Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 148 of 230
Found at i:43576631 original size:15 final size:14
Alignment explanation
Indices: 43576613--43576641 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43576603 AAAAAGAAGG
43576613 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
43576627 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
43576641 A
1 A
43576642 TACGGTCTAG
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:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Found at i:43577386 original size:15 final size:15
Alignment explanation
Indices: 43577354--43577387 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
43577344 GTTCAACGAA
*
43577354 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
43577369 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
43577384 GAGG
1 GAGG
43577388 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:43583059 original size:15 final size:16
Alignment explanation
Indices: 43583020--43583060 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
43583010 AACAACACTC
43583020 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
43583036 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
43583050 CTTTCTTTTTC
1 CTTTCTTTTTC
43583061 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:43585231 original size:13 final size:13
Alignment explanation
Indices: 43585213--43585271 Score: 66
Period size: 13 Copynumber: 4.4 Consensus size: 13
43585203 TTGGAGTAAC
43585213 AAAAAAA-TCAAA
1 AAAAAAATTCAAA
43585225 AAAAAAATTCGAAA
1 AAAAAAATTC-AAA
* *
43585239 AAAAATTGATTCAGA
1 AAAAA--AATTCAAA
43585254 AAAAAAATTCAAA
1 AAAAAAATTCAAA
43585267 AAAAA
1 AAAAA
43585272 TCGAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 7 0.18
13 13 0.33
14 8 0.21
15 7 0.18
16 4 0.10
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:43585250 original size:16 final size:17
Alignment explanation
Indices: 43585231--43585262 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43585221 CAAAAAAAAA
43585231 ATTC-GAAAAAAAATTG
1 ATTCAGAAAAAAAATTG
43585247 ATTCAGAAAAAAAATT
1 ATTCAGAAAAAAAATT
43585263 CAAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.25
Consensus pattern (17 bp):
ATTCAGAAAAAAAATTG
Found at i:43585279 original size:12 final size:12
Alignment explanation
Indices: 43585213--43585281 Score: 52
Period size: 12 Copynumber: 5.4 Consensus size: 12
43585203 TTGGAGTAAC
*
43585213 AAAAAAATCAAA
1 AAAAAAATCGAA
43585225 AAAAAAATTCGAA
1 AAAAAAA-TCGAA
43585238 AAAAAATTGATTCAGAA
1 AAAAAA---A-TC-GAA
*
43585255 AAAAAATTC--A
1 AAAAAAATCGAA
43585265 AAAAAAATCGAA
1 AAAAAAATCGAA
43585277 AAAAA
1 AAAAA
43585282 GGAAAAAAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
10 9 0.19
12 13 0.28
13 12 0.26
16 4 0.09
17 9 0.19
ACGTcount: A:0.72, C:0.07, G:0.06, T:0.14
Consensus pattern (12 bp):
AAAAAAATCGAA
Found at i:43585324 original size:10 final size:10
Alignment explanation
Indices: 43585309--43585347 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
43585299 AAATCGAGTT
43585309 AAAAAAAAGA
1 AAAAAAAAGA
*
43585319 AAAAAAAAGT
1 AAAAAAAAGA
*
43585329 AAAAGAAAGA
1 AAAAAAAAGA
43585339 ACAAAAAAA
1 A-AAAAAAA
43585348 AGTGAAAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:43585331 original size:20 final size:21
Alignment explanation
Indices: 43585308--43585347 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
43585298 AAAATCGAGT
43585308 TAAAAAAAAGAA-AAAAAAAG
1 TAAAAAAAAGAACAAAAAAAG
*
43585328 TAAAAGAAAGAACAAAAAAA
1 TAAAAAAAAGAACAAAAAAA
43585348 AGTGAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (21 bp):
TAAAAAAAAGAACAAAAAAAG
Found at i:43586398 original size:17 final size:18
Alignment explanation
Indices: 43586366--43586399 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43586356 AAAAGAGAGT
*
43586366 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
43586384 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
43586400 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:43589614 original size:30 final size:30
Alignment explanation
Indices: 43589574--43589644 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
43589564 TTTCAATCAC
43589574 TCTT-TTTTTTTCAATT-TCG-ATTTTTTTT
1 TCTTCTTTTTTTCAATTCT-GAATTTTTTTT
* *
43589602 CTTTTCTTTTTTTTAATTCTGAATTTTTTTT
1 -TCTTCTTTTTTTCAATTCTGAATTTTTTTT
43589633 TCTTCTTTTTTT
1 TCTTCTTTTTTT
43589645 TCTTCAATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 3 0.08
30 23 0.64
31 10 0.28
ACGTcount: A:0.10, C:0.11, G:0.03, T:0.76
Consensus pattern (30 bp):
TCTTCTTTTTTTCAATTCTGAATTTTTTTT
Found at i:43589645 original size:30 final size:31
Alignment explanation
Indices: 43589577--43589646 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
43589567 CAATCACTCT
*
43589577 TTTTTTTTCAATTTCGATTTTTTTTCTTTTC
1 TTTTTTTTCAATTTCGATTTTTTTTCTCTTC
43589608 TTTTTTTT-AA-TTCTGAATTTTTTTT-TCTTC
1 TTTTTTTTCAATTTC-G-ATTTTTTTTCTCTTC
43589638 TTTTTTTTC
1 TTTTTTTTC
43589647 TTCAATACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 3 0.09
30 15 0.43
31 17 0.49
ACGTcount: A:0.10, C:0.11, G:0.03, T:0.76
Consensus pattern (31 bp):
TTTTTTTTCAATTTCGATTTTTTTTCTCTTC
Found at i:43589708 original size:13 final size:13
Alignment explanation
Indices: 43589690--43589736 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
43589680 GAATACAAAC
43589690 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
**
43589703 TTTTTTTTCAAATT
1 TTTTTTTTTGAA-T
43589717 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
43589730 TTTTTTT
1 TTTTTTT
43589737 ACAATACCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:43601016 original size:46 final size:42
Alignment explanation
Indices: 43600964--43601053 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 42
43600954 ATAGTGTGGC
*
43600964 GTTCATCATAAACCAAGGTTCTTATCATCATTGATAGTGGGTCGAG
1 GTTCATCATAAACCAAGGTTCCTATCAT--TTGATAGT--GTCGAG
**
43601010 GTTCATCATATGCCAAGGTTCCTATCATTTGATAGTGTCGAG
1 GTTCATCATAAACCAAGGTTCCTATCATTTGATAGTGTCGAG
43601052 GT
1 GT
43601054 CTTTTCTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
42 8 0.20
44 8 0.20
46 25 0.61
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (42 bp):
GTTCATCATAAACCAAGGTTCCTATCATTTGATAGTGTCGAG
Found at i:43619437 original size:16 final size:16
Alignment explanation
Indices: 43619398--43619437 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
43619388 CGTTTGGTTC
43619398 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
43619414 GCTCTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
43619430 GGTGTAAT
1 GCTGTAAT
43619438 AGTAATTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:43619588 original size:27 final size:27
Alignment explanation
Indices: 43619551--43619625 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
43619541 TAATATAAAT
* * *
43619551 AATAAATAATTTAATCATATTTTAACAT
1 AATATATAATTTAAT-ATAATTTAACAA
* *
43619579 AAT-TATAATTAAATATAATTTAATAA
1 AATATATAATTTAATATAATTTAACAA
*
43619605 AATATATAATTTAATAAAATT
1 AATATATAATTTAATATAATT
43619626 CTTAATATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
26 12 0.31
27 24 0.62
28 3 0.08
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
AATATATAATTTAATATAATTTAACAA
Found at i:43619631 original size:17 final size:17
Alignment explanation
Indices: 43619591--43619624 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43619581 TTATAATTAA
43619591 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
43619608 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
43619625 TCTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:43619685 original size:61 final size:61
Alignment explanation
Indices: 43619605--43619805 Score: 216
Period size: 61 Copynumber: 3.3 Consensus size: 61
43619595 AATTTAATAA
* *
43619605 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACCAAAATCAT
1 AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
* * * * * ** * *
43619666 AATATATAATACT-ATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATTTAATAAA
1 AATATATAAT-CTAATAAAATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAATCAT
*
43619725 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
43619786 AATATATAATACT-ATAAAAT
1 AATATATAAT-CTAATAAAAT
43619806 ATAATTTAAA
Statistics
Matches: 109, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
58 3 0.03
59 34 0.31
60 16 0.15
61 52 0.48
62 4 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (61 bp):
AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:43619756 original size:120 final size:120
Alignment explanation
Indices: 43619571--43619842 Score: 510
Period size: 120 Copynumber: 2.3 Consensus size: 120
43619561 TTAATCATAT
* *
43619571 TTTAACATAATTATAATTAAATATAATTTAAT-AAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
43619635 AAATATTCTTATATGAATTTACCAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACCAAAATCATAATATATAATACTATAAAATATAA
43619690 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
43619755 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACCAAAATCATAATATATAATACTATAAAATATAA
43619810 TTTAAAATAATTATTATTAAATATAATTTAATA
1 TTTAAAATAATTATTATTAAATATAATTTAATA
43619843 CATGAATCAA
Statistics
Matches: 149, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
119 30 0.20
120 119 0.80
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACCAAAATCATAATATATAATACTATAAAATATAA
Found at i:43619877 original size:47 final size:49
Alignment explanation
Indices: 43619828--43619924 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
43619818 AATTATTATT
* * * *
43619828 AAATATAATTT-AATA-CATGAATCAAAAGGTGAACACTTTATAAAATTA
1 AAAT-TAATTTCAATATAATGAATCAAAAGCTCAACACTGTATAAAATTA
43619876 AAATTAATTTCAATATAATGAATCAAAAGCTCAACACTGTATAAAATTA
1 AAATTAATTTCAATATAATGAATCAAAAGCTCAACACTGTATAAAATTA
43619925 TAACACATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 6 0.14
48 8 0.19
49 29 0.67
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (49 bp):
AAATTAATTTCAATATAATGAATCAAAAGCTCAACACTGTATAAAATTA
Found at i:43623336 original size:14 final size:14
Alignment explanation
Indices: 43623317--43623344 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43623307 ATTCCAATCG
43623317 CTAATGAGTTTTGA
1 CTAATGAGTTTTGA
43623331 CTAATGAGTTTTGA
1 CTAATGAGTTTTGA
43623345 TTTAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
CTAATGAGTTTTGA
Found at i:43627193 original size:39 final size:39
Alignment explanation
Indices: 43627139--43627259 Score: 197
Period size: 39 Copynumber: 3.1 Consensus size: 39
43627129 ATTTTCAATA
* * *
43627139 CACCGGCACATAGCCTGCTAGGCACATAGCCTGAATAAT
1 CACCGGCACAAAGCCTACTAGGCACATAGCCCGAATAAT
43627178 CACCGGCACAAAGCCTACTAGGCACATAGCCCGAATAAT
1 CACCGGCACAAAGCCTACTAGGCACATAGCCCGAATAAT
* *
43627217 CACCGGCACACAGCCTACTAGGCACATAGCCCAAATAAT
1 CACCGGCACAAAGCCTACTAGGCACATAGCCCGAATAAT
43627256 CACC
1 CACC
43627260 AGATTTCTAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.34, C:0.35, G:0.17, T:0.14
Consensus pattern (39 bp):
CACCGGCACAAAGCCTACTAGGCACATAGCCCGAATAAT
Found at i:43636633 original size:27 final size:27
Alignment explanation
Indices: 43636594--43636698 Score: 113
Period size: 27 Copynumber: 3.9 Consensus size: 27
43636584 ATTCTTAGTG
*
43636594 GTTGTGCTTGTAGATATGTTTTGGCGA
1 GTTGTGCTCGTAGATATGTTTTGGCGA
43636621 GTTGTGCTCGTAGATATGTTTTGGCGA
1 GTTGTGCTCGTAGATATGTTTTGGCGA
* * * * * *
43636648 GTTGTGTTCATAGGTTTGATGT-GCGA
1 GTTGTGCTCGTAGATATGTTTTGGCGA
* * *
43636674 GCTATGCTCGTAGATGTGTTTTGGC
1 GTTGTGCTCGTAGATATGTTTTGGC
43636699 AAACCATGCT
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
26 18 0.29
27 44 0.71
ACGTcount: A:0.14, C:0.10, G:0.33, T:0.42
Consensus pattern (27 bp):
GTTGTGCTCGTAGATATGTTTTGGCGA
Found at i:43642266 original size:43 final size:43
Alignment explanation
Indices: 43642216--43642495 Score: 425
Period size: 43 Copynumber: 6.5 Consensus size: 43
43642206 AGATAAGCAT
* * *
43642216 CGCTAAAGGTCATGTTCTTTAGCGGTGCTTCTATAGAAAATGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
* *
43642259 CACTAAAGGTCATGTTCTTTAGTGGCGCTTCTATAGCAAACGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
* *
43642302 CGTTAAATGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
*
43642345 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACAC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
* * * *
43642388 CGCTAAAGGTCATGTTCTTTAGTGGTGCTTCTATAGAAAATGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
*
43642431 CGCTAAAGGTCATGTTCTTTAGCGGCGATTCTATAGCAAACGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
* *
43642474 CGTTAAAGGTCACGTTCTTTAG
1 CGCTAAAGGTCATGTTCTTTAG
43642496 TGGCACTTTT
Statistics
Matches: 213, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 213 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (43 bp):
CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
Found at i:43642556 original size:129 final size:129
Alignment explanation
Indices: 43642216--43642565 Score: 341
Period size: 129 Copynumber: 2.7 Consensus size: 129
43642206 AGATAAGCAT
* ** * * * *
43642216 CGCTAAAGGTCATGTTCTTTAGCGGTGCTTCTATAG-AAAATGCCACTAAAGGTCATGTTCTTTA
1 CGCTAAAGGTCACGTTCTTTAGCGGCACTTCTATAGCAAAA-ACCGCTAAAAGTCACGTTCTTTA
** * * * * * *
43642280 GTGGCGCTTCTATAGCAAACGCCGTTAAATGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGC
65 GACGTGCTTCTACAGAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGATTCTATAGCAAACGC
* * * * *
43642345 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACACCGCTAAAGGTCATGTTCTTTAG
1 CGCTAAAGGTCACGTTCTTTAGCGGCACTTCTATAGCAAAAACCGCTAAAAGTCACGTTCTTTAG
** * *
43642410 TGGTGCTTCTATAGAAAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGATTCTATAGCAAACGC
66 ACGTGCTTCTACAGAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGATTCTATAGCAAACGC
* * * *
43642474 CGTTAAAGGTCACGTTCTTTAGTGGCACTT-TTTATCAAAAATGCCGCTAAAAG-CACCGTTCTT
1 CGCTAAAGGTCACGTTCTTTAGCGGCACTTCTATAGCAAAAA--CCGCTAAAAGTCA-CGTTCTT
* * *
43642537 TA-ACG-GCATTTTACGGAAAACGCCACTAA
63 TAGACGTGC-TTCTACAGAAAACGCCGCTAA
43642566 CTTTGGTAGA
Statistics
Matches: 190, Mismatches: 26, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
128 10 0.05
129 160 0.84
130 20 0.11
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (129 bp):
CGCTAAAGGTCACGTTCTTTAGCGGCACTTCTATAGCAAAAACCGCTAAAAGTCACGTTCTTTAG
ACGTGCTTCTACAGAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGATTCTATAGCAAACGC
Found at i:43642558 original size:86 final size:86
Alignment explanation
Indices: 43642216--43642565 Score: 301
Period size: 86 Copynumber: 4.1 Consensus size: 86
43642206 AGATAAGCAT
* * ** * * * *
43642216 CGCTAAAGGTCATGTTCTTTAGCGGTGCTTCTATAGAAAATGCCACTAAAGGTCATGTTCTTTAG
1 CGCTAAAGGTCACGTTCTTTAGTGGCACTTCTATAGAAAATGCCGCTAAAAGTCACGTTCTTTAA
* * * *
43642281 TGGCGCTTCTATAGCAAACGC
66 CGGCGATTCTACAGAAAACGC
* * * * * * * * * *
43642302 CGTTAAATGTCATGTTCTTTAGCGGCGCTTCTATAGCAAACGCCGCTAAAGGTCATGTTCTTTAG
1 CGCTAAAGGTCACGTTCTTTAGTGGCACTTCTATAGAAAATGCCGCTAAAAGTCACGTTCTTTAA
* * * *
43642367 CGGCGCTTCTATAGCAAACAC
66 CGGCGATTCTACAGAAAACGC
* ** * * *
43642388 CGCTAAAGGTCATGTTCTTTAGTGGTGCTTCTATAGAAAATGCCGCTAAAGGTCATGTTCTTTAG
1 CGCTAAAGGTCACGTTCTTTAGTGGCACTTCTATAGAAAATGCCGCTAAAAGTCACGTTCTTTAA
* *
43642453 CGGCGATTCTATAGCAAACGC
66 CGGCGATTCTACAGAAAACGC
* *
43642474 CGTTAAAGGTCACGTTCTTTAGTGGCACTTTTTATCA-AAAATGCCGCTAAAAG-CACCGTTCTT
1 CGCTAAAGGTCACGTTCTTTAGTGGCAC-TTCTAT-AGAAAATGCCGCTAAAAGTCA-CGTTCTT
* *
43642537 TAACGGC-ATTTTACGGAAAACGC
63 TAACGGCGATTCTACAGAAAACGC
*
43642560 CACTAA
1 CGCTAA
43642566 CTTTGGTAGA
Statistics
Matches: 231, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
86 198 0.86
87 32 0.14
88 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (86 bp):
CGCTAAAGGTCACGTTCTTTAGTGGCACTTCTATAGAAAATGCCGCTAAAAGTCACGTTCTTTAA
CGGCGATTCTACAGAAAACGC
Found at i:43642896 original size:21 final size:21
Alignment explanation
Indices: 43642858--43642903 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
43642848 TTCTACTCTG
*
43642858 CTCTGCTTCCCTCGCTGCTAC
1 CTCTGCTTCCCTCACTGCTAC
* *
43642879 CTCTGCTTCCCTTACTGCTGC
1 CTCTGCTTCCCTCACTGCTAC
43642900 CTCT
1 CTCT
43642904 ACTTTAAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.46, G:0.13, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCCCTCACTGCTAC
Found at i:43645345 original size:22 final size:23
Alignment explanation
Indices: 43645292--43645346 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
43645282 ATGCAATCGT
* *
43645292 AGATTTGA-TATGTAATCTTAGA
1 AGATTTGATTTTGCAATCTTAGA
**
43645314 AGATACGATTTTGCAATCTTAG-
1 AGATTTGATTTTGCAATCTTAGA
43645336 AGATTTGATTT
1 AGATTTGATTT
43645347 GTAGATACCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (23 bp):
AGATTTGATTTTGCAATCTTAGA
Found at i:43650455 original size:22 final size:21
Alignment explanation
Indices: 43650430--43650487 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
43650420 TATGTATCAT
*
43650430 AGATTTGATATGTAATCTTAG
1 AGATTTGATTTGTAATCTTAG
** *
43650451 AAGATACGATTTTGCAATCTTAG
1 -AGATTTGA-TTTGTAATCTTAG
43650474 AGATTTGATTTGTA
1 AGATTTGATTTGTA
43650488 GATACCTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 5 0.18
22 12 0.43
23 11 0.39
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:43655907 original size:84 final size:83
Alignment explanation
Indices: 43655596--43656114 Score: 468
Period size: 84 Copynumber: 6.2 Consensus size: 83
43655586 ATTACTTTCG
* * * * * *
43655596 TAGTTGCGGTGTTTTCCGCAAAAAACGCTAGTACAAAATTAAATTCCTATACTGAAACGACGCCG
1 TAGTTGCGGCGTTTTCCG-AAAAAACGCCACTA-AAAATTAAATTCCTGTAGTGAAACGGCGCCG
*
43655661 -TTTGAAGAAACTTTAATATA
64 TTTTG-AGAAACTTTAATACA
* * * * * * *
43655681 TAGTTGCGGCGTTTTTCGTAAAAACGCCACTAAAAATTAAATTTCTGAAGAGAAACAGCGACGTT
1 TAGTTGCGGCGTTTTCCGAAAAAACGCCACTAAAAATTAAATTCCTGTAGTGAAACGGCGCCGTT
*
43655746 TTGAGAAACATTAATACA
66 TTGAGAAACTTTAATACA
** * * * *
43655764 TTTTTGCAGCGTTTTCAAC-AAAAAACCCCACTAAAAGATTACATTCCTGTAGTGAAACGGAGCC
1 TAGTTGCGGCGTTTTC--CGAAAAAACGCCACTAAAA-ATTAAATTCCTGTAGTGAAACGGCGCC
* *
43655828 GTTTTGATAAATTTTAATACA
63 GTTTTGAGAAACTTTAATACA
* * * ** **
43655849 TATTTACGTCGTTTTCCGAAAAAACGCCACTAAAAATTTAAATTCCTAAACAGAAACGGCGCCGT
1 TAGTTGCGGCGTTTTCCGAAAAAACGCCACTAAAAA-TTAAATTCCTGTAGTGAAACGGCGCCGT
* * *
43655914 TTAGAAAAACTTGAATACA
65 TTTGAGAAACTTTAATACA
* * * * * * *
43655933 TAGTTCCGGCATTTTCAGTAAAAACGCCACTAAAAAATTTAATTCTTGTGGTGAAACGGCGCCGT
1 TAGTTGCGGCGTTTTCCGAAAAAACGCCACT-AAAAATTAAATTCCTGTAGTGAAACGGCGCCGT
*
43655998 TTTGAGAAATTTTAATACA
65 TTTGAGAAACTTTAATACA
** * * * ** *
43656017 TAGTTGCGGCGTTTT-TAAAAAAACGCCACTAAGAAATTAAATTCTTATAGCGAAATAGCGCTGT
1 TAGTTGCGGCGTTTTCCGAAAAAACGCCACTAA-AAATTAAATTCCTGTAGTGAAACGGCGCCGT
* * *
43656081 TTTGGGGAATTTTAATACA
65 TTTGAGAAACTTTAATACA
43656100 TAGTTGCGGCGTTTT
1 TAGTTGCGGCGTTTT
43656115 TTTCTGAAAA
Statistics
Matches: 349, Mismatches: 77, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
82 2 0.01
83 118 0.34
84 157 0.45
85 72 0.21
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (83 bp):
TAGTTGCGGCGTTTTCCGAAAAAACGCCACTAAAAATTAAATTCCTGTAGTGAAACGGCGCCGTT
TTGAGAAACTTTAATACA
Found at i:43656653 original size:7 final size:7
Alignment explanation
Indices: 43656643--43656667 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43656633 AACTTTAACA
43656643 CCTATCC
1 CCTATCC
43656650 CCTATCC
1 CCTATCC
43656657 CCTATCC
1 CCTATCC
43656664 CCTA
1 CCTA
43656668 AACCCTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.56, G:0.00, T:0.28
Consensus pattern (7 bp):
CCTATCC
Found at i:43656673 original size:7 final size:7
Alignment explanation
Indices: 43656663--43656740 Score: 52
Period size: 7 Copynumber: 11.0 Consensus size: 7
43656653 ATCCCCTATC
43656663 CCCTAAA
1 CCCTAAA
*
43656670 CCCTGAA
1 CCCTAAA
*
43656677 TCCTAAA
1 CCCTAAA
*
43656684 CCCTTAAC
1 CCC-TAAA
*
43656692 CCCTAAC
1 CCCTAAA
43656699 CCCTAAA
1 CCCTAAA
*
43656706 CCTTAAA
1 CCCTAAA
43656713 TCCC--AA
1 -CCCTAAA
43656719 CCCTTAAA
1 CCC-TAAA
*
43656727 CCATAAA
1 CCCTAAA
*
43656734 CCTTAAA
1 CCCTAAA
43656741 ATAGTAACTC
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
5 3 0.05
6 2 0.04
7 39 0.70
8 12 0.21
ACGTcount: A:0.38, C:0.40, G:0.01, T:0.21
Consensus pattern (7 bp):
CCCTAAA
Found at i:43656709 original size:21 final size:21
Alignment explanation
Indices: 43656678--43656735 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
43656668 AACCCTGAAT
43656678 CCTAAACCCTT-AACCCCTAACC
1 CCTAAA-CCTTAAACCCC-AACC
*
43656700 CCTAAACCTTAAATCCCAACC
1 CCTAAACCTTAAACCCCAACC
* *
43656721 CTTAAACCATAAACC
1 CCTAAACCTTAAACC
43656736 TTAAAATAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (21 bp):
CCTAAACCTTAAACCCCAACC
Found at i:43657173 original size:40 final size:40
Alignment explanation
Indices: 43657126--43657222 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
43657116 CGTTTTTGAC
43657126 AAAGCGCCGCTAATGCTCGATATATAGCGGCATTTTTTAT
1 AAAGCGCCGCTAATGCTCGATATATAGCGGCATTTTTTAT
* *
43657166 AAAGCGCCGCTAATACTCGATATATAGCGGCGTTTTTTAT
1 AAAGCGCCGCTAATGCTCGATATATAGCGGCATTTTTTAT
* *
43657206 GAAGCGCCAACTAATGC
1 AAAGCGCC-GCTAATGC
43657223 CACTAAAGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 45 0.88
41 6 0.12
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (40 bp):
AAAGCGCCGCTAATGCTCGATATATAGCGGCATTTTTTAT
Found at i:43657314 original size:40 final size:40
Alignment explanation
Indices: 43657267--43657359 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
43657257 ATAAATTTTT
43657267 GCGGCATTTTTTAAAAAGCGCCGCTAATACTCGATCTATA
1 GCGGCATTTTTTAAAAAGCGCCGCTAATACTCGATCTATA
* * * * *
43657307 GCTGCATTTCTCAAAATGCGCCGCTAATGCTCGATCTATA
1 GCGGCATTTTTTAAAAAGCGCCGCTAATACTCGATCTATA
*
43657347 GCGGCGTTTTTTA
1 GCGGCATTTTTTA
43657360 TCCAAAAGCC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (40 bp):
GCGGCATTTTTTAAAAAGCGCCGCTAATACTCGATCTATA
Found at i:43659734 original size:12 final size:11
Alignment explanation
Indices: 43659719--43659811 Score: 60
Period size: 12 Copynumber: 7.4 Consensus size: 11
43659709 TTAATGATTA
43659719 AAAACTTGATGG
1 AAAACTTGAT-G
*
43659731 AAAACTTGATT
1 AAAACTTGATG
*
43659742 AATGACTTGATG
1 AA-AACTTGATG
43659754 AAAAACACTTGATG
1 --AAA-ACTTGATG
43659768 AAAGACTTGATG
1 AAA-ACTTGATG
43659780 AAAAAAACACTTGATG
1 ----AAA-ACTTGATG
43659796 AAAGACTTGATG
1 AAA-ACTTGATG
43659808 AAAA
1 AAAA
43659812 AAACACTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
11 3 0.05
12 42 0.64
14 10 0.15
16 11 0.17
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (11 bp):
AAAACTTGATG
Found at i:43659740 original size:24 final size:24
Alignment explanation
Indices: 43659713--43659812 Score: 101
Period size: 28 Copynumber: 3.9 Consensus size: 24
43659703 AAAAACTTAA
* *
43659713 TGATTAAAAACTTGATGGAAAACT
1 TGATTAAAGACTTGATGAAAAACT
*
43659737 TGATTAATGACTTGATGAAAAACACT
1 TGATTAAAGACTTGATG-AAAA-ACT
*
43659763 TGATGAAAGACTTGATGAAAAAAACACT
1 TGATTAAAGACTTGATG---AAAA-ACT
*
43659791 TGATGAAAGACTTGATGAAAAA
1 TGATTAAAGACTTGATGAAAAA
43659813 AACACTTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
24 16 0.24
25 7 0.10
26 18 0.27
28 26 0.39
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (24 bp):
TGATTAAAGACTTGATGAAAAACT
Found at i:43659793 original size:16 final size:14
Alignment explanation
Indices: 43659746--43659812 Score: 70
Period size: 12 Copynumber: 4.9 Consensus size: 14
43659736 TTGATTAATG
43659746 ACTTGATGAAAAAC
1 ACTTGATGAAAAAC
*
43659760 ACTTGATG--AAAG
1 ACTTGATGAAAAAC
43659772 ACTTGATGAAAAAAAC
1 ACTTGATG--AAAAAC
*
43659788 ACTTGATG--AAAG
1 ACTTGATGAAAAAC
43659800 ACTTGATGAAAAA
1 ACTTGATGAAAAA
43659813 AACACTTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 22 0.50
14 11 0.25
16 11 0.25
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.22
Consensus pattern (14 bp):
ACTTGATGAAAAAC
Found at i:43659794 original size:28 final size:28
Alignment explanation
Indices: 43659734--43659837 Score: 149
Period size: 28 Copynumber: 3.8 Consensus size: 28
43659724 TTGATGGAAA
* *
43659734 ACTTGATTAATGACTTGATG--AAAAAC
1 ACTTGATGAAAGACTTGATGAAAAAAAC
43659760 ACTTGATGAAAGACTTGATGAAAAAAAC
1 ACTTGATGAAAGACTTGATGAAAAAAAC
43659788 ACTTGATGAAAGACTTGATGAAAAAAAC
1 ACTTGATGAAAGACTTGATGAAAAAAAC
* * *
43659816 ACTTAATGAATGACTTAATGAA
1 ACTTGATGAAAGACTTGATGAA
43659838 TGACTTGATC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
26 18 0.25
28 53 0.75
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (28 bp):
ACTTGATGAAAGACTTGATGAAAAAAAC
Found at i:43659824 original size:16 final size:16
Alignment explanation
Indices: 43659746--43659825 Score: 63
Period size: 16 Copynumber: 5.6 Consensus size: 16
43659736 TTGATTAATG
43659746 ACTTGATG--AAAAAC
1 ACTTGATGAAAAAAAC
*
43659760 ACTTGATG----AAAG
1 ACTTGATGAAAAAAAC
43659772 ACTTGATGAAAAAAAC
1 ACTTGATGAAAAAAAC
*
43659788 ACTTGATG----AAAG
1 ACTTGATGAAAAAAAC
43659800 ACTTGATGAAAAAAAC
1 ACTTGATGAAAAAAAC
*
43659816 ACTTAATGAA
1 ACTTGATGAA
43659826 TGACTTAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
12 22 0.42
14 8 0.15
16 23 0.43
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (16 bp):
ACTTGATGAAAAAAAC
Found at i:43659833 original size:12 final size:12
Alignment explanation
Indices: 43659816--43659843 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
43659806 TGAAAAAAAC
43659816 ACTTAATGAATG
1 ACTTAATGAATG
43659828 ACTTAATGAATG
1 ACTTAATGAATG
43659840 ACTT
1 ACTT
43659844 GATCCAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (12 bp):
ACTTAATGAATG
Found at i:43660365 original size:21 final size:21
Alignment explanation
Indices: 43660341--43660381 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
43660331 AATTTTAAAA
*
43660341 TATTTTTAAAATATATTTTTT
1 TATTTTTAAAATAAATTTTTT
43660362 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAATAAATTTTT
43660382 GGTGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTT
Found at i:43662580 original size:15 final size:16
Alignment explanation
Indices: 43662555--43662584 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43662545 ATTTTTTTTG
43662555 TTTTTATAAAATATAA
1 TTTTTATAAAATATAA
43662571 TTTTTA-AAAATATA
1 TTTTTATAAAATATA
43662585 TATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTTATAAAATATAA
Found at i:43662938 original size:104 final size:98
Alignment explanation
Indices: 43662709--43662940 Score: 331
Period size: 98 Copynumber: 2.3 Consensus size: 98
43662699 TAATGTAAAA
*
43662709 TTATTTTGTTAGTAATTTATGATTAGCTTATAAATTGTCAGTGTTTTGTGTTTTATGAAGTTTTA
1 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTCAGTGTTTTGTGTTTTATGAAGTTTTA
*
43662774 GTAATGTAAATTCTTTTTAAAAAAATGTTATAG
66 GTAATGTAAATTCTTTTTAAAAAAATATTATAG
* * *
43662807 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTTGTGTTTTGTGTTTTGTGA
1 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTCAGTGTTTTGTG---T-T-TTATG-AA
* *
43662872 TTTATTAGTAATGTAAATTCTTTTT-TAAAAATATTATAG
60 GTT-TTAGTAATGTAAATTCTTTTTAAAAAAATATTATAG
43662911 TTATTTTGTTAGTAATTTATGATTAGTTTA
1 TTATTTTGTTAGTAATTTATGATTAGTTTA
43662941 GGGTTTTGTG
Statistics
Matches: 120, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
98 48 0.40
101 1 0.01
102 1 0.01
103 4 0.03
104 45 0.38
105 21 0.17
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.55
Consensus pattern (98 bp):
TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTCAGTGTTTTGTGTTTTATGAAGTTTTA
GTAATGTAAATTCTTTTTAAAAAAATATTATAG
Found at i:43663011 original size:80 final size:80
Alignment explanation
Indices: 43662863--43663016 Score: 224
Period size: 80 Copynumber: 1.9 Consensus size: 80
43662853 TGTGTTTTGT
* *
43662863 GTTTTGTGATTTATTAGTAATGTAAATTCTTTTTTAAAAATATTATAGTTATTTTGTTAGTAATT
1 GTTTTGTGATTTATTAGTAATGTAAATTCTTTTTTAAAAATATTATAATTATGTTGTTAGTAATT
43662928 TATGATTAGTTTAGG
66 TATGATTAGTTTAGG
* *
43662943 GTTTTGTGATTTTTTAGTAAT-TTAATT-TTTTTTAAAAATAATTGTATAATTATGTTGTTAGTA
1 GTTTTGTGATTTATTAGTAATGTAAATTCTTTTTTAAAAAT-A-T-TATAATTATGTTGTTAGTA
43663006 A-TTATGATTAG
63 ATTTATGATTAG
43663017 GTTATATAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
78 12 0.18
79 6 0.09
80 31 0.46
81 18 0.27
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (80 bp):
GTTTTGTGATTTATTAGTAATGTAAATTCTTTTTTAAAAATATTATAATTATGTTGTTAGTAATT
TATGATTAGTTTAGG
Found at i:43663231 original size:198 final size:207
Alignment explanation
Indices: 43662933--43663484 Score: 715
Period size: 197 Copynumber: 2.7 Consensus size: 207
43662923 TAATTTATGA
* * * * * * *
43662933 TTAGTTTAGGGTTTTGTGATTTTTTAGTAATTTAATTTT--T-TTTA-A-AAATAATTGTATAAT
1 TTAGTTTAAGATTTTGTGAATTTTTAGTAATGTAATTTTAATATATAGATATATAATT-TATAGT
*
43662993 TATGTTGTTAGTAA-TTATGATTAGGTTATATAAATTGTTAGTGTTTTGTGTTTTGTGATTTATT
65 TATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTTGTGTTTTGTGATTTATT
* *
43663057 AGTAATGTAAATTCTTTTTAAAAAAATGTTATAGTTATTTTGTTAGTAATTTATAATTAGTTTAT
130 AGTAATGTAAATTCTTTTTAAAAAAATGTTATAATTATTTTGTTACTAATTTATAATTAGTTTAT
*
43663122 AAATTGTTAGTGT
195 AAATTATTAGTGT
43663135 TTAGTTTAAGATTTTGTGAATTTTTAGTAATGTAA-TTT-A-A-A-AGA-A-A-AA-TTATAGTT
1 TTAGTTTAAGATTTTGTGAATTTTTAGTAATGTAATTTTAATATATAGATATATAATTTATAGTT
*
43663191 GTTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTTGTGTTTTGTGATTTATTA
66 ATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTTGTGTTTTGTGATTTATTA
* *
43663256 GTAATGT-AATTCTTTTTAAAAAAATGTTATAATTATTTTTTTACTAATTTATGATTAGTTTATA
131 GTAATGTAAATTCTTTTTAAAAAAATGTTATAATTATTTTGTTACTAATTTATAATTAGTTTATA
43663320 AATTATTAGTGT
196 AATTATTAGTGT
* * * *
43663332 TTAGTTTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTAAATATATATATATATAATTTTATAG
1 TTAGTTTAAGATTTTGTGAATTTTTAGTAATGTAATTTT-AATATATAGATATATAA-TTTATAG
* *
43663397 TTATTTTGTTAGTAATTTATGATTAAGTTATATAAACTGTTAGTGTTTAGTTTAGTGTTTTGTGA
64 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTG--T--TTT-GTGTTTTGTGA
* *
43663462 TTTTTTATTAATGTAAATT-TTTT
124 TTTATTAGTAATGTAAATTCTTTT
43663485 ATAATATAAT
Statistics
Matches: 307, Mismatches: 22, Indels: 31
0.85 0.06 0.09
Matches are distributed among these distances:
197 113 0.37
198 62 0.20
199 2 0.01
200 3 0.01
201 6 0.02
202 32 0.10
203 2 0.01
204 1 0.00
205 1 0.00
206 2 0.01
208 48 0.16
210 1 0.00
212 3 0.01
213 27 0.09
214 4 0.01
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.54
Consensus pattern (207 bp):
TTAGTTTAAGATTTTGTGAATTTTTAGTAATGTAATTTTAATATATAGATATATAATTTATAGTT
ATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTTGTGTTTTGTGATTTATTA
GTAATGTAAATTCTTTTTAAAAAAATGTTATAATTATTTTGTTACTAATTTATAATTAGTTTATA
AATTATTAGTGT
Found at i:43663474 original size:111 final size:103
Alignment explanation
Indices: 43662933--43663485 Score: 599
Period size: 99 Copynumber: 5.4 Consensus size: 103
43662923 TAATTTATGA
* * * *
43662933 TTAGTTTAGGGTTTTGTGATTTTTTAGTAATTTAATTTTTTTTAAAAATAAT-TGTATAATTATG
1 TTAGTTTAGTGTTTTGTGATTTTTTAGTAATGTAA-TTTTTTTAAAAA-AATGT-TATAGTTATT
*
43662997 TTGTTAGTAA-TTATGATTAGGTTATATAAATTGTTAGTG-
63 TTGTTAGTAATTTATGATTAAGTTATATAAATTGTTAGTGT
*
43663036 -T--TTT-GTGTTTTGTGATTTATTAGTAATGTAAATTCTTTTTAAAAAAATGTTATAGTTATTT
1 TTAGTTTAGTGTTTTGTGATTTTTTAGTAATGT-AATT-TTTTTAAAAAAATGTTATAGTTATTT
*
43663097 TGTTAGTAATTTATAATT-AGTT-TATAAATTGTTAGTGT
64 TGTTAGTAATTTATGATTAAGTTATATAAATTGTTAGTGT
* * ** *
43663135 TTAGTTTAAG-ATTTTGTGAATTTTTAGTAATGTAA----TTTAAAAGAAAAATTATAGTTGTTT
1 TTAGTTT-AGTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTAAAA-AAATGTTATAGTTATTT
*
43663195 TGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTG-
64 TGTTAGTAATTTATGATTAAGTTATATAAATTGTTAGTGT
* *
43663234 -T--TTT-GTGTTTTGTGATTTATTAGTAATGTAATTCTTTTTAAAAAAATGTTATAATTATTTT
1 TTAGTTTAGTGTTTTGTGATTTTTTAGTAATGTAATT-TTTTTAAAAAAATGTTATAGTTATTTT
* * *
43663295 TTTACTAATTTATGATT-AGTT-TATAAATTATTAGTGT
65 GTTAGTAATTTATGATTAAGTTATATAAATTGTTAGTGT
* * *
43663332 TTAGTTTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTAAATATATATATATATAATTTTATAG
1 TTAGTTTAGTGTTTTGTGATTTTTTAGTAATGTAATTTT---T-T-TA-A-A-AAAATGTTATAG
*
43663397 TTATTTTGTTAGTAATTTATGATTAAGTTATATAAACTGTTAGTGT
58 TTATTTTGTTAGTAATTTATGATTAAGTTATATAAATTGTTAGTGT
* *
43663443 TTAGTTTAGTGTTTTGTGATTTTTTATTAATGTAAATTTTTTA
1 TTAGTTTAGTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTA
43663486 TAATATAATT
Statistics
Matches: 378, Mismatches: 38, Indels: 65
0.79 0.08 0.14
Matches are distributed among these distances:
94 1 0.00
95 22 0.06
96 3 0.01
97 21 0.06
98 50 0.13
99 81 0.21
100 46 0.12
101 5 0.01
102 33 0.09
103 20 0.05
104 2 0.01
105 1 0.00
106 4 0.01
107 2 0.01
108 2 0.01
109 31 0.08
110 4 0.01
111 50 0.13
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.54
Consensus pattern (103 bp):
TTAGTTTAGTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAAAATGTTATAGTTATTTTG
TTAGTAATTTATGATTAAGTTATATAAATTGTTAGTGT
Found at i:43663505 original size:111 final size:109
Alignment explanation
Indices: 43663183--43663502 Score: 378
Period size: 111 Copynumber: 3.0 Consensus size: 109
43663173 AAAAGAAAAA
* *
43663183 TTATAGTTGTTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTG--T--TTT-GTGTT
1 TTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATATAAATTGTTAGTGTTTAGTTTAGTGTT
* *
43663243 TTGTGATTTATTAGTAATGTAATTCTTTT-TAA-A-AA---AATG
66 TTGTGATTTTTTAGTAATGTAATT-TTTTATAATATAATTTAATT
* * * * *
43663282 TTATAATTATTTTTTTACTAATTTATGATT-AGTT-TATAAATTATTAGTGTTTAGTTTAGGGTT
1 TTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATATAAATTGTTAGTGTTTAGTTTAGTGTT
** *
43663345 TTGTGATTTTTTAGTAATGTAATTTTAAATATATATATATATAATT
66 TTGTGATTTTTTAGTAATGTAATTTTTTATA-ATATA-ATTTAATT
*
43663391 TTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATATAAACTGTTAGTGTTTAGTTTAGTGTT
1 TTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATATAAATTGTTAGTGTTTAGTTTAGTGTT
* *
43663456 TTGTGATTTTTTATTAATGTAAATTTTTTATAATATAATTTTATT
66 TTGTGATTTTTTAGTAATGT-AATTTTTTATAATATAATTTAATT
43663501 TT
1 TT
43663503 TATTTGACAA
Statistics
Matches: 183, Mismatches: 22, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
97 14 0.08
98 3 0.02
99 27 0.15
101 5 0.03
102 29 0.16
103 1 0.01
104 1 0.01
105 1 0.01
106 1 0.01
109 30 0.16
110 12 0.07
111 50 0.27
112 9 0.05
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (109 bp):
TTATAGTTATTTTGTTAGTAATTTATGATTAAGTTATATAAATTGTTAGTGTTTAGTTTAGTGTT
TTGTGATTTTTTAGTAATGTAATTTTTTATAATATAATTTAATT
Found at i:43667582 original size:17 final size:17
Alignment explanation
Indices: 43667560--43667598 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
43667550 TTTTTTTTTA
43667560 TCAAAAACAGAATAATT
1 TCAAAAACAGAATAATT
** *
43667577 TCAAAATTAGAATATTT
1 TCAAAAACAGAATAATT
43667594 TCAAA
1 TCAAA
43667599 CTTTCGATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (17 bp):
TCAAAAACAGAATAATT
Found at i:43668468 original size:41 final size:41
Alignment explanation
Indices: 43668411--43668550 Score: 235
Period size: 41 Copynumber: 3.4 Consensus size: 41
43668401 CCTTGTGGGT
*
43668411 CTTTAGCAGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
*
43668452 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGTGCAGAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
* *
43668493 CTTTAACGGCGTTTTTTCAAGAAGCGCCGCTAATGCGCAAAC
1 CTTTAGCGGCG-TTTTTCAAGAAGCGCCGCTAATGCGCAGAC
43668535 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
43668551 GGTAAAGCGT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
41 54 0.59
42 38 0.41
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
Found at i:43669250 original size:21 final size:21
Alignment explanation
Indices: 43669224--43669264 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43669214 GGTTATGGGT
* *
43669224 TTAAGGTTTTAAGGTTTAGGG
1 TTAAGGGTTCAAGGTTTAGGG
*
43669245 TTAAGGGTTCAGGGTTTAGG
1 TTAAGGGTTCAAGGTTTAGG
43669265 ATTTAGGGGT
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:0.22, C:0.02, G:0.37, T:0.39
Consensus pattern (21 bp):
TTAAGGGTTCAAGGTTTAGGG
Found at i:43669252 original size:29 final size:30
Alignment explanation
Indices: 43669212--43669281 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
43669202 TTAGGGACTG
* *
43669212 GGGGTTATGGGTTTAAGGTTTTAAGG-TTTA
1 GGGGTTAAGGGTTTAAGGGTTT-AGGATTTA
*
43669242 -GGGTTAAGGG-TTCAGGGTTTAGGATTTA
1 GGGGTTAAGGGTTTAAGGGTTTAGGATTTA
43669270 GGGGTTAAGGGT
1 GGGGTTAAGGGT
43669282 CGGGTTAGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 3 0.09
28 12 0.35
29 19 0.56
ACGTcount: A:0.20, C:0.01, G:0.41, T:0.37
Consensus pattern (30 bp):
GGGGTTAAGGGTTTAAGGGTTTAGGATTTA
Found at i:43669258 original size:14 final size:14
Alignment explanation
Indices: 43669213--43669281 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
43669203 TAGGGACTGG
*
43669213 GGGTTATGGGTTTAA
1 GGGTTAAGGGTTT-A
*
43669228 GGTTTTAA-GGTTTA
1 GG-GTTAAGGGTTTA
*
43669242 GGGTTAAGGGTTCA
1 GGGTTAAGGGTTTA
* *
43669256 GGGTTTAGGATTTA
1 GGGTTAAGGGTTTA
43669270 GGGGTTAAGGGT
1 -GGGTTAAGGGT
43669282 CGGGTTAGAG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
13 4 0.10
14 19 0.45
15 16 0.38
16 3 0.07
ACGTcount: A:0.20, C:0.01, G:0.41, T:0.38
Consensus pattern (14 bp):
GGGTTAAGGGTTTA
Found at i:43669272 original size:21 final size:22
Alignment explanation
Indices: 43669232--43669281 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
43669222 GTTTAAGGTT
*
43669232 TTAA-GGTTTAGGGTTAA-GGG
1 TTAAGGGTTTAGGATTAAGGGG
* *
43669252 TTCAGGGTTTAGGATTTAGGGG
1 TTAAGGGTTTAGGATTAAGGGG
43669274 TTAAGGGT
1 TTAAGGGT
43669282 CGGGTTAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 3 0.12
21 11 0.46
22 10 0.42
ACGTcount: A:0.22, C:0.02, G:0.40, T:0.36
Consensus pattern (22 bp):
TTAAGGGTTTAGGATTAAGGGG
Found at i:43669407 original size:21 final size:21
Alignment explanation
Indices: 43669373--43669434 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
43669363 ATTGGTGTAA
43669373 TTAGGG-TTATGAGTTTGGGA-
1 TTAGGGTTTA-GAGTTTGGGAT
* *
43669393 TTAGAGGTTTAGAGTTAGAGAT
1 TTAG-GGTTTAGAGTTTGGGAT
43669415 TTAGGGTTTAGAGATTTGGG
1 TTAGGGTTTAGAG-TTTGGG
43669435 GTCAAGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.12
21 19 0.56
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (21 bp):
TTAGGGTTTAGAGTTTGGGAT
Found at i:43670206 original size:12 final size:12
Alignment explanation
Indices: 43670189--43670221 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
43670179 CGTGATTTAA
43670189 AATTTTAAAATG
1 AATTTTAAAATG
43670201 AATTTTAAAA-G
1 AATTTTAAAATG
43670212 -ATTTTAAAAT
1 AATTTTAAAAT
43670222 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 1 0.05
12 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (12 bp):
AATTTTAAAATG
Found at i:43670217 original size:10 final size:10
Alignment explanation
Indices: 43670190--43670249 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
43670180 GTGATTTAAA
43670190 ATTTTAAAATG
1 ATTTTAAAA-G
43670201 AATTTTAAAAG
1 -ATTTTAAAAG
*
43670212 ATTTTAAAAT
1 ATTTTAAAAG
*
43670222 TTTTTAAAA-
1 ATTTTAAAAG
*
43670231 ATTTAAAAAAG
1 ATTT-TAAAAG
43670242 ATTTTAAA
1 ATTTTAAA
43670250 CTTTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 3 0.07
10 24 0.59
11 5 0.12
12 9 0.22
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (10 bp):
ATTTTAAAAG
Found at i:43670220 original size:30 final size:29
Alignment explanation
Indices: 43670184--43670255 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
43670174 TTTTTCGTGA
*
43670184 TTTAAAATTTTAAAATGAATTT-TAAAAGAT
1 TTTAAAATTTTAAAA--AATTTAAAAAAGAT
*
43670214 TTTAAAATTTTTTAAAAATTTAAAAAAGAT
1 TTTAAAA-TTTTAAAAAATTTAAAAAAGAT
*
43670244 TTTAAACTTTTA
1 TTTAAAATTTTA
43670256 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 9 0.25
30 20 0.56
31 7 0.19
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (29 bp):
TTTAAAATTTTAAAAAATTTAAAAAAGAT
Found at i:43671866 original size:59 final size:57
Alignment explanation
Indices: 43671774--43671891 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 57
43671764 TTTTGAATGT
*
43671774 CTCATAGCTTTTTCTCCTCATTAGTTGTGCTTTTTTTTATATAACTACTATAATTGGCA
1 CTCATAGCTTTTTCTCATCATTAGTTGTGC-TTTTTTT-TATAACTACTATAATTGGCA
43671833 CTCATAGCTTTTTCTCATCATTAGTTGTGCTTTTTTTTATAACTACTATAATTGGCA
1 CTCATAGCTTTTTCTCATCATTAGTTGTGCTTTTTTTTATAACTACTATAATTGGCA
43671890 CT
1 CT
43671892 TTTTAGATTA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 22 0.38
58 7 0.12
59 29 0.50
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.49
Consensus pattern (57 bp):
CTCATAGCTTTTTCTCATCATTAGTTGTGCTTTTTTTTATAACTACTATAATTGGCA
Found at i:43675037 original size:42 final size:42
Alignment explanation
Indices: 43674978--43675065 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
43674968 ATAATTTTTT
* * * *
43674978 TAAAGATTATGTTTTTAGCGGTATTTTTGCTAGAAGCGCCGC
1 TAAAGATTATGTTTTTAGCGGCATTTTCGATAAAAGCGCCGC
* *
43675020 TAAAGGTT-TGTTCTTTAGCGGCGTTTTCGATAAAAGCGCCGC
1 TAAAGATTATGTT-TTTAGCGGCATTTTCGATAAAAGCGCCGC
43675062 TAAA
1 TAAA
43675066 TGTCATAGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 4 0.10
42 35 0.90
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (42 bp):
TAAAGATTATGTTTTTAGCGGCATTTTCGATAAAAGCGCCGC
Found at i:43675100 original size:43 final size:43
Alignment explanation
Indices: 43675011--43675281 Score: 318
Period size: 43 Copynumber: 6.3 Consensus size: 43
43675001 TTTTTGCTAG
* *
43675011 AAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTT-T-CGAT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAT
* * * *
43675051 AAAAGCGCCGCTAAATGTCATAGTCTATAGCGGCGTTTGTGGGAT
1 --AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAT
43675096 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGA-
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-GGGAT
** * * *
43675139 AAATGTCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGTGCGAT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAT
* * * *
43675182 AAGCGCCACTAAAGGTCTTAGTCTTTAGTGGCTTTTGTGGGAT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAT
* *
43675225 AAACGCCGCTAAAGGTCTTGGTCTTTAGCGGTGTTTGTGGGGA-
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-GGGAT
43675268 AAGCGCCGCTAAAG
1 AAGCGCCGCTAAAG
43675282 TTAGCGACGC
Statistics
Matches: 192, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
42 18 0.09
43 162 0.84
44 9 0.05
45 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAT
Found at i:43675278 original size:129 final size:127
Alignment explanation
Indices: 43675011--43675281 Score: 382
Period size: 129 Copynumber: 2.1 Consensus size: 127
43675001 TTTTTGCTAG
* * * *
43675011 AAGCGCCGCTAAAGGTTTGTTCTTTAGCGGCGTTTTCGATAAAAGCGCCGCTAAATGTCATAGTC
1 AAGCGCCGCTAAAGGTTTGGTCTTTAGCAGCGTTTTCGAT-AAAGCGCCACTAAAGGTCATAGTC
*
43675076 TATAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGA
65 TATAGCGGCGTTTGTGGGATAAACGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGA
** * *
43675139 AAATGTCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTGTGCGAT-AAGCGCCACTAAAGGTCTTAG
1 AAGCGCCGCTAAAGGT-TTGGTCTTTAGCAGCGTTT-T-CGATAAAGCGCCACTAAAGGTCATAG
* * * *
43675203 TCTTTAGTGGCTTTTGTGGGATAAACGCCGCTAAAGGTCTTGGTCTTTAGCGGTGTTTGTGGGGA
63 TCTATAGCGGCGTTTGTGGGATAAACGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGA
43675268 AAGCGCCGCTAAAG
1 AAGCGCCGCTAAAG
43675282 TTAGCGACGC
Statistics
Matches: 124, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
128 13 0.10
129 106 0.85
130 1 0.01
131 4 0.03
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (127 bp):
AAGCGCCGCTAAAGGTTTGGTCTTTAGCAGCGTTTTCGATAAAGCGCCACTAAAGGTCATAGTCT
ATAGCGGCGTTTGTGGGATAAACGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGA
Found at i:43678216 original size:20 final size:20
Alignment explanation
Indices: 43678174--43678232 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
43678164 GACTTGTTTG
*
43678174 AAAATCATTTTGA-TGTG-TT
1 AAAATCATTTTAACT-TGATT
*
43678193 AAAATGATTTTAACTTGATT
1 AAAATCATTTTAACTTGATT
*
43678213 AAAATCATTTTCACTTGATT
1 AAAATCATTTTAACTTGATT
43678233 TTAAAATTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (20 bp):
AAAATCATTTTAACTTGATT
Found at i:43681705 original size:21 final size:21
Alignment explanation
Indices: 43681658--43681733 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
43681648 TACGGAACAT
* **
43681658 AAGTGCCTGAAACGACAAACG
1 AAGTGCCTGATACGACAAATA
*
43681679 AGGTGCCTGATACGACAAATA
1 AAGTGCCTGATACGACAAATA
*
43681700 AAGTGCCTGAGATACGACACATA
1 AAGTGCCT--GATACGACAAATA
*
43681723 AAGTACCTGAT
1 AAGTGCCTGAT
43681734 CGGCAAAGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 27 0.59
23 19 0.41
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.17
Consensus pattern (21 bp):
AAGTGCCTGATACGACAAATA
Found at i:43682852 original size:30 final size:28
Alignment explanation
Indices: 43682809--43682866 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
43682799 TTTTCTTCCC
43682809 CTGTTTTCATCTCTTTCTCTATTTCTTTT
1 CTGTTTTCATCTCTTTCTCTA-TTCTTTT
* *
43682838 CTGTTCTTCTTCTCTTTTTCTATTCTTTT
1 CTGTT-TTCATCTCTTTCTCTATTCTTTT
43682867 ATTTCATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.67
Consensus pattern (28 bp):
CTGTTTTCATCTCTTTCTCTATTCTTTT
Found at i:43684249 original size:23 final size:24
Alignment explanation
Indices: 43684223--43684293 Score: 101
Period size: 23 Copynumber: 3.0 Consensus size: 24
43684213 GGCTTTGCCG
*
43684223 ATTAGGCACTTTACGTGTCGTA-C
1 ATTAGGCACTTTATGTGTCGTATC
*
43684246 ATTAGGCACTTTATGTGACGTATC
1 ATTAGGCACTTTATGTGTCGTATC
*
43684270 -TCAGGCACTTTATGTGTCGTATC
1 ATTAGGCACTTTATGTGTCGTATC
43684293 A
1 A
43684294 GGCACCTCGT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 41 0.98
24 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (24 bp):
ATTAGGCACTTTATGTGTCGTATC
Found at i:43684296 original size:21 final size:21
Alignment explanation
Indices: 43684226--43684332 Score: 99
Period size: 23 Copynumber: 5.0 Consensus size: 21
43684216 TTTGCCGATT
* *
43684226 AGGCACTTTACGTGTCGTACATT
1 AGGCACTTTATGTGTCGT--ATC
*
43684249 AGGCACTTTATGTGACGTATCTC
1 AGGCACTTTATGTGTCGTA--TC
43684272 AGGCACTTTATGTGTCGTATC
1 AGGCACTTTATGTGTCGTATC
* ** * *
43684293 AGGCACCTCGTGTGTTGTTTC
1 AGGCACTTTATGTGTCGTATC
43684314 AGGCAC-TTATGTGTCGTAT
1 AGGCACTTTATGTGTCGTAT
43684333 GCTGATCAGG
Statistics
Matches: 69, Mismatches: 13, Indels: 7
0.78 0.15 0.08
Matches are distributed among these distances:
20 9 0.13
21 25 0.36
23 35 0.51
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (21 bp):
AGGCACTTTATGTGTCGTATC
Found at i:43690761 original size:137 final size:137
Alignment explanation
Indices: 43690603--43690876 Score: 503
Period size: 137 Copynumber: 2.0 Consensus size: 137
43690593 TTCTTCTACT
*
43690603 ACTAAAGTTCTTTTGTTAAAAACTTGATAAGCTTTAGAATTTAAAAAATAACCAAGAAAATTTTC
1 ACTAAAGTTCTTTTGTTAAAAACTCGATAAGCTTTAGAATTTAAAAAATAACCAAGAAAATTTTC
* *
43690668 TTTATAACTTTTTACATCAAATTTACCAAGATTATCTTTGTCATTGTTTACAACAAAATATTTTC
66 TTTATAACTTTTTACATCAAATTTACCAAGATTATCTTTGTCATTGTTTAAAACAAAACATTTTC
43690733 ATCCAAA
131 ATCCAAA
43690740 ACTAAAGTTCTTTTGTTAAAAACTCGATAAGCTTTAGAATTTAAAAAATAACCAAGAAAATTTTC
1 ACTAAAGTTCTTTTGTTAAAAACTCGATAAGCTTTAGAATTTAAAAAATAACCAAGAAAATTTTC
* *
43690805 TTTATCATTTTTTACATCAAATTTACCAAGATTATCTTTGTCATTGTTTAAAACAAAACATTTTC
66 TTTATAACTTTTTACATCAAATTTACCAAGATTATCTTTGTCATTGTTTAAAACAAAACATTTTC
43690870 ATCCAAA
131 ATCCAAA
43690877 GGGATGAAAA
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 132 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (137 bp):
ACTAAAGTTCTTTTGTTAAAAACTCGATAAGCTTTAGAATTTAAAAAATAACCAAGAAAATTTTC
TTTATAACTTTTTACATCAAATTTACCAAGATTATCTTTGTCATTGTTTAAAACAAAACATTTTC
ATCCAAA
Found at i:43694525 original size:15 final size:16
Alignment explanation
Indices: 43694498--43694527 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43694488 TTATTTATAG
43694498 TGTTTCTTTTCCCCAT
1 TGTTTCTTTTCCCCAT
43694514 TGTTTC-TTTCCCCA
1 TGTTTCTTTTCCCCA
43694528 CCTTCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.07, C:0.33, G:0.07, T:0.53
Consensus pattern (16 bp):
TGTTTCTTTTCCCCAT
Found at i:43703819 original size:13 final size:13
Alignment explanation
Indices: 43703801--43703841 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
43703791 TAGATTTTTT
43703801 CTAAATATTATCA
1 CTAAATATTATCA
*
43703814 CTAAATA--AT-T
1 CTAAATATTATCA
43703824 CTAAATATTATCA
1 CTAAATATTATCA
43703837 CTAAA
1 CTAAA
43703842 CAATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
10 7 0.30
11 2 0.09
12 2 0.09
13 12 0.52
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:43703826 original size:23 final size:23
Alignment explanation
Indices: 43703799--43703850 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
43703789 GTTAGATTTT
*
43703799 TTCTAAATATTATCACTAAATAA
1 TTCTAAATATTATCACTAAACAA
43703822 TTCTAAATATTATCACTAAACAA
1 TTCTAAATATTATCACTAAACAA
43703845 TT-TAAA
1 TTCTAAA
43703851 AATCAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.38
Consensus pattern (23 bp):
TTCTAAATATTATCACTAAACAA
Found at i:43707032 original size:12 final size:12
Alignment explanation
Indices: 43707015--43707039 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43707005 TTTGAAGGTG
43707015 TGGGGTGGTCTT
1 TGGGGTGGTCTT
43707027 TGGGGTGGTCTT
1 TGGGGTGGTCTT
43707039 T
1 T
43707040 TTCTATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.48, T:0.44
Consensus pattern (12 bp):
TGGGGTGGTCTT
Found at i:43709744 original size:20 final size:21
Alignment explanation
Indices: 43709719--43709757 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43709709 GGGACTAAAC
43709719 CGAAAAC-TTAAAAATTTTTT
1 CGAAAACATTAAAAATTTTTT
*
43709739 CGAAAACATTTAAAATTTT
1 CGAAAACATTAAAAATTTT
43709758 CAAAGCTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (21 bp):
CGAAAACATTAAAAATTTTTT
Found at i:43711047 original size:24 final size:22
Alignment explanation
Indices: 43711005--43711050 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
43710995 CAATTATCCA
*
43711005 CATTTCATATACATGTATCATT
1 CATTTCATATACATATATCATT
43711027 CATTTCATATATCAATATATCATT
1 CATTTCATATA-C-ATATATCATT
43711051 TAACATCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 1 0.05
24 9 0.43
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (22 bp):
CATTTCATATACATATATCATT
Found at i:43711338 original size:25 final size:25
Alignment explanation
Indices: 43711285--43711362 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
43711275 TGAGCTAACG
* * *
43711285 GTAAGCTCATGCGAGCTGAATATCG
1 GTAAGCTCATACGAGCTGAAAATCA
43711310 GTAAGCTCATACGAGCT-AAGAATCA
1 GTAAGCTCATACGAGCTGAA-AATCA
*
43711335 GTAAGCTC-TCATGAGCTG-AAATCA
1 GTAAGCTCAT-ACGAGCTGAAAATCA
43711359 GTAA
1 GTAA
43711363 CCTTAATGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
24 12 0.26
25 34 0.74
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (25 bp):
GTAAGCTCATACGAGCTGAAAATCA
Found at i:43716642 original size:40 final size:39
Alignment explanation
Indices: 43716596--43716780 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 39
43716586 GCTCCTCGTT
*
43716596 CAAATGCCTTCGGGACATAGCCCGG-TTAGAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT--AGTAACTCGCA
*
43716636 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
*
43716676 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCA
* * * * *
43716715 CAAATGCCTT-AGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
43716756 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43716781 CATCATTCAA
Statistics
Matches: 125, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 77 0.62
41 11 0.09
42 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:43716698 original size:79 final size:80
Alignment explanation
Indices: 43716596--43716780 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 80
43716586 GCTCCTCGTT
* *
43716596 CAAATGCCTTCGGGACATAGCCCGG-TTAGAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT--AGTAACTCGCACAAATGCCTT-AGGATCTTAACCC
* *
43716659 GGATTTAGTAAC-TCGCA
63 GGATATAGTAACTTAGCA
* **
43716676 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTAGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCACAAATGCCTTAGGATCTTAACCCGG
* *
43716740 ATATGGTCACTTAGCA
65 ATATAGTAACTTAGCA
43716756 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43716781 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 32 0.35
81 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCACAAATGCCTTAGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:43724661 original size:79 final size:81
Alignment explanation
Indices: 43724559--43724743 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
43724549 GCTCCTCGTT
* * * *
43724559 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCACACAAAGGCCTTC-GGATCTTAACCC
* *
43724622 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
43724639 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACACAAAGGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCACACAAAGGCCTTCGGATCTTAACCCGG
* *
43724703 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
43724719 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43724744 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.59
80 34 0.38
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCACACAAAGGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:43724743 original size:40 final size:40
Alignment explanation
Indices: 43724559--43724743 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
43724549 GCTCCTCGTT
* * *
43724559 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
* * *
43724599 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
*
43724639 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCA-CA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACT-AGCA
* * * *
43724678 CAAAGGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TAGCA
43724719 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43724744 CATCATTCAA
Statistics
Matches: 123, Mismatches: 14, Indels: 16
0.80 0.09 0.10
Matches are distributed among these distances:
38 2 0.02
39 29 0.24
40 81 0.66
41 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
Found at i:43737569 original size:17 final size:18
Alignment explanation
Indices: 43737542--43737577 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
43737532 AGCCAGCAAT
43737542 AGAAGAAAAACATGGAGA
1 AGAAGAAAAACATGGAGA
*
43737560 AGAA-AAAAACATTGAGA
1 AGAAGAAAAACATGGAGA
43737577 A
1 A
43737578 AATGAGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.64, C:0.06, G:0.22, T:0.08
Consensus pattern (18 bp):
AGAAGAAAAACATGGAGA
Found at i:43744664 original size:40 final size:40
Alignment explanation
Indices: 43744580--43744764 Score: 152
Period size: 40 Copynumber: 4.7 Consensus size: 40
43744570 TTGAATGATG
* * *
43744580 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGA-T-ACTAAA
* * *
43744620 TCCGGACTAAGATCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
* * *
43744660 TCCGGGCTAA-ACCCGAAGGCATTTGTGCTAGTTACTAAA
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
*
43744699 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA-AA
*
43744740 -CCGGGCTATG-TCCCGAAGGCATTTG
1 TCCGGGCTAAGAT-CCGAAGGCATTTG
43744765 AACGAGGAGC
Statistics
Matches: 121, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
39 33 0.27
40 75 0.62
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:43744716 original size:79 final size:80
Alignment explanation
Indices: 43744580--43744764 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 80
43744570 TTGAATGATG
* *
43744580 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCCTT
1 TCCGGGCTAA-TCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
43744644 TGTGCGAGA-TACTA-A
65 TGTGCGA-ATTACTATA
* * * **
43744659 TTCCGGGCTAAACCCGAAGGCATTTGTGCT-AGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAATCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
43744722 TTGTGCGAATTACTATA
64 TTGTGCGAATTACTATA
* *
43744739 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTA-ATCCCGAAGGCATTTG
43744765 AACGAGGAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
78 2 0.02
79 55 0.61
80 33 0.37
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAATCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAATTACTATA
Found at i:43752814 original size:39 final size:40
Alignment explanation
Indices: 43752709--43752893 Score: 164
Period size: 40 Copynumber: 4.7 Consensus size: 40
43752699 TTGAATGATG
* * * *
43752709 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* * * *
43752749 TCCGGACTAAGATCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAAA
* *
43752789 TCCGGGCTAA-ACCCGAAGGCATTTGTGCTAGTTACTAAA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAAA
* * *
43752828 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACTATAA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGA-TACTA-AA
* *
43752869 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGACCCGAAGGCATTTG
43752894 AACGAGGAGC
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 33 0.28
40 75 0.62
41 11 0.09
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:43752865 original size:79 final size:80
Alignment explanation
Indices: 43752709--43752893 Score: 200
Period size: 79 Copynumber: 2.3 Consensus size: 80
43752699 TTGAATGATG
* *
43752709 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCCTT
1 TCCGGGCTAA-TCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
43752773 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
43752788 TTCCGGGCTAAACCCGAAGGCATTTGTGCT-AGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAATCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
43752851 TTGTGTGA-ATTACTATA
64 TTGTGCGAGA-TACTATA
* *
43752868 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTA-ATCCCGAAGGCATTTG
43752894 AACGAGGAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
78 2 0.02
79 54 0.61
80 33 0.37
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAATCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATA
Found at i:43754559 original size:18 final size:18
Alignment explanation
Indices: 43754510--43754559 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
43754500 AACTGAACTT
*
43754510 TTATTTTTATTTTTTGGA
1 TTATTTTTAATTTTTGGA
* *
43754528 TTA-TATTAGTTTTTGGA
1 TTATTTTTAATTTTTGGA
43754545 TTATTTTTAAATTTT
1 TTATTTTT-AATTTT
43754560 AATTTGTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 15 0.58
18 6 0.23
19 5 0.19
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.68
Consensus pattern (18 bp):
TTATTTTTAATTTTTGGA
Found at i:43773652 original size:54 final size:54
Alignment explanation
Indices: 43773559--43773663 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 54
43773549 TGAGGTCAAT
43773559 AAATAACCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCCATAGGGTG
1 AAATAACCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCCATAGGGTG
* * * *
43773613 AAATGACCGAAATACCCCCAT-AGGATGAAATGAAC-GAAATACCCTCATAGG
1 AAATAACCAAAATACCCCCATAAGG-TAAAATG-ACTGAAATACCCCCATAGG
43773664 TCCATAATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
53 3 0.07
54 40 0.89
55 2 0.04
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (54 bp):
AAATAACCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCCATAGGGTG
Found at i:43773662 original size:27 final size:26
Alignment explanation
Indices: 43773568--43773664 Score: 124
Period size: 27 Copynumber: 3.6 Consensus size: 26
43773558 TAAATAACCA
*
43773568 AAATACCCCCATAAGGTAAAATG-ACTG
1 AAATACCCCCAT-AGGTGAAATGAAC-G
*
43773595 AAATACCCCCATAGGGTGAAATGACCG
1 AAATACCCCCATA-GGTGAAATGAACG
43773622 AAATACCCCCATAGGATGAAATGAACG
1 AAATACCCCCATAGG-TGAAATGAACG
*
43773649 AAATACCCTCATAGGT
1 AAATACCCCCATAGGT
43773665 CCATAATAGG
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
26 4 0.06
27 58 0.92
28 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (26 bp):
AAATACCCCCATAGGTGAAATGAACG
Found at i:43773976 original size:370 final size:369
Alignment explanation
Indices: 43773291--43773989 Score: 1148
Period size: 370 Copynumber: 1.9 Consensus size: 369
43773281 TTCATGGGCT
* *
43773291 TAGGCCATAATGGGTAAGATAGGGCTGAAATGGGCCGTGTGGGGTCAAAGGGCTTGTAGGCCCCA
1 TAGGCCATAATGGCTAAGATAGGGCTGAAATGGGCCGTGTGGGCTCAAAGGGCTTGTAGGCCCCA
* * * *
43773356 CGCAAATGAAATCTACGAATTATGGAAAATACAGGACTAGGCGATATAGATCGCATAGCCGTGGT
66 CACAAATGAAATCCACGAATTATGGAAAATACAGGACTAGGCGATATAGATCCCATAGCCGTGGC
* ** * * *
43773421 AAATTCTGGGCTGAATAGGCCACACGAATATGTGGGCCCAATTGGGCCGAGTGATGGTCCTTGGG
131 AAATTCTAGGCTGAATAGGCCACACGAATATGTGGGCCCAATTGGGCCGAGAAAAGGGCATTGGG
* * * *
43773486 CCTATTTACACTATTTTACCATTTAGGTTATCTGAGTCGCTCGAGGCGACTACGAACCTTTTGTG
196 CCCATTTACACTATTTTACCATTTAGGTTACCTAAGTCGCTCGAGGCGACTACGAACCTTTTGAG
*
43773551 AGGTCAATAAATAACCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCCATAGGGTGAAA
261 AGGTCAATAAATAACCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCCATAGGGTAAAA
43773616 TGACCGAAATACCCCCATAGGATGAAATGAACGAAATACCCTCA
326 TGACCGAAATACCCCCATAGGATGAAATGAACGAAATACCCTCA
*
43773660 TAGGTCCATAATAGGCT-AGATAGGGCTGAAATGGGTCGTGTGGGCTCAAAGGGCTTGTAGGCCC
1 TAGG-CCATAAT-GGCTAAGATAGGGCTGAAATGGGCCGTGTGGGCTCAAAGGGCTTGTAGGCCC
** *
43773724 CACACCGATGAAATCCACGAATTATGGAAAATATAGGACTAGGCGATATAGATCCCATAGCCGTG
64 CACACAAATGAAATCCACGAATTATGGAAAATACAGGACTAGGCGATATAGATCCCATAGCCGTG
* * *
43773789 GCAAATTCTATGCTGAATGGGCCGCACGAATATGTGGGCCCAATTGGGCCGAGAAAAGGGCATTG
129 GCAAATTCTAGGCTGAATAGGCCACACGAATATGTGGGCCCAATTGGGCCGAGAAAAGGGCATTG
*
43773854 GGCCCATTTACACTATTTTACCATTTAGGTTACCTAAGTCGCTCGAGGCGACTACGGACCTTTTG
194 GGCCCATTTACACTATTTTACCATTTAGGTTACCTAAGTCGCTCGAGGCGACTACGAACCTTTTG
43773919 AGAGGTCAATAAATAACCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCCATAGGGTAA
259 AGAGGTCAATAAATAACCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCCATAGGGTAA
43773984 AATGAC
324 AATGAC
43773990 TGTTTACCCC
Statistics
Matches: 303, Mismatches: 25, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
369 4 0.01
370 296 0.98
371 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (369 bp):
TAGGCCATAATGGCTAAGATAGGGCTGAAATGGGCCGTGTGGGCTCAAAGGGCTTGTAGGCCCCA
CACAAATGAAATCCACGAATTATGGAAAATACAGGACTAGGCGATATAGATCCCATAGCCGTGGC
AAATTCTAGGCTGAATAGGCCACACGAATATGTGGGCCCAATTGGGCCGAGAAAAGGGCATTGGG
CCCATTTACACTATTTTACCATTTAGGTTACCTAAGTCGCTCGAGGCGACTACGAACCTTTTGAG
AGGTCAATAAATAACCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCCATAGGGTAAAA
TGACCGAAATACCCCCATAGGATGAAATGAACGAAATACCCTCA
Found at i:43773998 original size:26 final size:27
Alignment explanation
Indices: 43773938--43773991 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
43773928 TAAATAACCA
43773938 AAATACCCCCATAAGGTAAAATGACTG
1 AAATACCCCCATAAGGTAAAATGACTG
*
43773965 AAATACCCCCATAGGGTAAAATGACTG
1 AAATACCCCCATAAGGTAAAATGACTG
43773992 TTTACCCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAAGGTAAAATGACTG
Found at i:43774185 original size:26 final size:26
Alignment explanation
Indices: 43774155--43774231 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
43774145 GGAAATATAT
* *
43774155 TGTTACTGGCAGCTTTGCTGCGATGC
1 TGTTACTGGAAGCTTTGCTGCGATAC
*
43774181 TGTTACT-GATAGGTTTGCTGCGATAC
1 TGTTACTGGA-AGCTTTGCTGCGATAC
* * *
43774207 TATTACTAGAAGCTTTGCTGTGATA
1 TGTTACTGGAAGCTTTGCTGCGATA
43774232 TTGGTGTGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
25 1 0.02
26 40 0.93
27 2 0.05
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (26 bp):
TGTTACTGGAAGCTTTGCTGCGATAC
Found at i:43781739 original size:27 final size:27
Alignment explanation
Indices: 43781675--43781772 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
43781665 AGAGGTCAGT
* *
43781675 AAATGACCGAAATACCCTCATA-GGTA
1 AAATGACTGAAATACCCCCATAGGGTA
*
43781701 AAATGA-TCGAAATACCCCCATAGGGTG
1 AAATGACT-GAAATACCCCCATAGGGTA
* *
43781728 AAATGACTGAAATGCCCCAATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* **
43781755 AAATAACTGTTATACCCC
1 AAATGACTGAAATACCCC
43781773 TAGGAGATGA
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
26 19 0.32
27 39 0.66
28 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACTGAAATACCCCCATAGGGTA
Found at i:43782259 original size:20 final size:20
Alignment explanation
Indices: 43782234--43782283 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
43782224 CCTAAAGGGG
43782234 ACACACGGCTATGTCGCCTA
1 ACACACGGCTATGTCGCCTA
*
43782254 ACACACGGCAATGTCGCCTA
1 ACACACGGCTATGTCGCCTA
*
43782274 ACACAAGGCT
1 ACACACGGCT
43782284 GAGTCACATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.20, T:0.16
Consensus pattern (20 bp):
ACACACGGCTATGTCGCCTA
Found at i:43783500 original size:12 final size:12
Alignment explanation
Indices: 43783477--43783511 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
43783467 TTTCCATTTT
*
43783477 TTTAAGTCAATA
1 TTTAATTCAATA
*
43783489 TTTCATTCAATA
1 TTTAATTCAATA
43783501 TTTAATTCAAT
1 TTTAATTCAAT
43783512 TCCACACATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (12 bp):
TTTAATTCAATA
Found at i:43792171 original size:39 final size:40
Alignment explanation
Indices: 43792054--43792277 Score: 239
Period size: 40 Copynumber: 5.7 Consensus size: 40
43792044 GCTCCTCGTT
* *
43792054 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
43792094 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
43792134 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
43792173 CAAATGCCTT-GGGGCTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * * *
43792212 CAAATGCCTTC-GGATCTTGGTCCGGATATT-CTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
43792253 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43792278 CATCATTCAA
Statistics
Matches: 160, Mismatches: 15, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
38 3 0.02
39 69 0.43
40 71 0.44
41 17 0.11
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:43800149 original size:40 final size:40
Alignment explanation
Indices: 43799926--43800149 Score: 230
Period size: 39 Copynumber: 5.7 Consensus size: 40
43799916 GCTCCTCGTT
* * * *
43799926 CAAATGCCTTCGGGACATAGCCTGG-TTATAGTAAT-TTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
43799966 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
43800006 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
43800045 CAAATGCCTT-GGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * * *
43800084 CAAATGCCTTC-GGATCTTGGTCCGGATATT-CTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
43800125 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43800150 CATCATTCAA
Statistics
Matches: 160, Mismatches: 15, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
38 3 0.02
39 70 0.44
40 70 0.44
41 17 0.11
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:43813554 original size:40 final size:40
Alignment explanation
Indices: 43813510--43813774 Score: 285
Period size: 40 Copynumber: 6.7 Consensus size: 40
43813500 GCTCCTCGTT
*
43813510 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAATTCGCA
* *
43813550 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
* *
43813590 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
* *
43813630 CAAATGCCTTCGGG-CTAAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAAT-TCGCA
* *
43813669 CAAATGCCTTC-GGATCTTGGTCCGGATTTAGT-ATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAT-TCGCA
* * * * *
43813709 CAAATGCCTTC-GGATCTTGGTCCGGATATT-CTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGT-AATTCGCA
43813750 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43813775 CATCATTCAA
Statistics
Matches: 201, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
38 3 0.01
39 30 0.15
40 152 0.76
41 15 0.07
42 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
Found at i:43813694 original size:79 final size:80
Alignment explanation
Indices: 43813510--43813721 Score: 288
Period size: 79 Copynumber: 2.7 Consensus size: 80
43813500 GCTCCTCGTT
* * *
43813510 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
*
43813574 GATTTAGTAACTCGCA
65 GAATTAGTAACTCGCA
43813590 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-C-TAAGCCCG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAA-CCCG
*
43813653 GAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
*** *
43813669 CAAATGCCTTC-GGATCTTGGTCCGGATTTAGTATCTCGCACAAATGCCTTCGG
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGG
43813722 ATCTTGGTCC
Statistics
Matches: 120, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
78 6 0.05
79 64 0.53
80 48 0.40
81 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCA
Found at i:43813734 original size:119 final size:122
Alignment explanation
Indices: 43813510--43813774 Score: 307
Period size: 119 Copynumber: 2.2 Consensus size: 122
43813500 GCTCCTCGTT
*
43813510 CAAATGCCTTCGGGAC-ATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGGACTA-AGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCC
* *
43813573 GGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT-TTAGTAAC-TCGCA
65 GGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATT-CTAACTTAGCA
***
43813630 CAAATGCCTTCGGG-CTAAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTGGTC
1 CAAATGCCTTCGGGACTAAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
* *** *
43813691 CGGATTTAGTATCTCGCACAAATGCCTTC-GGATCTTGGTCCGGATATTCTCACTTAGCA
64 CGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATTCTAACTTAGCA
*
43813750 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTAAGCCCGGA
43813775 CATCATTCAA
Statistics
Matches: 125, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
118 8 0.06
119 81 0.65
120 36 0.29
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (122 bp):
CAAATGCCTTCGGGACTAAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
GATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATTCTAACTTAGCA
Found at i:43821619 original size:79 final size:78
Alignment explanation
Indices: 43821517--43821739 Score: 265
Period size: 79 Copynumber: 2.8 Consensus size: 78
43821507 GCTCCTCGTT
* *
43821517 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
43821582 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
43821597 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
43821660 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * *
43821675 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
43821738 GA
63 GA
43821740 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 47 0.38
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:43821634 original size:39 final size:40
Alignment explanation
Indices: 43821517--43821739 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
43821507 GCTCCTCGTT
* *
43821517 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
43821557 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
43821597 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
43821636 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
43821675 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
43821716 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43821740 CATCATTCAA
Statistics
Matches: 166, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:43829596 original size:79 final size:78
Alignment explanation
Indices: 43829494--43829716 Score: 265
Period size: 79 Copynumber: 2.8 Consensus size: 78
43829484 GCTCCTCGTT
* *
43829494 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
43829559 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
43829574 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
43829637 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * *
43829652 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
43829715 GA
63 GA
43829717 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 47 0.38
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:43829611 original size:39 final size:40
Alignment explanation
Indices: 43829494--43829716 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
43829484 GCTCCTCGTT
* *
43829494 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
43829534 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
43829574 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
43829613 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
43829652 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
43829693 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43829717 CATCATTCAA
Statistics
Matches: 166, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:43837330 original size:169 final size:166
Alignment explanation
Indices: 43837032--43837347 Score: 510
Period size: 169 Copynumber: 1.9 Consensus size: 166
43837022 GAACTCAGGT
* *
43837032 ACTTACTTTTCCGCTTCCAAAATTGACTCGGTAAGTCGCACCCATCATGTAATAATTATAGAAAA
1 ACTTACTTTTCCGCTTCCAAAATCGACTCGGTAAGTCGCACCCATAATGTAATAATTATAGAAAA
*
43837097 TATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGCACTTTAA
66 TATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGCACTTTAA
43837162 ACTCACACACTTAGTGCCATGCATTCAAGTTCGCAC
131 ACTCACACACTTAGTGCCATGCATTCAAGTTCGCAC
43837198 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGTCGCACCC-TAATGTAAATAATTTATAG
1 ACTTA-CTTTTCCGCT-TCCAAAATCGACTCGGTAAGTCGCACCCATAATGT-AATAA-TTATAG
* * *
43837262 AAAATATATATTGGTTGGCACACATAGTGCTTAATAAT-AACCACGCACACTTAGTGCCATGTAC
62 AAAATATAT-TGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGCAC
*
43837326 TTTAAACTCGCACACTTAGTGC
126 TTTAAACTCACACACTTAGTGC
43837348 TGTACAATTT
Statistics
Matches: 138, Mismatches: 7, Indels: 7
0.91 0.05 0.05
Matches are distributed among these distances:
166 5 0.04
167 15 0.11
168 32 0.23
169 60 0.43
170 26 0.19
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (166 bp):
ACTTACTTTTCCGCTTCCAAAATCGACTCGGTAAGTCGCACCCATAATGTAATAATTATAGAAAA
TATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGCACTTTAA
ACTCACACACTTAGTGCCATGCATTCAAGTTCGCAC
Found at i:43837339 original size:29 final size:29
Alignment explanation
Indices: 43837299--43837377 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
43837289 TGCTTAATAA
43837299 TAACCACGCACACTTAGTGCCATGTAC-TT
1 TAACC-CGCACACTTAGTGCCATGTACATT
*
43837328 TAAACTCGCACACTTAGTG-C-TGTACAATT
1 T-AACCCGCACACTTAGTGCCATGTAC-ATT
*
43837357 TAACCCACACACTTAGTGCCA
1 TAACCCGCACACTTAGTGCCA
43837378 ATTCATGACC
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
27 5 0.12
28 16 0.38
29 18 0.43
30 3 0.07
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (29 bp):
TAACCCGCACACTTAGTGCCATGTACATT
Found at i:43840341 original size:21 final size:22
Alignment explanation
Indices: 43840304--43840344 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
43840294 TGAAGAGTAT
43840304 AGTATGTGAAGATTGATGTACG
1 AGTATGTGAAGATTGATGTACG
43840326 AGTAT-TGAA-ATATGATGTA
1 AGTATGTGAAGAT-TGATGTA
43840345 TGGCTGGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 11 0.61
22 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (22 bp):
AGTATGTGAAGATTGATGTACG
Found at i:43843921 original size:40 final size:39
Alignment explanation
Indices: 43843872--43844053 Score: 131
Period size: 40 Copynumber: 4.6 Consensus size: 39
43843862 GCTCCTCGTT
* *
43843872 CAAATGCCTTCGGGACATAGCCCAGTTATAGTAACTCGCA
1 CAAAAGCCTTCGGGACTTAGCCC-GTTATAGTAACTCGCA
* * *
43843912 CAAAAGCCTTCGGGACTTAACCGGATT-TAATAACTCGCA
1 CAAAAGCCTTCGGGACTTAGCCCG-TTATAGTAACTCGCA
** *
43843951 -AAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAAA-GCCTTCGGGACTTAGCCCGTTA-TAGTAACTCGCA
* ** * * * *
43843990 CAAATGCCTTC-GGATCTTAGTCTGGATATTGTCACTTAGCA
1 CAAAAGCCTTCGGGA-CTTAG-CCCGTTATAGTAAC-TCGCA
43844031 C-AAAGCCTTCGGGACTTAGCCCG
1 CAAAAGCCTTCGGGACTTAGCCCG
43844054 GACATCATTC
Statistics
Matches: 109, Mismatches: 23, Indels: 21
0.71 0.15 0.14
Matches are distributed among these distances:
38 13 0.12
39 39 0.36
40 46 0.42
41 11 0.10
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAAAGCCTTCGGGACTTAGCCCGTTATAGTAACTCGCA
Found at i:43843960 original size:39 final size:39
Alignment explanation
Indices: 43843903--43844002 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 39
43843893 CCAGTTATAG
*
43843903 TAACTCGCACAAAA-GCCTTCGGGACTTA-ACCGGATTTAA
1 TAACTCGCA-AAAATGCCTTCGGG-CTTAGACCGGAATTAA
* *
43843942 TAACTCGCAAAAATGCCTTCGGGCTTAGCCCGGAATTAG
1 TAACTCGCAAAAATGCCTTCGGGCTTAGACCGGAATTAA
* *
43843981 TATCTCGCACAAATGCCTTCGG
1 TAACTCGCAAAAATGCCTTCGG
43844003 ATCTTAGTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
38 8 0.15
39 46 0.85
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (39 bp):
TAACTCGCAAAAATGCCTTCGGGCTTAGACCGGAATTAA
Found at i:43855406 original size:79 final size:79
Alignment explanation
Indices: 43855295--43855519 Score: 226
Period size: 79 Copynumber: 2.8 Consensus size: 79
43855285 GCTCCTCGTT
* * * *
43855295 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGAATTAACCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCG
43855359 GATTTAGTAACTCGCA
64 GATTTAGTAACTCGCA
* * * *
43855375 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGTACAAATGCCTT-TGGATCTTGGTCCG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAGCCCG
*
43855438 GATTTAGTATCTCGCA
64 GATTTAGTAACTCGCA
* * * * *
43855454 CAAATGCCTTCGGATCTTGGTCCGGATATT-GTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCC
43855517 GGA
63 GGA
43855520 CATCATTCAA
Statistics
Matches: 119, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
78 5 0.04
79 60 0.50
80 40 0.34
81 13 0.11
82 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGA
TTTAGTAACTCGCA
Found at i:43855519 original size:40 final size:40
Alignment explanation
Indices: 43855295--43855519 Score: 207
Period size: 40 Copynumber: 5.7 Consensus size: 40
43855285 GCTCCTCGTT
* *
43855295 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGT-ATTCGCA
* * *
43855335 CAAATGCCTTCGGGAATTAACCCGGAT-TTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGT-ATTCGCA
*
43855375 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAT-TCGCA
* * *
43855414 CAAATGCCTT-TGGATCTTGGTCCGGAT-TTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATTAGTAT-TCGCA
* * *
43855454 CAAATGCCTTC-GGATCTTGGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATTAGT-A-TTCGCA
43855495 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43855520 CATCATTCAA
Statistics
Matches: 158, Mismatches: 16, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
38 3 0.02
39 28 0.18
40 112 0.71
41 14 0.09
42 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATTAGTATTCGCA
Found at i:43859179 original size:17 final size:17
Alignment explanation
Indices: 43859153--43859186 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43859143 AGGGTCAATA
*
43859153 TACCATATAAGGCCTTC
1 TACCACATAAGGCCTTC
43859170 TACCACATAAGGCCTTC
1 TACCACATAAGGCCTTC
43859187 CAACTATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (17 bp):
TACCACATAAGGCCTTC
Found at i:43865634 original size:40 final size:40
Alignment explanation
Indices: 43865580--43865682 Score: 107
Period size: 40 Copynumber: 2.6 Consensus size: 40
43865570 TGTCTAACTG
* * ** *
43865580 CACATGCGTACCCCTGTTTGTACTTTGGTACCCCTAAATG
1 CACATACGTGCCCCTGTTTGTACTTCAGTACCCCTAAATA
* * * *
43865620 TACATACGTGCCCCTATTTATACTTCAGTACCCCTGAATA
1 CACATACGTGCCCCTGTTTGTACTTCAGTACCCCTAAATA
* *
43865660 CACATACGTGCCCTTGTTGGTAC
1 CACATACGTGCCCCTGTTTGTAC
43865683 CTCGGTACTC
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (40 bp):
CACATACGTGCCCCTGTTTGTACTTCAGTACCCCTAAATA
Found at i:43866231 original size:56 final size:56
Alignment explanation
Indices: 43866145--43866264 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
43866135 ACAAGGGATG
43866145 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
43866201 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
43866257 ATGGGCAA
1 ATGGGCAA
43866265 TAAACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:43875114 original size:50 final size:50
Alignment explanation
Indices: 43875015--43875165 Score: 185
Period size: 50 Copynumber: 2.9 Consensus size: 50
43875005 AATGAGATGC
*
43875015 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCA
*
43875071 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCA
** * * *
43875121 CCCGTAAGACCGTGTCTGGGACATGGCATGGGCACCGATATGAGA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGA
43875166 ACTTCCATTG
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
50 50 0.57
53 3 0.03
55 1 0.01
56 34 0.39
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCA
Found at i:43875505 original size:20 final size:20
Alignment explanation
Indices: 43875467--43875505 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43875457 TAAGCAAGCA
*
43875467 AGTAAGTAAACAAGTAAGTG
1 AGTAAGTAAACAAGAAAGTG
*
43875487 AGTAAGTAAAGAAGAAAGT
1 AGTAAGTAAACAAGAAAGT
43875506 AAAGATCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.26, T:0.18
Consensus pattern (20 bp):
AGTAAGTAAACAAGAAAGTG
Found at i:43882216 original size:50 final size:50
Alignment explanation
Indices: 43882110--43882302 Score: 190
Period size: 50 Copynumber: 3.7 Consensus size: 50
43882100 GGGAATGAGA
*
43882110 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-TA--AGAGG
* * *
43882166 TCCCATGTAATACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
* * * * * **
43882216 TCCCCCGCAAGACCATGTCTGGGACATGGCA-TGGTCATCGATATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGG-CACCGAGATAAGAGG
* * *
43882266 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
43882303 GTACAGGAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
49 3 0.03
50 69 0.59
51 3 0.03
52 2 0.02
53 4 0.03
55 1 0.01
56 34 0.29
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
Found at i:43883884 original size:40 final size:40
Alignment explanation
Indices: 43883835--43884080 Score: 316
Period size: 40 Copynumber: 6.1 Consensus size: 40
43883825 TAATTAATGT
* *
43883835 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* *
43883875 CT-AAGTGCACATACGTGCCCTTGTTTGTACTTCGATACCC
1 CTGAA-TGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* * * *
43883915 TTGAATGCACATATGTGCCCTTGTTTGTACTTTGGTACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* *
43883955 CTAAATGCACATACATGCCCCTGTTTGTACTTCGGTACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* *
43883995 CTGAATGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTA-CCC
* * *
43884036 CTGAATGCACATGCGTGCCCCTGTTAGTACCTTC-GTACTC
1 CTGAATGCACATACGTGCCCCTGTTTGTA-CTTCGGTACCC
43884076 CTGAA
1 CTGAA
43884081 GGCATATTCA
Statistics
Matches: 179, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.01
40 140 0.78
41 33 0.18
42 4 0.02
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (40 bp):
CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
Found at i:43883929 original size:80 final size:79
Alignment explanation
Indices: 43883835--43884080 Score: 350
Period size: 80 Copynumber: 3.1 Consensus size: 79
43883825 TAATTAATGT
*
43883835 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCCCTAAGTGCACATACGTGCCCTTGTT
1 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCCCTAA-TGCACATACGTGCCCCTGTT
43883900 TGTACTTCGATACCC
65 TGTACTTCGATACCC
* * *
43883915 TTGAATGCACATATGTGCCCTTGTTTGTACTTTGGTACCCCTAAATGCACATACATGCCCCTGTT
1 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCCCT-AATGCACATACGTGCCCCTGTT
*
43883980 TGTACTTCGGTACCC
65 TGTACTTCGATACCC
* * *
43883995 CTGAATGCACATATGTGCCCCTATTTGTACTTCGGTACCCCCTGAATGCACATGCGTGCCCCTGT
1 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTA-CCCCT-AATGCACATACGTGCCCCTGT
* *
43884060 TAGTACCTTCG-TACTC
64 TTGTA-CTTCGATACCC
43884076 CTGAA
1 CTGAA
43884081 GGCATATTCA
Statistics
Matches: 149, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
80 105 0.70
81 39 0.26
82 5 0.03
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (79 bp):
CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCCCTAATGCACATACGTGCCCCTGTTT
GTACTTCGATACCC
Found at i:43883995 original size:20 final size:20
Alignment explanation
Indices: 43883972--43884035 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
43883962 CACATACATG
43883972 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
** * * ** *
43883992 CCCCTGAATGCACATATGTG
1 CCCCTGTTTGTACTTCGGTA
*
43884012 CCCCTATTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
43884032 CCCC
1 CCCC
43884036 CTGAATGCAC
Statistics
Matches: 29, Mismatches: 15, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.34, G:0.17, T:0.33
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:43886195 original size:20 final size:20
Alignment explanation
Indices: 43886135--43886208 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
43886125 TTGTACGAGA
* *
43886135 TTTGCACTTTGATGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* *
43886155 GTTGCACTTCGTTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
43886175 TTTGCACTTCGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* *
43886195 TATACACTTCGGTG
1 TTTGCACTTCGGTG
43886209 TTCCTATCCG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.09, C:0.31, G:0.23, T:0.36
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:43890987 original size:50 final size:50
Alignment explanation
Indices: 43890880--43891059 Score: 171
Period size: 50 Copynumber: 3.5 Consensus size: 50
43890870 GGGAATGAGA
* * *
43890880 TCCCATGTAAGACCATGTATGGGACATGGCATTGGCATCATTGAGATTGTAAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-TG--AGAGG
43890936 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * * **
43890986 TCCCCCGTAAGGCCATGTCTAGCACATGGCATGGGCACCGATATGGGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
43891036 TCCCATGTAAGACTATATCTGGGA
1 TCCCACGTAAGACCATGTCTGGGA
43891060 TATGACATCG
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
50 63 0.60
52 2 0.02
53 4 0.04
55 1 0.01
56 35 0.33
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:43895420 original size:18 final size:18
Alignment explanation
Indices: 43895399--43895439 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
43895389 GTTGATTAAA
43895399 GATTATGAGTTAGTGGTC
1 GATTATGAGTTAGTGGTC
43895417 GATTATGAGTTAGTGGTC
1 GATTATGAGTTAGTGGTC
43895435 GATTA
1 GATTA
43895440 CGACCCGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.05, G:0.32, T:0.39
Consensus pattern (18 bp):
GATTATGAGTTAGTGGTC
Done.