Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007909.1 Hibiscus syriacus cultivar Beakdansim tig00110303_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3382237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 17
Found at i:1535259 original size:21 final size:22
Alignment explanation
Indices: 1535229--1535294 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
1535219 ATTACATATC
*
1535229 TTTAAAAAAAGTATCGATC-CTT
1 TTTACAAAAAGTATCGA-CACTT
* *
1535251 TTTATAAAAAGTATGGACACTT
1 TTTACAAAAAGTATCGACACTT
*
1535273 TTTAC-AAAAGTGTCGACA-TT
1 TTTACAAAAAGTATCGACACTT
1535293 TT
1 TT
1535295 ACACATCGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 4 0.11
21 12 0.32
22 22 0.58
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (22 bp):
TTTACAAAAAGTATCGACACTT
Found at i:1535587 original size:184 final size:184
Alignment explanation
Indices: 1535273--1536167 Score: 1736
Period size: 184 Copynumber: 4.9 Consensus size: 184
1535263 ATGGACACTT
*
1535273 TTTACAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
*
1535338 ATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
66 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
1535403 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
131 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
1535457 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
1535522 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
66 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
1535587 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
131 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
1535641 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
1535706 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
66 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
1535771 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
131 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
1535825 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
1535890 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
66 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
*
1535955 TAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGA
131 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
1536009 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
* *
1536074 ATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTA
66 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
*
1536139 TAATATTGTGTCGGTACTTTATGTCCATA
131 TAATATTGTGTCGGTACTTTATATCCATA
1536168 CCATTTAAAA
Statistics
Matches: 706, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 706 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
Found at i:1539391 original size:407 final size:408
Alignment explanation
Indices: 1538633--1539444 Score: 1576
Period size: 408 Copynumber: 2.0 Consensus size: 408
1538623 CAGTACACTG
1538633 TTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
1 TTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
1538698 ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAG
66 ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAG
1538763 GTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGA
131 GTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGA
1538828 AAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
196 AAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
1538893 TAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTTAAAATTCTAAATAATATTTT
261 TAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTTAAAATTCTAAATAATATTTT
1538958 ATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGTAGGT
326 ATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGTAGGT
1539023 GGAAAACATGAAACATAC
391 GGAAAACATGAAACATAC
1539041 TTAAAAAATATTGAAACATAAATTACAT-A-TCTTTAAAAAAAGTATCGATCCTTTTTATAAAAA
1 TTAAAAAA-ATTGAAACATAAATTACATAAGT-TTTAAAAAAAGTATCGATCCTTTTTATAAAAA
1539104 GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
64 GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
1539169 AGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
129 AGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
1539234 GAAAACATTAATTTAAGGTTATC-TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
194 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
1539298 TCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTTAAAATTCTAAATAATATT
259 TCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTTAAAATTCTAAATAATATT
*
1539363 TTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGTAG
324 TTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGTAG
1539428 GTGGAAAACATGAAACA
389 GTGGAAAACATGAAACA
1539445 CTGTTAAAGT
Statistics
Matches: 401, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
407 188 0.47
408 194 0.48
409 19 0.05
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (408 bp):
TTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAG
GTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGA
AAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
TAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTTAAAATTCTAAATAATATTTT
ATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGTAGGT
GGAAAACATGAAACATAC
Found at i:1543942 original size:115 final size:115
Alignment explanation
Indices: 1543740--1543977 Score: 476
Period size: 115 Copynumber: 2.1 Consensus size: 115
1543730 TAAATGTTAG
1543740 TCTAATTATCAAAAAATGAAACAGTTGGTTAAATAATTTGGACACTCCAATTCCATCCTAAAGAA
1 TCTAATTATCAAAAAATGAAACAGTTGGTTAAATAATTTGGACACTCCAATTCCATCCTAAAGAA
1543805 CCCAAGGTTAAACTTCTAATAAATACAAGATATCATCTATTTATTTTCTT
66 CCCAAGGTTAAACTTCTAATAAATACAAGATATCATCTATTTATTTTCTT
1543855 TCTAATTATCAAAAAATGAAACAGTTGGTTAAATAATTTGGACACTCCAATTCCATCCTAAAGAA
1 TCTAATTATCAAAAAATGAAACAGTTGGTTAAATAATTTGGACACTCCAATTCCATCCTAAAGAA
1543920 CCCAAGGTTAAACTTCTAATAAATACAAGATATCATCTATTTATTTTCTT
66 CCCAAGGTTAAACTTCTAATAAATACAAGATATCATCTATTTATTTTCTT
1543970 TCTAATTA
1 TCTAATTA
1543978 AAGGTGACAT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 123 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.34
Consensus pattern (115 bp):
TCTAATTATCAAAAAATGAAACAGTTGGTTAAATAATTTGGACACTCCAATTCCATCCTAAAGAA
CCCAAGGTTAAACTTCTAATAAATACAAGATATCATCTATTTATTTTCTT
Found at i:1554271 original size:16 final size:16
Alignment explanation
Indices: 1554250--1554283 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1554240 TTACTATTCA
*
1554250 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1554266 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1554282 CG
1 CG
1554284 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1571836 original size:20 final size:20
Alignment explanation
Indices: 1571811--1571903 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1571801 TTTTCCCAAT
1571811 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1571831 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1571851 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1571872 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1571893 TCGCAATGCGA
1 TCGCAATGCGA
1571904 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1571853 original size:41 final size:41
Alignment explanation
Indices: 1571808--1571903 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1571798 CGATTTTCCC
1571808 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1571849 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1571890 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1571904 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1571857 original size:21 final size:20
Alignment explanation
Indices: 1571811--1571903 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1571801 TTTTCCCAAT
*
1571811 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1571831 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1571851 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1571872 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1571893 TCGCAATGCGA
1 TCGCAATGCGA
1571904 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1571917 original size:20 final size:20
Alignment explanation
Indices: 1571892--1571985 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1571882 AATTGGGAAA
*
1571892 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1571912 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1571933 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
1571953 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1571973 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1571986 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1571966 original size:41 final size:41
Alignment explanation
Indices: 1571889--1571966 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1571879 GCGAATTGGG
* * **
1571889 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
1571930 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
1571967 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:1572548 original size:19 final size:19
Alignment explanation
Indices: 1572505--1572569 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
1572495 CGAGAATGAT
* *
1572505 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATAAA
*
1572525 TATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
1572544 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
1572563 AATCGCA
1 AATCGCA
1572570 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:1572587 original size:19 final size:19
Alignment explanation
Indices: 1572565--1572749 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
1572555 GAAACCAAAA
*
1572565 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1572584 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1572603 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
1572622 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
1572642 TCGTGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1572658 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1572675 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1572689 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1572708 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1572728 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1572748 TC
1 TC
1572750 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.44
20 47 0.35
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1572642 original size:39 final size:38
Alignment explanation
Indices: 1572565--1572654 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
1572555 GAAACCAAAA
* *
1572565 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
1572603 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
*
1572642 TCGTGTTGCGATT
1 TCGCGTTGCGATT
1572655 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:1572674 original size:33 final size:33
Alignment explanation
Indices: 1572637--1572724 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
1572627 GTTGCGATTT
* * **
1572637 TCATTTCGTGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
1572670 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
1572703 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1572725 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 34 0.69
34 15 0.31
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:1572726 original size:20 final size:20
Alignment explanation
Indices: 1572703--1572749 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1572693 ATTGCGATAG
1572703 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
1572723 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
1572743 TCATTTC
1 TCATTTC
1572750 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:1574810 original size:42 final size:42
Alignment explanation
Indices: 1574750--1574872 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1574740 GCCCGACTCG
* * *
1574750 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1574792 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1574834 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1574873 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1574830 original size:21 final size:21
Alignment explanation
Indices: 1574806--1574872 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1574796 TCATTCCTCG
1574806 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1574827 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1574848 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1574869 AGAG
1 AGAG
1574873 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1576252 original size:14 final size:14
Alignment explanation
Indices: 1576233--1576266 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1576223 TGTTTAATTT
1576233 ATTTGTAAAAGGTG
1 ATTTGTAAAAGGTG
*
1576247 ATTTGTAAAAGTTG
1 ATTTGTAAAAGGTG
1576261 ATTTGT
1 ATTTGT
1576267 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGGTG
Found at i:1576467 original size:19 final size:19
Alignment explanation
Indices: 1576445--1576562 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
1576435 CGAAATTAAA
1576445 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1576464 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1576479 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1576497 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1576512 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1576530 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1576549 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1576563 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1576491 original size:33 final size:33
Alignment explanation
Indices: 1576449--1576542 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
1576439 ATTAAATTCG
1576449 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1576482 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1576515 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1576543 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1577914 original size:14 final size:14
Alignment explanation
Indices: 1577895--1577952 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1577885 TTTCATTTCG
1577895 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1577909 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1577925 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
1577941 CGTTGTGATTTT
1 CGTTGCGATTTT
1577953 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1577959 original size:33 final size:33
Alignment explanation
Indices: 1577878--1577968 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1577868 GACCTACGCA
1577878 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1577911 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
1577943 TTGTGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
1577969 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:1577987 original size:20 final size:19
Alignment explanation
Indices: 1577953--1578007 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1577943 TTGTGATTTT
*
1577953 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1577972 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1577992 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1578008 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1578506 original size:18 final size:18
Alignment explanation
Indices: 1578480--1578524 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1578470 GTCGATCAGA
*
1578480 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
1578498 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
1578516 TGATGGCTC
1 TGATGGCTC
1578525 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:1579858 original size:20 final size:20
Alignment explanation
Indices: 1579833--1579870 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1579823 AATAGTTTCT
1579833 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1579853 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1579871 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1580159 original size:22 final size:22
Alignment explanation
Indices: 1580134--1580177 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1580124 GATTTAGATA
1580134 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1580156 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1580178 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1580390 original size:20 final size:20
Alignment explanation
Indices: 1580365--1580458 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1580355 GATTATGTAT
1580365 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1580385 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1580405 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1580426 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1580446 TATCGCATTGCGA
1 TATCGCGTTGCGA
1580459 TTTACTTATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1580459 original size:20 final size:20
Alignment explanation
Indices: 1580345--1580459 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1580335 CGCTTTGAAA
*
1580345 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1580366 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1580386 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1580406 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1580427 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1580447 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1580460 TTACTTATTC
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1580471 original size:20 final size:20
Alignment explanation
Indices: 1580448--1580519 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
1580438 ATAGTCAGTA
1580448 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
1580468 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
* *
1580489 TTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
1580509 TCGCATTGCGA
1 TCGCATTGCGA
1580520 ATTGGGAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:1581017 original size:45 final size:47
Alignment explanation
Indices: 1580933--1581029 Score: 180
Period size: 45 Copynumber: 2.1 Consensus size: 47
1580923 AAGTTAAAAA
1580933 AATATTAAAATAATTATAATATATATATATAAAGTATATATTAATAT
1 AATATTAAAATAATTATAATATATATATATAAAGTATATATTAATAT
1580980 AATATTAAAATAATTAT-A-ATATATATATAAAGTATATATTAATAT
1 AATATTAAAATAATTATAATATATATATATAAAGTATATATTAATAT
1581025 AATAT
1 AATAT
1581030 AAATAAACTA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 32 0.64
46 1 0.02
47 17 0.34
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (47 bp):
AATATTAAAATAATTATAATATATATATATAAAGTATATATTAATAT
Found at i:1581034 original size:11 final size:11
Alignment explanation
Indices: 1580933--1581034 Score: 70
Period size: 11 Copynumber: 8.9 Consensus size: 11
1580923 AAGTTAAAAA
1580933 AATATTAAA-AT
1 AATA-TAAATAT
1580944 AATTATAATATAT
1 AA-TATAA-ATAT
1580957 ATATATAAAGTAT
1 A-ATATAAA-TAT
*
1580970 -ATATTAATAT
1 AATATAAATAT
1580980 AATATTAAA-AT
1 AATA-TAAATAT
1580991 AAT-TATAATAT
1 AATATA-AATAT
1581002 ATATATAAAGTAT
1 A-ATATAAA-TAT
*
1581015 -ATATTAATAT
1 AATATAAATAT
1581025 AATATAAATA
1 AATATAAATA
1581035 AACTATATAG
Statistics
Matches: 74, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
9 2 0.03
10 8 0.11
11 36 0.49
12 11 0.15
13 16 0.22
14 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
AATATAAATAT
Found at i:1581265 original size:50 final size:51
Alignment explanation
Indices: 1581137--1581265 Score: 136
Period size: 50 Copynumber: 2.5 Consensus size: 51
1581127 TATTACCACA
* * * * *
1581137 TGTTTAATTAATATTGGATTGATAAATAATTTAGAGGATCTATTTATTATG
1 TGTTTAATTAGTATTGGGTTGATAAATAATTTAGAAGATCTATTTATCACG
** * * *
1581188 TGTTTAATTAGTATTATGTTAAAAAATACTTTA-AAGATCTATTT-TGCACG
1 TGTTTAATTAGTATTGGGTTGATAAATAATTTAGAAGATCTATTTAT-CACG
*
1581238 TGTTTAATCAGTATTGGGTTGATAAATA
1 TGTTTAATTAGTATTGGGTTGATAAATA
1581266 TTTTGGAGGA
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
49 1 0.02
50 35 0.56
51 26 0.42
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.45
Consensus pattern (51 bp):
TGTTTAATTAGTATTGGGTTGATAAATAATTTAGAAGATCTATTTATCACG
Found at i:1581471 original size:51 final size:51
Alignment explanation
Indices: 1581233--1581712 Score: 379
Period size: 51 Copynumber: 9.4 Consensus size: 51
1581223 GATCTATTTT
* * *
1581233 GCACGTGTTTAATCAGTATTGGGTTGATAAATATTTTGGAGGATTCACTCA
1 GCACGTGTTTAATCAGTATTGAGTTGATAAATACTTTGAAGGATTCACTCA
* * * * * * * *
1581284 ACACATG-TT-ATCGGTA-TCAGGTTGATAAATACTCT-AGAGAATTCCCTTA
1 GCACGTGTTTAATCAGTATTGA-GTTGATAAATACTTTGA-AGGATTCACTCA
* * * * * *
1581333 GCACGTGCTTAATTAGTATTGAGTTGACAAATGCTTTGGAGGATTCACTTTA
1 GCACGTGTTTAATCAGTATTGAGTTGATAAATACTTTGAAGGATTCAC-TCA
* * * * * *
1581385 GTC-CATGTTTAATCAATATTG-GATTCACAAGTACTTTGAAGGATTCACTCG
1 G-CACGTGTTTAATCAGTATTGAG-TTGATAAATACTTTGAAGGATTCACTCA
* *
1581436 GCACGTGTTTAATCAGTATTGAGTTGACAAATACTTTGGAGGATTCACTTCA
1 GCACGTGTTTAATCAGTATTGAGTTGATAAATACTTTGAAGGATTCAC-TCA
* * *
1581488 GCACATGTTTAATCAGTATT-AGGTTGATAAATATTTTGGAGGATTCACTCA
1 GCACGTGTTTAATCAGTATTGA-GTTGATAAATACTTTGAAGGATTCACTCA
* * * * *
1581539 ACACATGTTGAATTAGTATTG-GATTGACAAATACTTTAGAA-GATTCACTCA
1 GCACGTGTTTAATCAGTATTGAG-TTGATAAATACTTT-GAAGGATTCACTCA
* * * * * *
1581590 ACACGTGTTTAATCGGTATTGAGTTGATAAATACTTCAGAA-AATTCAGTTA
1 GCACGTGTTTAATCAGTATTGAGTTGATAAATACTT-TGAAGGATTCACTCA
* * * * *
1581641 ACATGTGTTTAATCGGTATTGAGTTGATAAATACTTTAGAA-GATTCAATTA
1 GCACGTGTTTAATCAGTATTGAGTTGATAAATACTTT-GAAGGATTCACTCA
*
1581692 GCACGTGTTTAATCAATATTG
1 GCACGTGTTTAATCAGTATTG
1581713 GGTTAGGATT
Statistics
Matches: 346, Mismatches: 64, Indels: 38
0.77 0.14 0.08
Matches are distributed among these distances:
48 1 0.00
49 33 0.10
50 6 0.02
51 215 0.62
52 90 0.26
53 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (51 bp):
GCACGTGTTTAATCAGTATTGAGTTGATAAATACTTTGAAGGATTCACTCA
Found at i:1581584 original size:154 final size:154
Alignment explanation
Indices: 1581238--1581713 Score: 430
Period size: 154 Copynumber: 3.1 Consensus size: 154
1581228 ATTTTGCACG
* * * * * * * * *
1581238 TGTTTAATCAGTATTGGGTTGATAAATATTTTGGAGGATTCACTCAACACATG-TT-ATCGGTA-
1 TGTTGAATCAATATTGGATTCACAAATACTTTGAAGGATTCACTCAACACGTGTTTAATCAGTAT
* * * * *
1581300 TCAGGTTGATAAATACTCTAGAGAATTCCCTTAGCACGTGCTTAATTAGTATTGAGTTGACAAAT
66 TGA-GTTGATAAATACTTTAGAGAATTCACTTAGCACATGCTTAATCAGTATTGAGTTGACAAAT
* * *
1581365 GCTTTGGAGGATTCACTTTAGTCCA
130 ACTTTGGAGGATTCACTTCAGACCA
* * **
1581390 TGTTTAATCAATATTGGATTCACAAGTACTTTGAAGGATTCACTCGGCACGTGTTTAATCAGTAT
1 TGTTGAATCAATATTGGATTCACAAATACTTTGAAGGATTCACTCAACACGTGTTTAATCAGTAT
* * * * *
1581455 TGAGTTGACAAATACTTTGGAGGATTCACTTCAGCACATGTTTAATCAGTATT-AGGTTGATAAA
66 TGAGTTGATAAATACTTTAGAGAATTCACTT-AGCACATGCTTAATCAGTATTGA-GTTGACAAA
*
1581519 TATTTTGGAGGATTCAC-TCA-ACACA
129 TACTTTGGAGGATTCACTTCAGAC-CA
* * * *
1581544 TGTTGAATTAGTATTGGATTGACAAATACTTTAGAA-GATTCACTCAACACGTGTTTAATCGGTA
1 TGTTGAATCAATATTGGATTCACAAATACTTT-GAAGGATTCACTCAACACGTGTTTAATCAGTA
* * * * ** * * *
1581608 TTGAGTTGATAAATACTTCAGAAAATTCAGTTAACATGTGTTTAATCGGTATTGAGTTGATAAAT
65 TTGAGTTGATAAATACTTTAGAGAATTCACTTAGCACATGCTTAATCAGTATTGAGTTGACAAAT
* * * *
1581673 ACTTTAGAAGATTCAATT-AG-CACG
130 ACTTTGGAGGATTCACTTCAGAC-CA
*
1581697 TGTTTAATCAATATTGG
1 TGTTGAATCAATATTGG
1581714 GTTAGGATTC
Statistics
Matches: 263, Mismatches: 51, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
152 43 0.16
153 60 0.23
154 114 0.43
155 46 0.17
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (154 bp):
TGTTGAATCAATATTGGATTCACAAATACTTTGAAGGATTCACTCAACACGTGTTTAATCAGTAT
TGAGTTGATAAATACTTTAGAGAATTCACTTAGCACATGCTTAATCAGTATTGAGTTGACAAATA
CTTTGGAGGATTCACTTCAGACCA
Found at i:1581660 original size:102 final size:102
Alignment explanation
Indices: 1581234--1581716 Score: 388
Period size: 103 Copynumber: 4.7 Consensus size: 102
1581224 ATCTATTTTG
* * * * * * * *
1581234 CACGTGTTTAATCAGTATTGGGTTGATAAATATTTTGGAGGATTCACTCAACACATG-TT-ATCG
1 CACGTGTTTAATCAGTATTGAGTTGACAAATACTTTAGAAGATTCACTCAGCACGTGTTTAATCA
* * * * *
1581297 GTATCAGGTTGATAAATAC-TCTAGAGAATTCCCTTAG
66 GTATTAGGTTGATAAATACTTC-AGAAAATTCACTCAA
* * * * * * *
1581334 CACGTGCTTAATTAGTATTGAGTTGACAAATGCTTTGGAGGATTCACTTTAGTC-CATGTTTAAT
1 CACGTGTTTAATCAGTATTGAGTTGACAAATACTTTAGAAGATTCAC-TCAG-CACGTGTTTAAT
* * * * * * **
1581398 CAATATT-GGATTCACAAGTACTT-TGAAGGATTCACTCGG
64 CAGTATTAGG-TTGATAAATACTTCAGAA-AATTCACTCAA
* * *
1581437 CACGTGTTTAATCAGTATTGAGTTGACAAATACTTTGGAGGATTCACTTCAGCACATGTTTAATC
1 CACGTGTTTAATCAGTATTGAGTTGACAAATACTTTAGAAGATTCAC-TCAGCACGTGTTTAATC
* ** **
1581502 AGTATTAGGTTGATAAATATTTTGGAGGATTCACTCAA
65 AGTATTAGGTTGATAAATACTTCAGAAAATTCACTCAA
* * * *
1581540 CACATGTTGAATTAGTATTG-GATTGACAAATACTTTAGAAGATTCACTCAACACGTGTTTAATC
1 CACGTGTTTAATCAGTATTGAG-TTGACAAATACTTTAGAAGATTCACTCAGCACGTGTTTAATC
* * *
1581604 GGTATT-GAGTTGATAAATACTTCAGAAAATTCAGTTAA
65 AGTATTAG-GTTGATAAATACTTCAGAAAATTCACTCAA
* * * * *
1581642 CATGTGTTTAATCGGTATTGAGTTGATAAATACTTTAGAAGATTCAATTAGCACGTGTTTAATCA
1 CACGTGTTTAATCAGTATTGAGTTGACAAATACTTTAGAAGATTCACTCAGCACGTGTTTAATCA
* *
1581707 ATATTGGGTT
66 GTATTAGGTT
1581717 AGGATTCACT
Statistics
Matches: 310, Mismatches: 59, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
100 41 0.13
101 7 0.02
102 112 0.36
103 145 0.47
104 5 0.02
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (102 bp):
CACGTGTTTAATCAGTATTGAGTTGACAAATACTTTAGAAGATTCACTCAGCACGTGTTTAATCA
GTATTAGGTTGATAAATACTTCAGAAAATTCACTCAA
Found at i:1581789 original size:88 final size:88
Alignment explanation
Indices: 1581632--1581797 Score: 217
Period size: 88 Copynumber: 1.9 Consensus size: 88
1581622 ACTTCAGAAA
* * * * * * * *
1581632 ATTCAGTTAACATGTGTTTAATCGGTATTGAGTTGATAAATACTTTAGAAGATTCAATTAGCACG
1 ATTCACTTAACATGTGTTTAATCAGCATTGAATTAACAAATACTTTAGAAGATTCAATTAACACA
1581697 TGTTTAATCAATATTGGGTTAGG
66 TGTTTAATCAATATTGGGTTAGG
* * *
1581720 ATTCACTTAACATGTGTTTCATTAGCATTGAATTAACAAATACTTT-GAAAGATTCACTTAACAC
1 ATTCACTTAACATGTGTTTAATCAGCATTGAATTAACAAATACTTTAG-AAGATTCAATTAACAC
1581784 ATGTTTAATCAATA
65 ATGTTTAATCAATA
1581798 CTGGATTGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
87 1 0.02
88 65 0.98
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (88 bp):
ATTCACTTAACATGTGTTTAATCAGCATTGAATTAACAAATACTTTAGAAGATTCAATTAACACA
TGTTTAATCAATATTGGGTTAGG
Found at i:1584889 original size:347 final size:347
Alignment explanation
Indices: 1584254--1584947 Score: 1334
Period size: 347 Copynumber: 2.0 Consensus size: 347
1584244 ATATTGTTTT
*
1584254 TTACTTCTCTAAGTTGTAAGGTTACCCCAAACAAATGTGAGTAGCCACTAGTGGATCTCCTTTCA
1 TTACTTCTCCAAGTTGTAAGGTTACCCCAAACAAATGTGAGTAGCCACTAGTGGATCTCCTTTCA
*
1584319 GTAAGGTCTCCGGCCCAACTAGAGTCTGTAAAAATTTTAACAGTTCTGTCTTGTGTCTTCTTAAA
66 GTAAGGTCTCCGGCCCAACTAGAGTCTGTAAAAATTTTAACAGTTCTGTCTTGTGCCTTCTTAAA
* *
1584384 CATTAAGCCGTGTCCTGGAGTTTTCTTCAAGTACTTGAGAATTCTATTTGTTGTTGCCATATGCT
131 CATTAAGCCGTGTCCTGGAGTTTTCTTCAAGTACTTGAGAATTCTATTTGCTGCTGCCATATGCT
1584449 CTTCAATAGGATTAGTCATGTGTTGACTTATCACATTACGGGAAAGGCTATATCTGGCCTTGTCA
196 CTTCAATAGGATTAGTCATGTGTTGACTTATCACATTACGGGAAAGGCTATATCTGGCCTTGTCA
1584514 AGGATAAATAAATTAGTTTCCCAACTAATCTTTGAAATTTCTCTTTGTCTACTAAGGACCCTTAT
261 AGGATAAATAAATTAGTTTCCCAACTAATCTTTGAAATTTCTCTTTGTCTACTAAGGACCCTTAT
1584579 TCTTTGCTAAATTTCAAGCTTG
326 TCTTTGCTAAATTTCAAGCTTG
1584601 TTACTTCTCCAAGTTGTAAGGTTACCCCAAACAAATGTGAGTAGCCACTAGTGGATCTCCTTTCA
1 TTACTTCTCCAAGTTGTAAGGTTACCCCAAACAAATGTGAGTAGCCACTAGTGGATCTCCTTTCA
*
1584666 GTAAGGTCTCCGGCCCAACTAGAGTCTGTAAAAATTTTAATAGTTCTGTCTTGTGCCTTCTTAAA
66 GTAAGGTCTCCGGCCCAACTAGAGTCTGTAAAAATTTTAACAGTTCTGTCTTGTGCCTTCTTAAA
1584731 CATTAAGCCGTGTCCTGGAGTTTTCTTCAAGTACTTGAGAATTCTATTTGCTGCTGCCATATGCT
131 CATTAAGCCGTGTCCTGGAGTTTTCTTCAAGTACTTGAGAATTCTATTTGCTGCTGCCATATGCT
1584796 CTTCAATAGGATTAGTCATGTGTTGACTTATCACATTACGGGAAAGGCTATATCTGGCCTTGTCA
196 CTTCAATAGGATTAGTCATGTGTTGACTTATCACATTACGGGAAAGGCTATATCTGGCCTTGTCA
*
1584861 AGGATAAATAAATTAGTTTCCCAACTAATCTTTGAAATTTCTCTTTGTCTACTAAGGACCCTTTT
261 AGGATAAATAAATTAGTTTCCCAACTAATCTTTGAAATTTCTCTTTGTCTACTAAGGACCCTTAT
1584926 TCTTTGCTAAATTTCAAGCTTG
326 TCTTTGCTAAATTTCAAGCTTG
1584948 CCTCCATTGG
Statistics
Matches: 341, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
347 341 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (347 bp):
TTACTTCTCCAAGTTGTAAGGTTACCCCAAACAAATGTGAGTAGCCACTAGTGGATCTCCTTTCA
GTAAGGTCTCCGGCCCAACTAGAGTCTGTAAAAATTTTAACAGTTCTGTCTTGTGCCTTCTTAAA
CATTAAGCCGTGTCCTGGAGTTTTCTTCAAGTACTTGAGAATTCTATTTGCTGCTGCCATATGCT
CTTCAATAGGATTAGTCATGTGTTGACTTATCACATTACGGGAAAGGCTATATCTGGCCTTGTCA
AGGATAAATAAATTAGTTTCCCAACTAATCTTTGAAATTTCTCTTTGTCTACTAAGGACCCTTAT
TCTTTGCTAAATTTCAAGCTTG
Found at i:1590088 original size:27 final size:27
Alignment explanation
Indices: 1590057--1590115 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1590047 TCTATTTACA
1590057 AAATCACATCTCTATAGGAATGGTAAC
1 AAATCACATCTCTATAGGAATGGTAAC
*
1590084 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCACATCTCTATAGGAATGGTAAC
1590111 AAATC
1 AAATC
1590116 CTTAGTAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (27 bp):
AAATCACATCTCTATAGGAATGGTAAC
Found at i:1592434 original size:27 final size:27
Alignment explanation
Indices: 1592403--1592470 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1592393 TCTATTTACA
1592403 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1592430 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1592457 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
1592471 ATTCCTACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:1607838 original size:4 final size:4
Alignment explanation
Indices: 1607829--1607855 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1607819 TCCTACTAGC
1607829 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1607856 GTAATAGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1610806 original size:22 final size:24
Alignment explanation
Indices: 1610772--1610816 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1610762 AAAATTAGCT
* *
1610772 AAATAAATTAAAGA-ATAAAAATA
1 AAATAAATAAAAGAGAAAAAAATA
1610795 AAAT-AATAAAAGAGAAAAAAAT
1 AAATAAATAAAAGAGAAAAAAAT
1610817 GGAAAAGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.18
Consensus pattern (24 bp):
AAATAAATAAAAGAGAAAAAAATA
Found at i:1610850 original size:5 final size:5
Alignment explanation
Indices: 1610835--1610930 Score: 56
Period size: 5 Copynumber: 19.4 Consensus size: 5
1610825 TATTACAATA
* * *
1610835 AAAAT AGAAT AAAAT -AAAT AAAGAT AAAAT AAAAC AAAAT -TAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT
* * * * * *
1610884 -TAAT AAAAC AACAT TAAAT AAAACA AAAATT AAAAC AAAA- AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAA-T AAAAT AAAAT AAAAT AA
1610931 TGGAAACAAA
Statistics
Matches: 67, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
4 14 0.21
5 40 0.60
6 13 0.19
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1610856 original size:20 final size:20
Alignment explanation
Indices: 1610831--1610868 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1610821 AAGATATTAC
*
1610831 AATAAAAATAGAATAAAATA
1 AATAAAAATAAAATAAAATA
*
1610851 AATAAAGATAAAATAAAA
1 AATAAAAATAAAATAAAA
1610869 CAAAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (20 bp):
AATAAAAATAAAATAAAATA
Found at i:1610892 original size:23 final size:24
Alignment explanation
Indices: 1610845--1610906 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
1610835 AAAATAGAAT
*
1610845 AAAA-TAAATAAAGATAAAATAAAAC
1 AAAATTAAATAAA-AT-TAATAAAAC
1610870 AAAATT-AATAAAATTAATAAAAC
1 AAAATTAAATAAAATTAATAAAAC
*
1610893 AACATTAAATAAAA
1 AAAATTAAATAAAA
1610907 CAAAAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 13 0.39
24 9 0.27
25 10 0.30
26 1 0.03
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAATTAAATAAAATTAATAAAAC
Found at i:1611569 original size:12 final size:12
Alignment explanation
Indices: 1611539--1611567 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1611529 AGTAAAAACG
1611539 AAAAAAGAATGA
1 AAAAAAGAATGA
1611551 AAAAAAGAA-GA
1 AAAAAAGAATGA
1611562 AAAAAA
1 AAAAAA
1611568 AGCCACATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (12 bp):
AAAAAAGAATGA
Found at i:1620719 original size:84 final size:84
Alignment explanation
Indices: 1620515--1621527 Score: 996
Period size: 84 Copynumber: 12.2 Consensus size: 84
1620505 TATACATACT
* * * * *
1620515 ATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTACCATCCAAAGACCTTCTAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* ** *
1620580 CTCAACTTTGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
* * * * *
1620600 ATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
1620665 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * *
1620684 ATTTGTAGTATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
1620749 TTCAGCTCCAAGGAACATC
66 CTCAGCTCCAAGGCACATC
* * * * * *
1620768 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * *
1620829 CTCAGCTTCGAGAGCACATA
66 CTCAGCTCCAAG-GCACATC
* * * * * * *
1620849 ATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTAGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
*
1620913 GCTCAGCTCCAAGGCATATC
65 GCTCAGCTCCAAGGCACATC
* * * *
1620933 ATTTGCAGTATAACTTAAGTCGAGAAGGATTATCTGCCAACCAAATACCTTCGAGTTCAACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1620998 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* ** * * * *
1621017 ATTTGCAGTATTGCTTAAGTTGAGAAGGGTTATCTTCC-A--AAA-ACCTTCGAGTTTGACTATG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
1621078 CTCAGCTCAAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * * * * *
1621097 ATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * *
1621162 TTAAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * * * *
1621181 ATTTACAACATAACTCAA-TGCTAGAAGGGTTATCTGTC-ACCAAATACCTTCGAGTTTGACTAC
1 ATTTGCAGCATAACTTAAGT-CGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
1621244 GCTCAGCTCCAAGGCATATC
65 GCTCAGCTCCAAGGCACATC
* * * ** *
1621264 ATTTGCAGCATAACTTAAGTCGATAAGGGTTATCTACCAACCAAAGAACTTTAAGTTCGACTATG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1621329 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * *
1621348 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
1621409 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
* * * * * ** * * * *
1621429 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTTAA-CAAATACCTTTGAGTTCGACTCCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * *
1621493 CTCACCTCAAAGGCACGTC
66 CTCAGCTCCAAGGCACATC
*
1621512 ATTTTACAGCATAACT
1 A-TTTGCAGCATAACT
1621528 CATGGCAAGA
Statistics
Matches: 768, Mismatches: 141, Indels: 39
0.81 0.15 0.04
Matches are distributed among these distances:
80 117 0.15
81 78 0.10
83 85 0.11
84 397 0.52
85 91 0.12
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATC
Found at i:1620960 original size:249 final size:249
Alignment explanation
Indices: 1620515--1621524 Score: 1063
Period size: 249 Copynumber: 4.0 Consensus size: 249
1620505 TATACATACT
* * * *
1620515 ATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTACCATCCAAAGACCTTCTAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT----TCCAAAGACCTTCGAGTTCGATTTCG
* * * *
1620580 CTCAACTTTGAGGGCACATCATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAA
62 CTCAGCTTCGAGAGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAA
* * *
1620645 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGTATAACTTAAGTTGAGAA
127 GACCTTCGAGTTAGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTCGAGAA
* * *
1620710 GGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGAACATC
192 GGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * *
1620768 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTTCACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTTCCAAAGACCTTCGAGTTCGATTTCGCTCA
* * * * *
1620833 GCTTCGAGAGCACATAATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACC
66 GCTTCGAGAGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACC
*
1620898 TTCGAGTTAGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTCGAGAAGGAT
131 TTCGAGTTAGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTCGAGAAGGGT
*
1620963 TATCTGCCAACCAAATACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATC
196 TATCTGCCAACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * * * *
1621017 ATTTGCAGTATTGCTTAAGTTGAGAAGGGTTATCTTCCAAAAACCTTCGAGTTTGACTAT-GCTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTTCCAAAGACCTTCGAGTTCGA-TTTCGCTC
* * * * *
1621081 AGC-TC-AAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGA
65 AGCTTCGAGA-GCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGA
* * * * ** * *
1621144 CCTTCGAGTTTGACTACGTTAAGCTCCAAGGCATATCATTTACAACATAACTCAA-TGCTAGAAG
129 CCTTCGAGTTAGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGT-CGAGAAG
* * *
1621208 GGTTATCTGTC-ACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATC
193 GGTTATCTGCCAACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * * ** *
1621264 ATTTGCAGCATAACTTAAGTCGATAAGGGTTATCTACCAACCAAAGAACTTTAAGTTCGACTAT-
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT----TCCAAAGACCTTCGAGTTCGA-TTTC
* * * * * * *
1621328 GCTCAGCTCCAAG-GCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AA
61 GCTCAGCTTCGAGAGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA
* * * * * * * * ** * * *
1621388 AGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAG
126 AGACCTTCGAGTTAGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGTATAACTTAAGTCGAG
** * * * * * *
1621453 AAGGGTTATCTGTTAA-CAAATACCTTTGAGTTCGACTCCACTCACCTCAAAGGCACGTC
190 AAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
1621512 ATTTTACAGCATA
1 A-TTTGCAGCATA
1621525 ACTCATGGCA
Statistics
Matches: 648, Mismatches: 96, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
247 98 0.15
248 192 0.30
249 256 0.40
250 3 0.00
251 63 0.10
252 1 0.00
253 35 0.05
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (249 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTTCCAAAGACCTTCGAGTTCGATTTCGCTCA
GCTTCGAGAGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACC
TTCGAGTTAGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTCGAGAAGGGT
TATCTGCCAACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:1623173 original size:21 final size:24
Alignment explanation
Indices: 1623140--1623186 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
1623130 GTTCCCCCTC
1623140 TTTTATCTAGTA-TTT-TTTTATT
1 TTTTATCTAGTATTTTATTTTATT
*
1623162 TTTTAT-TTGTATTTTATTTTATT
1 TTTTATCTAGTATTTTATTTTATT
1623185 TT
1 TT
1623187 CCCCTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 9 0.41
23 9 0.41
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (24 bp):
TTTTATCTAGTATTTTATTTTATT
Found at i:1627928 original size:12 final size:11
Alignment explanation
Indices: 1627911--1627957 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
1627901 ATTAAACCTA
1627911 AAAAATGAAAAT
1 AAAAAT-AAAAT
1627923 AAAAATAAAATT
1 AAAAATAAAA-T
1627935 AAAAAT-AAAT
1 AAAAATAAAAT
1627945 -AAAATAAAAT
1 AAAAATAAAAT
1627955 AAA
1 AAA
1627958 TAAAAATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.16
10 5 0.16
11 9 0.28
12 13 0.41
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1627932 original size:5 final size:5
Alignment explanation
Indices: 1627912--1627962 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
1627902 TTAAACCTAA
1627912 AAAAT GAAAAT AAAAAT AAAATT AAAA- ATAAAT AAAAT AAAAT -AAAT
1 AAAAT -AAAAT -AAAAT AAAA-T AAAAT A-AAAT AAAAT AAAAT AAAAT
1627959 AAAA
1 AAAA
1627963 ATGTATATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
4 5 0.12
5 19 0.47
6 16 0.40
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1628110 original size:38 final size:37
Alignment explanation
Indices: 1628011--1628339 Score: 341
Period size: 38 Copynumber: 8.9 Consensus size: 37
1628001 TTTCAAAACC
* *
1628011 CAAACACGTTTTCTAAA--ATATATTATATATATTTT
1 CAAAAACGTTTTCAAAACTATATATTATATATATTTT
* *
1628046 CCAAAAACGTCTT-AAAACTATATATTATACATATTTT
1 -CAAAAACGTTTTCAAAACTATATATTATATATATTTT
* *
1628083 CAAAAAATGATTTCAAAACTATATATTATATATATATTTT
1 C-AAAAACGTTTTCAAAACTATATA-T-TATATATATTTT
** *
1628123 CAAAAACGTTTTTTAAACCATATATTATAT-T-TTTT
1 CAAAAACGTTTTCAAAACTATATATTATATATATTTT
* *
1628158 --TAAACGTTTTCAAAACTATATATTATATATGTTTTT
1 CAAAAACGTTTTCAAAACTATATATTATATAT-ATTTT
** * *
1628194 TTAAAATGTTTTCAAAATTATATATTATATATATTTT
1 CAAAAACGTTTTCAAAACTATATATTATATATATTTT
* * *
1628231 -AAAAATGTTTTCAAAACTACATATTGTATATATTTT
1 CAAAAACGTTTTCAAAACTATATATTATATATATTTT
* * * *
1628267 CGAACAATGTTTTCAAAACTATATACTATATATTTTTT
1 C-AAAAACGTTTTCAAAACTATATATTATATATATTTT
*
1628305 CAAAAACGTTTTCAAAACCATATATTATATATATT
1 CAAAAACGTTTTCAAAACTATATATTATATATATT
1628340 ATGTATATAT
Statistics
Matches: 245, Mismatches: 35, Indels: 25
0.80 0.11 0.08
Matches are distributed among these distances:
33 24 0.10
34 1 0.00
35 7 0.03
36 48 0.20
37 63 0.26
38 71 0.29
39 19 0.08
40 12 0.05
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (37 bp):
CAAAAACGTTTTCAAAACTATATATTATATATATTTT
Found at i:1628261 original size:74 final size:74
Alignment explanation
Indices: 1628011--1628336 Score: 326
Period size: 74 Copynumber: 4.4 Consensus size: 74
1628001 TTTCAAAACC
* * * * *
1628011 CAAACACGTTTTCTAAA--ATATATTATATATATTTTCCAAAAACGTCTT-AAAACTATATATTA
1 CAAAAACGTTTTCAAAACTATATATTATATAT-TTTTTCAAAAATGTTTTCAAAACTATATATTA
*
1628073 TACATATTTT
65 TATATATTTT
* * * ** *
1628083 CAAAAAATGATTTCAAAACTATATATTATATATATATTTTCAAAAACGTTTTTTAAACCATATAT
1 C-AAAAACGTTTTCAAAACTATATATTATATAT-T-TTTTCAAAAATGTTTTCAAAACTATATAT
1628148 TATAT-T-TTTT
63 TATATATATTTT
* ** *
1628158 --TAAACGTTTTCAAAACTATATATTATATATGTTTTTTTAAAATGTTTTCAAAATTATATATTA
1 CAAAAACGTTTTCAAAACTATATATTATATAT-TTTTTCAAAAATGTTTTCAAAACTATATATTA
1628221 TATATATTTT
65 TATATATTTT
* * * * * *
1628231 -AAAAATGTTTTCAAAACTACATATTGTATATATTTTCGAACAATGTTTTCAAAACTATATACTA
1 CAAAAACGTTTTCAAAACTATATATTATATATTTTTTC-AAAAATGTTTTCAAAACTATATATTA
*
1628295 TATATTTTTT
65 TATATATTTT
*
1628305 CAAAAACGTTTTCAAAACCATATATTATATAT
1 CAAAAACGTTTTCAAAACTATATATTATATAT
1628337 ATTATGTATA
Statistics
Matches: 209, Mismatches: 35, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
71 27 0.13
72 30 0.14
73 20 0.10
74 57 0.27
75 46 0.22
76 15 0.07
77 14 0.07
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (74 bp):
CAAAAACGTTTTCAAAACTATATATTATATATTTTTTCAAAAATGTTTTCAAAACTATATATTAT
ATATATTTT
Found at i:1630146 original size:23 final size:23
Alignment explanation
Indices: 1630120--1630164 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1630110 TTGATTTACA
* *
1630120 AAGAATAAAAAGATTGCATGGTG
1 AAGAAGAAAAACATTGCATGGTG
*
1630143 AAGAAGAAGAACATTGCATGGT
1 AAGAAGAAAAACATTGCATGGT
1630165 CGTCATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.27, T:0.20
Consensus pattern (23 bp):
AAGAAGAAAAACATTGCATGGTG
Found at i:1638024 original size:20 final size:20
Alignment explanation
Indices: 1637999--1638043 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1637989 GTCATCCAAT
*
1637999 TTTTTAAACCCCAGACCGGA
1 TTTTTAAACCCCAAACCGGA
*
1638019 TTTTTAAACCTCAAACCGGA
1 TTTTTAAACCCCAAACCGGA
1638039 TTTTT
1 TTTTT
1638044 TTCCTGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTTTAAACCCCAAACCGGA
Found at i:1646231 original size:39 final size:41
Alignment explanation
Indices: 1646188--1646265 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 41
1646178 AATTAGGGTT
*
1646188 GTAAACGAGTAGACTCAAGTTC-A-ATTTCTAATTAGATCG
1 GTAAACGAGTAGAATCAAGTTCAATATTTCTAATTAGATCG
* *
1646227 GTAAATGAGTCGAATCAAGTTCAATATTTCTAATTAGAT
1 GTAAACGAGTAGAATCAAGTTCAATATTTCTAATTAGAT
1646266 TTGTAAACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 19 0.56
40 1 0.03
41 14 0.41
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (41 bp):
GTAAACGAGTAGAATCAAGTTCAATATTTCTAATTAGATCG
Found at i:1646288 original size:41 final size:39
Alignment explanation
Indices: 1646177--1646273 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 39
1646167 ACGAAGGTTT
** *
1646177 TAATTAGGGTTGTAAACGAGTAGACTCAAGTTCAATTTC
1 TAATTAGATTTGTAAACGAGTAGAATCAAGTTCAATTTC
** * *
1646216 TAATTAGATCGGTAAATGAGTCGAATCAAGTTCAATATTTC
1 TAATTAGATTTGTAAACGAGTAGAATCAAGTTC-A-ATTTC
1646257 TAATTAGATTTGTAAAC
1 TAATTAGATTTGTAAAC
1646274 AAGTTGAGTA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
39 26 0.57
40 1 0.02
41 19 0.41
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (39 bp):
TAATTAGATTTGTAAACGAGTAGAATCAAGTTCAATTTC
Found at i:1646634 original size:28 final size:29
Alignment explanation
Indices: 1646589--1646648 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1646579 GGCTCCCAAT
***
1646589 TTAGGGCTCCC-AATTTTTTTATTTATAA
1 TTAGGGCTCCCAAATTTTAAAATTTATAA
1646617 TTAGGGC-CCTCAAATTTTAAAATTTATAA
1 TTAGGGCTCC-CAAATTTTAAAATTTATAA
1646646 TTA
1 TTA
1646649 AGATCCCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 2 0.07
28 8 0.30
29 17 0.63
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (29 bp):
TTAGGGCTCCCAAATTTTAAAATTTATAA
Found at i:1648019 original size:17 final size:17
Alignment explanation
Indices: 1647999--1648032 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1647989 AACTCGTTAA
1647999 AAAT-TTAAGTTAAATTT
1 AAATATTAA-TTAAATTT
1648016 AAATATTAATTAAATTT
1 AAATATTAATTAAATTT
1648033 TAACCAGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AAATATTAATTAAATTT
Found at i:1649506 original size:52 final size:49
Alignment explanation
Indices: 1649403--1649513 Score: 141
Period size: 52 Copynumber: 2.2 Consensus size: 49
1649393 AAACCCACCT
* * *
1649403 TTAATTTTAAATTAATATTTAAATTTCACAAATATAATATTACATAACC
1 TTAATATTAAATTAATATATAAATTTCACAAATATAATATTAAATAACC
* * *
1649452 TTAATATTAATATTATATATATAAATTTCATAAATTATTATGTTAAATAACC
1 TTAATATTAA-ATTA-ATATATAAATTTCACAAA-TATAATATTAAATAACC
1649504 TTAATATTAA
1 TTAATATTAA
1649514 CAGTTAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
49 9 0.17
50 4 0.08
51 16 0.30
52 24 0.45
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (49 bp):
TTAATATTAAATTAATATATAAATTTCACAAATATAATATTAAATAACC
Found at i:1650093 original size:31 final size:31
Alignment explanation
Indices: 1650055--1650119 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1650045 TTGTAATACA
1650055 ATATCTGATTTAATTGAGTTACTAAGTGAGC
1 ATATCTGATTTAATTGAGTTACTAAGTGAGC
1650086 ATATCTGATTTAATTGAGTTACTAAGTGAGC
1 ATATCTGATTTAATTGAGTTACTAAGTGAGC
1650117 ATA
1 ATA
1650120 ATTAAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (31 bp):
ATATCTGATTTAATTGAGTTACTAAGTGAGC
Found at i:1652746 original size:19 final size:20
Alignment explanation
Indices: 1652707--1652747 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1652697 TAAAGTAAAA
1652707 TTATTTTTATTATAATATAT
1 TTATTTTTATTATAATATAT
1652727 TTATTTTATATT-TAAT-TAT
1 TTATTTT-TATTATAATATAT
1652746 TT
1 TT
1652748 GACCAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTTATTATAATATAT
Found at i:1653979 original size:3 final size:3
Alignment explanation
Indices: 1653973--1654007 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1653963 CTTAAAAAAA
1653973 TAT TAT TAT TAT TAT TAT TAT TAT TAAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
1654008 CATATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1658661 original size:21 final size:22
Alignment explanation
Indices: 1658637--1658694 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1658627 TAAAGCAGAA
*
1658637 AAAAAAGCAAAGAA-CAAAAAT
1 AAAAAAGCAAAGAAGCAAAAAG
* *
1658658 AAAAAAGAAAAGAAGCAAAGAG
1 AAAAAAGCAAAGAAGCAAAAAG
*
1658680 AAAATAAACAAAGAA
1 AAAA-AAGCAAAGAA
1658695 AAAGGGACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 13 0.43
22 9 0.30
23 8 0.27
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.03
Consensus pattern (22 bp):
AAAAAAGCAAAGAAGCAAAAAG
Found at i:1658698 original size:29 final size:30
Alignment explanation
Indices: 1658633--1658698 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
1658623 AAATTAAAGC
*
1658633 AGAAAAAAAAGCAAAGAACAAAAATAAAAA
1 AGAAAAAGAAGCAAAGAACAAAAATAAAAA
*
1658663 AG-AAAAGAAGCAAAG-A-GAAAATAAACAA
1 AGAAAAAGAAGCAAAGAACAAAAATAAA-AA
1658691 AGAAAAAG
1 AGAAAAAG
1658699 GGACAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 8 0.25
28 5 0.16
29 17 0.53
30 2 0.06
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (30 bp):
AGAAAAAGAAGCAAAGAACAAAAATAAAAA
Found at i:1659801 original size:32 final size:32
Alignment explanation
Indices: 1659758--1659820 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1659748 TTGAAGATTC
*
1659758 AATATTAGGGCATTTTTGGAGATTCAACATCG
1 AATATTAGGGCATCTTTGGAGATTCAACATCG
* *
1659790 AATATTGGGGCATCTTTGGGGATTCAACATC
1 AATATTAGGGCATCTTTGGAGATTCAACATC
1659821 CTGATGCGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (32 bp):
AATATTAGGGCATCTTTGGAGATTCAACATCG
Found at i:1661844 original size:18 final size:18
Alignment explanation
Indices: 1661821--1661855 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1661811 CTAGGAGATT
1661821 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1661839 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1661856 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1662900 original size:23 final size:23
Alignment explanation
Indices: 1662867--1662911 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1662857 ATCATTATAT
*
1662867 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1662890 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1662912 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1664026 original size:85 final size:85
Alignment explanation
Indices: 1663891--1664116 Score: 258
Period size: 85 Copynumber: 2.6 Consensus size: 85
1663881 AAAGCATAGT
* * * * * *
1663891 TCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCAAGTTCGATTACATTCAACTCAAGGACA
1 TCAAGGCGAGAAAGGCTATCTGTCAACAAAAATCTTCGAGTTTGATTACATTCAAATCAAGGACA
1663956 TACCAAATTTACAGCATAAC
66 TACCAAATTTACAGCATAAC
* * *
1663976 TCAAGGCGAGAAAGGTTATCTGTCAACAAAAATCTTCGAGTTTGATTACATTTAAATCAAGGGCA
1 TCAAGGCGAGAAAGGCTATCTGTCAACAAAAATCTTCGAGTTTGATTACATTCAAATCAAGGACA
* * *
1664041 TATCACATTTACAGCATAGC
66 TACCAAATTTACAGCATAAC
* * * *
1664061 T-TAGGTCGAGAAAAGCTATCGGTCAACAAAAAAAT-TATCGAGTTTGATTCCATTCA
1 TCAAGG-CGAGAAAGGCTATCTGTCAAC--AAAAATCT-TCGAGTTTGATTACATTCA
1664117 GCTCGATGAC
Statistics
Matches: 119, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
84 3 0.03
85 92 0.77
86 1 0.01
87 23 0.19
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (85 bp):
TCAAGGCGAGAAAGGCTATCTGTCAACAAAAATCTTCGAGTTTGATTACATTCAAATCAAGGACA
TACCAAATTTACAGCATAAC
Found at i:1665441 original size:22 final size:22
Alignment explanation
Indices: 1665411--1665452 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1665401 AATAACCAAA
*
1665411 TTTTATCAAGAACCAAAACAAT
1 TTTTATCAACAACCAAAACAAT
* *
1665433 TTTTTTCAACAATCAAAACA
1 TTTTATCAACAACCAAAACA
1665453 GAAACGAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (22 bp):
TTTTATCAACAACCAAAACAAT
Found at i:1668758 original size:23 final size:24
Alignment explanation
Indices: 1668704--1668767 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
1668694 CTCAAGTGAA
1668704 AATTAAATAAAAAAATTACAAACT
1 AATTAAATAAAAAAATTACAAACT
*
1668728 AAAT-AATAATAAAAATTA-AAAC-
1 AATTAAATAA-AAAAATTACAAACT
* *
1668750 AATTAAATAGAAACATTA
1 AATTAAATAAAAAAATTA
1668768 AATACAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 10 0.29
23 13 0.38
24 11 0.32
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (24 bp):
AATTAAATAAAAAAATTACAAACT
Found at i:1670788 original size:17 final size:17
Alignment explanation
Indices: 1670766--1670804 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1670756 TGAATCAAAT
1670766 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1670783 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1670800 -AATTA
1 TAATTA
1670805 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1670962 original size:32 final size:32
Alignment explanation
Indices: 1670921--1670999 Score: 158
Period size: 32 Copynumber: 2.5 Consensus size: 32
1670911 AATATTTTTG
1670921 AAAAAAAGTTCGGTTCGGTTAACGGTTAAAGA
1 AAAAAAAGTTCGGTTCGGTTAACGGTTAAAGA
1670953 AAAAAAAGTTCGGTTCGGTTAACGGTTAAAGA
1 AAAAAAAGTTCGGTTCGGTTAACGGTTAAAGA
1670985 AAAAAAAGTTCGGTT
1 AAAAAAAGTTCGGTT
1671000 AATTCGAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.25
Consensus pattern (32 bp):
AAAAAAAGTTCGGTTCGGTTAACGGTTAAAGA
Found at i:1674000 original size:2 final size:2
Alignment explanation
Indices: 1673987--1674016 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1673977 ATTTTTGAGG
*
1673987 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1674017 TAAGGATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1676869 original size:21 final size:21
Alignment explanation
Indices: 1676839--1676884 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1676829 ATTCGCGTTG
*
1676839 CGATAATTGAGAATCGAGTTA
1 CGATAATTGAAAATCGAGTTA
* * *
1676860 CGATAGTTGAAAATCGCGTTG
1 CGATAATTGAAAATCGAGTTA
1676881 CGAT
1 CGAT
1676885 TTTCCAGTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (21 bp):
CGATAATTGAAAATCGAGTTA
Found at i:1676898 original size:20 final size:20
Alignment explanation
Indices: 1676873--1676932 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 20
1676863 TAGTTGAAAA
1676873 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
*
1676893 TCGCGTTGCGATAGTTTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
1676915 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
1676933 AATTCGTTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 17 0.49
21 1 0.03
22 17 0.49
ACGTcount: A:0.13, C:0.22, G:0.25, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:1676921 original size:22 final size:22
Alignment explanation
Indices: 1676876--1676989 Score: 105
Period size: 22 Copynumber: 5.4 Consensus size: 22
1676866 TTGAAAATCG
*
1676876 CGTTGCGAT--TTTCCAGTTCG-
1 CGTTGCGATAGTTTACAGTT-GT
1676896 CGTTGCGATAGTTTACAGTTGT
1 CGTTGCGATAGTTTACAGTTGT
* **
1676918 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTTTACAGTTGT
* *
1676937 CGTTGCAATAGTCTACAGTTGT
1 CGTTGCGATAGTTTACAGTTGT
* *
1676959 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTTTACAGTTGT
1676981 CGTTGCGAT
1 CGTTGCGAT
1676990 TTTCCAAATT
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
19 9 0.12
20 15 0.20
21 6 0.08
22 46 0.61
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTTTACAGTTGT
Found at i:1676941 original size:41 final size:41
Alignment explanation
Indices: 1676876--1676967 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
1676866 TTGAAAATCG
* * *
1676876 CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTTACAGTTGT
1 CGTTGCGATTTTCCAATTC-CGTTGCAATAGTCTACAGTTGT
1676918 CGTTGCGATTTTCCAAATT-CGTTGCAATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-AATTCCGTTGCAATAGTCTACAGTTGT
*
1676959 TGTTGCGAT
1 CGTTGCGAT
1676968 AGTCTACAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
41 28 0.62
42 14 0.31
43 3 0.07
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAATTCCGTTGCAATAGTCTACAGTTGT
Found at i:1677286 original size:22 final size:22
Alignment explanation
Indices: 1677257--1677309 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1677247 AATTTGGAAA
1677257 ATCGCAACGACAACTATAGACT
1 ATCGCAACGACAACTATAGACT
* * *
1677279 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTATAGACT
1677301 ATCGCAACG
1 ATCGCAACG
1677310 CGAAATGCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTATAGACT
Found at i:1683605 original size:42 final size:40
Alignment explanation
Indices: 1683556--1683647 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 40
1683546 GTATTCTAAG
* *
1683556 TTAGAGTTTAAAATTTCA-GATTTTAGGGTTTGAAGGTTAGAT
1 TTAGAGTTTAAAA-TTCATGA-TTTAGGATTT-AAAGTTAGAT
* *
1683598 TTAGAGTTTAAGATTCATGATTTAGGATTTAAAGTTATAT
1 TTAGAGTTTAAAATTCATGATTTAGGATTTAAAGTTAGAT
1683638 TTAGAGTTTA
1 TTAGAGTTTA
1683648 GGGTTTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
40 18 0.40
41 13 0.29
42 14 0.31
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.45
Consensus pattern (40 bp):
TTAGAGTTTAAAATTCATGATTTAGGATTTAAAGTTAGAT
Found at i:1702066 original size:104 final size:104
Alignment explanation
Indices: 1701908--1702129 Score: 288
Period size: 104 Copynumber: 2.1 Consensus size: 104
1701898 AAAACAACTT
* * *
1701908 TTAATCTCACTTGAGATTGTTATTTCTTTCAAAACATATTTCATCTCGCTTGAGACATTTTTCCT
1 TTAATCTCACTTGAGATTGTTATTTATTTCAAAACAAATTTCATCTCACTTGAGACA-TTTTCC-
* ** * *
1701973 TTG-AT-ATACAAATTTTGAATTTGCTTCACTT-TAACAAAA
64 -CGCATAATACAAATTTCAAAGTTGCTTCACTTGAAACAAAA
* *
1702012 TTAATCTCACTTGAGATTGTTGTTTATTTCAAAACAAATTTCGTCTCACTTGAGACATTTTCCCG
1 TTAATCTCACTTGAGATTGTTATTTATTTCAAAACAAATTTCATCTCACTTGAGACATTTTCCCG
* *
1702077 CATAATACAAATTTCAAAGTTGTTTTACTTGAAACAAAA
66 CATAATACAAATTTCAAAGTTGCTTCACTTGAAACAAAA
1702116 TTAATCTCACTTGA
1 TTAATCTCACTTGA
1702130 AATTTTCAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
101 1 0.01
102 2 0.02
103 27 0.26
104 73 0.71
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (104 bp):
TTAATCTCACTTGAGATTGTTATTTATTTCAAAACAAATTTCATCTCACTTGAGACATTTTCCCG
CATAATACAAATTTCAAAGTTGCTTCACTTGAAACAAAA
Found at i:1702911 original size:28 final size:28
Alignment explanation
Indices: 1702830--1702895 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
1702820 AAAACACATC
*
1702830 ATCTTTGAGTTTGTTTTTCTTGAAAGAA
1 ATCTTTGAGTTTGTTTTTCTTGAAACAA
1702858 ATCTTTGAGTTTGTTTTTCTTGAAACAA
1 ATCTTTGAGTTTGTTTTTCTTGAAACAA
1702886 ATCTTTGAGT
1 ATCTTTGAGT
1702896 CGGTTTCCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (28 bp):
ATCTTTGAGTTTGTTTTTCTTGAAACAA
Found at i:1703171 original size:134 final size:134
Alignment explanation
Indices: 1702938--1703220 Score: 399
Period size: 134 Copynumber: 2.1 Consensus size: 134
1702928 GACCAGACTA
* *
1702938 CCTCATCGCGTAGGAGCAGTGTCAACCATAGATAACCAGCCATCCTCATCACGTAGGAACCATGT
1 CCTCATCACGTAGGAGCAGTGTCAACAATAGATAACCAGCCATCCTCATCACGTAGGAACCATGT
* * * * *
1703003 TATCGCCTTTCCTAAAGATGGCCATAACTCTTCATCAAGTATGAG-CAGTGTCATCCACCGACCA
66 TATCACCCTTCCTAAAGATGACCAGAACTCTTCATCAAGTATGAGCCA-TGTCAACCACCGACCA
1703067 AACCT
130 AACCT
* * * *
1703072 CCTCATCACGTAGGAGCCGTGTCAACAATAGATAACTAGCCGTCCTCATCGCGTAGGAACCGA-G
1 CCTCATCACGTAGGAGCAGTGTCAACAATAGATAACCAGCCATCCTCATCACGTAGGAACC-ATG
* * *
1703136 TTATCACCCTTCCTAAAGATGACCAGAATTGTTCATCACGTATGAGCCATGTCAACCACCGACCA
65 TTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCAAGTATGAGCCATGTCAACCACCGACCA
*
1703201 GACCT
130 AACCT
1703206 CCTCATCACGTAGGA
1 CCTCATCACGTAGGA
1703221 ACCGAGTTAT
Statistics
Matches: 132, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
134 129 0.98
135 3 0.02
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (134 bp):
CCTCATCACGTAGGAGCAGTGTCAACAATAGATAACCAGCCATCCTCATCACGTAGGAACCATGT
TATCACCCTTCCTAAAGATGACCAGAACTCTTCATCAAGTATGAGCCATGTCAACCACCGACCAA
ACCT
Found at i:1703232 original size:91 final size:92
Alignment explanation
Indices: 1703114--1703312 Score: 251
Period size: 92 Copynumber: 2.2 Consensus size: 92
1703104 TAACTAGCCG
* * * * *
1703114 TCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAAAGA-TGACC-AGAATTGTTCATCACGT
1 TCCTCATCACGTAGGAACCGAGTTATCACACTTCCTAAAGATTG-CCAAAAACTCTTCATCACGT
* *
1703177 ATGAGCCATGTCAACCACC-GACCAGACC
65 ATGAGCAATGTCAACC-CCTGACCAGAAC
* *
1703205 TCCTCATCACGTAGGAACCGAGTTATCACACTTCCTAAAGATTGCCAAAAACTCTTTATCATGTA
1 TCCTCATCACGTAGGAACCGAGTTATCACACTTCCTAAAGATTGCCAAAAACTCTTCATCACGTA
*
1703270 TGAGCAATGTCATCCCCTGACCAGAAC
66 TGAGCAATGTCAACCCCTGACCAGAAC
* *
1703297 TCTTCATCATGTAGGA
1 TCCTCATCACGTAGGA
1703313 GTTGTATCAC
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
91 43 0.46
92 50 0.54
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (92 bp):
TCCTCATCACGTAGGAACCGAGTTATCACACTTCCTAAAGATTGCCAAAAACTCTTCATCACGTA
TGAGCAATGTCAACCCCTGACCAGAAC
Found at i:1703525 original size:3 final size:3
Alignment explanation
Indices: 1703517--1703584 Score: 84
Period size: 3 Copynumber: 22.0 Consensus size: 3
1703507 TTTTTTCTAT
*
1703517 TTA TTA TTA CCTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1703563 TGT- TTA TTAA CTA TTA TTA TTA
1 T-TA TTA TT-A TTA TTA TTA TTA
1703585 ATACAAATAC
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
2 1 0.02
3 51 0.89
4 5 0.09
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1705179 original size:16 final size:16
Alignment explanation
Indices: 1705154--1705188 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1705144 ATATTTATGC
* *
1705154 TTTATTATTTTGTCCT
1 TTTATAATTTAGTCCT
1705170 TTTATAATTTAGTCCT
1 TTTATAATTTAGTCCT
1705186 TTT
1 TTT
1705189 TTTTAATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTATAATTTAGTCCT
Found at i:1705347 original size:19 final size:17
Alignment explanation
Indices: 1705307--1705354 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
1705297 TGTTTTTTTA
*
1705307 TATATTATTTATTTCAT
1 TATATTATTTATCTCAT
1705324 TATATTATTTTATCTCAT
1 TATATTA-TTTATCTCAT
1705342 TCATATTAATTTA
1 T-ATATT-ATTTA
1705355 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 7 0.26
18 10 0.37
19 9 0.33
20 1 0.04
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTATTTATCTCAT
Found at i:1711859 original size:14 final size:14
Alignment explanation
Indices: 1711802--1711891 Score: 74
Period size: 14 Copynumber: 6.5 Consensus size: 14
1711792 CGCCTGGTGC
*
1711802 AGTCCACTCA-CCG
1 AGTCAACTCATCCG
* *
1711815 AGTCAACCCATCCA
1 AGTCAACTCATCCG
* *
1711829 AGTCAACTTATCTG
1 AGTCAACTCATCCG
*
1711843 AGTCAACTCGTCCG
1 AGTCAACTCATCCG
* *
1711857 AGTCAACCCGTCCG
1 AGTCAACTCATCCG
* * *
1711871 AGTAAACTCCTCTG
1 AGTCAACTCATCCG
1711885 AGTCAAC
1 AGTCAAC
1711892 CTGTTGACTT
Statistics
Matches: 60, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
13 8 0.13
14 52 0.87
ACGTcount: A:0.28, C:0.36, G:0.16, T:0.21
Consensus pattern (14 bp):
AGTCAACTCATCCG
Found at i:1711885 original size:42 final size:42
Alignment explanation
Indices: 1711812--1711891 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
1711802 AGTCCACTCA
* *
1711812 CCGAGTCAACCCATCCAAGTCAACTTATCTGAGTCAACTCGT
1 CCGAGTCAACCCATCCAAGTAAACTCATCTGAGTCAACTCGT
* * *
1711854 CCGAGTCAACCCGTCCGAGTAAACTCCTCTGAGTCAAC
1 CCGAGTCAACCCATCCAAGTAAACTCATCTGAGTCAAC
1711892 CTGTTGACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.28, C:0.35, G:0.16, T:0.21
Consensus pattern (42 bp):
CCGAGTCAACCCATCCAAGTAAACTCATCTGAGTCAACTCGT
Found at i:1713849 original size:21 final size:20
Alignment explanation
Indices: 1713803--1713877 Score: 113
Period size: 18 Copynumber: 3.9 Consensus size: 20
1713793 ACTGAATATT
1713803 TGTCCCGAAGGACCACTATA
1 TGTCCCGAAGGACCACTATA
1713823 --TCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACT-ATA
1713842 TGTCCCGAAGGACCAC--TA
1 TGTCCCGAAGGACCACTATA
1713860 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1713878 ATAATCCCTC
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
18 33 0.66
19 3 0.06
21 14 0.28
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.17
Consensus pattern (20 bp):
TGTCCCGAAGGACCACTATA
Found at i:1718863 original size:18 final size:18
Alignment explanation
Indices: 1718840--1718931 Score: 121
Period size: 18 Copynumber: 4.9 Consensus size: 18
1718830 ACTGAATATT
1718840 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1718858 TGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCAC---TA
1718879 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * *
1718897 TGTCCCAAAAGACGACTA
1 TGTCCCGAAGGACCACTA
*
1718915 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1718932 GATAATCCCT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
18 46 0.72
21 18 0.28
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1718886 original size:39 final size:38
Alignment explanation
Indices: 1718840--1718931 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 38
1718830 ACTGAATATT
* *
1718840 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTATGTCCCAAAAGACCACT-ATA
*
1718879 TGTCCCGAAGGACCACTATGTCCCAAAAGACGACTATA
1 TGTCCCGAAGGACCACTATGTCCCAAAAGACCACTATA
1718917 --TCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1718932 GATAATCCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 15 0.30
38 3 0.06
39 32 0.64
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (38 bp):
TGTCCCGAAGGACCACTATGTCCCAAAAGACCACTATA
Found at i:1720511 original size:24 final size:22
Alignment explanation
Indices: 1720461--1720516 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 22
1720451 AATAAAGGTA
1720461 TGCATCGATGCATTCTATAGTG
1 TGCATCGATGCATTCTATAGTG
1720483 T--ATCGATGCATTCCT-TAACGTG
1 TGCATCGATGCATT-CTAT-A-GTG
1720505 TGCATCGATGCA
1 TGCATCGATGCA
1720517 CTACATGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 12 0.41
21 3 0.10
22 5 0.17
24 9 0.31
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (22 bp):
TGCATCGATGCATTCTATAGTG
Found at i:1722099 original size:66 final size:66
Alignment explanation
Indices: 1721976--1722100 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
1721966 TGTATGAAGA
* * * *
1721976 CTCTGGTAGGTTCAGTCGCTGCTGGTAATTCCTTGTATAGGTTCAACACCGATTGGTAATTCATA
1 CTCTGGTAAGTTCAGTCGCTGCTAGTAATTCCTTGAATAGGTTCAACACCGACTGGTAATTCATA
1722041 T
66 T
* * * *
1722042 CTCTGGTAAGTTCAGTCGCTGCTAGTAATTCCTTGAATAGTTTTAGCATCGACTGGTAA
1 CTCTGGTAAGTTCAGTCGCTGCTAGTAATTCCTTGAATAGGTTCAACACCGACTGGTAA
1722101 ATCCTTATGG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (66 bp):
CTCTGGTAAGTTCAGTCGCTGCTAGTAATTCCTTGAATAGGTTCAACACCGACTGGTAATTCATA
T
Found at i:1727006 original size:16 final size:17
Alignment explanation
Indices: 1726981--1727013 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1726971 TAACAAAAAG
1726981 TATTAAATA-TTAAATA
1 TATTAAATATTTAAATA
*
1726997 TATTATATATTTAAATA
1 TATTAAATATTTAAATA
1727014 CATATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAAATATTTAAATA
Found at i:1728213 original size:21 final size:21
Alignment explanation
Indices: 1728189--1728229 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1728179 TCAAATTAAT
1728189 ATAAAATAATTTTAAATTTTG
1 ATAAAATAATTTTAAATTTTG
* * *
1728210 ATAATATATTTTTAACTTTT
1 ATAAAATAATTTTAAATTTT
1728230 CGCTTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
ATAAAATAATTTTAAATTTTG
Found at i:1734747 original size:15 final size:14
Alignment explanation
Indices: 1734735--1734832 Score: 72
Period size: 15 Copynumber: 6.4 Consensus size: 14
1734725 TATGTAATTT
1734735 TATTTTTTGTAATTG
1 TATTTTTTGT-ATTG
*
1734750 TATTTTCTCGTATTG
1 TATTTT-TTGTATTG
*
1734765 TATTTTTTGGTATTA
1 TATTTTTT-GTATTG
*
1734780 TATTTTATAT-TATTT
1 TATTTT-T-TGTATTG
1734795 TAATTTTTTGGTATTG
1 T-ATTTTTT-GTATTG
*
1734811 TATTTTTTTAGTATTA
1 TA-TTTTTT-GTATTG
1734827 TATTTT
1 TATTTT
1734833 ATGTTATTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
14 2 0.03
15 38 0.56
16 27 0.40
17 1 0.01
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.67
Consensus pattern (14 bp):
TATTTTTTGTATTG
Found at i:1734771 original size:30 final size:30
Alignment explanation
Indices: 1734735--1734832 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
1734725 TATGTAATTT
* *
1734735 TATTTTTT-GTAATTGTATTTTCTCGTATTG
1 TATTTTTTGGT-ATTGTATTTTATAGTATTG
* * *
1734765 TATTTTTTGGTATTATATTTTATATTATTT
1 TATTTTTTGGTATTGTATTTTATAGTATTG
* *
1734795 TAATTTTTTGGTATTGTATTTTTTTAGTATTA
1 T-ATTTTTTGGTATTGTA-TTTTATAGTATTG
1734827 TATTTT
1 TATTTT
1734833 ATGTTATTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
30 23 0.41
31 22 0.39
32 11 0.20
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.67
Consensus pattern (30 bp):
TATTTTTTGGTATTGTATTTTATAGTATTG
Found at i:1734809 original size:16 final size:16
Alignment explanation
Indices: 1734766--1734849 Score: 64
Period size: 16 Copynumber: 5.4 Consensus size: 16
1734756 CTCGTATTGT
1734766 ATTTTTTGGTATTAT-
1 ATTTTTTGGTATTATA
* ** *
1734781 ATTTTATATTATTTTA
1 ATTTTTTGGTATTATA
*
1734797 ATTTTTTGGTATTGTA
1 ATTTTTTGGTATTATA
* *
1734813 TTTTTTTAGTATTAT-
1 ATTTTTTGGTATTATA
* * *
1734828 ATTTTATGTTATTTTA
1 ATTTTTTGGTATTATA
1734844 ATTTTT
1 ATTTTT
1734850 GGTGGTGTGT
Statistics
Matches: 50, Mismatches: 17, Indels: 3
0.71 0.24 0.04
Matches are distributed among these distances:
15 21 0.42
16 29 0.58
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (16 bp):
ATTTTTTGGTATTATA
Found at i:1734832 original size:31 final size:31
Alignment explanation
Indices: 1734735--1734832 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
1734725 TATGTAATTT
* * *
1734735 TATTTTTT-GTAATTGTA-TTTTCTCGTATTG
1 TATTTTTTGGT-ATTGTATTTTTTTAGTATTA
* *
1734765 TATTTTTTGGTATTATATTTTATATTA-TTTTA
1 TATTTTTTGGTATTGTATTTT-T-TTAGTATTA
1734797 -ATTTTTTGGTATTGTATTTTTTTAGTATTA
1 TATTTTTTGGTATTGTATTTTTTTAGTATTA
1734827 TATTTT
1 TATTTT
1734833 ATGTTATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
29 3 0.05
30 18 0.33
31 29 0.53
32 4 0.07
33 1 0.02
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.67
Consensus pattern (31 bp):
TATTTTTTGGTATTGTATTTTTTTAGTATTA
Found at i:1734833 original size:47 final size:46
Alignment explanation
Indices: 1734759--1734849 Score: 155
Period size: 47 Copynumber: 2.0 Consensus size: 46
1734749 GTATTTTCTC
*
1734759 GTATTGTATTTTTTGGTATTATATTTTATATTATTTTAATTTTTTG
1 GTATTGTATTTTTTAGTATTATATTTTATATTATTTTAATTTTTTG
*
1734805 GTATTGTATTTTTTTAGTATTATATTTTATGTTATTTTAATTTTT
1 GTATTGTA-TTTTTTAGTATTATATTTTATATTATTTTAATTTTT
1734850 GGTGGTGTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
46 8 0.19
47 34 0.81
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.68
Consensus pattern (46 bp):
GTATTGTATTTTTTAGTATTATATTTTATATTATTTTAATTTTTTG
Found at i:1734840 original size:15 final size:15
Alignment explanation
Indices: 1734724--1734840 Score: 58
Period size: 15 Copynumber: 7.7 Consensus size: 15
1734714 TAGACCATAA
* *
1734724 TTATGTAATTTTATT
1 TTATGTTATTGTATT
* *
1734739 TTTTGTAATTGTATT
1 TTATGTTATTGTATT
*
1734754 TTCTCG-TATTGTATT
1 TTAT-GTTATTGTATT
* * *
1734769 TTTTGGTATTATATT
1 TTATGTTATTGTATT
* *
1734784 TTATATTATTTTAATT
1 TTATGTTATTGT-ATT
* *
1734800 TTTTGGTATTGTATT
1 TTATGTTATTGTATT
* *
1734815 TT-TTTAGTATTATATT
1 TTATGT--TATTGTATT
1734831 TTATGTTATT
1 TTATGTTATT
1734841 TTAATTTTTG
Statistics
Matches: 78, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
14 2 0.03
15 52 0.67
16 22 0.28
17 2 0.03
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (15 bp):
TTATGTTATTGTATT
Found at i:1746068 original size:37 final size:38
Alignment explanation
Indices: 1746008--1746091 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
1745998 TGGTAACCAA
1746008 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
1746045 CTTTGAAAAATA-GTTTTTTAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
1746082 -GTTGAAAAAT
1 CTTTGAAAAAT
1746092 GATAATGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.21
37 32 0.76
38 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1750638 original size:37 final size:38
Alignment explanation
Indices: 1750583--1750666 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
1750573 TGGTAACCAA
1750583 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
1750620 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
1750657 -GTTGAAAAAT
1 CTTTGAAAAAT
1750667 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1756817 original size:3 final size:3
Alignment explanation
Indices: 1756811--1756876 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
1756801 ATTTGTCACT
1756811 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1756859 ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
1756877 GGAGTCTGTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1758023 original size:2 final size:2
Alignment explanation
Indices: 1758016--1758048 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1758006 GAATAACTTG
1758016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1758049 ATAAGAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1758847 original size:22 final size:22
Alignment explanation
Indices: 1758819--1758876 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
1758809 AAATCAAATT
1758819 TTTACATAAATACGTGTTCACC
1 TTTACATAAATACGTGTTCACC
1758841 TTTACATAAATACGTGTTCACC
1 TTTACATAAATACGTGTTCACC
1758863 TTTACATAAATACG
1 TTTACATAAATACG
1758877 GATCCTTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTACATAAATACGTGTTCACC
Found at i:1760533 original size:14 final size:14
Alignment explanation
Indices: 1760514--1760542 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1760504 ATACCATCCA
1760514 TTTGATATGAATTC
1 TTTGATATGAATTC
1760528 TTTGATATGAATTC
1 TTTGATATGAATTC
1760542 T
1 T
1760543 CTTACACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (14 bp):
TTTGATATGAATTC
Found at i:1763022 original size:15 final size:15
Alignment explanation
Indices: 1763004--1763034 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1762994 AAGTTTTGAT
1763004 AGTCTAAGTAATTAA
1 AGTCTAAGTAATTAA
*
1763019 AGTCTAGGTAATTAA
1 AGTCTAAGTAATTAA
1763034 A
1 A
1763035 TTATATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.32
Consensus pattern (15 bp):
AGTCTAAGTAATTAA
Found at i:1764564 original size:57 final size:56
Alignment explanation
Indices: 1764434--1764585 Score: 162
Period size: 56 Copynumber: 2.7 Consensus size: 56
1764424 GTTGTGCTCC
* * * *
1764434 AATCTAGAAATTTA-CACCTCTATGCTTTTAAAAAACAATTTAGTATGTTGTGCTTT
1 AATCTAGAAA-CTAGCACCTCTATGCTTTTAATAAACAATTGAGTATGTTGTGCCTT
* * * ** *
1764490 AATTTAGAAATTGGCACCTCTATGCTTTTAATAAATGATTGAGTTTTGTTGTGCCTT
1 AATCTAGAAACTAGCACCTCTATGCTTTTAATAAACAATTGAG-TATGTTGTGCCTT
* *
1764547 AATCTAGGAACTAGCACCTCTAATGCTTTTAATATACAA
1 AATCTAGAAACTAGCACCTCT-ATGCTTTTAATAAACAA
1764586 GCAATAGAGT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
55 2 0.03
56 34 0.44
57 28 0.36
58 14 0.18
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (56 bp):
AATCTAGAAACTAGCACCTCTATGCTTTTAATAAACAATTGAGTATGTTGTGCCTT
Found at i:1769938 original size:60 final size:60
Alignment explanation
Indices: 1769746--1769940 Score: 256
Period size: 60 Copynumber: 3.2 Consensus size: 60
1769736 ACCCAGTTTC
* *
1769746 CAAATTCGCAACTCGAATATGTAAATCGCAACGTGAATTTGTAAATCGCAACACAGAAGT
1 CAAATTCGCAACGCGAATATGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGT
* * *
1769806 CAAATTCGCAACAC--ATAAGTCAAATTCGCAACGCTGAA---GTCAAATTCGCAACACTGAAGT
1 CAAATTCGCAACGCGAATATGT-AAA-TCGCAACGC-GAATTTGT-AAA-TCGCAACACAGAAGT
*
1769866 CAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGT
1 CAAATTCGCAACGCGAATATGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGT
1769926 CAAATTCGCAACGCG
1 CAAATTCGCAACGCG
1769941 GTAGTCAAAT
Statistics
Matches: 117, Mismatches: 8, Indels: 20
0.81 0.06 0.14
Matches are distributed among these distances:
58 7 0.06
59 9 0.08
60 86 0.74
61 9 0.08
62 6 0.05
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.21
Consensus pattern (60 bp):
CAAATTCGCAACGCGAATATGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGT
Found at i:1769955 original size:60 final size:61
Alignment explanation
Indices: 1769746--1769966 Score: 253
Period size: 60 Copynumber: 3.7 Consensus size: 61
1769736 ACCCAGTTTC
* *
1769746 CAAATTCGCAACTCGAATATGTAAATCGCAACG-TGAATTTGTAAATCGCAACACAGAAGT
1 CAAATTCGCAACGCGAATAAGTAAATCGCAACGCTGAATTTGTAAATCGCAACACAGAAGT
* *
1769806 CAAATTCGCAACAC--ATAAGTCAAATTCGCAACGCTGAA---GTCAAATTCGCAACACTGAAGT
1 CAAATTCGCAACGCGAATAAGT-AAA-TCGCAACGCTGAATTTGT-AAA-TCGCAACACAGAAGT
**
1769866 CAAATTCGCAACGCGAATCTGTAAATCGCAACGC-GAATTTGTAAATCGCAACACAGAAGT
1 CAAATTCGCAACGCGAATAAGTAAATCGCAACGCTGAATTTGTAAATCGCAACACAGAAGT
* *
1769926 CAAATTCGCAACGCG-GT-AGTCAAATTCGCAACACTGAATTT
1 CAAATTCGCAACGCGAATAAGT-AAA-TCGCAACGCTGAATTT
1769967 CAAATTCGCA
Statistics
Matches: 138, Mismatches: 10, Indels: 25
0.80 0.06 0.14
Matches are distributed among these distances:
58 9 0.07
59 13 0.09
60 94 0.68
61 16 0.12
62 6 0.04
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (61 bp):
CAAATTCGCAACGCGAATAAGTAAATCGCAACGCTGAATTTGTAAATCGCAACACAGAAGT
Found at i:1769989 original size:60 final size:62
Alignment explanation
Indices: 1769746--1769997 Score: 251
Period size: 60 Copynumber: 4.2 Consensus size: 62
1769736 ACCCAGTTTC
* * * *
1769746 CAAATTCGCAACTCGAATATGT-AAA-TCGCAACG-TGAATTTGTAAA-TCGCAACACAGAAGT
1 CAAATTCGCAACGCG-ATAAGTCAAATTCGCAACGCTGAATTT-CAAATTCGCAACACTGAAGT
* *
1769806 CAAATTCGCAACAC-ATAAGTCAAATTCGCAACGCTGAA-GTCAAATTCGCAACACTGAAGT
1 CAAATTCGCAACGCGATAAGTCAAATTCGCAACGCTGAATTTCAAATTCGCAACACTGAAGT
** * *
1769866 CAAATTCGCAACGCGAATCTGT-AAA-TCGCAACGC-GAATTTGTAAA-TCGCAACACAGAAGT
1 CAAATTCGCAACGCG-ATAAGTCAAATTCGCAACGCTGAATTT-CAAATTCGCAACACTGAAGT
* * *
1769926 CAAATTCGCAACGCGGT-AGTCAAATTCGCAACACTGAATTTCAAATTCGC-A-ACTGAATTT
1 CAAATTCGCAACGCGATAAGTCAAATTCGCAACGCTGAATTTCAAATTCGCAACACTGAA-GT
1769986 CAAATTCGCAAC
1 CAAATTCGCAAC
1769998 TGAATTTCAA
Statistics
Matches: 162, Mismatches: 17, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
58 7 0.04
59 18 0.11
60 113 0.70
61 20 0.12
62 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (62 bp):
CAAATTCGCAACGCGATAAGTCAAATTCGCAACGCTGAATTTCAAATTCGCAACACTGAAGT
Found at i:1770008 original size:38 final size:39
Alignment explanation
Indices: 1769945--1770055 Score: 136
Period size: 39 Copynumber: 2.8 Consensus size: 39
1769935 AACGCGGTAG
*
1769945 TCAAATTCGCAACACTGAATTTCAAATTCGCAACTGAA-TT
1 TCAAATTCGC-A-ACTGAATTTCAAATTCGCAACTCAATTT
*
1769985 TCAAATTCGCAACTGAATTTCAAATTCGTAACTCAATTT
1 TCAAATTCGCAACTGAATTTCAAATTCGCAACTCAATTT
* * *
1770024 TCGAATTCGCAACACGAATTT-AATTTCGCAAC
1 TCAAATTCGCAAC-TGAATTTCAAATTCGCAAC
1770056 AGGTTTTAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
38 23 0.37
39 24 0.38
40 16 0.25
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.32
Consensus pattern (39 bp):
TCAAATTCGCAACTGAATTTCAAATTCGCAACTCAATTT
Found at i:1770030 original size:20 final size:19
Alignment explanation
Indices: 1769945--1770055 Score: 134
Period size: 19 Copynumber: 5.7 Consensus size: 19
1769935 AACGCGGTAG
1769945 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
1769966 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
1769985 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
1770004 TCAAATTCGTAACTCAATTT
1 TCAAATTCGCAACTGAA-TT
* *
1770024 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
1770044 T-AATTTCGCAAC
1 TCAAATTCGCAAC
1770056 AGGTTTTAGT
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 51 0.64
20 17 0.21
21 12 0.15
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:1770056 original size:19 final size:20
Alignment explanation
Indices: 1769687--1770056 Score: 191
Period size: 20 Copynumber: 18.6 Consensus size: 20
1769677 AAATGACCAA
** *
1769687 CAAATTCGCAACTTG-ATCT
1 CAAATTCGCAACACGAATTT
* * *
1769706 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACACGAATTT
* * *
1769726 CAATTTCGCAAC-CCAGTTT
1 CAAATTCGCAACACGAATTT
*
1769745 CCAAATTCGCAACTCGAATATGT
1 -CAAATTCGCAACACGAAT-T-T
**
1769768 -AAA-TCGCAACGTGAATTT
1 CAAATTCGCAACACGAATTT
* *
1769786 GTAAA-TCGCAACACAGAA-GT
1 -CAAATTCGCAACAC-GAATTT
**
1769806 CAAATTCGCAACAC-ATAAGT
1 CAAATTCGCAACACGA-ATTT
* *
1769826 CAAATTCGCAACGCTGAA-GT
1 CAAATTCGCAACAC-GAATTT
*
1769846 CAAATTCGCAACACTGAA-GT
1 CAAATTCGCAACAC-GAATTT
*
1769866 CAAATTCGCAACGCGAATCTGT
1 CAAATTCGCAACACGAAT-T-T
*
1769888 -AAA-TCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
* *
1769906 GTAAA-TCGCAACACAGAA-GT
1 -CAAATTCGCAACAC-GAATTT
* * *
1769926 CAAATTCGCAACGCG-GTAGT
1 CAAATTCGCAACACGAAT-TT
1769946 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
*
1769967 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
*
1769986 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* *
1770005 CAAATTCGTAACTC-AATTTT
1 CAAATTCGCAACACGAA-TTT
*
1770025 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
1770045 -AATTTCGCAACA
1 CAAATTCGCAACA
1770057 GGTTTTAGTT
Statistics
Matches: 285, Mismatches: 39, Indels: 54
0.75 0.10 0.14
Matches are distributed among these distances:
18 3 0.01
19 77 0.27
20 168 0.59
21 32 0.11
22 4 0.01
23 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:1770923 original size:24 final size:24
Alignment explanation
Indices: 1770896--1770949 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1770886 GTATTCGAAA
*
1770896 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1770920 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1770944 TTTGAT
1 TTTGAT
1770950 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1773226 original size:6 final size:6
Alignment explanation
Indices: 1773215--1773249 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1773205 AAGCAAAAGG
* *
1773215 AAATCA AAATCA AAATCG CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
1773250 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:1773239 original size:18 final size:18
Alignment explanation
Indices: 1773216--1773261 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1773206 AGCAAAAGGA
*
1773216 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
1773234 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
*
1773252 AATCACAATC
1 AATCAAAATC
1773262 GGCTTCAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.54, C:0.26, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:1773771 original size:14 final size:14
Alignment explanation
Indices: 1773754--1773788 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1773744 CAAATTAAAA
1773754 AAATCAACTTTTAC
1 AAATCAACTTTTAC
1773768 AAATCAACTTTTAC
1 AAATCAACTTTTAC
1773782 AAATCAA
1 AAATCAA
1773789 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:1775229 original size:21 final size:21
Alignment explanation
Indices: 1775200--1775314 Score: 108
Period size: 21 Copynumber: 5.5 Consensus size: 21
1775190 GTGAATCGGG
1775200 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGAC
* ** *
1775221 C-CATTGAACGATGACAGGGGC
1 CTC-TTGAACGGTGGGAGGGAC
*
1775242 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGAC
* *
1775263 CTCTTGAACGATGAGA-GGAGC
1 CTCTTGAACGGTGGGAGGGA-C
* * *
1775284 CTCTTGAACGATAGGAGGCAC
1 CTCTTGAACGGTGGGAGGGAC
1775305 CTCTTGAACG
1 CTCTTGAACG
1775315 ATGACAGGTG
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
20 3 0.04
21 71 0.92
22 3 0.04
ACGTcount: A:0.23, C:0.22, G:0.36, T:0.19
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGAC
Done.