247496 AAA
66 AAA
1247499 GGCTAAGATAGAA
1 GGCTAAGATAGAA
1247512 TCTCTCAATC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 77 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (68 bp):
GGCTAAGATAGAAACCTCCCTATCTTTTCACGAGCTAAGATAGAACCTCTCTCCCTATCTTTTTC
AAA
Found at i:1247993 original size:22 final size:22
Alignment explanation
Indices: 1247965--1248037 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
1247955 TACTATTCAC
*
1247965 ATGTATCGATGCATGAACAGTG
1 ATGTATCGATACATGAACAGTG
* *
1247987 ATGTATCGATACATGAATAGGG
1 ATGTATCGATACATGAACAGTG
* *
1248009 ATGTATCAATACATGAACAGTA
1 ATGTATCGATACATGAACAGTG
1248031 ATGTATC
1 ATGTATC
1248038 AATTTAAAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (22 bp):
ATGTATCGATACATGAACAGTG
Found at i:1248122 original size:19 final size:18
Alignment explanation
Indices: 1248072--1248126 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
1248062 TGCCAATTTT
*
1248072 ATGTATCGATACAAT-TC
1 ATGTATCGATACAATGAC
1248089 ATGATATAGCGATACAATGAAC
1 ATG-TAT--CGATACAATG-AC
1248111 ATGTATCGATACAATG
1 ATGTATCGATACAATG
1248127 TATCGATACT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 3 0.09
18 3 0.09
19 10 0.31
20 9 0.28
21 3 0.09
22 4 0.12
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (18 bp):
ATGTATCGATACAATGAC
Found at i:1248129 original size:13 final size:13
Alignment explanation
Indices: 1248111--1248135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1248101 TACAATGAAC
1248111 ATGTATCGATACA
1 ATGTATCGATACA
1248124 ATGTATCGATAC
1 ATGTATCGATAC
1248136 TAAGCAAAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1249718 original size:168 final size:167
Alignment explanation
Indices: 1249371--1250080 Score: 603
Period size: 167 Copynumber: 4.3 Consensus size: 167
1249361 ATCAAACATC
* ** * * * * *
1249371 AAAATTCTTCAAATATTATCATTTAATTCCCATAAAATCAGTTTTGAAAAATTCCTTTTATGTTC
1 AAAATTCATCAAATATTATCATTTAATTCATATTAAATCAG-TTTAAAAAATT-CATTCATTTTC
* * * ** * * *
1249436 -TGAGTTATTG-ATTTTCTT--TTGAAATTCTTTTTATTTT-TAAATTACGG-GATTTTCTTCTC
64 ATAAGTTTTTGAATTTT-TTCCTTGAAATTGTCCTTATTTTCGAAA-AACGGAG-TTTTCTACTC
* * * *
1249495 CGTAAAAT-TTTTCATGAGGA-TTTTCATGTGTTTAAAATTTTT
126 CGT-AAATGTTTTCAAGGGGATTTTTCTTGTTTTTAAAA-TTTT
* * * *
1249537 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTATTCAGAAATGCATTCATTTTCA
1 AAAATTCATCAAATATTATCATTTAATTCATATTAAATCAGT-TTAAAAAATTCATTCATTTTCA
*
1249602 TAAGTTTTTGAATTTTTTTCCTTGAAATTGTCC-TATTTTCAAAAAACGGAGTTTTCTACTCCGT
65 TAAGTTTTTGAA-TTTTTTCCTTGAAATTGTCCTTATTTTCGAAAAACGGAGTTTTCTACTCCGT
*
1249666 AAATGTTTTCAAGGGGATTTTTCTTGTTTTTTAAATTTT
129 AAATGTTTTCAAGGGGATTTTTCTTGTTTTTAAAATTTT
* * * *
1249705 AAAATTTATCAAATATTATCATTTGATTCATATTAAATCAATTTGAAAAAATTCACTT-ATTTGC
1 AAAATTCATCAAATATTATCATTTAATTCATATTAAATCAGTTT-AAAAAATTCA-TTCATTTTC
* * * * * *
1249769 ATAAATGTTTT-AACTTTTTCCTTGAAATT-TCCTTATTTTTGAAATATGGAGTTTTTTACTCCG
64 ATAAGT-TTTTGAATTTTTTCCTTGAAATTGTCCTTATTTTCGAAAAACGGAGTTTTCTACTCCG
* *
1249832 TAAATGTTTTCAAGGGGATTTTTCTTGGTTTTT-GATTTTT
128 TAAATGTTTTCAAGGGGATTTTTCTT-GTTTTTAAAATTTT
* * * * * *
1249872 GAAACTCAT-AAACTATTGTCATTTGATTCATATTAAATTAGTTTTAAAAAATTAATTCATTTTC
1 AAAATTCATCAAA-TATTATCATTTAATTCATATTAAATCAG-TTTAAAAAATTCATTCATTTTC
* * * * *
1249936 ATAAG-TTTTGGATTTTTTCTTTGAAA-TG-CCATTTTTTTCGAAAAACTGAGTTTTCTACTCTG
64 ATAAGTTTTTGAATTTTTTCCTTGAAATTGTCC-TTATTTTCGAAAAACGGAGTTTTCTACTCCG
* ** *
1249998 TAAATATTTT-TTGGGGATTTTTCTTG-ATTTAAAATTTT
128 TAAATGTTTTCAAGGGGATTTTTCTTGTTTTTAAAATTTT
* * * ** *
1250036 CAAAATTCATCTAATATTATTATTTAACTCCCATTAAATTAGTTT
1 -AAAATTCATCAAATATTATCATTTAATTCATATTAAATCAGTTT
1250081 TGAAAATTTT
Statistics
Matches: 445, Mismatches: 75, Indels: 50
0.78 0.13 0.09
Matches are distributed among these distances:
163 3 0.01
164 9 0.02
165 58 0.13
166 107 0.24
167 129 0.29
168 106 0.24
169 33 0.07
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (167 bp):
AAAATTCATCAAATATTATCATTTAATTCATATTAAATCAGTTTAAAAAATTCATTCATTTTCAT
AAGTTTTTGAATTTTTTCCTTGAAATTGTCCTTATTTTCGAAAAACGGAGTTTTCTACTCCGTAA
ATGTTTTCAAGGGGATTTTTCTTGTTTTTAAAATTTT
Found at i:1252372 original size:19 final size:19
Alignment explanation
Indices: 1252328--1252383 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1252318 CTGCCAGTTT
* **
1252328 CATGTATCGATACAATTGTC
1 CATGTATTGATACAA-TGAA
1252348 CATGTATTGATACAATGAA
1 CATGTATTGATACAATGAA
1252367 CATGTATTGATACAATG
1 CATGTATTGATACAATG
1252384 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (19 bp):
CATGTATTGATACAATGAA
Found at i:1253961 original size:16 final size:14
Alignment explanation
Indices: 1253940--1253982 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 14
1253930 AATAGTAACC
1253940 CATGTATCGATACA
1 CATGTATCGATACA
1253954 TTCATGTATCGATACA
1 --CATGTATCGATACA
1253970 -ATGTATCGATACA
1 CATGTATCGATACA
1253983 AAGAATATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.48
16 14 0.52
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (14 bp):
CATGTATCGATACA
Found at i:1253975 original size:13 final size:13
Alignment explanation
Indices: 1253941--1254016 Score: 65
Period size: 13 Copynumber: 6.1 Consensus size: 13
1253931 ATAGTAACCC
1253941 ATGTATCGATACA
1 ATGTATCGATACA
1253954 TTCATGTATCGATACA
1 ---ATGTATCGATACA
1253970 ATGTATCGATACA
1 ATGTATCGATACA
*
1253983 A---A--GA-ATA
1 ATGTATCGATACA
*
1253990 TTGTATCGATACA
1 ATGTATCGATACA
1254003 ATGTATCGATACA
1 ATGTATCGATACA
1254016 A
1 A
1254017 AGAATATTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
7 2 0.04
8 2 0.04
10 2 0.04
12 2 0.04
13 29 0.58
16 13 0.26
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1253996 original size:20 final size:20
Alignment explanation
Indices: 1253971--1254035 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
1253961 ATCGATACAA
1253971 TGTATCGATACAAAGAATAT
1 TGTATCGATACAAAGAATAT
1253991 TGTATCGATAC-----A-A-
1 TGTATCGATACAAAGAATAT
1254004 TGTATCGATACAAAGAATAT
1 TGTATCGATACAAAGAATAT
1254024 TGTATCGATACA
1 TGTATCGATACA
1254036 TCTGGGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 23 0.61
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAAAGAATAT
Found at i:1254000 original size:33 final size:33
Alignment explanation
Indices: 1253958--1254035 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
1253948 GATACATTCA
1253958 TGTATCGATACAATGTATCGATACAAAGAATAT
1 TGTATCGATACAATGTATCGATACAAAGAATAT
1253991 TGTATCGATACAATGTATCGATACAAAGAATAT
1 TGTATCGATACAATGTATCGATACAAAGAATAT
1254024 TGTATCGATACA
1 TGTATCGATACA
1254036 TCTGGGTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATACAAAGAATAT
Found at i:1258036 original size:13 final size:13
Alignment explanation
Indices: 1258017--1258047 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1258007 ACAATTCATC
1258017 ATGTATCGATACA
1 ATGTATCGATACA
*
1258030 TTGTATCGATACA
1 ATGTATCGATACA
1258043 ATGTA
1 ATGTA
1258048 CCATGTATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1258134 original size:32 final size:33
Alignment explanation
Indices: 1258093--1258157 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1258083 TGCCAGTTTC
*
1258093 ATGTATCAATACAATG-A-ACATGTATCGATACA
1 ATGTATCAATACAAAGCATA-ATGTATCGATACA
1258125 ATGTATCAATACAAAGCATAATGTATCGATACA
1 ATGTATCAATACAAAGCATAATGTATCGATACA
1258158 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.50
33 14 0.47
34 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
ATGTATCAATACAAAGCATAATGTATCGATACA
Found at i:1265173 original size:9 final size:9
Alignment explanation
Indices: 1265159--1265192 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1265149 TCCAAGTCAC
1265159 CATCATTAT
1 CATCATTAT
1265168 CATCATTAT
1 CATCATTAT
1265177 CATC-TTCAT
1 CATCATT-AT
1265186 CATCATT
1 CATCATT
1265193 GATGGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (9 bp):
CATCATTAT
Found at i:1266914 original size:19 final size:19
Alignment explanation
Indices: 1266874--1266942 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
1266864 CAATTTCATA
**
1266874 TATCGATACAATTGTCCATG
1 TATCGATACAA-TGAACATG
1266894 TATCGATACAATGAACATG
1 TATCGATACAATGAACATG
*
1266913 TATCGATACAAAGCATA-ATG
1 TATCGATACAATG-A-ACATG
1266933 TATCGATACA
1 TATCGATACA
1266943 TCTCGGTGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 18 0.41
20 25 0.57
21 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (19 bp):
TATCGATACAATGAACATG
Found at i:1268407 original size:9 final size:9
Alignment explanation
Indices: 1268393--1268426 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1268383 TTCGAGTCAC
*
1268393 CATCATCAT
1 CATCATTAT
1268402 CATCATTAT
1 CATCATTAT
*
1268411 CATCTTTAT
1 CATCATTAT
1268420 CATCATT
1 CATCATT
1268427 GATGGTTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (9 bp):
CATCATTAT
Found at i:1276216 original size:13 final size:13
Alignment explanation
Indices: 1276190--1276220 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1276180 TCTTTGTATA
*
1276190 GATACATTGTATC
1 GATACATTGCATC
1276203 GATACATTGCATC
1 GATACATTGCATC
1276216 GATAC
1 GATAC
1276221 TTGGGTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (13 bp):
GATACATTGCATC
Found at i:1278736 original size:19 final size:19
Alignment explanation
Indices: 1278693--1278765 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
1278683 CACACCCAAA
*
1278693 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
1278713 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
* *
1278732 TGTATCGATACATGGATAAT
1 TGTATCGATACAT-GTTCAT
*
1278752 TGTATTGATACATG
1 TGTATCGATACATG
1278766 AAACTGGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 16 0.34
20 30 0.64
21 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1278837 original size:33 final size:33
Alignment explanation
Indices: 1278795--1278859 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1278785 TACCACTGTT
*
1278795 TGTATCGATACATGGT-ACATTGCATCGATACAG
1 TGTATCGATACATGATGA-ATTGCATCGATACAG
*
1278828 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGATGAATTGCATCGATACA
1278860 TTGCTTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGCATCGATACAG
Found at i:1283640 original size:21 final size:20
Alignment explanation
Indices: 1283616--1283663 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1283606 CAAATCTGTT
*
1283616 TCAAAATTCTTCATTTTCACA
1 TCAAAATTATTCATTTT-ACA
* *
1283637 TCAAAATTATTTATTTTTCA
1 TCAAAATTATTCATTTTACA
1283657 TCAAAAT
1 TCAAAAT
1283664 CATCTATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.46
Consensus pattern (20 bp):
TCAAAATTATTCATTTTACA
Found at i:1283660 original size:20 final size:20
Alignment explanation
Indices: 1283616--1283683 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1283606 CAAATCTGTT
* * *
1283616 TCAAAATTCTTCATTTTCACA
1 TCAAAATTATTTATTTT-TCA
1283637 TCAAAATTATTTATTTTTCA
1 TCAAAATTATTTATTTTTCA
* * *
1283657 TCAAAATCATCTATTTGTCA
1 TCAAAATTATTTATTTTTCA
1283677 TCAAAAT
1 TCAAAAT
1283684 CATCAACAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.37, C:0.18, G:0.01, T:0.44
Consensus pattern (20 bp):
TCAAAATTATTTATTTTTCA
Found at i:1283684 original size:20 final size:20
Alignment explanation
Indices: 1283635--1283687 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1283625 TTCATTTTCA
* * *
1283635 CATCAAAATTATTTATTTTT
1 CATCAAAATCATCTATTTGT
1283655 CATCAAAATCATCTATTTGT
1 CATCAAAATCATCTATTTGT
1283675 CATCAAAATCATC
1 CATCAAAATCATC
1283688 AACAAAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.42
Consensus pattern (20 bp):
CATCAAAATCATCTATTTGT
Found at i:1285165 original size:18 final size:18
Alignment explanation
Indices: 1285142--1285204 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 18
1285132 ACCCTAGAAA
1285142 GTATCGATACATATCATT
1 GTATCGATACATATCATT
1285160 GTATCG----ATA-CATT
1 GTATCGATACATATCATT
*
1285173 GTATCGATACAATATGCTTT
1 GTATCGATAC-ATAT-CATT
1285193 GTATCGATACAT
1 GTATCGATACAT
1285205 TGTATCTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 10 0.27
14 3 0.08
18 9 0.24
19 2 0.05
20 13 0.35
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (18 bp):
GTATCGATACATATCATT
Found at i:1285174 original size:13 final size:13
Alignment explanation
Indices: 1285156--1285183 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1285146 CGATACATAT
1285156 CATTGTATCGATA
1 CATTGTATCGATA
1285169 CATTGTATCGATA
1 CATTGTATCGATA
1285182 CA
1 CA
1285184 ATATGCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1285200 original size:33 final size:32
Alignment explanation
Indices: 1285142--1285235 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 32
1285132 ACCCTAGAAA
1285142 GTATCGATAC-ATATCATTGTATCGATACATT
1 GTATCGATACAATATCATTGTATCGATACATT
*
1285173 GTATCGATACAATATGCTTTGTATCGATACATT
1 GTATCGATACAATAT-CATTGTATCGATACATT
* * *
1285206 GTATCTATAC-ATGTTCATTGTGTCGATACA
1 GTATCGATACAAT-ATCATTGTATCGATACA
1285236 CACTTAATTG
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
31 10 0.18
32 19 0.35
33 26 0.47
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (32 bp):
GTATCGATACAATATCATTGTATCGATACATT
Found at i:1285320 original size:13 final size:13
Alignment explanation
Indices: 1285302--1285328 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1285292 AATACATGGA
1285302 ACATTGTATCGAT
1 ACATTGTATCGAT
1285315 ACATTGTATCGAT
1 ACATTGTATCGAT
1285328 A
1 A
1285329 TATGAAGAAT
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:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:1287226 original size:13 final size:13
Alignment explanation
Indices: 1287208--1287232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1287198 TACAGTGGTC
1287208 ATGTATCGATACA
1 ATGTATCGATACA
1287221 ATGTATCGATAC
1 ATGTATCGATAC
1287233 TGTGCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1287250 original size:33 final size:32
Alignment explanation
Indices: 1287191--1287253 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1287181 ATCTTTGCAA
*
1287191 GTATCGATACAGTGGTCATGTATCGATACAAT
1 GTATCGATACAGTGATCATGTATCGATACAAT
* *
1287223 GTATCGATACTGTGCATTATGTATCGATACA
1 GTATCGATACAGTG-ATCATGTATCGATACA
1287254 TCTGAAAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (32 bp):
GTATCGATACAGTGATCATGTATCGATACAAT
Found at i:1295705 original size:13 final size:13
Alignment explanation
Indices: 1295673--1295708 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 13
1295663 ACATTTGGTC
1295673 ATGTATCGATACA
1 ATGTATCGATACA
1295686 A---ATCGATACA
1 ATGTATCGATACA
1295696 ATGTATCGATACA
1 ATGTATCGATACA
1295709 TCTTGTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
10 10 0.50
13 10 0.50
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1295815 original size:13 final size:13
Alignment explanation
Indices: 1295797--1295821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1295787 TACAGTGGTC
1295797 ATGTATCGATACA
1 ATGTATCGATACA
1295810 ATGTATCGATAC
1 ATGTATCGATAC
1295822 TGTGCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1295839 original size:33 final size:32
Alignment explanation
Indices: 1295780--1295842 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1295770 ATCTTTGCAA
*
1295780 GTATCGATACAGTGGTCATGTATCGATACAAT
1 GTATCGATACAGTGATCATGTATCGATACAAT
* *
1295812 GTATCGATACTGTGCATTATGTATCGATACA
1 GTATCGATACAGTG-ATCATGTATCGATACA
1295843 TCTGAAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (32 bp):
GTATCGATACAGTGATCATGTATCGATACAAT
Found at i:1297728 original size:13 final size:14
Alignment explanation
Indices: 1297704--1297732 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1297694 CTTTTTGTTA
1297704 TTTTCCTATTTTCT
1 TTTTCCTATTTTCT
1297718 TTTTCCT-TTTTCT
1 TTTTCCTATTTTCT
1297731 TT
1 TT
1297733 GATCTTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCCTATTTTCT
Found at i:1298451 original size:62 final size:61
Alignment explanation
Indices: 1298380--1298501 Score: 217
Period size: 62 Copynumber: 2.0 Consensus size: 61
1298370 TCAACTTATC
1298380 CAATCAATTGAAACAGAAATTCCAAGATCATCAAGTCTTACAAGAAACTTTGCTTCATATGT
1 CAATCAATTGAAACAGAAATTCCAAGATCATCAAGTCTTACAAGAAACTTTGC-TCATATGT
* *
1298442 CAATCAATTGAAATAGAAATTCCAAGATCATCAAGTCTTACATGAAACTTTGCTCATATG
1 CAATCAATTGAAACAGAAATTCCAAGATCATCAAGTCTTACAAGAAACTTTGCTCATATG
1298502 AAAACCAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 7 0.12
62 51 0.88
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (61 bp):
CAATCAATTGAAACAGAAATTCCAAGATCATCAAGTCTTACAAGAAACTTTGCTCATATGT
Found at i:1300484 original size:48 final size:50
Alignment explanation
Indices: 1300391--1300485 Score: 131
Period size: 48 Copynumber: 1.9 Consensus size: 50
1300381 CTGTTGCTGC
* *
1300391 TGCAGCTGGTGCATCTGGAGCTGCTGCTGCTCCTATTGGTGTGCCTGGTGT
1 TGCAGCTGGTGCATCAGAAGC-GCTGCTGCTCCTATTGGTGTGCCTGGTGT
* *
1300442 TGCAGCTGGTGCATCAGAAG-G-TGGTGCTCCTATTGGTTTGCCTG
1 TGCAGCTGGTGCATCAGAAGCGCTGCTGCTCCTATTGGTGTGCCTG
1300486 ATACTCCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 21 0.52
49 1 0.03
51 18 0.45
ACGTcount: A:0.11, C:0.22, G:0.35, T:0.33
Consensus pattern (50 bp):
TGCAGCTGGTGCATCAGAAGCGCTGCTGCTCCTATTGGTGTGCCTGGTGT
Found at i:1306654 original size:367 final size:367
Alignment explanation
Indices: 1305981--1306706 Score: 1364
Period size: 367 Copynumber: 2.0 Consensus size: 367
1305971 AAAGTAATAG
1305981 AAAGAGGTGAATGCTGGAAAAGTACTACCATAAAAACATAAAAGATATATCAATGAATAAAAGTT
1 AAAGAGGTGAATGCTGGAAAAGTACTACCATAAAAACATAAAAGATATATCAATGAATAAAAGTT
* **
1306046 TTAAAGCAACAAAAGCAAACTAGTAGCCAAATTATATATAACACGCTAATGCGAACCAAACATGC
66 CTAAAGCAACAAAAGCAAACTAGTAGCCAAATTATATATAACAAACTAATGCGAACCAAACATGC
1306111 AATCAATTGAAAAGTCACCAGTAATAACCAGAAGAACGCCACTAAAATGCAACATTTCCAAATTC
131 AATCAATTGAAAAGTCACCAGTAATAACCAGAAGAACGCCACTAAAATGCAACATTTCCAAATTC
1306176 TAAAAGCAAGTAATCAACTAAAAGAAGAACTGGATTTTCCAACTTTCACTGTGCCAAATCCATAG
196 TAAAAGCAAGTAATCAACTAAAAGAAGAACTGGATTTTCCAACTTTCACTGTGCCAAATCCATAG
* *
1306241 CCTCATTTATGCAACAAATTTAAAGGTCAATCACAAAATGGATAAAGACAACATTGGGGGCAAAT
261 CCTCATTTATGCAACAAATTTAAAGGTCAAGCACAAAATAGATAAAGACAACATTGGGGGCAAAT
1306306 TTTTAAGTGATGAAATTCTTTGGCAAACCATTGATTTTATAT
326 TTTTAAGTGATGAAATTCTTTGGCAAACCATTGATTTTATAT
1306348 AAAGAGGTGAATGCTGGAAAAGTACTACCATAAAAACATAAAAGATATATCAATGAATAAAAGTT
1 AAAGAGGTGAATGCTGGAAAAGTACTACCATAAAAACATAAAAGATATATCAATGAATAAAAGTT
*
1306413 CTAAAGCAACAAAAGCAAACTAGTGGCCAAATTATATATAACAAACTAATGCGAACCAAACATGC
66 CTAAAGCAACAAAAGCAAACTAGTAGCCAAATTATATATAACAAACTAATGCGAACCAAACATGC
1306478 AATCAATTGAAAAGTCACCAGTAATAACCAGAAGAACGCCACTAAAATGCAACATTTCCAAATTC
131 AATCAATTGAAAAGTCACCAGTAATAACCAGAAGAACGCCACTAAAATGCAACATTTCCAAATTC
*
1306543 TAAAATCAAGTAATCAACTAAAAGAAGAACTGGA-TTTCCAACTTTGCACTGTGCCAAATCCATA
196 TAAAAGCAAGTAATCAACTAAAAGAAGAACTGGATTTTCCAACTTT-CACTGTGCCAAATCCATA
1306607 GCCTCATTTATGCAACAAATTTAAAGGTCAAGCACAAAATAGATAAAGACAACATTGGGGGCAAA
260 GCCTCATTTATGCAACAAATTTAAAGGTCAAGCACAAAATAGATAAAGACAACATTGGGGGCAAA
*
1306672 TTTTTAAGTGATGAAATTCTTTGGCAAGCCATTGA
325 TTTTTAAGTGATGAAATTCTTTGGCAAACCATTGA
1306707 ATTTCTCAGA
Statistics
Matches: 350, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
366 11 0.03
367 339 0.97
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.23
Consensus pattern (367 bp):
AAAGAGGTGAATGCTGGAAAAGTACTACCATAAAAACATAAAAGATATATCAATGAATAAAAGTT
CTAAAGCAACAAAAGCAAACTAGTAGCCAAATTATATATAACAAACTAATGCGAACCAAACATGC
AATCAATTGAAAAGTCACCAGTAATAACCAGAAGAACGCCACTAAAATGCAACATTTCCAAATTC
TAAAAGCAAGTAATCAACTAAAAGAAGAACTGGATTTTCCAACTTTCACTGTGCCAAATCCATAG
CCTCATTTATGCAACAAATTTAAAGGTCAAGCACAAAATAGATAAAGACAACATTGGGGGCAAAT
TTTTAAGTGATGAAATTCTTTGGCAAACCATTGATTTTATAT
Found at i:1311326 original size:6 final size:6
Alignment explanation
Indices: 1311297--1311334 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
1311287 AGCAGCAGTA
*
1311297 GCAGCT GCTGCT GCAGCCT G-AGCT GCAGCT GCAGCT GC
1 GCAGCT GCAGCT GCAG-CT GCAGCT GCAGCT GCAGCT GC
1311335 TTCTTTAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 3 0.11
6 22 0.79
7 3 0.11
ACGTcount: A:0.13, C:0.34, G:0.34, T:0.18
Consensus pattern (6 bp):
GCAGCT
Found at i:1313034 original size:2 final size:2
Alignment explanation
Indices: 1313023--1313057 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1313013 AGAGCAATAG
1313023 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1313058 AACTTATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1315866 original size:2 final size:2
Alignment explanation
Indices: 1315859--1315890 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1315849 AAGATACATC
*
1315859 TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1315891 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1316171 original size:6 final size:6
Alignment explanation
Indices: 1316160--1316191 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1316150 TCCAACACAT
*
1316160 CTCTCC CTCTCC CTCTCC CTCTCC CCCTCC CT
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CT
1316192 TTCTCTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CTCTCC
Found at i:1321733 original size:14 final size:14
Alignment explanation
Indices: 1321716--1321749 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1321706 TTTGTGTCTA
1321716 TATATTAT-TTATAT
1 TATATTATGTTAT-T
1321730 TATATTATGTTATT
1 TATATTATGTTATT
1321744 TATATT
1 TATATT
1321750 TTATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TATATTATGTTATT
Found at i:1321853 original size:15 final size:16
Alignment explanation
Indices: 1321823--1321856 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1321813 AATTAAAGTT
1321823 TTAAATATATAATTAAA
1 TTAAATATAT-ATTAAA
1321840 TTAAATATAT-TTAAA
1 TTAAATATATATTAAA
1321855 TT
1 TT
1321857 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATATATATTAAA
Found at i:1321877 original size:13 final size:13
Alignment explanation
Indices: 1321859--1321893 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1321849 TTTAAATTTT
1321859 TTAATTTTAAAAA
1 TTAATTTTAAAAA
*
1321872 TTAATTACTAAAAA
1 TTAATT-TTAAAAA
1321886 TTAATTTT
1 TTAATTTT
1321894 TAATATACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAATTTTAAAAA
Found at i:1324054 original size:21 final size:21
Alignment explanation
Indices: 1324013--1324054 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1324003 TGAATCATAT
*
1324013 AATAATTTATGATTATCTTTA
1 AATAATTTATGATTATATTTA
*
1324034 AATAATATTAT-ATTCTATTTA
1 AATAAT-TTATGATTATATTTA
1324055 GACCTAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (21 bp):
AATAATTTATGATTATATTTA
Found at i:1324358 original size:18 final size:17
Alignment explanation
Indices: 1324304--1324358 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1324294 TACTATATTT
*
1324304 ATAAATTGCGAAAACTAA
1 ATAAATTGC-AAAAATAA
* *
1324322 AT-AATGGCAAGAA-AA
1 ATAAATTGCAAAAATAA
1324337 ATAAATTGCAAAAAATAA
1 ATAAATTGC-AAAAATAA
1324355 ATAA
1 ATAA
1324359 TCATAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 4 0.14
16 8 0.28
17 9 0.31
18 8 0.28
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (17 bp):
ATAAATTGCAAAAATAA
Found at i:1324368 original size:17 final size:17
Alignment explanation
Indices: 1324346--1324379 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1324336 AATAAATTGC
1324346 AAAAAATAAATAATCAT
1 AAAAAATAAATAATCAT
1324363 AAAAAATAAATAATCAT
1 AAAAAATAAATAATCAT
1324380 GAGAAGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAATAAATAATCAT
Found at i:1326486 original size:13 final size:13
Alignment explanation
Indices: 1326468--1326492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1326458 TACCTGAATG
1326468 TATCGATACAATA
1 TATCGATACAATA
1326481 TATCGATACAAT
1 TATCGATACAAT
1326493 GAATAATATA
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:1326502 original size:20 final size:20
Alignment explanation
Indices: 1326477--1326530 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1326467 GTATCGATAC
1326477 AATATATCGATACAATGAAT
1 AATATATCGATACAATGAAT
*
1326497 AATATATC-ATTATAATGAAT
1 AATATATCGA-TACAATGAAT
* *
1326517 AATGTATTGATACA
1 AATATATCGATACA
1326531 TCGGGGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
AATATATCGATACAATGAAT
Found at i:1327175 original size:41 final size:42
Alignment explanation
Indices: 1327130--1327278 Score: 128
Period size: 41 Copynumber: 3.6 Consensus size: 42
1327120 CTGCTCTTTA
* * *
1327130 AGGACAAAGG-AAAAGGAGAATGAAATGGGTCTTGTTCCTTG
1 AGGACAAAGGAAAAAGGAGAATAAAATGCGTCATGTTCCTTG
* * * **
1327171 AGGACAAAGGAAAATGG-GAAATAAAATGCATCCT-ACCCTTTG
1 AGGACAAAGGAAAAAGGAG-AATAAAATGCGTCATGTTCC-TTG
* * * *
1327213 AAGACAAAGGAAAAAGGA-AATTAAATGTGTCATGCTT-TTTG
1 AGGACAAAGGAAAAAGGAGAATAAAATGCGTCATG-TTCCTTG
1327254 AGGACAAAGGAAAAAGGAGAATAAA
1 AGGACAAAGGAAAAAGGAGAATAAA
1327279 GTGCATCCTG
Statistics
Matches: 83, Mismatches: 18, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
41 44 0.53
42 39 0.47
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (42 bp):
AGGACAAAGGAAAAAGGAGAATAAAATGCGTCATGTTCCTTG
Found at i:1327296 original size:83 final size:84
Alignment explanation
Indices: 1327118--1327296 Score: 215
Period size: 83 Copynumber: 2.2 Consensus size: 84
1327108 GAAGGGGGAG
*
1327118 TCCTGCTCTTT-AAGGACAAAGGAAAAGGAGAATGAAATGGGTCTTGTTCCTTGAGGACAAAGGA
1 TCCTGCTCTTTGAAGGACAAAGGAAAAGGAGAATGAAATGGGTCATGTTCCTTGAGGACAAAGGA
*
1327182 AAATGGGAAATAAAATGCA
66 AAAAGGGAAATAAAATGCA
* * * * *
1327201 TCCTACCCTTTGAA-GACAAAGGAAAAAGGA-AATTAAATGTGTCATGCTT-TTTGAGGACAAAG
1 TCCTGCTCTTTGAAGGACAAAGG-AAAAGGAGAATGAAATGGGTCATG-TTCCTTGAGGACAAAG
*
1327263 GAAAAA-GGAGAATAAAGTGCA
64 GAAAAAGGGA-AATAAAATGCA
*
1327284 TCCTGCTTTTTGA
1 TCCTGCTCTTTGA
1327297 GAATTAGAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
82 3 0.04
83 67 0.83
84 11 0.14
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (84 bp):
TCCTGCTCTTTGAAGGACAAAGGAAAAGGAGAATGAAATGGGTCATGTTCCTTGAGGACAAAGGA
AAAAGGGAAATAAAATGCA
Found at i:1327497 original size:62 final size:61
Alignment explanation
Indices: 1327358--1327940 Score: 722
Period size: 61 Copynumber: 9.5 Consensus size: 61
1327348 AAGGAGAAAG
* * * * * *
1327358 GGAAAAGGCGTCCTGCTCCTTGAAGACTAAAAAGTACCACCAACTCGTGTGGGCTTAAAAA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * ** *
1327419 GAAAAAGGCATCCTGCTCTTTGAGGACTCAAGGGTGCCACCAACTTGTATGGGCTTTAAAAA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * * * *
1327481 GAAAAAGGTGTCCTGCTCTTTAAGGACT-AGAGGTGCCACCAACTTGTGTAGGCTTTGAAAA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAA
* ** * * *
1327542 GAAAAAGGTTTCCTACTCTTTGAGGACTAGAGAGGTGCCACCAACTTGTGTGGGCTTTAAAA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * *
1327604 GGAAAAGGCATCCTGCTCCTTGAGGACTAAAAAGTGCTACCAACTTGTGTGGGCTTTAAAA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
*
1327665 GGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * *
1327727 GGAAAAGGCGTCTTGCTCCTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTATAAAA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* ** *
1327788 GGAAAAGACGTCCTGCTCTTTGAGGACT-AATGGTGCCACCAAATTGTGTGGGCTTTAAAA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* *
1327848 -GAGAAAGGCGTTCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTATAAAA
1 GGA-AAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* *
1327910 GGAAAATGTGTCCTGCTCTTTGAGGACTGAA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
1327941 GGTGAAAGGA
Statistics
Matches: 457, Mismatches: 57, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
59 2 0.00
60 51 0.11
61 214 0.47
62 161 0.35
63 29 0.06
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (61 bp):
GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
Found at i:1327604 original size:123 final size:122
Alignment explanation
Indices: 1327360--1327944 Score: 748
Period size: 123 Copynumber: 4.8 Consensus size: 122
1327350 GGAGAAAGGG
* * * *
1327360 AAAAGGCGTCCTGCTCCTTGAA-GACTAAAAAGTACCACCAACTCGTGTGGGCTTAAAAAGAAAA
1 AAAAGGCGTCCTGCTCCTT-AAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* *
1327424 AGGCATCCTGCTCTTTGAGGACTCA-AGGGTGCCACCAACTTGTATGGGCTTTAAAAAGA
65 AGGCATCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGA
* * * * * *
1327483 AAAAGGTGTCCTGCTCTTTAAGGACT-AGAGGTGCCACCAACTTGTGTAGGCTTTGAAAAGAAAA
1 AAAAGGCGTCCTGCTCCTTAAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAA
** * *
1327547 AGGTTTCCTACTCTTTGAGGACTAGAGAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
65 AGGCATCCTGCTCTTTGAGGACTAGA-AGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * *
1327606 AAAAGGCATCCTGCTCCTTGAGGACTAAAAAGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAA
1 AAAAGGCGTCCTGCTCCTTAAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* *
1327671 GGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
66 GGCATCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * *
1327729 AAAAGGCGTCTTGCTCCTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTATAAAAGGAAAA
1 AAAAGGCGTCCTGCTCCTTAAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* * * *
1327794 GACGTCCTGCTCTTTGAGGACTA-ATGGTGCCACCAAATTGTGTGGGCTTTAAAAGA
66 GGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * * * *
1327850 GAAAGGCGTTCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTATAAAAGGAAA
1 AAAAGGCGTCCTGCTCCTTAAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* **
1327915 ATGTGTCCTGCTCTTTGAGGACT-GAAGGTG
65 AGGCATCCTGCTCTTTGAGGACTAGAAGGTG
1327945 AAAGGAGAGA
Statistics
Matches: 405, Mismatches: 49, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
121 50 0.12
122 87 0.21
123 219 0.54
124 49 0.12
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (122 bp):
AAAAGGCGTCCTGCTCCTTAAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
GGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
Found at i:1328027 original size:99 final size:100
Alignment explanation
Indices: 1327855--1328039 Score: 300
Period size: 99 Copynumber: 1.9 Consensus size: 100
1327845 AAAGAGAAAG
* * * *
1327855 GCGTTCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTATAAAAGGAAAATGTG
1 GCGTTCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTATAAAAAGAAAAGGCG
1327920 TCCTGCTCTTTGAGGACTGAAGGTGAAAGGAGAGA
66 TCCTGCTCTTTGAGGACTGAAGGTGAAAGGAGAGA
* * *
1327955 GCGTTCTGCTCTTTGAGGACTAG-GAAGTGCCACCAACTTATGTGGGCTTTAAAAAGAGAAGGCG
1 GCGTTCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTATAAAAAGAAAAGGCG
1328019 TCCTGCTCTTTGAGGACTGAA
66 TCCTGCTCTTTGAGGACTGAA
1328040 AAATGAAAGG
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
99 55 0.71
100 23 0.29
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (100 bp):
GCGTTCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTATAAAAAGAAAAGGCG
TCCTGCTCTTTGAGGACTGAAGGTGAAAGGAGAGA
Found at i:1329025 original size:1 final size:1
Alignment explanation
Indices: 1329019--1329077 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
1329009 CTTTTCTCTC
* * * * * * *
1329019 TTTTTTTTTCTTTTTTTTCTTTGTTTTGTTTTGTTTTTTTTTATTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1329078 AAAAAAAGAA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.02, C:0.03, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:1329032 original size:9 final size:9
Alignment explanation
Indices: 1329005--1329069 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
1328995 AAGCAGGTTC
1329005 TTTTCTTTT
1 TTTTCTTTT
* *
1329014 CTCTCTTTTT
1 TTTTC-TTTT
1329024 TTTTCTTTT
1 TTTTCTTTT
*
1329033 TTTTCTTTG
1 TTTTCTTTT
*
1329042 TTTTGTTTT
1 TTTTCTTTT
1329051 GTTTT-TTTT
1 -TTTTCTTTT
1329060 TATTT-TTTT
1 T-TTTCTTTT
1329069 T
1 T
1329070 GTTTTTTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
8 1 0.02
9 34 0.74
10 11 0.24
ACGTcount: A:0.02, C:0.09, G:0.05, T:0.85
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:1329039 original size:19 final size:19
Alignment explanation
Indices: 1329005--1329077 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
1328995 AAGCAGGTTC
* *
1329005 TTTTCTTTTCTCTCTTTTT
1 TTTTCTTTTTTTTCTTTTT
1329024 TTTTCTTTTTTTTCTTTGTT
1 TTTTCTTTTTTTTCTTT-TT
* *
1329044 TTGTTTTGTTTTTTTTTATTTT
1 TT-TTCT-TTTTTTTCT-TTTT
*
1329066 TTTTGTTTTTTT
1 TTTTCTTTTTTT
1329078 AAAAAAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 15 0.33
20 10 0.22
21 6 0.13
22 12 0.27
23 2 0.04
ACGTcount: A:0.01, C:0.08, G:0.05, T:0.85
Consensus pattern (19 bp):
TTTTCTTTTTTTTCTTTTT
Found at i:1340739 original size:79 final size:80
Alignment explanation
Indices: 1340589--1340746 Score: 230
Period size: 79 Copynumber: 2.0 Consensus size: 80
1340579 CTGACTATAG
* ** * * *
1340589 AAAATCGGTGTTCTAGAAATAAAATCAGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGT
1 AAAATCAGTGTTCTAGAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGAAAT
1340654 ATCCCCGATTATGAA
66 ATCCCCGATTATGAA
*
1340669 AAAATCAGTGTTCTAGAAATAAAA-CTGGGTTGGAGTAT-CCCTCAAAAATAACGGGATTAGAAA
1 AAAATCAGTGTTCTAGAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAACGGGATT-GAAA
1340732 TATCCCCGATTATGA
65 TATCCCCGATTATGA
1340747 GAAATTGATT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
78 17 0.24
79 30 0.43
80 23 0.33
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (80 bp):
AAAATCAGTGTTCTAGAAATAAAATCAGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGAAAT
ATCCCCGATTATGAA
Found at i:1343180 original size:13 final size:13
Alignment explanation
Indices: 1343131--1343160 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1343121 GTAAACCCAG
*
1343131 AATGTATTGATAC
1 AATGTATAGATAC
1343144 AATGTATAGATAC
1 AATGTATAGATAC
1343157 AATG
1 AATG
1343161 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATAGATAC
Found at i:1343206 original size:24 final size:20
Alignment explanation
Indices: 1343142--1343198 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1343132 ATGTATTGAT
*
1343142 ACAATGTATAGATACAATGA
1 ACAATGTATCGATACAATGA
1343162 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
1343182 ATAATGTATCGATACAA
1 ACAATGTATCGATACAA
1343199 ATTGTGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.26
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:1348269 original size:21 final size:22
Alignment explanation
Indices: 1348239--1348294 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
1348229 ACAATGACCT
*
1348239 ATGAATAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
1348261 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
1348282 ATGAACAGTGATG
1 ATGAACAGTGATG
1348295 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.29
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:1348301 original size:10 final size:10
Alignment explanation
Indices: 1348282--1348312 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1348272 GTATCGATAC
1348282 ATGAACAGTG
1 ATGAACAGTG
*
1348292 ATGAATAGTG
1 ATGAACAGTG
1348302 ATGAACAGTG
1 ATGAACAGTG
1348312 A
1 A
1348313 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1348372 original size:18 final size:19
Alignment explanation
Indices: 1348336--1348372 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1348326 CTACTACCAA
1348336 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1348355 TGTATCGATACA-ATTTTG
1 TGTATCGATACATATTTTG
1348373 GCTACTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1348400 original size:53 final size:53
Alignment explanation
Indices: 1348336--1348472 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
1348326 CTACTACCAA
*
1348336 TGTATCGATACATATTTTGTGTATCGATACAATTTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
1348389 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1348442 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1348473 TATGCAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1348508 original size:21 final size:20
Alignment explanation
Indices: 1348460--1348514 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
1348450 TACATATTTG
**
1348460 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATAAAA
* *
1348480 TCTGTATCGATACATTTAAAA
1 TGTGTATCGATAC-TATAAAA
1348501 TGTGTATCGATACT
1 TGTGTATCGATACT
1348515 TTTCAGAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (20 bp):
TGTGTATCGATACTATAAAA
Found at i:1348579 original size:21 final size:21
Alignment explanation
Indices: 1348553--1348593 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1348543 GTCAACCTTG
1348553 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1348574 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1348594 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1351414 original size:79 final size:77
Alignment explanation
Indices: 1351321--1351584 Score: 260
Period size: 79 Copynumber: 3.4 Consensus size: 77
1351311 TCATTGATGT
* * *
1351321 TTTTATTTCC-AAAACATCGATTTTACACTATCGGGGATACTCCAACACCGTTATTTTTGAGGGC
1 TTTTA-TTCCTAAAACATCGATTTTTCACCATCGGGGATACTCCAAC-CCGTTATTTTCGAGGG-
1351385 ATACTCCAACCTCGG
63 ATACTCCAACCTCGG
* *
1351400 TTTTATTCCTAAAACATCGATTTTTCACCATCGAGGATACTCCAACCCCGTTATATTCGAAGGGA
1 TTTTATTCCTAAAACATCGATTTTTCACCATCGGGGATACTCCAA-CCCGTTATTTTCG-AGGGA
* **
1351465 TACTCCAACCCCAA
64 TACTCCAACCTCGG
** * * * ** * *
1351479 TTTTATTTATAAAATAACGATTTTTCACCATTGGGGATACTTTAACCCTGTTATTTCCAAGGGGA
1 TTTTATTCCTAAAACATCGATTTTTCACCATCGGGGATACTCCAACCC-GTTATTTTCGA-GGGA
* * *
1351544 CACTTCAACTTCGG
64 TACTCCAACCTCGG
* *
1351558 TTTTATTTCTAAAACACCGATTTTTCA
1 TTTTATTCCTAAAACATCGATTTTTCA
1351585 TAATCGGAGA
Statistics
Matches: 152, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
78 8 0.05
79 139 0.91
80 5 0.03
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (77 bp):
TTTTATTCCTAAAACATCGATTTTTCACCATCGGGGATACTCCAACCCGTTATTTTCGAGGGATA
CTCCAACCTCGG
Found at i:1352053 original size:8 final size:8
Alignment explanation
Indices: 1352036--1352079 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
1352026 AAAAGAATTC
1352036 CATGCTTT
1 CATGCTTT
*
1352044 CATGCCTT
1 CATGCTTT
* *
1352052 CATGCATA
1 CATGCTTT
1352060 CATGCATTT
1 CATGC-TTT
1352069 CATGCTTT
1 CATGCTTT
1352077 CAT
1 CAT
1352080 TTCATGCATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 24 0.80
9 6 0.20
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.41
Consensus pattern (8 bp):
CATGCTTT
Found at i:1364183 original size:23 final size:23
Alignment explanation
Indices: 1364143--1364186 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1364133 GGGGCCACTC
*
1364143 TTTTTTTATTGATGTTCATTCTT
1 TTTTTTTATTGATATTCATTCTT
* *
1364166 TTTTTTTCTTGCTATTCATTC
1 TTTTTTTATTGATATTCATTC
1364187 CCATTACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.14, G:0.07, T:0.68
Consensus pattern (23 bp):
TTTTTTTATTGATATTCATTCTT
Found at i:1373906 original size:12 final size:12
Alignment explanation
Indices: 1373888--1373938 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 12
1373878 TCCTTCATAC
1373888 AAAAAAAAA-AA
1 AAAAAAAAACAA
* *
1373899 ACAAAAAAACCA
1 AAAAAAAAACAA
* *
1373911 AAAAAAAGAC-C
1 AAAAAAAAACAA
1373922 AAAAAAAAACAA
1 AAAAAAAAACAA
1373934 AAAAA
1 AAAAA
1373939 CCAAGGAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
11 17 0.55
12 14 0.45
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:1373926 original size:31 final size:32
Alignment explanation
Indices: 1373891--1373960 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
1373881 TTCATACAAA
*
1373891 AAAAAAAAACAAAAAAACCAA-AAAAAAGACC
1 AAAAAAAAACAAAAAAACCAAGAAAAAAGAAC
* *
1373922 AAAAAAAAACAAAAAAACCAAGGAAAAATAAC
1 AAAAAAAAACAAAAAAACCAAGAAAAAAGAAC
1373954 AAAAAAA
1 AAAAAAA
1373961 TAGAAAAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.81, C:0.13, G:0.04, T:0.01
Consensus pattern (32 bp):
AAAAAAAAACAAAAAAACCAAGAAAAAAGAAC
Found at i:1375265 original size:30 final size:29
Alignment explanation
Indices: 1375214--1375392 Score: 184
Period size: 29 Copynumber: 6.0 Consensus size: 29
1375204 AGAATGTTCA
*
1375214 TCTTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 TCTTTTCAAAG-CC-CACAAGTCAGTGGC-AC
*
1375246 TCTTTTCAAAGCTCACAAGTCAGTGGCA-
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1375274 TCTCTACAAAAGCCCACAAGTCAGTGGCAC
1 TCTTTTC-AAAGCCCACAAGTCAGTGGCAC
* *
1375304 -CCTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 TCTTTTCAAAG-CC-CACAAGTCAGTGGC-AC
*
1375335 TCTTTTCAAAGCCCATAAGTCAGTGGCA-
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1375363 TCTCTTCAAAAGCCCACAAGTCTGTGGCAC
1 TCTTTTC-AAAGCCCACAAGTCAGTGGCAC
1375393 CCACAAGTCG
Statistics
Matches: 124, Mismatches: 15, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
28 15 0.12
29 46 0.37
30 38 0.31
31 5 0.04
32 20 0.16
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (29 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:1375295 original size:29 final size:28
Alignment explanation
Indices: 1375212--1376042 Score: 470
Period size: 30 Copynumber: 28.7 Consensus size: 28
1375202 CTAGAATGTT
* *
1375212 CATCTTTTCAAAGCCCACACAAGTCGGTGG
1 CATCTCTTCAAAG-CC-CACAAGTCAGTGG
* *
1375242 CAACTCTTTTCAAAGCTCACAAGTCAGTGG
1 C-A-TCTCTTCAAAGCCCACAAGTCAGTGG
*
1375272 CATCTCTACAAAAGCCCACAAGTCAGTGG
1 CATCTCTTC-AAAGCCCACAAGTCAGTGG
* *
1375301 CA-CCCTTTCAAAGCCCACACAAGTCGGTGG
1 CATCTC-TTCAAAG-CC-CACAAGTCAGTGG
* *
1375331 CAACTCTTTTCAAAGCCCATAAGTCAGTGG
1 C-A-TCTCTTCAAAGCCCACAAGTCAGTGG
*
1375361 CATCTCTTCAAAAGCCCACAAGTCTGTGG
1 CATCTCTTC-AAAGCCCACAAGTCAGTGG
* * * ***
1375390 CA-C-C--CACAAG---TC-GGT-GGCAC
1 CATCTCTTCA-AAGCCCACAAGTCAGTGG
* * ** *** * * *
1375410 CCTTTC-AAAGCCCACACAAGTCGGCGG
1 CATCTCTTCAAAGCCCACAAGTCAGTGG
*
1375437 CAACTCTTTTCAAAGCCCACAAGTCAGTGG
1 C-A-TCTCTTCAAAGCCCACAAGTCAGTGG
* *
1375467 CATCTCTTCAAAAGACCACAAGTCGGTGG
1 CATCTCTTC-AAAGCCCACAAGTCAGTGG
* *
1375496 CA-CCCTTTCAAAGCCCACACAAGTCGGTGG
1 CATCTC-TTCAAAG-CC-CACAAGTCAGTGG
*
1375526 CAACTCTTTTCAAAGCCCACAAGTCAGTGG
1 C-A-TCTCTTCAAAGCCCACAAGTCAGTGG
* *
1375556 CTTCTCTTCAAAAGCTCACAAGTCAGTGG
1 CATCTCTTC-AAAGCCCACAAGTCAGTGG
* *
1375585 CACCAT-TTCAAAGTCCACACAAGTCGGTGG
1 CATC-TCTTCAAAG-CC-CACAAGTCAGTGG
*
1375615 CAACTCTTTTCAAAGCCCACAAGTCAGTGG
1 C-A-TCTCTTCAAAGCCCACAAGTCAGTGG
* * * *
1375645 CATCTCTTCAAAAGACCATAAGTTAGTGA
1 CATCTCTTC-AAAGCCCACAAGTCAGTGG
1375674 CATC-CTTTCAAAGCCCACAAGTCAGTGG
1 CATCTC-TTCAAAGCCCACAAGTCAGTGG
*
1375702 CATACCCTTTCAAAGCCCACAAGTCAGTGG
1 CAT-CTC-TTCAAAGCCCACAAGTCAGTGG
*
1375732 CA-CCCTTTCAAAGGCCACACAAGTC-GATGG
1 CATCTC-TTCAAA-GCC-CACAAGTCAG-TGG
* * * *
1375762 CAACTATTTTCAAAGCCCACATAAATCGGTGG
1 C-A-TCTCTTCAAAGCCCAC--AAGTCAGTGG
* *
1375794 CA-CCCTTCCAAAGCCCACAAGTCAGTGA
1 CATCTCTT-CAAAGCCCACAAGTCAGTGG
* *
1375822 CA-CCCTTTCAAAGCCCATAAGTCAGTGG
1 CATCTC-TTCAAAGCCCACAAGTCAGTGG
* *
1375850 CATACCCTTTCAAAGCCCACAAGTTAGTGG
1 CAT-CTC-TTCAAAGCCCACAAGTCAGTGG
* *
1375880 CATACCCTTTCAAAGCCCACACAAATCAGTGG
1 CAT-CTC-TTCAAAG-CC-CACAAGTCAGTGG
*
1375912 CA-CCCTTCCAAAGCCCACAAGTCAGTGG
1 CATCTCTT-CAAAGCCCACAAGTCAGTGG
* *
1375940 CA-CCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCTC-TTCAAAGCCCACAAGTCAGTGG
* *
1375968 CA-CCCTTTCAGAA-CCCATAAGTCAGTGG
1 CATCTC-TTCA-AAGCCCACAAGTCAGTGG
1375996 CA-CAT-TTCCAAAGCCCACAAGTCAGTGG
1 CATC-TCTT-CAAAGCCCACAAGTCAGTGG
1376024 CATC-CTTTCAAAGCCCACA
1 CATCTC-TTCAAAGCCCACA
1376043 CAAGTCGGTG
Statistics
Matches: 647, Mismatches: 90, Indels: 130
0.75 0.10 0.15
Matches are distributed among these distances:
20 2 0.00
21 2 0.00
22 2 0.00
23 1 0.00
24 1 0.00
25 5 0.01
26 2 0.00
27 9 0.01
28 198 0.31
29 138 0.21
30 205 0.32
31 19 0.03
32 60 0.09
33 3 0.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (28 bp):
CATCTCTTCAAAGCCCACAAGTCAGTGG
Found at i:1375373 original size:89 final size:85
Alignment explanation
Indices: 1375217--1376042 Score: 678
Period size: 89 Copynumber: 9.5 Consensus size: 85
1375207 ATGTTCATCT
* * * *
1375217 TTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCTCACAAGTCAGTGGCATCTCTACA
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTC-
1375282 AAAGCCCACAAGTCAGTGGCACCC
62 AAAGCCCACAAGTCAGTGGCACCC
* * *
1375306 TTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCATAAGTCAGTGGCATCTCTTCA
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTC-
*
1375371 AAAGCCCACAAGTCTGTGG-----
62 AAAGCCCACAAGTCAGTGGCACCC
* * * *
1375390 ---C--A-CCCACAAGTCGGTGGCAC-CCTTTCAAAGCCCACACAAGTCGGCGGCAACTCTTTTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-TCTCTTC
*
1375448 AAAGCCCACAAGTCAGTGGCA-TC
62 AAAGCCCACAAGTCAGTGGCACCC
* * * *
1375471 TCTTCAAAAGACCACAAGTCGGTGGCAC-CCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTT
1 T-TTC-AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-TCTCT
**
1375535 TCAAAGCCCACAAGTCAGTGGC-TTC
60 TCAAAGCCCACAAGTCAGTGGCACCC
* * * *
1375560 TCTTCAAAAGCTCACAAGTCAGTGGCAC-CATTTCAAAGTCCACACAAGTCGGTGGCAACTCTTT
1 T-TTC-AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-TCTCT
*
1375624 TCAAAGCCCACAAGTCAGTGGCA-TC
60 TCAAAGCCCACAAGTCAGTGGCACCC
* * * * *
1375649 TCTTCAAAAGACCATAAGTTAGTGACA-TCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTC
1 T-TTC-AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAT-CTC-TTC
1375713 AAAGCCCACAAGTCAGTGGCACCC
62 AAAGCCCACAAGTCAGTGGCACCC
** * * *
1375737 TTTCAAAGGCCACACAAGTC-GATGGCAACTATTTTCAAAGCCCACATAAATCGGTGGCA-CCCT
1 TTTCAAA-GCC-CACAAGTCAG-TGGC-ACTCCTTTCAAAGCCCAC--AAGTCAGTGGCATCTCT
*
1375800 TCCAAAGCCCACAAGTCAGTGACACCC
60 T-CAAAGCCCACAAGTCAGTGGCACCC
* * *
1375827 TTTCAAAGCCCATAAGTCAGTGGCA-TACCCTTTCAAAGCCCACAAGTTAGTGGCATACCCTTTC
1 TTTCAAAGCCCACAAGTCAGTGGCACT--CCTTTCAAAGCCCACAAGTCAGTGGCAT-CTC-TTC
*
1375891 AAAGCCCACACAAATCAGTGGCACCC
62 AAAG-CC-CACAAGTCAGTGGCACCC
* * *
1375917 TTCCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCA-CCCTTTCAGA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATCTC-TTCA-A
* *
1375980 A-CCCATAAGTCAGTGGCA-CA
64 AGCCCACAAGTCAGTGGCACCC
1376000 TTTCCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACA
1 TTT-CAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA
1376043 CAAGTCGGTG
Statistics
Matches: 645, Mismatches: 50, Indels: 89
0.82 0.06 0.11
Matches are distributed among these distances:
74 9 0.01
75 4 0.01
76 25 0.04
77 21 0.03
78 6 0.01
79 1 0.00
81 1 0.00
83 3 0.00
84 51 0.08
85 4 0.01
86 23 0.04
87 46 0.07
88 73 0.11
89 281 0.44
90 87 0.13
92 10 0.02
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.21
Consensus pattern (85 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAG
CCCACAAGTCAGTGGCACCC
Found at i:1375397 original size:17 final size:17
Alignment explanation
Indices: 1375375--1375411 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1375365 TCTTCAAAAG
*
1375375 CCCACAAGTCTGTGGCA
1 CCCACAAGTCGGTGGCA
1375392 CCCACAAGTCGGTGGCA
1 CCCACAAGTCGGTGGCA
1375409 CCC
1 CCC
1375412 TTTCAAAGCC
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:0.22, C:0.41, G:0.24, T:0.14
Consensus pattern (17 bp):
CCCACAAGTCGGTGGCA
Found at i:1375429 original size:30 final size:28
Alignment explanation
Indices: 1375392--1376042 Score: 630
Period size: 30 Copynumber: 22.2 Consensus size: 28
1375382 GTCTGTGGCA
*
1375392 CCCACAAGTCGGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCACCCTTTCAAAG
* * *
1375420 CCCACACAAGTCGGCGGCAACTCTTTTCAAAG
1 -CC-CACAAGTCAGTGGC-AC-CCTTTCAAAG
*
1375452 CCCACAAGTCAGTGGCA-TCTCTTCAAAAG
1 CCCACAAGTCAGTGGCACCCT-TTC-AAAG
* *
1375481 ACCACAAGTCGGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCACCCTTTCAAAG
* *
1375509 CCCACACAAGTCGGTGGCAACTCTTTTCAAAG
1 -CC-CACAAGTCAGTGGC-AC-CCTTTCAAAG
**
1375541 CCCACAAGTCAGTGGC-TTCTCTTCAAAAG
1 CCCACAAGTCAGTGGCACCCT-TTC-AAAG
* *
1375570 CTCACAAGTCAGTGGCACCATTTCAAAG
1 CCCACAAGTCAGTGGCACCCTTTCAAAG
* *
1375598 TCCACACAAGTCGGTGGCAACTCTTTTCAAAG
1 -CC-CACAAGTCAGTGGC-AC-CCTTTCAAAG
*
1375630 CCCACAAGTCAGTGGCA-TCTCTTCAAAAG
1 CCCACAAGTCAGTGGCACCCT-TTC-AAAG
* * * * *
1375659 ACCATAAGTTAGTGACATCCTTTCAAAG
1 CCCACAAGTCAGTGGCACCCTTTCAAAG
1375687 CCCACAAGTCAGTGGCATACCCTTTCAAAG
1 CCCACAAGTCAGTGGC--ACCCTTTCAAAG
1375717 CCCACAAGTCAGTGGCACCCTTTCAAAGG
1 CCCACAAGTCAGTGGCACCCTTTCAAA-G
**
1375746 CCACACAAGTC-GATGGCAACTATTTTCAAAG
1 CC-CACAAGTCAG-TGGC-AC-CCTTTCAAAG
* * *
1375777 CCCACATAAATCGGTGGCACCCTTCCAAAG
1 CCCAC--AAGTCAGTGGCACCCTTTCAAAG
*
1375807 CCCACAAGTCAGTGACACCCTTTCAAAG
1 CCCACAAGTCAGTGGCACCCTTTCAAAG
*
1375835 CCCATAAGTCAGTGGCATACCCTTTCAAAG
1 CCCACAAGTCAGTGGC--ACCCTTTCAAAG
*
1375865 CCCACAAGTTAGTGGCATACCCTTTCAAAG
1 CCCACAAGTCAGTGGC--ACCCTTTCAAAG
* *
1375895 CCCACACAAATCAGTGGCACCCTTCCAAAG
1 -CC-CACAAGTCAGTGGCACCCTTTCAAAG
1375925 CCCACAAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCACCCTTTCAAAG
*
1375953 CCCACAAGTTAGTGGCACCCTTTCAGAA-
1 CCCACAAGTCAGTGGCACCCTTTCA-AAG
* *
1375981 CCCATAAGTCAGTGGCA-CATTTCCAAAG
1 CCCACAAGTCAGTGGCACCCTTT-CAAAG
*
1376009 CCCACAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCACCCTTTCAAAG
1376037 CCCACA
1 CCCACA
1376043 CAAGTCGGTG
Statistics
Matches: 524, Mismatches: 60, Indels: 77
0.79 0.09 0.12
Matches are distributed among these distances:
27 9 0.02
28 169 0.32
29 82 0.16
30 188 0.36
31 21 0.04
32 54 0.10
33 1 0.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.20
Consensus pattern (28 bp):
CCCACAAGTCAGTGGCACCCTTTCAAAG
Found at i:1375471 original size:106 final size:106
Alignment explanation
Indices: 1375286--1375500 Score: 385
Period size: 106 Copynumber: 2.0 Consensus size: 106
1375276 TCTACAAAAG
* *
1375286 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCAT
1 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGCGGCAACTCTTTTCAAAGCCCAC
* *
1375351 AAGTCAGTGGCATCTCTTCAAAAGCCCACAAGTCTGTGGCA
66 AAGTCAGTGGCATCTCTTCAAAAGACCACAAGTCGGTGGCA
*
1375392 CCCACAAGTCGGTGGCACCCTTTCAAAGCCCACACAAGTCGGCGGCAACTCTTTTCAAAGCCCAC
1 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGCGGCAACTCTTTTCAAAGCCCAC
1375457 AAGTCAGTGGCATCTCTTCAAAAGACCACAAGTCGGTGGCA
66 AAGTCAGTGGCATCTCTTCAAAAGACCACAAGTCGGTGGCA
1375498 CCC
1 CCC
1375501 TTTCAAAGCC
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (106 bp):
CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGCGGCAACTCTTTTCAAAGCCCAC
AAGTCAGTGGCATCTCTTCAAAAGACCACAAGTCGGTGGCA
Found at i:1375552 original size:195 final size:195
Alignment explanation
Indices: 1375217--1375588 Score: 663
Period size: 195 Copynumber: 1.9 Consensus size: 195
1375207 ATGTTCATCT
* *
1375217 TTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCTCACAAGTCAGTGGCATCTCTACA
1 TTTCAAAGCCCACACAAGTCGGCGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTACA
*
1375282 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGC
66 AAAGACCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGC
* *
1375347 CCATAAGTCAGTGGCATCTCTTCAAAAGCCCACAAGTCTGTGGCACCCACAAGTCGGTGGCACCC
131 CCACAAGTCAGTGGCATCTCTTCAAAAGCCCACAAGTCAGTGGCACCCACAAGTCGGTGGCACCC
*
1375412 TTTCAAAGCCCACACAAGTCGGCGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCA
1 TTTCAAAGCCCACACAAGTCGGCGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTACA
*
1375477 AAAGACCACAAGTCGGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGC
66 AAAGACCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGC
* *
1375542 CCACAAGTCAGTGGCTTCTCTTCAAAAGCTCACAAGTCAGTGGCACC
131 CCACAAGTCAGTGGCATCTCTTCAAAAGCCCACAAGTCAGTGGCACC
1375589 ATTTCAAAGT
Statistics
Matches: 168, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
195 168 1.00
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.21
Consensus pattern (195 bp):
TTTCAAAGCCCACACAAGTCGGCGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTACA
AAAGACCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGC
CCACAAGTCAGTGGCATCTCTTCAAAAGCCCACAAGTCAGTGGCACCCACAAGTCGGTGGCACCC
Found at i:1376078 original size:25 final size:26
Alignment explanation
Indices: 1376028--1376079 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1376018 CAGTGGCATC
*
1376028 CTTTCAAAGCCCACACAAGTCGGTGG
1 CTTTCAAAGCCCACACAAGTCAGTGG
* *
1376054 CTTT-AAAGCCCACATAAGTTAGTGG
1 CTTTCAAAGCCCACACAAGTCAGTGG
1376079 C
1 C
1376080 ACCTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (26 bp):
CTTTCAAAGCCCACACAAGTCAGTGG
Found at i:1376096 original size:33 final size:34
Alignment explanation
Indices: 1376058--1376121 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
1376048 CGGTGGCTTT
* * *
1376058 AAAGCCCACATAAGTTAGTGGC-ACCTTTTTTTA
1 AAAGCCCACACAAGTCAATGGCAACCTTTTTTTA
1376091 AAAGCCCACACAAGTCAATGGCAACCTTTTT
1 AAAGCCCACACAAGTCAATGGCAACCTTTTT
1376122 CAGATCACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 19 0.70
34 8 0.30
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (34 bp):
AAAGCCCACACAAGTCAATGGCAACCTTTTTTTA
Found at i:1376217 original size:48 final size:48
Alignment explanation
Indices: 1376156--1376468 Score: 491
Period size: 48 Copynumber: 6.5 Consensus size: 48
1376146 AAGTTCGATA
**
1376156 TCGCTGGTGTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
1376204 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
*
1376252 TCGCTGGCCTTGAATCAGGACATTGTCCACTTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
* *
1376300 TCGCTGGCCTTGAATCAGCATATTGTCCACTTTTCCCTCAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
* * * *
1376348 CCGCTGGCCTTGAATCAGTACATTATCCACTTTTCCCTTAGCTCCATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
* * *
1376396 TCGCTGGCCTTGAATCAGCACGTTGTCCATTTTTCCCTTAGCTCGATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
* **
1376444 TCGTTGGCCTTGAATTGGCACATTG
1 TCGCTGGCCTTGAATCAGCACATTG
1376469 GCACTCTTCT
Statistics
Matches: 243, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 243 1.00
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (48 bp):
TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
Found at i:1384457 original size:21 final size:20
Alignment explanation
Indices: 1384431--1384469 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1384421 AGGTCAAAAT
1384431 CCTAGAAAGTATCGATACACA
1 CCTAG-AAGTATCGATACACA
*
1384452 CCTAGATGTATCGATACA
1 CCTAGAAGTATCGATACA
1384470 TATTGCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CCTAGAAGTATCGATACACA
Found at i:1389774 original size:20 final size:20
Alignment explanation
Indices: 1389687--1389875 Score: 110
Period size: 20 Copynumber: 8.7 Consensus size: 20
1389677 GTTTAACTAG
1389687 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
1389707 ATAGAATCTATCGAT-CATTGAAGA
1 AT-G----TATCGATACATTGAAAA
* * * *
1389731 ATGTATCGATACAGTCATAC
1 ATGTATCGATACATTGAAAA
*
1389751 ATGTATTGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
1389771 ATGTATCAATACATCTTGCTAAAAAGATAGA
1 ATGTATCGATACA--TTG------A-A-A-A
* *
1389802 ATGTATTGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
1389822 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
1389842 ATGTATCGATAAATTGAAAA
1 ATGTATCGATACATTGAAAA
1389862 ATGTATCGATACAT
1 ATGTATCGATACAT
1389876 CTGGGTAAAA
Statistics
Matches: 126, Mismatches: 26, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
19 7 0.06
20 77 0.61
21 1 0.01
22 4 0.03
23 2 0.02
24 10 0.08
25 7 0.06
28 1 0.01
29 4 0.03
30 1 0.01
31 12 0.10
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:1389877 original size:91 final size:89
Alignment explanation
Indices: 1389703--1389886 Score: 278
Period size: 91 Copynumber: 2.0 Consensus size: 89
1389693 CGATACATTG
* *
1389703 AAAAATAGAATCTATCGATCATTGAAGAATGTATCGATACAGTCATACATGTATTGATACATTGA
1 AAAAATAGAATCTATCGATCATTGAAGAATGTATCGATACAGTCATACATGTATCGATAAATTGA
*
1389768 AAAATGTATCAATACATCTTGCTA
66 AAAATGTATCAATACATCTGGCTA
* * *
1389792 AAAAGATAGAATGTATTGATACATTGAAGAATGTATCGATACATTCATACATGTATCGATAAATT
1 AAAA-ATAGAATCTATCGAT-CATTGAAGAATGTATCGATACAGTCATACATGTATCGATAAATT
* *
1389857 GAAAAATGTATCGATACATCTGGGTA
64 GAAAAATGTATCAATACATCTGGCTA
1389883 AAAA
1 AAAA
1389887 TGTGATTTTC
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
89 4 0.05
90 13 0.15
91 68 0.80
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (89 bp):
AAAAATAGAATCTATCGATCATTGAAGAATGTATCGATACAGTCATACATGTATCGATAAATTGA
AAAATGTATCAATACATCTGGCTA
Found at i:1391079 original size:20 final size:20
Alignment explanation
Indices: 1391054--1391091 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1391044 TATCACTATT
1391054 TGTATCGATACATGGTATAA
1 TGTATCGATACATGGTATAA
*
1391074 TGTATCGATACATTGTAT
1 TGTATCGATACATGGTAT
1391092 CGATACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATGGTATAA
Found at i:1391090 original size:13 final size:13
Alignment explanation
Indices: 1391074--1391099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1391064 CATGGTATAA
1391074 TGTATCGATACAT
1 TGTATCGATACAT
1391087 TGTATCGATACAT
1 TGTATCGATACAT
1391100 GAAGAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1391090 original size:33 final size:32
Alignment explanation
Indices: 1391053--1391119 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
1391043 CTATCACTAT
1391053 TTGTATCGATACATG-GTATAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
1391086 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
1391119 T
1 T
1391120 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:1397444 original size:24 final size:22
Alignment explanation
Indices: 1397417--1397461 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1397407 TCATCAAATT
*
1397417 TTCAACAAATTTTCACTTTTTCAC
1 TTCAA-AAACTTTCA-TTTTTCAC
*
1397441 TTCAAATACTTTCATTTTTCA
1 TTCAAAAACTTTCATTTTTCA
1397462 TCAAAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (22 bp):
TTCAAAAACTTTCATTTTTCAC
Found at i:1399757 original size:20 final size:19
Alignment explanation
Indices: 1399734--1399804 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
1399724 CACCCAGATG
1399734 TATCGATACATGCTGCATTC
1 TATCGATACATG-TGCATTC
* *
1399754 TATCGATACATGTTCATTG
1 TATCGATACATGTGCATTC
*
1399773 TATCGATACATG-GACAATTG
1 TATCGATACATGTG-C-ATTC
1399793 TATCGATACATG
1 TATCGATACATG
1399805 AAACTGGCAG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 18 0.39
20 28 0.61
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (19 bp):
TATCGATACATGTGCATTC
Found at i:1399878 original size:33 final size:32
Alignment explanation
Indices: 1399833--1399896 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
1399823 CTATCACAAT
1399833 TTGTATCAATACATG-GTATAATGTATCGATATA
1 TTGTATCAATACATGAG-A-AATGTATCGATATA
*
1399866 TTGTATCGATACATGAAGAAATGTATCGATA
1 TTGTATCAATACATG-AGAAATGTATCGATA
1399897 CATAGCTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (32 bp):
TTGTATCAATACATGAGAAATGTATCGATATA
Found at i:1400899 original size:29 final size:29
Alignment explanation
Indices: 1400714--1402154 Score: 785
Period size: 28 Copynumber: 49.9 Consensus size: 29
1400704 CTAACTTATT
* *
1400714 TGGGCATTG-AAATGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
1400742 TGGGTTTTG-AAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
1400770 TGGGCTTTG-AAATGATGCCACTAACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
1400798 TGAGCTTTG-AAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
1400826 TGGGCTTTGAAAA-GATGCCACTGATTTGTG
1 TGGGCTTTGAAAAGGATGCCACTGA-CT-TG
* *
1400856 TGGGCTTTGAGAAGGATGCGACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
1400885 TGGGCTTTGAAAAGGATGCCATTGATTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
1400914 TGGGCTTTGAGAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
1400943 TGGGCTTTG-AAAGGATGCCACTGACTTA
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
1400971 TGGG-TTTG-AAAGGATGCCACTAACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
1400998 TGGGCTTTG-AAATGATGCCACTGATTTGTG
1 TGGGCTTTGAAAAGGATGCCACTGA-CT-TG
* *
1401028 TGGGCTTTGAGAAGGATGCCACTAACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
1401057 TGGGCTTTGAGAGGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
1401086 TGGGCTTTGAGAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* **
1401115 TGGGCATTG-AAAGGATATCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * *
1401143 TGGGCTTTGAAATGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAAA-AGGATGCCACTGAC-T-TG
* * *
1401175 TGGGCTTTGAGAAGGATGCCATTGATTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
1401204 TGGGCTTTGAGAAGGATGCCACT-ACCTTG
1 TGGGCTTTGAAAAGGATGCCACTGA-CTTG
* ** * *
1401233 TGAGCTTTGATATGGGCTACCACTGACTTGTG
1 TGGGCTTTGA-AAAGGATGCCACTGAC-T-TG
* * *
1401265 TGGGCTTTGAAATGGGTTGCTACTGACTTGTG
1 TGGGCTTTGAAA-AGGATGCCACTGAC-T-TG
* * * * * *
1401297 TGGGCTTTTAAATGGGTTACCACCGA-TTCA
1 TGGGCTTTGAAA-AGGATGCCACTGACTT-G
*
1401327 TGGGCTTTGAGAAA-GATGCTACTGACTTG
1 TGGGCTTTGA-AAAGGATGCCACTGACTTG
* * * * *
1401356 TTGGCTTTGAAATGGGTTACCACCGACTTGTG
1 TGGGCTTTGAAA-AGGATGCCACTGAC-T-TG
* * *
1401388 TGGGCTTTGAAATGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAAA-AGGATGCCACTGAC-T-TG
* * * *
1401420 TGGGCTTTCAAATGGGTTGCCACCGACTTG
1 TGGGCTTTGAAA-AGGATGCCACTGACTTG
* * *
1401450 TATGGGCTTTGAAATGGGTTGCCACCGACTTGTG
1 --TGGGCTTTGAAA-AGGATGCCACTGAC-T-TG
* * *
1401484 TGGGCTTTGAAATGGGTTGCCACCGACTTTTG
1 TGGGCTTTGAAA-AGGATGCCACTGAC--TTG
* * * * * *
1401516 TGGGTTTTCAAATGAGTTACCACCGACTTGTG
1 TGGGCTTTGAAAAG-GATGCCACTGAC-T-TG
*
1401548 TGGGCTTTGAACTA--ATGCCACTGACTTG
1 TGGGCTTTGAA-AAGGATGCCACTGACTTG
* * *
1401576 TGGGC-TTAAAAAGGGGTACCACTGACTTG
1 TGGGCTTTGAAAA-GGATGCCACTGACTTG
* *
1401605 TGGGCTTTG-GAA-GAGTGCCACTGACTTA
1 TGGGCTTTGAAAAGGA-TGCCACTGACTTG
* * *
1401633 TGGGC-TTAAAAAGGATGCCA-TGAAGTTA
1 TGGGCTTTGAAAAGGATGCCACTG-ACTTG
* * *
1401661 TGGACTTTGGAAAGG-TGCCACTCACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
1401689 TGGGGC-TTAAAAAGGATGCCA-TGAAGTTG
1 T-GGGCTTTGAAAAGGATGCCACTG-ACTTG
* * *
1401718 TGGAC-TT-AAAAGGATGCCA-TAAAGTTG
1 TGGGCTTTGAAAAGGATGCCACT-GACTTG
* *
1401745 TGGAC-TT-AAAA-GAGTGCCAC-GAAGTTG
1 TGGGCTTTGAAAAGGA-TGCCACTG-ACTTG
* * * *
1401772 TGGAC-TT-AAAAGGGTGCCACGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * * *
1401799 TGGACTTT-AAAAGAATGCCACGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * ** *
1401827 TGGAC-TTGAAATGGATGCCA-TGGGGTTA
1 TGGGCTTTGAAAAGGATGCCACT-GACTTG
* * * *
1401855 TGGAC-TTAAAAAGG-TGCCACAGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
1401882 TGGAC-TT-AAAAGGATGCCA-TAGAGTTG
1 TGGGCTTTGAAAAGGATGCCACT-GACTTG
** * * * *
1401909 T-GAATTTAAAAAGG-TGCCACGGAGTGG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * * * *
1401936 TGGACTTT-AAAAGAATGCCACGGAGTTA
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * * * *
1401964 TGGAC-TTGAAATGAATGCCACGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * ** *
1401992 TGGAC-TT-AAAAGGGTGCCACCCAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * *
1402019 TGGAC-TT-AAAAGGATGCCACGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * *
1402046 TGGACTTT-AAAAGGTTGCCA-TGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACT-GACTTG
* *
1402074 TGGACTTT-AAAAGGATGCCAC-GAAGTTG
1 TGGGCTTTGAAAAGGATGCCACTG-ACTTG
* * *
1402102 TGGAC-TT-AAAAGGATGCCACGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
1402129 TGGACTTTGAAAAGAAATGCCACTGA
1 TGGGCTTTGAAAAG-GATGCCACTGA
1402155 ATCGTGGACT
Statistics
Matches: 1182, Mismatches: 159, Indels: 142
0.80 0.11 0.10
Matches are distributed among these distances:
26 11 0.01
27 220 0.19
28 375 0.32
29 235 0.20
30 87 0.07
31 42 0.04
32 207 0.18
33 3 0.00
34 2 0.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.29
Consensus pattern (29 bp):
TGGGCTTTGAAAAGGATGCCACTGACTTG
Found at i:1401017 original size:172 final size:171
Alignment explanation
Indices: 1400714--1401692 Score: 759
Period size: 172 Copynumber: 5.5 Consensus size: 171
1400704 CTAACTTATT
* * *
1400714 TGGGCATTG-AAATGATGCCACTGACTTGTGGGTTTTGA-AAGGATGCCACTGACTTGTGGGCTT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTT
* * *
1400777 TGAAATGATGCCACTAACTTGTGAGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAT
66 TGAAAGGATGCCACTGACTTGTG-GGTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAT
*
1400842 GCCACTGATTTGTGTGGGCTTTGAGAAGGATGCGACTGACTTG
130 GCCACTGATTTGTGTGGGCTTTGAGAAGGATGCCACT-ACTTG
* *
1400885 TGGGCTTTGAAAAGGATGCCATTGATTTGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTT
* * *
1400950 TGAAAGGATGCCACTGACTTATGGGTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAATGATG
66 TGAAAGGATGCCACTGACTTGTGGGTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATG
1401015 CCACTGATTTGTGTGGGCTTTGAGAAGGATGCCACTAACTTG
131 CCACTGATTTGTGTGGGCTTTGAGAAGGATGCCACT-ACTTG
* * *
1401057 TGGGCTTTGAGAGGGATGCCACTGACTTGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCAT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTT
** * *
1401122 TGAAAGGATATCACTGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAGA
66 TGAAAGGATGCCACTGACTTGTGGG-TTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTGA-A
* *
1401187 AGGATGCCATTGA-TT-TGTGGGCTTTGAGAAGGATGCCACTACCTTG
125 AAGATGCCACTGATTTGTGTGGGCTTTGAGAAGGATGCCACTA-CTTG
* ** * * * *
1401233 TGAGCTTTGATATGGGCTACCACTGACTTGTGTGGGCTTTGA-AATGGGTTGCTACTGACTTGTG
1 TGGGCTTTGA-AAAGGATGCCACTGAC-T-TGTGGGCTTTGAGAA--GGATGCCACTGAC-T-TG
* * * * * * * *
1401297 TGGGCTTTTAAATGGGTTACCACCGA-TTCATGGGCTTTGAGAAAGATGCTACTGACTTGTTGGC
59 TGGGCTTTGAAA--GGATGCCACTGACTT-GTGGG-TTTGA-AAGGATGCCACTGACTTGTGGGC
* * * * * * *
1401361 TTTGAAATGGGTTACCACCGACTTGTGTGGGCTTTGA-AATGGGTTGCCACCGACTTGTG
119 TTTGAAA--AGATGCCACTGATTTGTGTGGGCTTTGAGAA--GGATGCCA-CTAC-T-TG
* * * * * *
1401420 TGGGCTTTCAAATGGGTTGCCACCGACTTGTATGGGCTTTGA-AATGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAAA-AGGATGCCACTGACTTG--TGGGCTTTGAGAA--GGATGCCACTGAC-T-TG
* * * * * *
1401484 TGGGCTTTGAAATGGGTTGCCACCGACTTTTGTGGGTTTTCAAATGAGTTACCACCGACTTGTGT
59 TGGGCTTTGAAA--GGATGCCACTGAC--TTGTGGG-TTTGAAA-G-GATGCCACTGAC-T-TGT
* * * * * *
1401549 GGGCTTTGAACTA-ATGCCACTGA-CT-TGTGGGC-TTAAAAAGGGGTACCACTGACTTG
115 GGGCTTTGAA-AAGATGCCACTGATTTGTGTGGGCTTTGAGAA-GGATGCCACT-ACTTG
* * * * * * *
1401605 TGGGCTTTG-GAA-GAGTGCCACTGACTTATGGGC-TTAAAAAGGATGCCA-TGAAGTTATGGAC
1 TGGGCTTTGAAAAGGA-TGCCACTGACTTGTGGGCTTTGAGAAGGATGCCACTG-ACTTGTGGGC
*
1401666 TTTGGAAAGG-TGCCACTCACTTGTGGG
64 TTT-GAAAGGATGCCACTGACTTGTGGG
1401693 GCTTAAAAAG
Statistics
Matches: 669, Mismatches: 93, Indels: 90
0.79 0.11 0.11
Matches are distributed among these distances:
171 8 0.01
172 186 0.28
173 59 0.09
175 19 0.03
176 41 0.06
177 34 0.05
178 21 0.03
179 20 0.03
180 16 0.02
181 19 0.03
182 22 0.03
183 26 0.04
184 32 0.05
185 22 0.03
186 7 0.01
187 87 0.13
188 11 0.02
189 9 0.01
190 17 0.03
191 1 0.00
192 12 0.02
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (171 bp):
TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTT
TGAAAGGATGCCACTGACTTGTGGGTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATG
CCACTGATTTGTGTGGGCTTTGAGAAGGATGCCACTACTTG
Found at i:1401180 original size:32 final size:29
Alignment explanation
Indices: 1400694--1401736 Score: 765
Period size: 29 Copynumber: 35.4 Consensus size: 29
1400684 CTTTTAAAAA
* * *
1400694 AAAGG-TGCCACTAACTTATTTGGGCATTG
1 AAAGGATGCCACTGACTT-TGTGGGCTTTG
* *
1400723 AAATGATGCCACTGAC-TTGTGGGTTTTG
1 AAAGGATGCCACTGACTTTGTGGGCTTTG
1400751 AAAGGATGCCACTGAC-TTGTGGGCTTTG
1 AAAGGATGCCACTGACTTTGTGGGCTTTG
* * *
1400779 AAATGATGCCACTAAC-TTGTGAGCTTTG
1 AAAGGATGCCACTGACTTTGTGGGCTTTG
1400807 AAAGGATGCCACTGAC-TTGTGGGCTTTG
1 AAAGGATGCCACTGACTTTGTGGGCTTTG
* *
1400835 AAAAGATGCCACTGATTTGTGTGGGCTTTG
1 AAAGGATGCCACTGACTT-TGTGGGCTTTG
*
1400865 AGAAGGATGCGACTGAC-TTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTTGTGGGCTTTG
*
1400894 AAAAGGATGCCATTGA-TTTGTGGGCTTTG
1 -AAAGGATGCCACTGACTTTGTGGGCTTTG
1400923 AGAAGGATGCCACTGAC-TTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTTGTGGGCTTTG
*
1400952 AAAGGATGCCACTGAC-TTATGGG-TTTG
1 AAAGGATGCCACTGACTTTGTGGGCTTTG
*
1400979 AAAGGATGCCACTAAC-TTGTGGGCTTTG
1 AAAGGATGCCACTGACTTTGTGGGCTTTG
* *
1401007 AAATGATGCCACTGATTTGTGTGGGCTTTG
1 AAAGGATGCCACTGACTT-TGTGGGCTTTG
*
1401037 AGAAGGATGCCACTAAC-TTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTTGTGGGCTTTG
*
1401066 AGAGGGATGCCACTGAC-TTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTTGTGGGCTTTG
*
1401095 AGAAGGATGCCACTGAC-TTGTGGGCATTG
1 A-AAGGATGCCACTGACTTTGTGGGCTTTG
**
1401124 AAAGGATATCACTGAC-TTGTGGGCTTTG
1 AAAGGATGCCACTGACTTTGTGGGCTTTG
* *
1401152 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--GGATGCCACTGACTT-TGTGGGCTTTG
*
1401184 AGAAGGATGCCATTGA-TTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTTGTGGGCTTTG
* *
1401213 AGAAGGATGCCACT-ACCTTGTGAGCTTTG
1 A-AAGGATGCCACTGACTTTGTGGGCTTTG
* * *
1401242 ATATGGGCTACCACTGACTTGTGTGGGCTTTG
1 A-A-AGGATGCCACTGACTT-TGTGGGCTTTG
* * *
1401274 AAATGGGTTGCTACTGACTTGTGTGGGCTTTT
1 AAA--GGATGCCACTGACTT-TGTGGGCTTTG
* * * **
1401306 AAATGGGTTACCACCGA-TTCATGGGCTTTG
1 AAA--GGATGCCACTGACTTTGTGGGCTTTG
* * *
1401336 AGAAAGATGCTACTGAC-TTGTTGGCTTTG
1 A-AAGGATGCCACTGACTTTGTGGGCTTTG
* * *
1401365 AAATGGGTTACCACCGACTTGTGTGGGCTTTG
1 AAA--GGATGCCACTGACTT-TGTGGGCTTTG
* * *
1401397 AAATGGGTTGCCACCGACTTGTGTGGGCTTTC
1 AAA--GGATGCCACTGACTT-TGTGGGCTTTG
* * *
1401429 AAATGGGTTGCCACCGACTTGTATGGGCTTTG
1 AAA--GGATGCCACTGACTT-TGTGGGCTTTG
* *
1401461 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--GGATGCCACTGACTT-TGTGGGCTTTG
* * * *
1401493 AAATGGGTTGCCACCGACTTTTGTGGGTTTTC
1 AAA--GGATGCCACTGAC-TTTGTGGGCTTTG
* * *
1401525 AAATGAGTTACCACCGACTTGTGTGGGCTTTG
1 AAA-G-GATGCCACTGACTT-TGTGGGCTTTG
*** **
1401557 AACTAATGCCACTGAC-TTGTGGGCTTAA
1 AAAGGATGCCACTGACTTTGTGGGCTTTG
* *
1401585 AAAGGGGTACCACTGAC-TTGTGGGCTTTG
1 AAA-GGATGCCACTGACTTTGTGGGCTTTG
* * **
1401614 GAA-GAGTGCCACTGAC-TTATGGGCTTAA
1 AAAGGA-TGCCACTGACTTTGTGGGCTTTG
** * *
1401642 AAAGGATGCCA-TGAAGTTATGGACTTTGG
1 AAAGGATGCCACTGACTTTGTGGGCTTT-G
* **
1401671 AAAGG-TGCCACTCAC-TTGTGGGGCTTAA
1 AAAGGATGCCACTGACTTTGT-GGGCTTTG
** * *
1401699 AAAGGATGCCA-TGAAGTTGTGGAC-TTA
1 AAAGGATGCCACTGACTTTGTGGGCTTTG
1401726 AAAGGATGCCA
1 AAAGGATGCCA
1401737 TAAAGTTGTG
Statistics
Matches: 848, Mismatches: 125, Indels: 84
0.80 0.12 0.08
Matches are distributed among these distances:
27 42 0.05
28 230 0.27
29 233 0.27
30 80 0.09
31 46 0.05
32 213 0.25
33 4 0.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (29 bp):
AAAGGATGCCACTGACTTTGTGGGCTTTG
Found at i:1401318 original size:64 final size:63
Alignment explanation
Indices: 1400731--1401558 Score: 532
Period size: 64 Copynumber: 13.9 Consensus size: 63
1400721 TGAAATGATG
* * * *
1400731 CCACTGAC-TTGTGGGTTTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTGAAAT--GATG
1 CCACTGACTTTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* * * * * *
1400787 CCACTAAC-TTGTGAGCTTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTGAAA--AGATG
1 CCACTGACTTTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* * * * * *
1400843 CCACTGATTTGTGTGGGCTTTGAGAA--GGATGCGACTGAC-T-TGTGGGCTTTGAAA-AGGATG
1 CCACTGACTT-TGTGGGCTTTGA-AATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* * * *
1400903 CCATTGA-TTTGTGGGCTTTGAGAA--GGATGCCACTGAC-T-TGTGGGCTTTGAAA--GGATG
1 CCACTGACTTTGTGGGCTTTGA-AATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* * * * *
1400960 CCACTGAC-TTATGGG-TTTGAAA--GGATGCCACTAAC-T-TGTGGGCTTTGAAAT--GATG
1 CCACTGACTTTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* * * * * *
1401015 CCACTGATTTGTGTGGGCTTTGAGAA--GGATGCCACTAAC-T-TGTGGGCTTTGAGA-GGGATG
1 CCACTGACTT-TGTGGGCTTTGA-AATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* * *
1401075 CCACTGAC-TTGTGGGCTTTGAGAA--GGATGCCACTGAC-T-TGTGGGCATTGAAA--GGATA
1 CCACTGACTTTGTGGGCTTTGA-AATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* * * *
1401132 TCACTGAC-TTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAGAA--GGATG
1 CCACTGACTTTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGA-AATGGGTTA
* * * * * *
1401193 CCATTGA-TTTGTGGGCTTTGAGAA--GGATGCCACT-ACCT-TGTGAGCTTTGATATGGGCTA
1 CCACTGACTTTGTGGGCTTTGA-AATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* *
1401252 CCACTGACTTGTGTGGGCTTTGAAATGGGTTGCTACTGACTTGTGTGGGCTTTTAAATGGGTTA
1 CCACTGACTT-TGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* ** * * *
1401316 CCACCGA-TTCATGGGCTTTGAGAA--AGATGCTACTGACTTGT-T-GGCTTTGAAATGGGTTA
1 CCACTGACTTTGTGGGCTTTGA-AATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* * * *
1401375 CCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAATGGGTTG
1 CCACTGACTT-TGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* * * *
1401439 CCACCGACTTGTATGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTG
1 CCACTGACTT-TGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
* * * * * *
1401503 CCACCGACTTTTGTGGGTTTTCAAATGAGTTACCACCGACTTGTGTGGGCTTTGAA
1 CCACTGAC-TTTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAA
1401559 CTAATGCCAC
Statistics
Matches: 672, Mismatches: 64, Indels: 64
0.84 0.08 0.08
Matches are distributed among these distances:
55 40 0.06
56 66 0.10
57 48 0.07
58 120 0.18
59 97 0.14
60 49 0.07
61 61 0.09
62 33 0.05
63 8 0.01
64 148 0.22
65 2 0.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.32
Consensus pattern (63 bp):
CCACTGACTTTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTA
Found at i:1401624 original size:57 final size:56
Alignment explanation
Indices: 1401546--1401720 Score: 178
Period size: 57 Copynumber: 3.1 Consensus size: 56
1401536 CACCGACTTG
* *
1401546 TGTGGGCTTT-GAACTAATGCCACTGACTTGTGGGCTTAAAAAGGGGTACCACTG-ACT
1 TGTGGGCTTTGGAA--AGTGCCACTGACTTGTGGGCTTAAAAAGGGATACCA-TGAACT
* * *
1401603 TGTGGGCTTTGGAAGAGTGCCACTGACTTATGGGCTTAAAAA-GGATGCCATGAAGT
1 TGTGGGCTTTGGAA-AGTGCCACTGACTTGTGGGCTTAAAAAGGGATACCATGAACT
* * * * *
1401659 TATGGACTTTGGAAAGGTGCCACTCACTTGTGGGGCTTAAAAA-GGATGCCATGAAGT
1 TGTGGGCTTTGGAAA-GTGCCACTGACTTGT-GGGCTTAAAAAGGGATACCATGAACT
1401716 TGTGG
1 TGTGG
1401721 ACTTAAAAGG
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
55 3 0.03
56 33 0.32
57 64 0.62
58 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (56 bp):
TGTGGGCTTTGGAAAGTGCCACTGACTTGTGGGCTTAAAAAGGGATACCATGAACT
Found at i:1401722 original size:57 final size:56
Alignment explanation
Indices: 1401563--1402108 Score: 225
Period size: 55 Copynumber: 9.9 Consensus size: 56
1401553 TTTGAACTAA
* * * *
1401563 TGCCACTGACTTGTGGGCTTAAAAAGGGGTACCACTG-ACTTGTGGGCTTTGGAAGAG
1 TGCCACTGACTTGTGGGCTTAAAAA-GGATGCCA-TGAAGTTGTGGACTTTGGAAGAG
* *
1401620 TGCCACTGACTTATGGGCTTAAAAAGGATGCCATGAAGTTATGGACTTTGGAA-AGG
1 TGCCACTGACTTGTGGGCTTAAAAAGGATGCCATGAAGTTGTGGACTTTGGAAGA-G
* **
1401676 TGCCACTCACTTGTGGGGCTTAAAAAGGATGCCATGAAGTTGTGGAC-TTAAAAG-G
1 TGCCACTGACTTGT-GGGCTTAAAAAGGATGCCATGAAGTTGTGGACTTTGGAAGAG
* * * * ** *
1401731 ATGCCA-TAAAGTTGTGGACTT-AAAA-GAGTGCCACGAAGTTGTGGAC-TTAAAAGGG
1 -TGCCACT-GACTTGTGGGCTTAAAAAGGA-TGCCATGAAGTTGTGGACTTTGGAAGAG
* * * * * * * *
1401786 TGCCACGGAGTTGTGGACTTTAAAAGAATGCCACGGAGTTGTGGAC-TTGAAATG-G
1 TGCCACTGACTTGTGGGCTTAAAAAGGATGCCATGAAGTTGTGGACTTTGGAA-GAG
** * * * **
1401841 ATGCCA-TGGGGTTATGGACTTAAAAAGG-TGCCA-CAGAGTTGTGGAC-TTAAAAG-G
1 -TGCCACT-GACTTGTGGGCTTAAAAAGGATGCCATGA-AGTTGTGGACTTTGGAAGAG
* *** * * * ** *
1401895 ATGCCA-TAGAGTTGTGAATTTAAAAAGG-TGCCACGGAGTGGTGGACTTTAAAAGAA
1 -TGCCACT-GACTTGTGGGCTTAAAAAGGATGCCATGAAGTTGTGGACTTTGGAAGAG
* * * * * * * * * ** *
1401951 TGCCACGGAGTTATGGACTTGAAATGAATGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACTGACTTGTGGGCTTAAAAAGGATGCCATGAAGTTGTGGACTTTGGAAGAG
** * * * * **
1402006 TGCCACCCAGTTGTGGACTT-AAAAGGATGCCACGGAGTTGTGGACTTTAAAAG-G
1 TGCCACTGACTTGTGGGCTTAAAAAGGATGCCATGAAGTTGTGGACTTTGGAAGAG
* * * *
1402060 TTGCCA-TGGAGTTGTGGACTTTAAAAGGATGCCACGAAGTTGTGGACTT
1 -TGCCACT-GACTTGTGGGCTTAAAAAGGATGCCATGAAGTTGTGGACTT
1402109 AAAAGGATGC
Statistics
Matches: 410, Mismatches: 55, Indels: 49
0.80 0.11 0.10
Matches are distributed among these distances:
53 2 0.00
54 108 0.26
55 132 0.32
56 113 0.28
57 55 0.13
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (56 bp):
TGCCACTGACTTGTGGGCTTAAAAAGGATGCCATGAAGTTGTGGACTTTGGAAGAG
Found at i:1401733 original size:27 final size:27
Alignment explanation
Indices: 1401698--1402135 Score: 522
Period size: 27 Copynumber: 16.0 Consensus size: 27
1401688 GTGGGGCTTA
* *
1401698 AAAAGGATGCCATGAAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
***
1401725 AAAAGGATGCCATAAAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
*
1401752 AAAA-GAGTGCCACGAAGTTGTGGACTT
1 AAAAGGA-TGCCACGGAGTTGTGGACTT
*
1401779 AAAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
*
1401807 AAAAGAATGCCACGGAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* * * *
1401834 GAAATGGATGCCATGGGGTTATGGACTT
1 -AAAAGGATGCCACGGAGTTGTGGACTT
*
1401862 AAAAAGG-TGCCACAGAGTTGTGGACTT
1 -AAAAGGATGCCACGGAGTTGTGGACTT
** * *
1401889 AAAAGGATGCCATAGAGTTGTGAATTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
*
1401916 AAAAAGG-TGCCACGGAGTGGTGGACTTT
1 -AAAAGGATGCCACGGAGTTGTGGAC-TT
* *
1401944 AAAAGAATGCCACGGAGTTATGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* *
1401971 GAAATGAATGCCACGGAGTTGTGGACTT
1 -AAAAGGATGCCACGGAGTTGTGGACTT
* **
1401999 AAAAGGGTGCCACCCAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
1402026 AAAAGGATGCCACGGAGTTGTGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
* *
1402054 AAAAGGTTGCCATGGAGTTGTGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
*
1402082 AAAAGGATGCCACGAAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
1402109 AAAAGGATGCCACGGAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
1402136 TGAAAAGAAA
Statistics
Matches: 356, Mismatches: 45, Indels: 20
0.85 0.11 0.05
Matches are distributed among these distances:
26 8 0.02
27 196 0.55
28 152 0.43
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (27 bp):
AAAAGGATGCCACGGAGTTGTGGACTT
Found at i:1401846 original size:110 final size:110
Alignment explanation
Indices: 1401698--1402166 Score: 556
Period size: 110 Copynumber: 4.3 Consensus size: 110
1401688 GTGGGGCTTA
* * * ** *
1401698 AAAAGGATGCCATGAAGTTGTGGAC-TTAAAAGGATGCCATAAAGTTGTGGACTTAAAAGAGTGC
1 AAAAGAATGCCACGGAGTTGTGGACTTTAAAAGGATGCCATGGAGTTATGGACTTAAAAGAGTGC
*
1401762 CACGAAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTT
66 CACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTT
* * *
1401807 AAAAGAATGCCACGGAGTTGTGGACTTGAAATGGATGCCATGGGGTTATGGACTTAAAA-AGGTG
1 AAAAGAATGCCACGGAGTTGTGGACTTTAAAAGGATGCCATGGAGTTATGGACTTAAAAGA-GTG
** *
1401871 CCAC-AGAGTTGTGGACTTAAAAGGATGCCATAGAGTTGT-GAATTT
65 CCACGA-AGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTT
* * * * * *
1401916 AAAA-AGGTGCCACGGAGTGGTGGACTTTAAAAGAATGCCACGGAGTTATGGACTTGAAATGAAT
1 AAAAGA-ATGCCACGGAGTTGTGGACTTTAAAAGGATGCCATGGAGTTATGGACTT-AAAAGAGT
* * **
1401980 GCCACGGAGTTGTGGACTTAAAAGGGTGCCACCCAGTTGTGGAC-TT
64 GCCACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTT
* * *
1402026 AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGTTGCCATGGAGTTGTGGACTTTAAAAG-GAT
1 AAAAGAATGCCACGGAGTTGTGGACTTTAAAAGGATGCCATGGAGTTATGGAC-TTAAAAGAG-T
1402090 GCCACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTT
64 GCCACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTT
* * *
1402137 GAAAAGAAATGCCACTGAATCGTGGACTTT
1 -AAAAG-AATGCCACGGAGTTGTGGACTTT
1402167 GGAGAAGTCA
Statistics
Matches: 301, Mismatches: 45, Indels: 24
0.81 0.12 0.06
Matches are distributed among these distances:
108 1 0.00
109 75 0.25
110 194 0.64
111 7 0.02
112 5 0.02
113 19 0.06
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (110 bp):
AAAAGAATGCCACGGAGTTGTGGACTTTAAAAGGATGCCATGGAGTTATGGACTTAAAAGAGTGC
CACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTT
Found at i:1401887 original size:137 final size:137
Alignment explanation
Indices: 1401702--1402135 Score: 597
Period size: 137 Copynumber: 3.2 Consensus size: 137
1401692 GGCTTAAAAA
* * *
1401702 GGATGCCATGAAGTTGTGGACTT-AAAAGGATGCCATAAAGTTGTGGACTTAAAA-GAGTGCCAC
1 GGATGCCACGGAGTTGTGGACTTAAAAAGG-TGCCACAAAGTTGTGGACTTAAAAGGA-TGCCAC
1401765 GAAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAATGCCACGGAGTTGTGG
64 GAAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAATGCCACGGAGTTGTGG
1401830 ACTTGAAAT
129 ACTTGAAAT
* * * * *
1401839 GGATGCCATGGGGTTATGGACTTAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCA-TA
1 GGATGCCACGGAGTTGTGGACTTAAAAAGGTGCCACAAAGTTGTGGACTTAAAAGGATGCCACGA
* * * * *
1401903 GAGTTGTGAATTTAAAAAGGTGCCACGGAGTGGTGGACTTTAAAAGAATGCCACGGAGTTATGGA
66 -AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAATGCCACGGAGTTGTGGA
1401968 CTTGAAAT
130 CTTGAAAT
* * ** *
1401976 GAATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACCCAGTTGTGGACTTAAAAGGATGCCACGG
1 GGATGCCACGGAGTTGTGGACTTAAAAAGGTGCCACAAAGTTGTGGACTTAAAAGGATGCCACGA
* * * *
1402041 AGTTGTGGACTTTAAAAGGTTGCCATGGAGTTGTGGACTTTAAAAGGATGCCACGAAGTTGTGGA
66 AGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAATGCCACGGAGTTGTGGA
*
1402106 CTT-AAAA
130 CTTGAAAT
1402113 GGATGCCACGGAGTTGTGGACTT
1 GGATGCCACGGAGTTGTGGACTT
1402136 TGAAAAGAAA
Statistics
Matches: 261, Mismatches: 31, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
136 1 0.00
137 202 0.77
138 58 0.22
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (137 bp):
GGATGCCACGGAGTTGTGGACTTAAAAAGGTGCCACAAAGTTGTGGACTTAAAAGGATGCCACGA
AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAATGCCACGGAGTTGTGGAC
TTGAAAT
Found at i:1405995 original size:13 final size:13
Alignment explanation
Indices: 1405977--1406003 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1405967 TACAAAGATT
1405977 AATGTATCGATAC
1 AATGTATCGATAC
1405990 AATGTATCGATAC
1 AATGTATCGATAC
1406003 A
1 A
1406004 TTTGAGTAAT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Done.