Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 176 of 226
Found at i:56300606 original size:47 final size:48
Alignment explanation
Indices: 56300539--56300631 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 48
56300529 TTTACATATT
* *
56300539 GATGCCATAGCCCAGCTATGGTCTTACACAG-TAGCACATATCACACC
1 GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACACC
* * * *
56300586 GATGCCATATCCCGGATATGGTCTTATACAGAAATCACATATCACA
1 GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACA
56300632 TGTTGCCATG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 27 0.69
48 12 0.31
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (48 bp):
GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACACC
Found at i:56303293 original size:46 final size:46
Alignment explanation
Indices: 56303218--56303332 Score: 194
Period size: 46 Copynumber: 2.5 Consensus size: 46
56303208 CCACACTAAT
* * *
56303218 ATGTAGCCGATGCTACCACTAATACGTAGCTGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
*
56303264 ATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
56303310 ATGTAGCCGAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAT
56303333 CAATAACACT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
Found at i:56303330 original size:23 final size:23
Alignment explanation
Indices: 56303218--56303331 Score: 158
Period size: 23 Copynumber: 5.0 Consensus size: 23
56303208 CCACACTAAT
*
56303218 ATGTAGCCGATGCTACCACT-AA
1 ATGTAGCCGAAGCTACCACTGAA
* * *
56303240 TACGTAGCTGTAGCTACCACTGAA
1 -ATGTAGCCGAAGCTACCACTGAA
*
56303264 ATGTAGCCGAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAA
*
56303287 ATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
56303310 ATGTAGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
56303332 TCAATAACAC
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
23 77 0.97
24 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:56306977 original size:3 final size:3
Alignment explanation
Indices: 56306969--56306994 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56306959 GAATCATGGA
56306969 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
56306995 ATTTTCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:56308814 original size:3 final size:3
Alignment explanation
Indices: 56308808--56308833 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56308798 TTATTATTAT
56308808 TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TA
56308834 TGGTATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:56312007 original size:6 final size:6
Alignment explanation
Indices: 56311996--56312037 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
56311986 CTTTTTCAAC
* * *
56311996 CCCAAA CCCAAA TCCAAA TCCAAA TCCAAA CCCAAA CCCAAA
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA
56312038 TCTAATTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (6 bp):
CCCAAA
Found at i:56312018 original size:12 final size:12
Alignment explanation
Indices: 56311997--56312037 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
56311987 TTTTTCAACC
56311997 CCAAACCCAAAT
1 CCAAACCCAAAT
*
56312009 CCAAATCCAAAT
1 CCAAACCCAAAT
*
56312021 CCAAACCCAAAC
1 CCAAACCCAAAT
56312033 CCAAA
1 CCAAA
56312038 TCTAATTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.51, C:0.41, G:0.00, T:0.07
Consensus pattern (12 bp):
CCAAACCCAAAT
Found at i:56314261 original size:13 final size:13
Alignment explanation
Indices: 56314243--56314274 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
56314233 TCATTACTCG
56314243 AAACTCATAGATT
1 AAACTCATAGATT
56314256 AAACTCATAGATT
1 AAACTCATAGATT
56314269 AAACTC
1 AAACTC
56314275 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (13 bp):
AAACTCATAGATT
Found at i:56315931 original size:20 final size:20
Alignment explanation
Indices: 56315906--56315943 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56315896 AATTTATTGA
56315906 TAATACAT-AAATTGTAACTT
1 TAATACATCAAATT-TAACTT
56315926 TAATACATCAAATTTAAC
1 TAATACATCAAATTTAAC
56315944 CCATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (20 bp):
TAATACATCAAATTTAACTT
Found at i:56316896 original size:27 final size:27
Alignment explanation
Indices: 56316838--56316900 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
56316828 TTAAATTATT
**
56316838 TATATTTTATAATTCAATATTTTTGTA
1 TATATTTTATAATTCAATATTTTAATA
56316865 TATATTTT-TAATTCAATATCATTTAATA
1 TATATTTTATAATTCAATAT--TTTAATA
56316893 -ATATTTTA
1 TATATTTTA
56316901 AAGCCTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 11 0.35
27 15 0.48
28 5 0.16
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (27 bp):
TATATTTTATAATTCAATATTTTAATA
Found at i:56317136 original size:19 final size:19
Alignment explanation
Indices: 56317105--56317150 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
56317095 GTTTATGGTA
*
56317105 ATTA-AATAATATTTATTT
1 ATTATAATAATATTTATCT
*
56317123 ATTATAATAGTATTTATCT
1 ATTATAATAATATTTATCT
56317142 -TTATAATAA
1 ATTATAATAA
56317151 ATAATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTATAATAATATTTATCT
Found at i:56317452 original size:163 final size:160
Alignment explanation
Indices: 56317237--56317550 Score: 438
Period size: 163 Copynumber: 1.9 Consensus size: 160
56317227 ATTTTGAAAA
*
56317237 TTAAACTAATTTCTTTAAAGATGAATAAAAATATTATTTAAATTAAATTTTCTA-TGAAAGTTTT
1 TTAAACTAATTTCTTTAAAGATAAATAAAAATATTATTTAAATTAAATTTTCTAGT-AAAGTTTT
* * *
56317301 AACTTTAAACTAAATATTAAAATTAGTAAATTTATAATTTATAATTTA-AATAAAAAATATTAAA
65 AACTTTAAACTAAATATTAAAATTA-AAAATTT-TAATTCAGAATTTAGAAT-AAAAATATTAAA
56317365 ATTAAATTGTGTTATAGATTTTTATGAAAGGATT
127 ATTAAATTGTGTTATAGATTTTTATGAAAGGATT
* * *
56317399 TTAAACTATATTT-TTTAATGATAAATAAAGATATATT-TTTAAATTAAATTTTCTAGTAGATTT
1 TTAAACTA-ATTTCTTTAAAGATAAATAAA-A-ATATTATTTAAATTAAATTTTCTAGTAAAGTT
*
56317462 TTAACTTTAAACTAAATATTAAAATTAAAAATTTTAATTCAGAATTTAGAATAAAAATATTGAAA
63 TTAACTTTAAACTAAATATTAAAATTAAAAATTTTAATTCAGAATTTAGAATAAAAATATTAAAA
* * *
56317527 TTAAATTTTTTTATGGATTTTTAT
128 TTAAATTGTGTTATAGATTTTTAT
56317551 TAAAATTAAT
Statistics
Matches: 136, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
161 45 0.33
162 31 0.23
163 54 0.40
164 6 0.04
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (160 bp):
TTAAACTAATTTCTTTAAAGATAAATAAAAATATTATTTAAATTAAATTTTCTAGTAAAGTTTTA
ACTTTAAACTAAATATTAAAATTAAAAATTTTAATTCAGAATTTAGAATAAAAATATTAAAATTA
AATTGTGTTATAGATTTTTATGAAAGGATT
Found at i:56317687 original size:13 final size:13
Alignment explanation
Indices: 56317656--56317688 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
56317646 ATGATAGATA
*
56317656 TTAAATTTAAAAT
1 TTAAATATAAAAT
56317669 TT-AATATAAAAT
1 TTAAATATAAAAT
56317681 TTAAATAT
1 TTAAATAT
56317689 TATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAATATAAAAT
Found at i:56324824 original size:18 final size:17
Alignment explanation
Indices: 56324801--56324849 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
56324791 AATCGTGTCG
56324801 TTCATTTCCAAAACATTA
1 TTCATTT-CAAAACATTA
*
56324819 TTCATTTACAAATCATTA
1 TTCATTT-CAAAACATTA
56324837 TTCAATTTCAAAA
1 TTC-ATTTCAAAA
56324850 TGTTTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (17 bp):
TTCATTTCAAAACATTA
Found at i:56328692 original size:50 final size:50
Alignment explanation
Indices: 56328580--56328822 Score: 324
Period size: 50 Copynumber: 4.8 Consensus size: 50
56328570 GATCATAACA
* * ** *
56328580 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *** *
56328631 TGCCCATGCCATGTCCCAAACATGGTCTTATGGGGGACTTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
56328681 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
56328731 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
56328781 TACCAACACCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56328823 TTACCCAAAT
Statistics
Matches: 171, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
50 141 0.82
51 30 0.18
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:56345604 original size:37 final size:37
Alignment explanation
Indices: 56345563--56345636 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
56345553 TGTTGTCATG
56345563 ATTAGTCTTCAATCACATCCTCAATTACAATAACAAT
1 ATTAGTCTTCAATCACATCCTCAATTACAATAACAAT
*
56345600 ATTAGTCTTCAATCACATCTTCAATTACAATAACAAT
1 ATTAGTCTTCAATCACATCCTCAATTACAATAACAAT
56345637 CACAATCTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.34
Consensus pattern (37 bp):
ATTAGTCTTCAATCACATCCTCAATTACAATAACAAT
Found at i:56354667 original size:14 final size:12
Alignment explanation
Indices: 56354642--56354676 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
56354632 TTCTCATTTC
56354642 TCATTCCCTTTT
1 TCATTCCCTTTT
56354654 TCATTCTCCTTTT
1 TCATTC-CCTTTT
*
56354667 TCTTTCCCTT
1 TCATTCCCTT
56354677 GCATAGCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTCCCTTTT
Found at i:56354673 original size:25 final size:26
Alignment explanation
Indices: 56354627--56354676 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
56354617 TCCCTCATCA
56354627 TTCATTTCTCATTTCTCATTCCCTTT
1 TTCATTTCTCATTTCTCATTCCCTTT
* * *
56354653 TTCA-TTCTCCTTTTTCTTTCCCTT
1 TTCATTTCTCATTTCTCATTCCCTT
56354677 GCATAGCCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.60
Consensus pattern (26 bp):
TTCATTTCTCATTTCTCATTCCCTTT
Found at i:56360273 original size:70 final size:70
Alignment explanation
Indices: 56360124--56360820 Score: 643
Period size: 70 Copynumber: 10.0 Consensus size: 70
56360114 GCAGTTAGTA
** * * * * ** *
56360124 CGAGCTCAAGCTCTTAGCTGTGATTTTAAGGCTCACAGTTTCAATGC-GCAGCCTCCAAAATAGT
1 CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACTGCAGCCTCTAAAATAGT
*
56360188 TAGCA
66 TAGCG
* * * *
56360193 CGAGCTCAAGCTTCCAACTATGGTCTTAAGGCTCGCAGGTTCAACACTGCAACCTCTAAAATAGT
1 CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACTGCAGCCTCTAAAATAGT
*
56360258 TAGTG
66 TAGCG
** * ** * * *
56360263 TTAGCTCAAGCTCCTAGTTGTGATTTTAAGGCTCGTAGGTTCAACA-TCGTAGCCTCTAAAATAG
1 CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACT-GCAGCCTCTAAAATAG
*
56360327 TTAGCA
65 TTAGCG
* * * * * * *
56360333 CGAGCTCGAGCTCCTAACTGTGATATTAAGGCTCGCAGGTTCACCACCGTAGCCTCCAAAATAGT
1 CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACTGCAGCCTCTAAAATAGT
56360398 TAGCG
66 TAGCG
* * * * *
56360403 CGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTCAACATTGTAGCCTCTAAAATAGC
1 CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACTGCAGCCTCTAAAATAGT
*
56360468 TAGCA
66 TAGCG
* * * * *
56360473 TGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGTAGGTTCAACA-TCACAACCTCTAAAACAG
1 CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACT-GCAGCCTCTAAAATAG
*
56360537 TTAGCA
65 TTAGCG
* * * * * *
56360543 TGAGCTCAAACTCCCAATTGTGATCTTAAGGCTTGCAGGTTTAACA-TCGCAACCTCCTAAACA-
1 CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACT-GCAGCCT-CTAAA-AT
56360606 A-TTAGCG
63 AGTTAGCG
* * * ** * *
56360613 CAAGCTCAAGCTCCCAGCTGTGATCTTAATGCTCATAAGTTCAACACTGCAGCCTCCAAAATAGT
1 CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACTGCAGCCTCTAAAATAGT
*
56360678 TAACG
66 TAGCG
* * * * ** *
56360683 CGAGGTCAAACTCTCAACTGTGATCTTAAGGCTCACAATTTCAACACTGCAGCCTCTTAAATAGT
1 CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACTGCAGCCTCTAAAATAGT
*
56360748 TAGCT
66 TAGCG
* * * * * *
56360753 AGAGCTCAAACTCCCAGCTGTGATCTTAAGGCTCGCAGGCTCAAAAACTCCA-CCTTCTAAAATA
1 CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTC-AACACTGCAGCC-TCTAAAATA
56360817 GTTA
64 GTTA
56360821 AAGCTTACGT
Statistics
Matches: 513, Mismatches: 104, Indels: 20
0.81 0.16 0.03
Matches are distributed among these distances:
68 1 0.00
69 43 0.08
70 442 0.86
71 26 0.05
72 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (70 bp):
CGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACTGCAGCCTCTAAAATAGT
TAGCG
Found at i:56360484 original size:210 final size:209
Alignment explanation
Indices: 56360116--56360791 Score: 730
Period size: 210 Copynumber: 3.2 Consensus size: 209
56360106 CCTTCAAAGC
* * ** * * * * *
56360116 AGTTAGTACGAGCTCAAGCTCTTAGCTGTGATTTTAAGGCTCACAGTTTCA-ATGCGCAGCCTCC
1 AGTTAGCACGAGCTCAAACTCCCAACTGTGATCTTAAGGCTCGCAGGTTCACA-CCGCAGCCTCC
* * * * * * *
56360180 AAAATAGTTAGCACGAGCTCAAGCTTCCAACTATGGTCTTAAGGCTCGCAGGTTCAACACTGCAA
65 AAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTCAACACTGCAG
* * ** *
56360245 CCTCTAAAATAGTTAGTGTTAGCTCAAGCTCCTAGTTGTGATTTTAAGGCTCGTAGGTTCAACAT
130 CCTCTAAAATAGTTAGCGTGAGCTCAAGCTCCTAACTGTGATCTTAAGGCTCGTAGGTTCAACAT
*
56360310 CGTAGCCTCTAAAAT
195 CGCAGCCTCTAAAAT
* * * * *
56360325 AGTTAGCACGAGCTCGAGCTCCTAACTGTGATATTAAGGCTCGCAGGTTCACCACCGTAGCCTCC
1 AGTTAGCACGAGCTCAAACTCCCAACTGTGATCTTAAGGCTCGCAGGTTCA-CACCGCAGCCTCC
* *
56360390 AAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTCAACATTGTAG
65 AAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTCAACACTGCAG
* * *
56360455 CCTCTAAAATAGCTAGCATGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGTAGGTTCAACAT
130 CCTCTAAAATAGTTAGCGTGAGCTCAAGCTCCTAACTGTGATCTTAAGGCTCGTAGGTTCAACAT
* * *
56360520 CACAACCTCTAAAAC
195 CGCAGCCTCTAAAAT
* * * * * *
56360535 AGTTAGCATGAGCTCAAACTCCCAATTGTGATCTTAAGGCTTGCAGGTTTAACATCGCAACCTCC
1 AGTTAGCACGAGCTCAAACTCCCAACTGTGATCTTAAGGCTCGCAGG-TTCACACCGCAGCCTCC
* * * * * * * *
56360600 TAAACAATTAGCGCAAGCTCAAGCTCCCAGCTGTGATCTTAATGCTCATAAGTTCAACACTGCAG
65 AAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTCAACACTGCAG
* * * * * ** **
56360665 CCTCCAAAATAGTTAACGCGAGGTCAAACT-CTCAACTGTGATCTTAAGGCTCACAATTTCAACA
130 CCTCTAAAATAGTTAGCGTGAGCTCAAGCTCCT-AACTGTGATCTTAAGGCTCGTAGGTTCAACA
*
56360729 -CTGCAGCCTCTTAAAT
194 TC-GCAGCCTCTAAAAT
*
56360745 AGTTAGCTA-GAGCTCAAACTCCCAGCTGTGATCTTAAGGCTCGCAGG
1 AGTTAGC-ACGAGCTCAAACTCCCAACTGTGATCTTAAGGCTCGCAGG
56360792 CTCAAAAACT
Statistics
Matches: 391, Mismatches: 70, Indels: 11
0.83 0.15 0.02
Matches are distributed among these distances:
209 46 0.12
210 340 0.87
211 5 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (209 bp):
AGTTAGCACGAGCTCAAACTCCCAACTGTGATCTTAAGGCTCGCAGGTTCACACCGCAGCCTCCA
AAATAGTTAGCGCGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTCAACACTGCAGC
CTCTAAAATAGTTAGCGTGAGCTCAAGCTCCTAACTGTGATCTTAAGGCTCGTAGGTTCAACATC
GCAGCCTCTAAAAT
Found at i:56362684 original size:37 final size:38
Alignment explanation
Indices: 56362630--56362702 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
56362620 TTTTCATAAT
* *
56362630 TTCACTTTTTCAGTTTCAA-TCACTATTCAATTCAAAA
1 TTCACTTTGTCAGTTTCAAGTCAATATTCAATTCAAAA
*
56362667 TTCACTTTGTCATTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTGTCAGTTTCAAGTCAATATTCAATTCAA
56362703 TTCCACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 17 0.53
38 15 0.47
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.44
Consensus pattern (38 bp):
TTCACTTTGTCAGTTTCAAGTCAATATTCAATTCAAAA
Found at i:56362733 original size:23 final size:22
Alignment explanation
Indices: 56362690--56362733 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
56362680 TTTCAAGTCA
56362690 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
56362713 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
56362734 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:56362964 original size:51 final size:51
Alignment explanation
Indices: 56362907--56363046 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 51
56362897 TTGGTTCACA
56362907 TAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACAAG
1 TAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACAAG
* * * * * *
56362958 TAGTAGCCTACACATAGTACTACACATGCGATC-T-ATCTTTCTGGTACACG
1 TAGTAGCCTACACATAGTACTACACATGTGACCATCA-CTATCCGATACAAG
* *
56363008 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTACACATAGTACTACACATGTGACCATCACT
56363047 TTCACTTTCA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
49 1 0.01
50 40 0.53
51 34 0.45
52 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACAAG
Found at i:56367160 original size:39 final size:39
Alignment explanation
Indices: 56367117--56367646 Score: 810
Period size: 39 Copynumber: 13.6 Consensus size: 39
56367107 CATATTCACT
** *
56367117 TTTAAGCATATATCACTTTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
56367156 TTTAAACATATATCACAATACTCATATAATCACATAACG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
56367195 TTTAAGCATATTTCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
56367234 TTTAAGCATATATCACAGTACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
56367273 TTTAAGCATATATCACAGTACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
56367312 TTTAAACATATATCACAATACTCATATAATCACATAACG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
56367351 TTTAAGCATATTTCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
56367390 TTTAAGCATATATCACAGTACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * **
56367429 TTTAAGCATATATC-TAGTACTCATATAATCACATAATG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * *
56367467 TTTAAGCATATATCACATTGCTCATATAATCACATAACG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
56367506 TTGAAGTATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* **
56367545 TTTAAGCATATATCACAATACTCATATAATCACAAAATG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
56367584 TTTAAGCATATATCACAATACTCATATAATTACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
56367623 TTAAAACATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
56367647 AAAACATATT
Statistics
Matches: 449, Mismatches: 41, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
38 35 0.08
39 414 0.92
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:56371362 original size:39 final size:39
Alignment explanation
Indices: 56371319--56371409 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 39
56371309 CATATTCACT
* * *
56371319 TTTAAGCATGTATCACATTACAT-ATATAATTACATAACA
1 TTTAAGCATATATCACAATAC-TCATATAATCACATAACA
**
56371358 TTTAAGTGTATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
56371397 TTTAAACATATAT
1 TTTAAGCATATAT
56371410 GTCGCATGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.02
39 42 0.98
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.36
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:56375925 original size:104 final size:105
Alignment explanation
Indices: 56375745--56375950 Score: 360
Period size: 104 Copynumber: 2.0 Consensus size: 105
56375735 CTTTCCCTTA
* *
56375745 TGATCTCGAATTCTCAATATCACTTGGCAAAGCTCCTTGTAGCCTTGAATTCAAAGCATTTGTTA
1 TGATCTCAAATTCTCAATATCACTTGGCAAAGCTCCTTGTAGCCTTGAATTCAAAGCATTTGCTA
* *
56375810 TCTGCCCCACTTGATTCTTAAGAGC-TAAAGGGAAGCTTG
66 TCTGCCCCACTTAATTCTCAAGAGCTTAAAGGGAAGCTTG
*
56375849 TGATCTCAAATTCTCAGTATCACTTGGCAAAGCTCCTTGTAGCCTTGAATTCAAAGCATTTGCTA
1 TGATCTCAAATTCTCAATATCACTTGGCAAAGCTCCTTGTAGCCTTGAATTCAAAGCATTTGCTA
56375914 TCTGCCCCACTTAATTCTCAAGAGCTTAAAGGGAAGC
66 TCTGCCCCACTTAATTCTCAAGAGCTTAAAGGGAAGC
56375951 AGCTTGACTC
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
104 85 0.89
105 11 0.11
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (105 bp):
TGATCTCAAATTCTCAATATCACTTGGCAAAGCTCCTTGTAGCCTTGAATTCAAAGCATTTGCTA
TCTGCCCCACTTAATTCTCAAGAGCTTAAAGGGAAGCTTG
Found at i:56378781 original size:127 final size:122
Alignment explanation
Indices: 56378624--56378883 Score: 387
Period size: 127 Copynumber: 2.1 Consensus size: 122
56378614 ACTAATTCCC
56378624 AACCT-TTAATCTACAATATAATACTCAATTCATAGTATCGACTTTTTGACATGTTTTATAGCTA
1 AACCTCTTAATCTACAATATAATACTCAATTCATAGTATCGACTTTTTGACATGTTTTATAGCTA
* * * * * * *
56378688 TTTTTTTGAAAATTCATTGAAACCTTAAGAAATTTTTAACGAAAATTCAACGTAAGTTCAGA
66 -TTTTCTAAAAACTCATTAAAACCTCAAGAAAATTTTAACAAAAATTC-A---AAGTTCAGA
*
56378750 AACCTCTTAATCTACAATATAATACTCAATTCATAGTATCGACTTTTTGACATGTTTTATGGCTA
1 AACCTCTTAATCTACAATATAATACTCAATTCATAGTATCGACTTTTTGACATGTTTTATAGCTA
*
56378815 TTTTCTAAAAACTCATTAAAACCTCAAGAAAATTTTAACAAAAATTCAAAGTTTAGA
66 TTTTCTAAAAACTCATTAAAACCTCAAGAAAATTTTAACAAAAATTCAAAGTTCAGA
56378872 AACCTCTTAATC
1 AACCTCTTAATC
56378884 ATGTGAAAAC
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
122 20 0.16
125 1 0.01
126 45 0.36
127 58 0.47
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (122 bp):
AACCTCTTAATCTACAATATAATACTCAATTCATAGTATCGACTTTTTGACATGTTTTATAGCTA
TTTTCTAAAAACTCATTAAAACCTCAAGAAAATTTTAACAAAAATTCAAAGTTCAGA
Found at i:56384067 original size:18 final size:19
Alignment explanation
Indices: 56384021--56384067 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
56384011 GTTCCCTAAG
*
56384021 TTAATTCAATTTATTCAAT
1 TTAATTCAATTAATTCAAT
* *
56384040 TTAAAT-AATTAATTTAAT
1 TTAATTCAATTAATTCAAT
56384058 TT-ATTCAATT
1 TTAATTCAATT
56384068 TTCAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.09
18 16 0.70
19 5 0.22
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATTCAATTAATTCAAT
Found at i:56384325 original size:26 final size:25
Alignment explanation
Indices: 56384296--56384367 Score: 92
Period size: 27 Copynumber: 2.8 Consensus size: 25
56384286 TATTTTTTAA
56384296 TTTTAATTTTAATTTTAAAATAATTT
1 TTTTAATTTTAATTTTAAAATAA-TT
* *
56384322 TTTTATTTTTTATTTTTAAAATAATT
1 TTTTA-ATTTTAATTTTAAAATAATT
56384348 TTTTAATGTTT-ATTTTAAAA
1 TTTTAAT-TTTAATTTTAAAA
56384368 ATGGGCCGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 9 0.22
26 15 0.38
27 16 0.40
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (25 bp):
TTTTAATTTTAATTTTAAAATAATT
Found at i:56384340 original size:27 final size:26
Alignment explanation
Indices: 56384296--56384369 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 26
56384286 TATTTTTTAA
*
56384296 TTTTAA-TTTTAATTTTAAAATAATTT
1 TTTTAATTTTTATTTTTAAAATAA-TT
*
56384322 TTTTATTTTTTATTTTTAAAATAATT
1 TTTTAATTTTTATTTTTAAAATAATT
* *
56384348 TTTTAATGTTTATTTTAAAAAT
1 TTTTAATTTTTATTTTTAAAAT
56384370 GGGCCGGGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 26 0.62
27 16 0.38
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (26 bp):
TTTTAATTTTTATTTTTAAAATAATT
Found at i:56385334 original size:3 final size:3
Alignment explanation
Indices: 56385326--56385351 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56385316 AAAGGTAACC
56385326 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
56385352 CTCGTGGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:56388140 original size:28 final size:28
Alignment explanation
Indices: 56388109--56388227 Score: 154
Period size: 28 Copynumber: 4.3 Consensus size: 28
56388099 TTCAAATATC
*
56388109 GCCACAGAGGCTGA-TCTTTTCATACTTT
1 GCCACAAAGGCT-ATTCTTTTCATACTTT
56388137 GCCACAAAGGCTATTCTTTTCATACTTT
1 GCCACAAAGGCTATTCTTTTCATACTTT
* * *
56388165 GCCACAAAGGTTATTATTTTCATACTTC
1 GCCACAAAGGCTATTCTTTTCATACTTT
*
56388193 GCCACAAAGGCT-TTCATTTCATGA-TTT
1 GCCACAAAGGCTATTCTTTTCAT-ACTTT
56388220 GCCACAAA
1 GCCACAAA
56388228 AGCATCATTT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
27 19 0.23
28 62 0.77
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (28 bp):
GCCACAAAGGCTATTCTTTTCATACTTT
Found at i:56390744 original size:25 final size:24
Alignment explanation
Indices: 56390660--56390749 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 24
56390650 CGACCCATAA
* * *
56390660 CTCATGTGAGCATATCGATTTATAG
1 CTCATATGAGCATACCGA-TTACAG
* *
56390685 CTCGTAAGAGCATACCGATATACAG
1 CTCATATGAGCATACCGAT-TACAG
*
56390710 CTCA-AGTGAGTATACCGATTCACAG
1 CTCATA-TGAGCATACCGATT-ACAG
56390735 CTCATATGAGCATAC
1 CTCATATGAGCATAC
56390750 ATGTACATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
24 3 0.06
25 48 0.92
26 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (24 bp):
CTCATATGAGCATACCGATTACAG
Found at i:56392829 original size:42 final size:42
Alignment explanation
Indices: 56392731--56392831 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
56392721 AAAGAGCACT
* *
56392731 TTGTAGAACACATTTTCACTGACACGAGAGTAACAACATGCA
1 TTGTAGAACACATTTTCACTGACACAAGACTAACAACATGCA
* ** * ** *
56392773 TTGTAGGATGCATTTTCACTGACACAATACTGAA-AATGTGCC
1 TTGTAGAACACATTTTCACTGACACAAGACT-AACAACATGCA
56392815 TTGTAGAACACATTTTC
1 TTGTAGAACACATTTTC
56392832 CTTTCTCTCT
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (42 bp):
TTGTAGAACACATTTTCACTGACACAAGACTAACAACATGCA
Found at i:56398808 original size:20 final size:20
Alignment explanation
Indices: 56398775--56398813 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
56398765 AATAATTGCT
56398775 TGATGATTATATTTGAATGA
1 TGATGATTATATTTGAATGA
*
56398795 TGATAGATTA-ATTTTAATG
1 TGAT-GATTATATTTGAATG
56398814 TTATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (20 bp):
TGATGATTATATTTGAATGA
Found at i:56409802 original size:41 final size:41
Alignment explanation
Indices: 56409721--56409816 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
56409711 AGGCTCTATG
* ** *
56409721 TGCCTAGCAGGCTTGATGCCGGTGAAATATTTTAGACTTTA
1 TGCCTAGCAGGCTTCATGCCGGTGAAATAAATCAGACTTTA
* * *
56409762 TGCCTAGCAGGCTTCATGCCGGTGTATTAAATCAGGCTTTA
1 TGCCTAGCAGGCTTCATGCCGGTGAAATAAATCAGACTTTA
*
56409803 AGCCTAGCAGGCTT
1 TGCCTAGCAGGCTT
56409817 TGTACCGGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (41 bp):
TGCCTAGCAGGCTTCATGCCGGTGAAATAAATCAGACTTTA
Found at i:56413436 original size:28 final size:28
Alignment explanation
Indices: 56413383--56413456 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
56413373 GCTAAGGCAT
* * *
56413383 ATTAAA-ACAGGTATTAGACTAGGACAA
1 ATTAAAGACATGTACTAAACTAGGACAA
* *
56413410 ATTAATGACATGTACTAAACTATGACAA
1 ATTAAAGACATGTACTAAACTAGGACAA
*
56413438 ATTAAAGACATGTATTAAA
1 ATTAAAGACATGTACTAAA
56413457 ATAAAACACA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 5 0.13
28 34 0.87
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (28 bp):
ATTAAAGACATGTACTAAACTAGGACAA
Found at i:56414077 original size:15 final size:16
Alignment explanation
Indices: 56414047--56414077 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56414037 AAGTGACAAG
56414047 AAACAAATCGTGCAGT
1 AAACAAATCGTGCAGT
56414063 AAACAAATC-TGCAGT
1 AAACAAATCGTGCAGT
56414078 TAATAGTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (16 bp):
AAACAAATCGTGCAGT
Found at i:56440183 original size:34 final size:34
Alignment explanation
Indices: 56440124--56440188 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
56440114 CTGTACTGTG
* *
56440124 ATGGGCTAAGGCCCTAATGCTTACTGTTACTAAA
1 ATGGGCTAAGGCCCTAATGCATACTGATACTAAA
56440158 ATGGGCTAAGG-CCTAAATTG-ATACTGATACT
1 ATGGGCTAAGGCCCT-AA-TGCATACTGATACT
56440189 GATATTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 3 0.11
34 22 0.81
35 2 0.07
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (34 bp):
ATGGGCTAAGGCCCTAATGCATACTGATACTAAA
Found at i:56443633 original size:88 final size:89
Alignment explanation
Indices: 56443527--56443780 Score: 280
Period size: 88 Copynumber: 2.8 Consensus size: 89
56443517 TTTAGAGTTG
* *
56443527 AAATGGTAATTTTTCTTTTCACCTTTATACTTAAAATCAGTAATTTTTTTTTCAATTGAACGCTG
1 AAATGGTAATTTTCCTTTTCACCTTTATACTTGAAATCAGTAATTTTTTTTTCAATTGAAC-CTG
*
56443592 AACTTGTACTTAA-T-TTGAAATTC
65 AACTTGTACTTAATTGTTGAAAATC
* * * * * * *
56443615 AAATGGTTATTTTCCTTTTCCCCTTTATAATTGAAATTAGT-TTTTTTTTTTCAGTTGAACTTCG
1 AAATGGTAATTTTCCTTTTCACCTTTATACTTGAAATCAGTAATTTTTTTTTCAATTGAACCT-G
*
56443679 AACTTGTACTTAATTTGGAGTTGAAAATG
65 AACTTGTACTTAA-TT---GTTGAAAATC
* *
56443708 AAATGGTAATTTTCCTTTTTCACCTTTACACTTGAAATCAATACATTTTTTTTTTCAATTGAACT
1 AAATGGTAATTTTCC-TTTTCACCTTTATACTTGAAATCAGTA-A-TTTTTTTTTCAATTGAAC-
56443773 CTGAACTT
62 CTGAACTT
56443781 AAATTTATTG
Statistics
Matches: 134, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
86 1 0.01
87 31 0.23
88 35 0.26
89 1 0.01
93 21 0.16
94 21 0.16
97 23 0.17
98 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.47
Consensus pattern (89 bp):
AAATGGTAATTTTCCTTTTCACCTTTATACTTGAAATCAGTAATTTTTTTTTCAATTGAACCTGA
ACTTGTACTTAATTGTTGAAAATC
Found at i:56444282 original size:37 final size:38
Alignment explanation
Indices: 56444212--56444316 Score: 104
Period size: 37 Copynumber: 2.7 Consensus size: 38
56444202 GTTTGGACAA
* *
56444212 AAAACGCCGCTAAAAATCGAGCATTAGCAGCGCTTAGG
1 AAAACGCCGCTAAAAATAGAGCACTAGCAGCGCTTAGG
* ** * *
56444250 AAAACGCCGCT-AAAATAGAGTACTAGTGGCGCTTTTTGA
1 AAAACGCCGCTAAAAATAGAGCACTAGCAGCGC--TTAGG
* *
56444289 AAAATGCCGCTAAAAATAGAGCATTAGC
1 AAAACGCCGCTAAAAATAGAGCACTAGC
56444317 GGTGTTTTCC
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
37 16 0.30
38 11 0.21
39 13 0.25
40 13 0.25
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (38 bp):
AAAACGCCGCTAAAAATAGAGCACTAGCAGCGCTTAGG
Found at i:56444921 original size:14 final size:14
Alignment explanation
Indices: 56444902--56445098 Score: 89
Period size: 14 Copynumber: 13.9 Consensus size: 14
56444892 TATCACTATA
*
56444902 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
* *
56444916 GTTTAGGGTTTTTA
1 GTTTAGGGTTTATG
*
56444930 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
56444944 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
*
56444958 GTTTAGGTGTTACCAT-
1 GTTTAGG-GTT--TATG
*
56444974 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
*
56444987 GATTATGGGTTTATG
1 GTTTA-GGGTTTATG
* * *
56445002 GGTTATGATTTATG
1 GTTTAGGGTTTATG
* **
56445016 GTTTATGGTTTAAA
1 GTTTAGGGTTTATG
** **
56445030 GACT-GGGATTTAAA
1 GTTTAGGG-TTTATG
*
56445044 ATTTAGTGGTTATAT-
1 GTTTAG-GGTT-TATG
*
56445059 GTTAAGGGTTTATG
1 GTTTAGGGTTTATG
56445073 GTTTTAGGGTTTA-G
1 G-TTTAGGGTTTATG
*
56445087 GTTTATGGTTTA
1 GTTTAGGGTTTA
56445099 GGATTTAGAT
Statistics
Matches: 139, Mismatches: 32, Indels: 25
0.71 0.16 0.13
Matches are distributed among these distances:
12 2 0.01
13 15 0.11
14 80 0.58
15 37 0.27
16 4 0.03
17 1 0.01
ACGTcount: A:0.21, C:0.02, G:0.29, T:0.48
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:56445024 original size:7 final size:7
Alignment explanation
Indices: 56444902--56445027 Score: 67
Period size: 7 Copynumber: 17.7 Consensus size: 7
56444892 TATCACTATA
*
56444902 GTTTAGG
1 GTTTATG
*
56444909 GTTTTTG
1 GTTTATG
*
56444916 GTTTAGG
1 GTTTATG
* *
56444923 GTTTTTA
1 GTTTATG
*
56444930 GTTTAGG
1 GTTTATG
*
56444937 GTATATG
1 GTTTATG
56444944 GTTTA-G
1 GTTTATG
*
56444950 AGTTTAAG
1 -GTTTATG
56444958 GTTTA-G
1 GTTTATG
**
56444964 GTGTTACCA
1 GT-TTA-TG
* *
56444973 TTTTAAG
1 GTTTATG
56444980 GTTTATG
1 GTTTATG
*
56444987 GATTATGG
1 GTTTAT-G
56444995 GTTTATG
1 GTTTATG
*
56445002 GGTTATG
1 GTTTATG
*
56445009 ATTTATG
1 GTTTATG
56445016 GTTTATG
1 GTTTATG
56445023 GTTTA
1 GTTTA
56445028 AAGACTGGGA
Statistics
Matches: 88, Mismatches: 25, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
6 4 0.05
7 73 0.83
8 10 0.11
9 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (7 bp):
GTTTATG
Found at i:56445081 original size:15 final size:14
Alignment explanation
Indices: 56445063--56445106 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
56445053 TTATATGTTA
56445063 AGGGTTTATGGTTTT
1 AGGGTTTA-GGTTTT
56445078 AGGGTTTAGG-TTT
1 AGGGTTTAGGTTTT
* *
56445091 ATGGTTTAGGATTT
1 AGGGTTTAGGTTTT
56445105 AG
1 AG
56445107 ATTAACTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 12 0.46
14 6 0.23
15 8 0.31
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (14 bp):
AGGGTTTAGGTTTT
Found at i:56445089 original size:21 final size:20
Alignment explanation
Indices: 56445065--56445106 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
56445055 ATATGTTAAG
*
56445065 GGTTTATGGTTTTAGGGTTTA
1 GGTTTATGG-TTTAGGATTTA
56445086 GGTTTATGGTTTAGGATTTA
1 GGTTTATGGTTTAGGATTTA
56445106 G
1 G
56445107 ATTAACTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (20 bp):
GGTTTATGGTTTAGGATTTA
Found at i:56452477 original size:27 final size:27
Alignment explanation
Indices: 56452447--56452508 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
56452437 CCTATCAGGT
56452447 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
56452474 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
56452501 AGGCGCCA
1 AGGCGCCA
56452509 TTACTAGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:56452642 original size:21 final size:19
Alignment explanation
Indices: 56452611--56452654 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 19
56452601 AATAAACACC
56452611 AAAAAATTTTTAAAAATAA
1 AAAAAATTTTTAAAAATAA
56452630 AAAAAAGTATTTTAAAAATAA
1 AAAAAA-T-TTTTAAAAATAA
56452651 AAAA
1 AAAA
56452655 TAAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 16 0.70
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAAATTTTTAAAAATAA
Found at i:56452838 original size:19 final size:19
Alignment explanation
Indices: 56452816--56452853 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
56452806 AATTTAATTT
*
56452816 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
56452835 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
56452854 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:56466134 original size:24 final size:22
Alignment explanation
Indices: 56466107--56466226 Score: 89
Period size: 22 Copynumber: 5.2 Consensus size: 22
56466097 AAAATAATCA
*
56466107 AAAAAAATTTTGAATTACAGGGAC
1 AAAAAAA--TTGAATTATAGGGAC
* *
56466131 AAAAAAATTGATTTATAGGGAT
1 AAAAAAATTGAATTATAGGGAC
* **
56466153 AAACAAATCAAATTATAGGGAC
1 AAAAAAATTGAATTATAGGGAC
* * *
56466175 AAAAAAACGTTAAATTACAAGGAC
1 AAAAAAA--TTGAATTATAGGGAC
*
56466199 ATAAAAAGGTTGAATTATAGGGA-
1 A-AAAAA-ATTGAATTATAGGGAC
56466222 AAAAA
1 AAAAA
56466227 TCGACTTACA
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
22 39 0.51
23 1 0.01
24 31 0.41
25 5 0.07
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.23
Consensus pattern (22 bp):
AAAAAAATTGAATTATAGGGAC
Found at i:56466141 original size:22 final size:22
Alignment explanation
Indices: 56466107--56466336 Score: 93
Period size: 24 Copynumber: 10.4 Consensus size: 22
56466097 AAAATAATCA
56466107 AAAAAAATTTTGAATTACAGGGAC
1 AAAAAAA--TTGAATTACAGGGAC
* * *
56466131 AAAAAAATTGATTTATAGGGAT
1 AAAAAAATTGAATTACAGGGAC
* ** *
56466153 AAACAAATCAAATTATAGGGAC
1 AAAAAAATTGAATTACAGGGAC
* *
56466175 AAAAAAACGTTAAATTACAAGGAC
1 AAAAAAA--TTGAATTACAGGGAC
* *
56466199 ATAAAAAGGTTGAATTATAGGG--
1 A-AAAAA-ATTGAATTACAGGGAC
* *
56466221 -AAAAAATCGACTTACA-GGA-
1 AAAAAAATTGAATTACAGGGAC
* *
56466240 AAAAAAA--GAACTAC-GTGAAC
1 AAAAAAATTGAATTACAG-GGAC
** *
56466260 TAAAAATTTTGAATTATAGGGAC
1 -AAAAAAATTGAATTACAGGGAC
* *
56466283 --AAAAATTCAATTTACAGTGAC
1 AAAAAAATTGAA-TTACAGGGAC
* *
56466304 AAAAAAATGTCGAATTACAAGGAG
1 AAAAAAAT-T-GAATTACAGGGAC
56466328 AAAAAAATT
1 AAAAAAATT
56466337 TGGACTTATA
Statistics
Matches: 151, Mismatches: 37, Indels: 37
0.67 0.16 0.16
Matches are distributed among these distances:
18 7 0.05
19 9 0.06
20 18 0.12
21 13 0.09
22 35 0.23
23 15 0.10
24 47 0.31
25 7 0.05
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.23
Consensus pattern (22 bp):
AAAAAAATTGAATTACAGGGAC
Found at i:56466346 original size:129 final size:134
Alignment explanation
Indices: 56466138--56466382 Score: 288
Period size: 129 Copynumber: 1.9 Consensus size: 134
56466128 GACAAAAAAA
* * * *
56466138 TTGATTTATAGGGATAAACAAATCAAATTATAGGGACAAAAAAACGTTAAATTACAAGGACATAA
1 TTGAATTATAGGGACAAACAAATCAAATTACAGGGACAAAAAAACGTCAAATTACAAGGACATAA
* * *
56466203 AAAGGTTGAATTATAG-G-GAA-AAAATC-GACTTACAGGAA-AAAAAAGAACTACGTGAACTAA
66 AAAAGTTGAATTATAGAGAGAACAAAAACAAAC-TACAGGAACAAAAAAGAACTACGTGAACTAA
56466263 AAATT
130 AAATT
* * * * * *
56466268 TTGAATTATAGGGACAAA-AATTCAATTTACAGTGACAAAAAAATGTCGAATTACAAGGAGA-AA
1 TTGAATTATAGGGACAAACAAATCAAATTACAGGGACAAAAAAACGTCAAATTACAAGGACATAA
* *
56466331 AAAATTTGGACTTATAGAGAGAACAAAAACAAACTACAGGAACAAAAAAGAA
66 AAAAGTT-GAATTATAGAGAGAACAAAAACAAACTACAGGAACAAAAAAGAA
56466383 ATAGAATTAT
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
128 7 0.07
129 43 0.46
130 17 0.18
131 3 0.03
132 13 0.14
133 11 0.12
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.21
Consensus pattern (134 bp):
TTGAATTATAGGGACAAACAAATCAAATTACAGGGACAAAAAAACGTCAAATTACAAGGACATAA
AAAAGTTGAATTATAGAGAGAACAAAAACAAACTACAGGAACAAAAAAGAACTACGTGAACTAAA
AATT
Found at i:56469297 original size:31 final size:29
Alignment explanation
Indices: 56469254--56469315 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
56469244 TTTTATAAAT
*
56469254 AATTAATATTTAT-TAATTAAAAATATTTAC
1 AATTAATATTTATAT-ATT-AAAATATTAAC
*
56469284 AATTTATATTTTATATATTAAAATATTAAC
1 AATTAATA-TTTATATATTAAAATATTAAC
56469314 AA
1 AA
56469316 CAAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 8 0.29
32 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTAATATTTATATATTAAAATATTAAC
Found at i:56472869 original size:48 final size:48
Alignment explanation
Indices: 56472798--56472894 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
56472788 GAAGTATGAG
56472798 AAACGGCCAATTCACCCTACCCATGTATCAAAGCTGAGAAACCTAACA
1 AAACGGCCAATTCACCCTACCCATGTATCAAAGCTGAGAAACCTAACA
56472846 AAACGGCCAATTCACCCTACCCATGTATCAAAGCTGAGAAACCTAACA
1 AAACGGCCAATTCACCCTACCCATGTATCAAAGCTGAGAAACCTAACA
56472894 A
1 A
56472895 TTCATCTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.40, C:0.31, G:0.12, T:0.16
Consensus pattern (48 bp):
AAACGGCCAATTCACCCTACCCATGTATCAAAGCTGAGAAACCTAACA
Found at i:56474826 original size:27 final size:27
Alignment explanation
Indices: 56474796--56474850 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
56474786 AAATAAAATA
56474796 TATATACATAATATAGTCATTTCATAT
1 TATATACATAATATAGTCATTTCATAT
56474823 TATATACATAATATAGTCATTTCATAT
1 TATATACATAATATAGTCATTTCATAT
56474850 T
1 T
56474851 TAGTATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (27 bp):
TATATACATAATATAGTCATTTCATAT
Found at i:56479254 original size:126 final size:126
Alignment explanation
Indices: 56478998--56479394 Score: 484
Period size: 126 Copynumber: 3.2 Consensus size: 126
56478988 GGCCAAACAG
* * * **
56478998 GAACTACTGTAGAAAAAAAACGTTCACGTGAGAGCTTTTTTCAGTAATTTTTTTGACAGTGCATC
1 GAACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTACTGACAGTGCATC
* * * * *
56479063 CTGCTTGACGCGTTTTTGACACTATTTTTTT-AGAA-TTGTCTTCTCAAAATTATTTCTTTAG
66 CTGCTTGAAGCTTTTTTGACACTATTTTTTTCAGAACCT-TCTTCTCAAAATTATTT-TTCAA
* *
56479124 GAACTACTGTAGAAAAAAAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTACTGTCAGTGCATC
1 GAACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTACTGACAGTGCATC
*
56479189 CTGCTTGAAGCTTTTTTGAAACTATTTTTTTCAGAACCTTCTTCTCAAAATTATTTTTCAA
66 CTGCTTGAAGCTTTTTTGACACTATTTTTTTCAGAACCTTCTTCTCAAAATTATTTTTCAA
* * *
56479250 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAG-TCTTTTT-AGTAATTTTGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCT-TTTTTCAGTAATTTTACTGACAGTGCAT
* * * * * *
56479313 CATGTTTGAAG-TGTTTTTGACATTA-TCTTTTCAGAACCGTCTTCTCAAAATTAACTTTTCTAA
65 CCTGCTTGAAGCT-TTTTTGACACTATTTTTTTCAGAACCTTCTTCTCAAAATT-ATTTTTC-AA
56479376 -AACTACTGTAGAAAGAAAA
1 GAACTACTGTAGAAA-AAAA
56479395 ACAAAATTCT
Statistics
Matches: 238, Mismatches: 26, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
124 26 0.11
125 60 0.25
126 130 0.55
127 21 0.09
128 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTACTGACAGTGCATC
CTGCTTGAAGCTTTTTTGACACTATTTTTTTCAGAACCTTCTTCTCAAAATTATTTTTCAA
Found at i:56479494 original size:34 final size:33
Alignment explanation
Indices: 56479453--56479558 Score: 140
Period size: 34 Copynumber: 3.2 Consensus size: 33
56479443 CACAAAATTA
*
56479453 TTTTTAAAAAAACTAAACCCTAATTTAATTAAT
1 TTTTTAAAAACACTAAACCCTAATTTAATTAAT
* *
56479486 TTTCTTAAAAACTCTAAACCTTAATTTAATTAAT
1 TTT-TTAAAAACACTAAACCCTAATTTAATTAAT
* * *
56479520 TTATTTAAAACCCCTAAAACCTAATTTAATTAAT
1 TT-TTTAAAAACACTAAACCCTAATTTAATTAAT
56479554 TTTTT
1 TTTTT
56479559 TTAAAATTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
33 6 0.09
34 57 0.89
35 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.43
Consensus pattern (33 bp):
TTTTTAAAAACACTAAACCCTAATTTAATTAAT
Found at i:56479527 original size:68 final size:68
Alignment explanation
Indices: 56479455--56479581 Score: 182
Period size: 68 Copynumber: 1.9 Consensus size: 68
56479445 CAAAATTATT
*
56479455 TTTAAAAAAACTAAACCCTAATTTAATTAATTTTCTTAAAAACTCTAAACCTTAATTTAATTAAT
1 TTTAAAAAAACTAAAACCTAATTTAATTAATTTTCTTAAAAACTCTAAACCTTAATTTAATTAAT
56479520 TTA
66 TTA
*** * * * *
56479523 TTTAAAACCCCTAAAACCTAATTTAATTAATTTTTTTTAAAATTCTAAACCTTGATTTA
1 TTTAAAAAAACTAAAACCTAATTTAATTAATTTTCTTAAAAACTCTAAACCTTAATTTA
56479582 TTTTTTAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 51 1.00
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.43
Consensus pattern (68 bp):
TTTAAAAAAACTAAAACCTAATTTAATTAATTTTCTTAAAAACTCTAAACCTTAATTTAATTAAT
TTA
Found at i:56479581 original size:34 final size:34
Alignment explanation
Indices: 56479465--56479581 Score: 139
Period size: 34 Copynumber: 3.4 Consensus size: 34
56479455 TTTAAAAAAA
* * *
56479465 CTAAACCCTAATTTAATTAATTTTCTTAAAAACT
1 CTAAACCTTAATTTAATTAATTTTATTTAAAACT
*
56479499 CTAAACCTTAATTTAATTAA-TTTATTTAAAACCC
1 CTAAACCTTAATTTAATTAATTTTATTTAAAA-CT
* *
56479533 CTAAAACC-TAATTTAATTAATTTTTTTTAAAATT
1 CT-AAACCTTAATTTAATTAATTTTATTTAAAACT
*
56479567 CTAAACCTTGATTTA
1 CTAAACCTTAATTTA
56479582 TTTTTTAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
33 14 0.20
34 42 0.59
35 15 0.21
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (34 bp):
CTAAACCTTAATTTAATTAATTTTATTTAAAACT
Found at i:56480794 original size:20 final size:20
Alignment explanation
Indices: 56480769--56480809 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
56480759 TTTTGGTAAG
56480769 ATAACAAAATATAGTAATAA
1 ATAACAAAATATAGTAATAA
*
56480789 ATAACAAAATATGGTAATAA
1 ATAACAAAATATAGTAATAA
56480809 A
1 A
56480810 ACATCATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.24
Consensus pattern (20 bp):
ATAACAAAATATAGTAATAA
Found at i:56483988 original size:268 final size:265
Alignment explanation
Indices: 56483496--56484031 Score: 729
Period size: 268 Copynumber: 2.0 Consensus size: 265
56483486 TAAACTTGCT
*
56483496 TAATAAAAGTACTTGTATATCATTTTAGTCATTTTATTTTATGTTAATAATATATATGTATATAT
1 TAATAAAAGTACTTGTACATCATTTTAGTCATTTTATTTTATGTTAATAATATATATGTATATAT
* * * * *
56483561 ACTACTTCGCTAATGGATCGGTTATGAGTGAAGGTTTTGGAAATGTGACCAAATTGAGTAACCGA
66 ACTACTCCGCTAATGAATAGGTTATGAGTGAAGATTTTGGAAATGTGACCAAATTAAGTAACCGA
*
56483626 GATAAGGTGCTTGAGTTGTCATCTCACCTCGCGTAAAAAGATTCAAGTGACGAACCAAAACCTGC
131 GATAAGGTGCTTGAGTTGTCATCTCACCTCGCATAAAAAGATTCAAGTGACGAACCAAAACCTGC
* * * * *
56483691 AAACACTCTGCTAGCTGAGTTTCCATGAGTAGGGGAAAAA-TAATTCGTTTAGAGACGTATCAAA
196 AAACACTCTGCTAGCTAAGTGTCCATGAGTAAGGAAAAAAGTAATCCGTTTAGAGACGTATCAAA
56483755 TCGAG
261 TCGAG
* * *
56483760 TAATAAAAGTACTTGTACCTCGTTTTAGTCATTTTGTTTTATGTTAATAATATATATAAGTATAA
1 TAATAAAAGTACTTGTACATCATTTTAGTCATTTTATTTTATGTTAATAATATATAT--GTAT--
* *
56483825 ATATACTACTCCGTTGATGAATAGGTTATGAGTGAAGATTTTGGAAATGTGACCAAATTAAGTAA
62 ATATACTACTCCGCTAATGAATAGGTTATGAGTGAAGATTTTGGAAATGTGACCAAATTAAGTAA
* * * * * *
56483890 TCGAGATAAGGTTCTTGGGTTGTTATCTCACCTCGCATAAAAAGA-TCTGAGTGACGAACCGAAA
127 CCGAGATAAGGTGCTTGAGTTGTCATCTCACCTCGCATAAAAAGATTC-AAGTGACGAACCAAAA
* * * *
56483954 CTTGCAAACACTCTGCTA-ATCAAGCTGT-CATGAGTAAGGAAAAAAGTAATCCGTTTGGAGATG
191 CCTGCAAACACTCTGCTAGCT-AAG-TGTCCATGAGTAAGGAAAAAAGTAATCCGTTTAGAGACG
*
56484017 TATCAAATTGAG
254 TATCAAATCGAG
56484029 TAA
1 TAA
56484032 CCTGGATGAG
Statistics
Matches: 236, Mismatches: 28, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
264 53 0.22
266 4 0.02
267 3 0.01
268 146 0.62
269 30 0.13
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (265 bp):
TAATAAAAGTACTTGTACATCATTTTAGTCATTTTATTTTATGTTAATAATATATATGTATATAT
ACTACTCCGCTAATGAATAGGTTATGAGTGAAGATTTTGGAAATGTGACCAAATTAAGTAACCGA
GATAAGGTGCTTGAGTTGTCATCTCACCTCGCATAAAAAGATTCAAGTGACGAACCAAAACCTGC
AAACACTCTGCTAGCTAAGTGTCCATGAGTAAGGAAAAAAGTAATCCGTTTAGAGACGTATCAAA
TCGAG
Found at i:56488042 original size:7 final size:7
Alignment explanation
Indices: 56488032--56488076 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
56488022 GTTTTTGGGT
56488032 TTTAGGG
1 TTTAGGG
56488039 TTTAGGG
1 TTTAGGG
56488046 TTTAGGG
1 TTTAGGG
**
56488053 TTTTAAAG
1 -TTTAGGG
*
56488061 TTTGGGG
1 TTTAGGG
56488068 TTTAGGG
1 TTTAGGG
56488075 TT
1 TT
56488077 AAAAATTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
7 26 0.84
8 5 0.16
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:56488053 original size:22 final size:22
Alignment explanation
Indices: 56488028--56488076 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
56488018 ACTTGTTTTT
**
56488028 GGGTTTTAGGGTTTAGGGTTTA
1 GGGTTTTAAAGTTTAGGGTTTA
*
56488050 GGGTTTTAAAGTTTGGGGTTTA
1 GGGTTTTAAAGTTTAGGGTTTA
56488072 GGGTT
1 GGGTT
56488077 AAAAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.45
Consensus pattern (22 bp):
GGGTTTTAAAGTTTAGGGTTTA
Found at i:56488295 original size:37 final size:39
Alignment explanation
Indices: 56488229--56488303 Score: 111
Period size: 37 Copynumber: 2.0 Consensus size: 39
56488219 TAAACACCAA
56488229 AAAAATTATTTTAAAAATAAAAAGAATAAAAAAGTATTTT
1 AAAAATTATTTTAAAAATAAAAAGAATAAAAAA-TATTTT
*
56488269 AAAAA-TATTTT-AAAAT-CAAAGAATAAAAAATATTT
1 AAAAATTATTTTAAAAATAAAAAGAATAAAAAATATTT
56488304 ATTTATTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 5 0.15
37 13 0.38
38 5 0.15
39 6 0.18
40 5 0.15
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (39 bp):
AAAAATTATTTTAAAAATAAAAAGAATAAAAAATATTTT
Found at i:56488529 original size:6 final size:6
Alignment explanation
Indices: 56488515--56488554 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
56488505 CAAAATTGGA
*
56488515 TTAGGG TTAGAG TTAGGG TTAGGG TTAGGG TTAGGG TTAG
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAG
56488555 AGTTTTGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.35
Consensus pattern (6 bp):
TTAGGG
Found at i:56492724 original size:50 final size:50
Alignment explanation
Indices: 56492649--56492889 Score: 365
Period size: 50 Copynumber: 4.8 Consensus size: 50
56492639 ATTTGGGTAA
56492649 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
**
56492699 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
56492749 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTAGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
56492799 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
56492849 AGAACATCCCATGTAAGACCATGTCTGGGACAAGGCTTTGG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
56492890 TATGTTATTA
Statistics
Matches: 173, Mismatches: 17, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
50 142 0.82
51 31 0.18
ACGTcount: A:0.26, C:0.22, G:0.32, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:56493312 original size:17 final size:17
Alignment explanation
Indices: 56493290--56493351 Score: 124
Period size: 17 Copynumber: 3.6 Consensus size: 17
56493280 AGTCTACTTT
56493290 CATATAAAAATAATGGG
1 CATATAAAAATAATGGG
56493307 CATATAAAAATAATGGG
1 CATATAAAAATAATGGG
56493324 CATATAAAAATAATGGG
1 CATATAAAAATAATGGG
56493341 CATATAAAAAT
1 CATATAAAAAT
56493352 CACCTAGTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.24
Consensus pattern (17 bp):
CATATAAAAATAATGGG
Found at i:56498844 original size:51 final size:51
Alignment explanation
Indices: 56498784--56498883 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
56498774 ATAATTAAAA
56498784 AAATAGGGATTTAAGAGAAA-TTTGAGAGGAAATTGAGAGCAAAATGAGATT
1 AAATAGGGATTTAAGAGAAATTTTGA-AGGAAATTGAGAGCAAAATGAGATT
* *
56498835 AAATAGGGATTTGAGAGAAATTTTGAAGGAAATTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTTGAAGGAAATTGAGAGCAAAATGAGA
56498884 GGAAATTGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 41 0.89
52 5 0.11
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTTGAAGGAAATTGAGAGCAAAATGAGATT
Found at i:56498891 original size:11 final size:11
Alignment explanation
Indices: 56498800--56498892 Score: 63
Period size: 11 Copynumber: 8.7 Consensus size: 11
56498790 GGATTTAAGA
56498800 GAAATTTGAGAG
1 GAAA-TTGAGAG
56498812 GAAATTGAGAG
1 GAAATTGAGAG
* * *
56498823 CAAAATGAGAT
1 GAAATTGAGAG
*
56498834 TAAA-T-AG-G
1 GAAATTGAGAG
*
56498842 G-ATTTGAGA-
1 GAAATTGAGAG
56498851 GAAATTTTGA-AG
1 GAAA--TTGAGAG
56498863 GAAATTGAGAG
1 GAAATTGAGAG
*
56498874 CAAATTGAGAG
1 GAAATTGAGAG
56498885 GAAATTGA
1 GAAATTGA
56498893 AAGAATAATA
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 5 0.08
10 6 0.10
11 38 0.60
12 12 0.19
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:56501960 original size:6 final size:6
Alignment explanation
Indices: 56501949--56501982 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
56501939 ATACAAAATG
56501949 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
56501983 GTTCAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:56505450 original size:47 final size:47
Alignment explanation
Indices: 56505397--56505541 Score: 158
Period size: 47 Copynumber: 3.1 Consensus size: 47
56505387 TCATATAAGA
*
56505397 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
* **
56505444 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATT
* * *
56505488 AAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
56505535 ATATTTA
1 ATATTTA
56505542 ATAATAATTA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.31
45 8 0.10
46 8 0.10
47 32 0.41
48 3 0.04
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
Found at i:56505494 original size:91 final size:91
Alignment explanation
Indices: 56505382--56505597 Score: 369
Period size: 91 Copynumber: 2.4 Consensus size: 91
56505372 ATGATTTTAG
*
56505382 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
56505447 TTTAATATTAATTATTTTAAATTATA
66 TTTAATAATAATTATTTTAAATTATA
* *
56505473 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
56505538 TTTAATAATAATTATTTTAAATTATA
66 TTTAATAATAATTATTTTAAATTATA
* * *
56505564 CAAATTCATATAAGAAAATTTATTAGTAATAATT
1 TAAATTCATATAAGAAAATTTATTATTAAGAATT
56505598 ATTTTAAATT
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 117 1.00
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATAATAATTATTTTAAATTATA
Found at i:56505528 original size:101 final size:92
Alignment explanation
Indices: 56505474--56505665 Score: 194
Period size: 101 Copynumber: 2.0 Consensus size: 92
56505464 TAAATTATAT
56505474 AAATTCATATAAGAAAATTTATTA-TCAAGAATT-TTATGA--AATTATATATTATTATTAAATT
1 AAATTCATATAAGAAAATTTATTAGT-AAGAATTATT-TGATTAATTATATA-TATTATTAAATT
*
56505535 ATATTTAATAATAATTATTTTAAATTATAC
63 ATATTTAATAATAATTATTTTAAATTATAT
* * *
56505565 AAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTTTATTAAATCATATATTTTAAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTA-TTT-GA-TTAATT--AT-ATATA--TT-AT
* *
56505630 TAAAATATATTTAATAATAATTATTTCAAATTATAT
57 TAAATTATATTTAATAATAATTATTTTAAATTATAT
56505666 TTTATAGTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
91 30 0.37
92 2 0.02
93 3 0.04
96 3 0.04
98 4 0.05
99 3 0.04
100 2 0.02
101 35 0.43
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (92 bp):
AAATTCATATAAGAAAATTTATTAGTAAGAATTATTTGATTAATTATATATATTATTAAATTATA
TTTAATAATAATTATTTTAAATTATAT
Found at i:56505555 original size:47 final size:47
Alignment explanation
Indices: 56505413--56505556 Score: 140
Period size: 47 Copynumber: 3.1 Consensus size: 47
56505403 ATTATTAAGA
* *
56505413 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATAATT
* * **
56505460 A-TTT-T-AAATTATATA-AATTCATATAAGA--AAATTT-ATTATCAAGA
1 ATTTTATGAAATTATATATAATT-AT-TAA-ATTATATTTAATAAT-AATT
*
56505504 ATTTTATGAAATTATATATTATTATTAAATTATATTTAATAATAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATAATT
56505551 ATTTTA
1 ATTTTA
56505557 AATTATACAA
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
43 6 0.08
44 20 0.27
45 8 0.11
46 8 0.11
47 26 0.35
48 7 0.09
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (47 bp):
ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATAATT
Found at i:56506011 original size:16 final size:16
Alignment explanation
Indices: 56505990--56506028 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
56505980 AATTGATTTG
*
56505990 CTATTACGTCTCTATT
1 CTATTACGCCTCTATT
56506006 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
*
56506022 CCATTAC
1 CTATTAC
56506029 AGCGAACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.31, G:0.05, T:0.44
Consensus pattern (16 bp):
CTATTACGCCTCTATT
Found at i:56506184 original size:32 final size:32
Alignment explanation
Indices: 56506148--56506209 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
56506138 GTGACAGTTA
*
56506148 AAAAAATCATTATAATAATAAATTTAACCCAC
1 AAAAAATCATTATAATAATAAATTCAACCCAC
*
56506180 AAAAAATTATTATAATAATAAATTCAACCC
1 AAAAAATCATTATAATAATAAATTCAACCC
56506210 TCAATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (32 bp):
AAAAAATCATTATAATAATAAATTCAACCCAC
Found at i:56507387 original size:22 final size:22
Alignment explanation
Indices: 56507352--56507394 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56507342 AGAAAAGATA
56507352 TTAAATATGGATGATAGTAATTT
1 TTAAATATGGATGATA-TAATTT
*
56507375 TTAAA-ATTGATGATATAATT
1 TTAAATATGGATGATATAATT
56507395 GATGCGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (22 bp):
TTAAATATGGATGATATAATTT
Found at i:56508403 original size:20 final size:21
Alignment explanation
Indices: 56508365--56508403 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
56508355 TAATATTAAA
*
56508365 AAATATATTTTTATATTTTTT
1 AAATATATTTTAATATTTTTT
*
56508386 AAATA-ATTTTAATCTTTT
1 AAATATATTTTAATATTTT
56508404 AATTTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
AAATATATTTTAATATTTTTT
Found at i:56512021 original size:45 final size:45
Alignment explanation
Indices: 56511896--56512067 Score: 177
Period size: 45 Copynumber: 3.8 Consensus size: 45
56511886 TTTGGATTGA
* * * * *
56511896 GAAATAAGAAAGACGATGGTTGAAAGATGCCATGACATTATACCC
1 GAAATGAGAAAGACCATAGTTGAAAGATACCATGGCATTATACCC
* * *
56511941 GAAACGAGAAAGACTATGGTTGAAAGATACCATGGCATTATACCC
1 GAAATGAGAAAGACCATAGTTGAAAGATACCATGGCATTATACCC
* * * *
56511986 GAAATGAGAAAGACCATAGTTGAAGGCA-ACTATGGCATTATATCG
1 GAAATGAGAAAGACCATAGTTGAAAG-ATACCATGGCATTATACCC
* * *
56512031 GAAATGTA-TAAGACCATAGTTGAAATATACTATGGCA
1 GAAATG-AGAAAGACCATAGTTGAAAGATACCATGGCA
56512068 ATACATCGGC
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
44 1 0.01
45 106 0.97
46 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (45 bp):
GAAATGAGAAAGACCATAGTTGAAAGATACCATGGCATTATACCC
Found at i:56512076 original size:45 final size:44
Alignment explanation
Indices: 56511986--56512112 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 44
56511976 CATTATACCC
* * *
56511986 GAAATGAGA-AAGACCATAGTTGAAGGCAACTATGGCATTATATCG
1 GAAATGA-ATAAGACCATAGTTGAA-ACAACTATGGCAATACATCG
* *
56512031 GAAATGTATAAGACCATAGTTGAAATATACTATGGCAATACATCG
1 GAAATGAATAAGACCATAGTTGAAACA-ACTATGGCAATACATCG
* * * * *
56512076 GCAATGAATAAGACTACAGTTTAAAGAGACTATGGCA
1 GAAATGAATAAGACCATAGTTGAAACA-ACTATGGCA
56512113 TCACTTTGGA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 2 0.03
45 66 0.97
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (44 bp):
GAAATGAATAAGACCATAGTTGAAACAACTATGGCAATACATCG
Found at i:56522313 original size:21 final size:22
Alignment explanation
Indices: 56522273--56522319 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
56522263 ATAAATATGA
*
56522273 CAATTCAAAATACATGTATAATT
1 CAATTCAAAATACATATAT-ATT
56522296 CAATT-AAAA-ACATATATATT
1 CAATTCAAAATACATATATATT
56522316 CAAT
1 CAAT
56522320 ATAATTACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 7 0.30
22 4 0.17
23 5 0.22
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (22 bp):
CAATTCAAAATACATATATATT
Found at i:56529819 original size:25 final size:24
Alignment explanation
Indices: 56529774--56529914 Score: 107
Period size: 25 Copynumber: 6.0 Consensus size: 24
56529764 AATTATTCAA
*
56529774 CAAATTGGACAGCAATA-ACATGCT
1 CAAATTGGACAGCATTATACAT-CT
*
56529798 CAAAATGGACAGCATTATACA--T
1 CAAATTGGACAGCATTATACATCT
* * * *
56529820 CAAATTAGACAGC-TTAAATATACC
1 CAAATTGGACAGCATTATACAT-CT
56529844 CAAAATTGGACAGCATTATACA--T
1 C-AAATTGGACAGCATTATACATCT
* * *
56529867 CAAATTAGACAGC-TTAAATATACT
1 CAAATTGGACAGCATTATACAT-CT
56529891 CACAATTGGACAGCATTATACATC
1 CA-AATTGGACAGCATTATACATC
56529915 AAATTATAAC
Statistics
Matches: 89, Mismatches: 17, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
21 10 0.11
22 23 0.26
23 1 0.01
24 19 0.21
25 25 0.28
26 11 0.12
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (24 bp):
CAAATTGGACAGCATTATACATCT
Found at i:56529854 original size:47 final size:47
Alignment explanation
Indices: 56529798--56529920 Score: 221
Period size: 47 Copynumber: 2.6 Consensus size: 47
56529788 ATAACATGCT
56529798 CAAAA-TGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
*
56529844 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACT
1 CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
*
56529891 CACAATTGGACAGCATTATACATCAAATTA
1 CAAAATTGGACAGCATTATACATCAAATTA
56529921 TAACACAAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
46 5 0.07
47 69 0.93
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (47 bp):
CAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACC
Found at i:56530883 original size:28 final size:27
Alignment explanation
Indices: 56530851--56530949 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
56530841 TTAATAAGTA
*
56530851 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT-ATAATTAAACT
* *
56530879 CGCACACTTAGTGCTT-TACCCTTATACT
1 CGCACACTTAGTGCTTATA--ATTAAACT
56530907 CGCACACTTAGTGCATT-TCAATTAAACT
1 CGCACACTTAGTGC-TTAT-AATTAAACT
56530935 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
56530950 AATCTCATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 55 0.89
29 3 0.05
30 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATTAAACT
Found at i:56535206 original size:20 final size:20
Alignment explanation
Indices: 56535170--56535209 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
56535160 TACACCACAC
*
56535170 CAGAGGCACCGAAGTGCAAA
1 CAGAGGCACCAAAGTGCAAA
56535190 CAGAGGCA-CAAATGTGCAAA
1 CAGAGGCACCAAA-GTGCAAA
56535210 GGCACCGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.42, C:0.23, G:0.28, T:0.07
Consensus pattern (20 bp):
CAGAGGCACCAAAGTGCAAA
Found at i:56542523 original size:45 final size:45
Alignment explanation
Indices: 56542456--56542664 Score: 274
Period size: 45 Copynumber: 4.6 Consensus size: 45
56542446 TTGATTTGAA
* ** * * *
56542456 GAAAAGGAAAAAATGATTATTGAAATATATCATTGCATTATAATC
1 GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATAATC
*
56542501 GAAAAGGAAAATACCATGATTGAAAGATATCATGGCATTATAATC
1 GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATAATC
* * * *
56542546 TAAAAGGAAAAGACCGTGATTGAAAGATATCAAGGCATTATAATT
1 GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATAATC
* **
56542591 GAAAAGGAAAAGACCATGATTGAAAGATATCACGGCATTATGCTC
1 GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATAATC
* *
56542636 GAAAAGAAAAAGACCATGGTTGAAAGATA
1 GAAAAGGAAAAGACCATGATTGAAAGATA
56542665 CTATGACATC
Statistics
Matches: 145, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 145 1.00
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.23
Consensus pattern (45 bp):
GAAAAGGAAAAGACCATGATTGAAAGATATCATGGCATTATAATC
Found at i:56544871 original size:22 final size:23
Alignment explanation
Indices: 56544842--56544884 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
56544832 TTAGGGGTGT
56544842 TACATTTAG-TGG-TATCAAAGC
1 TACATTTAGTTGGTTATCAAAGC
56544863 TACAGTTTAGTTGGTTATCAAA
1 TACA-TTTAGTTGGTTATCAAA
56544885 TGAATGTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
23 3 0.16
24 7 0.37
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (23 bp):
TACATTTAGTTGGTTATCAAAGC
Found at i:56554995 original size:15 final size:16
Alignment explanation
Indices: 56554968--56554997 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56554958 GATAATAATT
56554968 AATATATATTATATAA
1 AATATATATTATATAA
56554984 AATATA-ATTATATA
1 AATATATATTATATA
56554998 TTAGTTATTA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:56563823 original size:29 final size:29
Alignment explanation
Indices: 56563778--56563835 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
56563768 CATCAATAAA
56563778 GATAACCACAAAAAACATATGTAAATTAC
1 GATAACCACAAAAAACATATGTAAATTAC
* *
56563807 GATAACTACAAAGAACATATGTAAATTAC
1 GATAACCACAAAAAACATATGTAAATTAC
56563836 AGAAGCTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (29 bp):
GATAACCACAAAAAACATATGTAAATTAC
Found at i:56565407 original size:26 final size:24
Alignment explanation
Indices: 56565359--56565409 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
56565349 TTTAAAATAC
* *
56565359 TTTTAAAATATTTTTATTTTTTAT
1 TTTTAAAATATTTTTAATGTTTAT
56565383 TTTTAAAATAATTTTTTAATGTTTAT
1 TTTTAAAAT-A-TTTTTAATGTTTAT
56565409 T
1 T
56565410 AAAAAATGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
26 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTAAAATATTTTTAATGTTTAT
Found at i:56567025 original size:14 final size:16
Alignment explanation
Indices: 56567006--56567037 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
56566996 TAAGTCATAA
56567006 ATAATATA-AA-ATTT
1 ATAATATATAACATTT
56567020 ATAATATATAACATTT
1 ATAATATATAACATTT
56567036 AT
1 AT
56567038 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATATATAACATTT
Found at i:56572998 original size:10 final size:10
Alignment explanation
Indices: 56572985--56573011 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
56572975 GTTATTCACA
56572985 TTTATTTCAT
1 TTTATTTCAT
56572995 TTTATTTCAT
1 TTTATTTCAT
56573005 TTTATTT
1 TTTATTT
56573012 ATATACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTATTTCAT
Found at i:56585455 original size:132 final size:132
Alignment explanation
Indices: 56585218--56587045 Score: 2806
Period size: 132 Copynumber: 13.9 Consensus size: 132
56585208 AATAGATCAG
* * *
56585218 TGAAGATAGCATATCTTATCTCCCTAAGCAGTAGTGGGGCAAATCGAAGACGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* *
56585283 TTCCAAGATATTGGAAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
56585348 GT
131 GT
* * * *
56585350 TGAAGATAGCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGGATATGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* * *
56585415 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGCAA
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
56585480 GT
131 GT
* * * *
56585482 TGAAGATAGTAGATCTTATCTCCCTAA-TAGTAGTGAAGCAGAT-AAAGACGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* * *
56585545 TTCCAAGATAGTGGGAAGCAAATTTAAACAACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
56585610 GT
131 GT
* *
56585612 TGAAGATAGCAGATCTTATCTCCCTAATCAGTAGTGGAGCAGGTCGAAGACGGCAAATCTTATC-
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* * *
56585676 TTCCTAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGACCAGCAGTGGAGCA
66 TTCC-AAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTA
56585741 GGT
130 GGT
* * *
56585744 TGAAGATAGCAGATCTTATCTCCCTAAGAAGTAGTGGAGCAAATCGATGACGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* * * * * * *
56585809 TTCAAATATAGTGAGAAGCAGATTTAAACCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGCAA
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
56585874 GT
131 GT
* * * *
56585876 TGAAGATAGCAGATCTCATCTCCCTAA-TAGTAGTGAAGCAGAT-AAAGACGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* * *
56585939 TTCCAAGATAGTGGGAAGCAAATTTAAACAACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
56586004 GT
131 GT
* *
56586006 TGAAGATAGCAGATCTTATCTCCCTAATCAGTAGTGGAGCAGGTCGAAGACGGCAAATCTTATC-
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* * *
56586070 TTCCTAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGACCAGCAGTGGAGCA
66 TTCC-AAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTA
*
56586135 GAT
130 GGT
* * *
56586138 TGAAGATAGCAGATCTTATCTCCCTAAGAAGTAGTGGAGCAAATCGATGACGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* * * * *
56586203 TTCAAATATAGTGAGAAGCAGATTTAAACCACCAAGCCTTGTCTCCCTGAGCAGCAGCAGAGTAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
56586268 GT
131 GT
*
56586270 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* * * **
56586335 TTCCAAGATAGTGGGAAGTAGATTTAAGCCACCAAGCCCTGTCTCCCTGAGCAACAGATGAGTAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
56586400 GT
131 GT
* *
56586402 TGAAGATAGCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* *
56586467 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGAAGCAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
56586532 GT
131 GT
*
56586534 TGAAGATAGCAGATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
*
56586599 TTCCAAGATAGTGGGAAGCAGATTTAAACCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
56586664 GT
131 GT
* *
56586666 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCACATCGAAGATGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* * *
56586731 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCATTGTCTCCCTGAGCAGCAGCGTAGCAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
56586796 GT
131 GT
* * *
56586798 TGAAGATAGCAGATCTTATCTCCCTGAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATAT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* *
56586863 TTCCAAGATAGTGGGAAGCAGATTTAAACCACCAAGCCTTGTGTCCCTGAGCAGCAGC-GATGTA
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGA-GTA
56586927 GGT
130 GGT
** * * *
56586930 TGAAGACGGCAAATCTTATCTCCCTAAGCAGTAGTAGAGCAGATTGAAGACGGCAAATCTTATCT
1 TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
* ** *
56586995 GTCCAAGATAGTGCAAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAG
56587046 GTTGTAGTGG
Statistics
Matches: 1541, Mismatches: 146, Indels: 18
0.90 0.09 0.01
Matches are distributed among these distances:
130 206 0.13
131 63 0.04
132 1266 0.82
133 6 0.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (132 bp):
TGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAG
GT
Found at i:56587018 original size:44 final size:44
Alignment explanation
Indices: 56586018--56586994 Score: 130
Period size: 44 Copynumber: 22.2 Consensus size: 44
56586008 AAGATAGCAG
* ** * *
56586018 ATCTTATCTCCCTAATCAGTAGTGGAGCAGGTCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
* * * * **
56586062 ATCTTATCTTCCTAAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT--AAAGCAGATTGAAGACGGCAA
** * * * * ** ** *
56586106 GCCTTGTCTCCCTGACCAGCAGTGGAGCAGATTGAAGATAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
* ** * * *
56586150 ATCTTATCTCCCTAAGAAGTAGTGGAGCAAATCGATGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
** ** * **
56586194 ATCTTATCTTTC-AAATA-TAGTGAGAAGCAGATTTAA-ACCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT-A-AAGCAGATTGAAGA-CGGCAA
** * * * * * * * ** *
56586238 GCCTTGTCTCCCTGAGCAGCAGCAGAGTAGGTTGAAGATAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
** **
56586282 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
* * * * * **
56586326 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGTAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT--AAAGCAGATTGAAGACGGCAA
** * * * ** * * * ** *
56586370 GCCCTGTCTCCCTGAGCAACAG-ATGAGTAGGTTGAAGATAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTA-AAGCAGATTGAAGACGGCAA
* ** * *
56586414 ATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
* * * * **
56586458 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT--AAAGCAGATTGAAGACGGCAA
** * * * ** * ** *
56586502 GCCTTGTCTCCCTGAGCAGCAGCGAAGCAGGTTGAAGATAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
* ** *
56586546 ATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
* * * **
56586590 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAA-ACCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT--AAAGCAGATTGAAGA-CGGCAA
** * * * *** * * ** *
56586634 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
** * * *
56586678 ATCTTATCTCCCTAAGCAGTAGTGGAGCACATCGAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
* * * ** *
56586722 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT--AAAGCAGATTGAAGACGGCAA
* * * * *** * ** *
56586765 AGCATTGTCTCCCTGAGCAGCAGCGTAGCAGGTTGAAGATAGCAG
1 ATC-TTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
* ** * *
56586810 ATCTTATCTCCCTGAGCAGTAGTGGAGCAGATCGAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
* * * * **
56586854 ATCTTATATTTCC-AAG-A-TAGTGGGAAGCAGATTTAA-ACCACCAA
1 ATCTTAT-CTCCCTAAGCAGTAGT--AAAGCAGATTGAAGA-CGGCAA
** * * * * ** * * *
56586898 GCCTTGTGTCCCTGAGCAGCAGCGATGTAGGTTGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
*
56586942 ATCTTATCTCCCTAAGCAGTAGTAGAGCAGATTGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
56586986 ATCTTATCT
1 ATCTTATCT
56586995 GTCCAAGATA
Statistics
Matches: 635, Mismatches: 250, Indels: 96
0.65 0.25 0.10
Matches are distributed among these distances:
42 28 0.04
43 31 0.05
44 532 0.84
45 29 0.05
46 15 0.02
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATTGAAGACGGCAA
Found at i:56593573 original size:23 final size:24
Alignment explanation
Indices: 56593545--56593590 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
56593535 TATACGCTAT
*
56593545 ATTTTTGT-TGAATAAAATCAACA
1 ATTTTTATGTGAATAAAATCAACA
*
56593568 ATTTTTATGTGAATAATATCAAC
1 ATTTTTATGTGAATAAAATCAAC
56593591 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (24 bp):
ATTTTTATGTGAATAAAATCAACA
Found at i:56597037 original size:30 final size:30
Alignment explanation
Indices: 56596997--56597087 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
56596987 ACGGGTAACC
56596997 TTGATATAATGTCAGCTTGTGTGAGCAATT
1 TTGATATAATGTCAGCTTGTGTGAGCAATT
* * * *
56597027 TTGTTATAATGTCAGCTTATGTGAGCAGTC
1 TTGATATAATGTCAGCTTGTGTGAGCAATT
* * * *
56597057 CTGATATACTATTAGCTTGTGTGAGCAATT
1 TTGATATAATGTCAGCTTGTGTGAGCAATT
56597087 T
1 T
56597088 ATTCACATGT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (30 bp):
TTGATATAATGTCAGCTTGTGTGAGCAATT
Found at i:56602011 original size:15 final size:15
Alignment explanation
Indices: 56601983--56602023 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
56601973 TTATCCAATC
56601983 AAATAAAG-AAAAAT
1 AAATAAAGCAAAAAT
56601997 AAATAAAGCAAAAAT
1 AAATAAAGCAAAAAT
* *
56602012 GAATAAAACAAA
1 AAATAAAGCAAA
56602024 GAAGCTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (15 bp):
AAATAAAGCAAAAAT
Found at i:56602780 original size:26 final size:26
Alignment explanation
Indices: 56602736--56602810 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
56602726 AAATTAAACC
56602736 TAAACCCAAGTT-ACC-AGCCCAAAAT
1 TAAACCCAA-TTAACCTAGCCCAAAAT
*
56602761 CT-AACCCAATTAACCTAGCCCAAACT
1 -TAAACCCAATTAACCTAGCCCAAAAT
*
56602787 TAAACCCAACTACACCTAGCCCAA
1 TAAACCCAATTA-ACCTAGCCCAA
56602811 CTATCATACA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 2 0.05
25 11 0.26
26 19 0.44
27 11 0.26
ACGTcount: A:0.41, C:0.37, G:0.05, T:0.16
Consensus pattern (26 bp):
TAAACCCAATTAACCTAGCCCAAAAT
Found at i:56606598 original size:16 final size:16
Alignment explanation
Indices: 56606579--56606609 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56606569 TTATTTTTAA
56606579 ATAAATCTAATTAAAT
1 ATAAATCTAATTAAAT
56606595 ATAAATCTAATTAAA
1 ATAAATCTAATTAAA
56606610 AGATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATCTAATTAAAT
Found at i:56609352 original size:125 final size:125
Alignment explanation
Indices: 56609130--56609414 Score: 444
Period size: 125 Copynumber: 2.3 Consensus size: 125
56609120 TGTTAATTTA
* *
56609130 AAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGAAGACG
1 AAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTTGAGAAGACG
* * * * * *
56609195 TTTCTGAGCAAATAGTGTTAAAAACGCTTTAAGCAGGATGCTTTGTTAGGAAAAATACTG
66 GTTCAGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTAAGCAAAAATACTG
* * *
56609255 AAAAAGCTCTCACGTGGACGCGCTTTTACTACAGTAGCTCCTAAAAAAATAATTTTGAGTAGACG
1 AAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTTGAGAAGACG
*
56609320 GTTCAGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTAAGCAAAAGTACTG
66 GTTCAGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTAAGCAAAAATACTG
*
56609380 AAAGAAGCTCCCACGTGGATGCGCTTTTGCTACAG
1 AAA-AAGCTCCCACGTGGACGCGCTTTTGCTACAG
56609415 CAGTTCCTGT
Statistics
Matches: 144, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
125 116 0.81
126 28 0.19
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (125 bp):
AAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTTGAGAAGACG
GTTCAGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGACGCTTTGTAAGCAAAAATACTG
Found at i:56612671 original size:34 final size:35
Alignment explanation
Indices: 56612598--56612694 Score: 117
Period size: 34 Copynumber: 2.7 Consensus size: 35
56612588 ATTTAAAAGA
* *
56612598 ATTTCTATTATATTAAA-AATGTAAAAGTAAATTTCT
1 ATTT-TATTACATTAAATAATATAAAAG-AAATTTCT
*
56612634 ATTTTATTACATTAAATAATATAAAAG-AATTTTT
1 ATTTTATTACATTAAATAATATAAAAGAAATTTCT
*
56612668 ATTTTATTACATCAAATAATATCAAAA
1 ATTTTATTACATTAAATAATAT-AAAA
56612695 TATTCAAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
34 27 0.49
35 15 0.27
36 13 0.24
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (35 bp):
ATTTTATTACATTAAATAATATAAAAGAAATTTCT
Found at i:56612841 original size:21 final size:21
Alignment explanation
Indices: 56612825--56612871 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
56612815 GTGGGGGTTG
*
56612825 TGGTTGCTCCGGCGGGGATTC
1 TGGTTCCTCCGGCGGGGATTC
*
56612846 TGGTTCCTCCGGTAGGGGA-TC
1 TGGTTCCTCCGG-CGGGGATTC
56612867 TGGTT
1 TGGTT
56612872 GTCGGTGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.06, C:0.21, G:0.40, T:0.32
Consensus pattern (21 bp):
TGGTTCCTCCGGCGGGGATTC
Found at i:56613139 original size:18 final size:18
Alignment explanation
Indices: 56613113--56613155 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
56613103 GACTAGAAAA
* * *
56613113 AGGAAACATAGAAGGGTT
1 AGGATACATAAAAGGGCT
56613131 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
56613149 AGGATAC
1 AGGATAC
56613156 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.30, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:56613791 original size:7 final size:7
Alignment explanation
Indices: 56613781--56613805 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56613771 CATAATACAT
56613781 AATACTA
1 AATACTA
56613788 AATACTA
1 AATACTA
56613795 AATACTA
1 AATACTA
56613802 AATA
1 AATA
56613806 TCAATCGACT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:56615029 original size:11 final size:11
Alignment explanation
Indices: 56615015--56615095 Score: 112
Period size: 11 Copynumber: 7.4 Consensus size: 11
56615005 AGCATTTTTA
*
56615015 AGAGGAATTTG
1 AGAGGAAATTG
56615026 AGAGGAAATTG
1 AGAGGAAATTG
*
56615037 AAAGGAAATTG
1 AGAGGAAATTG
56615048 AGAGGAAATTG
1 AGAGGAAATTG
56615059 AGAGGAAATTG
1 AGAGGAAATTG
56615070 AGA-GAATATTG
1 AGAGGAA-ATTG
56615081 -GAGAGAAATTG
1 AGAG-GAAATTG
56615092 AGAG
1 AGAG
56615096 AAAGGATTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
10 5 0.08
11 52 0.83
12 6 0.10
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.20
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:56615801 original size:54 final size:54
Alignment explanation
Indices: 56615684--56615789 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
56615674 GGTTTTTTTC
* *
56615684 TTCAAAA-TTTAAATTTGGTTGAGGAATCTTAAAATTCAAATTTATAATTTTGT
1 TTCAAAATTTTGAATTTGATTGAGGAATCTTAAAATTCAAATTTATAATTTTGT
* * *
56615737 TTCAAAATTTTGAATTTGATTGATGCATCTTAAAATTCGAATTCT-TAATTTTG
1 TTCAAAATTTTGAATTTGATTGAGGAATCTTAAAATTCAAATT-TATAATTTTG
56615790 ATTTTATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
53 7 0.15
54 38 0.83
55 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (54 bp):
TTCAAAATTTTGAATTTGATTGAGGAATCTTAAAATTCAAATTTATAATTTTGT
Found at i:56620391 original size:6 final size:6
Alignment explanation
Indices: 56620380--56620446 Score: 66
Period size: 6 Copynumber: 11.0 Consensus size: 6
56620370 GAAGTCTAAG
* * *
56620380 AAATAA AAATAA CACAACT-A AAA-AA AAGTAA AAGTAA AAGTAA AAATAA
1 AAATAA AAATAA -A-AA-TAA AAATAA AAATAA AAATAA AAATAA AAATAA
56620429 AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA
56620447 TATTGAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
5 3 0.06
6 45 0.83
7 2 0.04
8 3 0.06
9 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:56622092 original size:4 final size:5
Alignment explanation
Indices: 56622035--56622111 Score: 64
Period size: 5 Copynumber: 14.0 Consensus size: 5
56622025 GAATAACAAT
*
56622035 AATAA GAATAA GAATAA ATACTAAA AATAA AATAA AAGAA AGATAA AATAA
1 AATAA -AATAA -AATAA A-A-T-AA AATAA AATAA AATAA A-ATAA AATAA
* *
56622086 AATAA ATTAG AATAAA AATAA AATAA
1 AATAA AATAA AAT-AA AATAA AATAA
56622112 GAAATAAATA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
5 34 0.57
6 21 0.35
7 2 0.03
8 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:56622103 original size:21 final size:20
Alignment explanation
Indices: 56622056--56622119 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
56622046 GAATAAATAC
56622056 TAAAAATAAAATAAAAGAAA
1 TAAAAATAAAATAAAAGAAA
*
56622076 GATAAAATAAAATAAATTAG-AA
1 TA-AAAATAAAATAAA--AGAAA
56622098 TAAAAATAAAAT--AAGAAA
1 TAAAAATAAAATAAAAGAAA
56622116 TAAA
1 TAAA
56622120 TAGATAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 2 0.05
18 6 0.16
19 1 0.03
20 1 0.03
21 23 0.61
22 3 0.08
23 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (20 bp):
TAAAAATAAAATAAAAGAAA
Found at i:56622121 original size:11 final size:11
Alignment explanation
Indices: 56622035--56622119 Score: 68
Period size: 11 Copynumber: 7.5 Consensus size: 11
56622025 GAATAACAAT
*
56622035 AATAAGAATAAG
1 AATAA-AATAAA
56622047 AATAAATACTAAA
1 AATAAA-A-TAAA
56622060 AATAAAATAAA
1 AATAAAATAAA
*
56622071 AGA-AAGAT-AA
1 A-ATAAAATAAA
56622081 AATAAAAT-AA
1 AATAAAATAAA
* *
56622091 ATTAGAATAAA
1 AATAAAATAAA
56622102 AATAAAATAAGA
1 AATAAAATAA-A
56622114 AATAAA
1 AATAAA
56622120 TAGATAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
9 1 0.02
10 15 0.25
11 20 0.33
12 15 0.25
13 9 0.15
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:56622126 original size:26 final size:26
Alignment explanation
Indices: 56622026--56622129 Score: 79
Period size: 26 Copynumber: 3.9 Consensus size: 26
56622016 AATAATAGTG
* *
56622026 AATAACAAT-AATAAGAATAAGAATAA
1 AATAA-AATAAATTAGAATAAAAATAA
* * * *
56622052 ATACTAAAAATAAAATAAAAGAAAGATAA
1 A-A-T-AAAATAAATTAGAATAAAAATAA
56622081 AATAAAATAAATTAGAATAAAAATAA
1 AATAAAATAAATTAGAATAAAAATAA
56622107 AATAAGAAATAAA-TAG-ATAAAAA
1 AAT-A-AAATAAATTAGAATAAAAA
56622130 GGGTAAATAG
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
26 30 0.48
27 6 0.10
28 12 0.19
29 14 0.23
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (26 bp):
AATAAAATAAATTAGAATAAAAATAA
Found at i:56624144 original size:50 final size:50
Alignment explanation
Indices: 56624068--56624265 Score: 234
Period size: 50 Copynumber: 3.8 Consensus size: 50
56624058 TTTTCTTTAC
* * **
56624068 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
56624118 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
56624168 TGCCAATGCCATGTTCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
56624224 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56624266 TTACCCAAAT
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 81 0.65
53 2 0.02
56 41 0.33
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:56626897 original size:40 final size:40
Alignment explanation
Indices: 56626830--56626935 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 40
56626820 AAATTATACT
* *
56626830 CTGATTGCACATACGTGACCTTATTTGTACTTCGGTA-CC
1 CTGATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCC
* * * *
56626869 TTCGATTACACATACGTGCCCCTGTTTGTACTTTGGTACCC
1 CT-GATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCC
*
56626910 CTGATTGCACTTACGTGCCCTTGTTT
1 CTGATTGCACATACGTGCCCTTGTTT
56626936 ACATTTTGGT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.02
40 51 0.93
41 3 0.05
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.38
Consensus pattern (40 bp):
CTGATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCC
Found at i:56631704 original size:7 final size:7
Alignment explanation
Indices: 56631666--56631714 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
56631656 AAATAAGAAA
56631666 TAGGGTT
1 TAGGGTT
*
56631673 TAGTGTT
1 TAGGGTT
*
56631680 TAAGGTT
1 TAGGGTT
*
56631687 T-GGATT
1 TAGGGTT
56631693 T-GGGTT
1 TAGGGTT
56631699 TAGGGTT
1 TAGGGTT
56631706 TAGGGTT
1 TAGGGTT
56631713 TA
1 TA
56631715 TTGTTTGTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 9 0.26
7 26 0.74
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (7 bp):
TAGGGTT
Found at i:56633241 original size:25 final size:24
Alignment explanation
Indices: 56633171--56633241 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 24
56633161 CGACTTATGT
*
56633171 TTCAATTTAAGGTTTGGTTTGGGGG
1 TTCAATTTAA-GTTTGGTTTGGGGA
* **
56633196 TTTAGATTT-AGTTTCAATTTGGGGA
1 TTCA-ATTTAAGTTT-GGTTTGGGGA
56633221 TTCAATTTCAAGTTTGGTTTG
1 TTCAATTT-AAGTTTGGTTTG
56633242 TGGTTTCATT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
24 8 0.23
25 18 0.51
26 9 0.26
ACGTcount: A:0.20, C:0.06, G:0.27, T:0.48
Consensus pattern (24 bp):
TTCAATTTAAGTTTGGTTTGGGGA
Found at i:56634029 original size:143 final size:143
Alignment explanation
Indices: 56633771--56634054 Score: 433
Period size: 143 Copynumber: 2.0 Consensus size: 143
56633761 CATCTTATGT
* *
56633771 TTGACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTATTTACCCAAATCTATTG
1 TTGACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTC
* *
56633836 AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTGGGGTCTGGTTTGGGGTTTTAGATTCG
66 AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTAGGGTCTAGTTTGGGGTTTTAGATTCG
*
56633901 TCTACGATTTGGG
131 TCCACGATTTGGG
* * * * *
56633914 TTGACTAGAATGAGCTACAATAGAATGTTTTAGAAAGCTTGAAATTTAGTTACCTAAATTTGTTC
1 TTGACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTC
* * * * *
56633979 ACAGCTTTAATTTGGGATTTTAAGTTATGTTTAAATTTAGGGTCTAGTTTGGGGTTTTAGATTTG
66 AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTAGGGTCTAGTTTGGGGTTTTAGATTCG
56634044 TCCACGATTTG
131 TCCACGATTTG
56634055 TTGATTTGAT
Statistics
Matches: 126, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
143 126 1.00
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (143 bp):
TTGACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAACTTAGTTACCCAAATCTATTC
AAAGCTTCAATTTGGGATTTTAACTTAGGTTTAAATTTAGGGTCTAGTTTGGGGTTTTAGATTCG
TCCACGATTTGGG
Found at i:56636420 original size:705 final size:697
Alignment explanation
Indices: 56634642--56638348 Score: 3436
Period size: 705 Copynumber: 5.4 Consensus size: 697
56634632 TAAAAGGTTT
* * * * * * ** *
56634642 TTGAAATCCTTCAATTTGGGATTTTGATTTAGGTTTTAATTTAG-GGTTTGGTTTGGGGTTTTAA
1 TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTAGATTTTTGGTTT-GGGTTTTAG
* ** * ** * * ** * * ** *
56634706 ATTCAATTTTGATTTGGGAATTTGATTTGATTTTTTATTTGAGGTCTCGATTCGAAG-GGTTTCG
65 ATTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTG
* * * * * * * * *
56634770 ATTGTTCGGTTACCTCTCGAGTAACTGAGCTAGTGTGGTAATTTTTTAAGTTTTTAATATATATA
130 GTTATTCGGTAACCTC-CGAGTAACTAAACAAGTGTGGTAATTCTATAAGTTTGTAATATATATA
* *
56634835 AATATATAAATTCAAC-AAAAAATATTCAAAATTAATTT-A-AT-ATGTTCACCTTAAT-AAA-A
194 AATATATAAATTCAACAAAAAAAT-TTAAAAATTAATTTAATATGATGTTTA-CTTAATAAAACA
* * * * *
56634894 -AACTTGACCAACAAT--TA-TAAAAT---CT---AT-AA-TTTTTATATTCTATATTTCAAAAC
257 TAATTTGACCAACAATAATATTAAAATGAAATAAAATAAATTTTTTATATTATATATTTCAGAAT
* * * **
56634947 CTCAATTACTTTTTGCCTCATTTTAAGTTATCAAAACTCTATGGTCTTTCAAAAATTTGGTGGTT
322 CTCCATAACTTTTTGACTCATTTTAAGTTATCAAAACTCTATACTCTTTCAAAAATTTGGTGGTT
* * * *
56635012 TTAATAATATTAATTTAGAGCTGAAATTTAATTCTAAAATAAGAAATTTTGTTTGATCAAAAAGA
387 TTAATAATATTAATTTAGAGTTGAAATGTAATTCTAAAACAAAAAATTTTGTTTGATCAAAAAGA
* *
56635077 GTAACCAAAAGCCTAAGATTCGGGGCTTAAAACATTCAAAATCGTCACAACTTG-CTCAAAATTT
452 GTAACCAAAAGCCTAAGATTCAGGGCTTAAAACATTCAAAATCGTCACAACTTGCCT-AGAATTT
* * * *
56635141 CAAAGTTTTCTATTTCAAGTAGGCTACTTTGGGAGCTTGGTTCTTTTAAGACACG-ACATAATTT
516 CAAAGTTTTCTGTTTCAAGTAGGCTACTTT-GGAGCTTGGTTCTTTTAACACA-GAACACATTTT
* * * *
56635205 GGCTTGGAAAACATACTAATGGAAAGATCACAGTTAATACAATATAAATCATCTCACGTTCAACT
579 GGCTTGGAAAACATACCAATGGAAAGATCACATTTCATACAATAGAAATCATCTCACGTTCAACT
* * * *
56635270 AAAATGAAAAATAATAAAAGGTTTTTTAAAGCC-TTATATTTAGTTATCCAAATCTA
644 AGAATG-AAAACAATAAAAGG-TTTTGAAAGCCTTTA-ATTTAGTTACCCAAATCTA
* * *
56635326 TTGAAAGCCTTAAATTTGGGATTTTGA-TATAGGTTTCACTTT--A----------GGGTTTTAG
1 TTGAAAGCCTTAAATTTGAGATTTCGACT-TAGGTTTCAATTTAGATTTTTGGTTTGGGTTTTAG
* * * * *
56635378 ATTTGGTTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATCCAAAGCTCTTTTG
65 ATTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTG
** * ** * *
56635443 GTTATTCGGTGTCCTCCAGAGGAACTAAACAAGTGTGACAATTCTATAAGTTTGTTATATATACA
130 GTTATTCGGTAACCTCC-GAGTAACTAAACAAGTGTGGTAATTCTATAAGTTTGTAATATATATA
* *
56635508 AATATATAAATTCAACAAAAAAAATTTAAAAATTAATTTAATATAATGTTTACCTTAATAAAAAA
194 AATATATAAATTCAAC-AAAAAAATTTAAAAATTAATTTAATATGATGTTTA-CTTAATAAAACA
** * * * * * **
56635573 TTGTTTGACCAACAACAATAATAATATGGAATAAAATATAAAGTTTTTATAACATATATTTCAGA
257 TAATTTGACCAACAATAATATTAAAATGAAAT-AAA-ATAAATTTTTTATATTATATATTTCAGA
* * * * *
56635638 ACCTCAATGACTTTTTCACTCATTTTAAGTTATCAAAACTCTATGA-TCTTTCAAAATTTTGGTG
320 ATCTCCATAACTTTTTGACTCATTTTAAGTTATCAAAACTCTAT-ACTCTTTCAAAAATTTGGTG
* * * *
56635702 GTTTTAATAATATTAATTTAGAGCTGGAATGTAATTCTAAAACAAAAAATTTTGCTTGATAAAAA
384 GTTTTAATAATATTAATTTAGAGTTGAAATGTAATTCTAAAACAAAAAATTTTGTTTGATCAAAA
* * * * * * *
56635767 AGAGTAACCGAAAGCCTAACACTCAGGGCTTAAAACATTCAAAATTGTCGCAAC-TGGCTCAAAA
449 AGAGTAACCAAAAGCCTAAGATTCAGGGCTTAAAACATTCAAAATCGTCACAACTTGCCT-AGAA
* * **
56635831 TTTCAAAGTTTTCTGTTTCAAGTAGGCTACTTTGAGAGCTTGGTTCTTTTAAGACACAACACAAC
513 TTTCAAAGTTTTCTGTTTCAAGTAGGCTACTTTG-GAGCTTGGTTCTTTTAACACAGAACACATT
* * * *
56635896 TTGGCTTGGAAAACATACTAATGGAAAGATCACATTTCATACAATACAAATCCTCTCACTTTCAA
577 TTGGCTTGGAAAACATACCAATGGAAAGATCACATTTCATACAATAGAAATCATCTCACGTTCAA
* *
56635961 TTAGAATGAGAAAAAATAAAAGGTTTCTGAAAGCCTTTAATTTAGTTACCCAAATCTA
642 CTAGAATGA-AAACAATAAAAGGTTT-TGAAAGCCTTTAATTTAGTTACCCAAATCTA
* * *
56636019 ATGAAAGCCTTAAATTTGGGATTTCGACATAGGTTTCAATTTAGATTTTTGGTTTGGGTTTTAGA
1 TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTAGATTTTTGGTTTGGGTTTTAGA
* ** * * *
56636084 TTTGGCTTCAATTTGGGGATTCAAGTTCAATTTTGGTTTGTGGTTGCAATTCGAAGCCCTTTTGG
66 TTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTGG
*
56636149 TTATTCGGTAACCTCCGGAGTAACTAAACAAGTGTGGCAATTCTATAAGTTTGTAATATATATAA
131 TTATTCGGTAACCTCC-GAGTAACTAAACAAGTGTGGTAATTCTATAAGTTTGTAATATATATAA
*
56636214 ATATATATATTCAACAAAAAAATTTTAAAAATTAATTTAATATGATGTTTATCTTAATAAAACAT
195 ATATATAAATTCAACAAAAAAA-TTTAAAAATTAATTTAATATGATGTTTA-CTTAATAAAACAT
* *
56636279 AATTTGACCAACAATAATATTAAAATAAAATAAAATCGAAATTTTTTTTATTATATATTTCAGAA
258 AATTTGACCAACAATAATATTAAAATGAAATAAAAT--AAATTTTTTATATTATATATTTCAGAA
* *
56636344 TCTCCATAACTTTTTGACTCATTTTAAGCTATCAAAACTCTATACTCTTTCAAAAATTTGGTTGT
321 TCTCCATAACTTTTTGACTCATTTTAAGTTATCAAAACTCTATACTCTTTCAAAAATTTGGTGGT
* * * * *
56636409 TTTATTAATATTAATTTAGAGTTCAAATGTAATTCTAAAAC--AATATTTTTTTTTATCAAACAA
386 TTTAATAATATTAATTTAGAGTTGAAATGTAATTCTAAAACAAAAAATTTTGTTTGATCAAA-AA
* * * *
56636472 -AGTAACCAAAAGCCTAAGGTTCAAGGCTTAAAACTTTGAAAATCGTCACAACTTGCCTAGAATT
450 GAGTAACCAAAAGCCTAAGATTCAGGGCTTAAAACATTCAAAATCGTCACAACTTGCCTAGAATT
* ** *
56636536 TTAAAG-TTTCTTGTTTCAAGTAGAATACTTTGGGAGCTTGGTTCTTTTAACATAGAACACATTT
515 TCAAAGTTTTC-TGTTTCAAGTAGGCTACTTT-GGAGCTTGGTTCTTTTAACACAGAACACATTT
* * * * * * * *
56636600 TGGCATGGAAAACAGACAAATGAAAAGATGACATTTTC-TACAATAGAAATAACCTCACGTTCGA
578 TGGCTTGGAAAACATACCAATGGAAAGATCACA-TTTCATACAATAGAAATCATCTCACGTTCAA
56636664 CTAGAATGAACAACAAT---A------G-AAG-----------G--------AT-T-
642 CTAGAATGAA-AACAATAAAAGGTTTTGAAAGCCTTTAATTTAGTTACCCAAATCTA
* * * *
56636690 TAGAAAGCTTTAAATTTGAGATTTTGACTTAAGTTTCAATTTAGGATTTTTGGTTTGGGTTTTAG
1 TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTA-GATTTTTGGTTTGGGTTTTAG
* * * * * * ** * **
56636755 ATTCAATTTCGATATGGAGAGT-AGATTT-ATGTTTTGGTCTTG-CCTTT-TATTCGAAGGTCTT
65 ATTCGATTTCAATTTGGGGATTCA-ATTTCA-ATTTTGGT-TTGTGGTTTCGATTCGAAGCCCTT
* ** * * * *
56636816 TTAGTTGCTCGGTAACCT-C--GCAACTAAACAATTGTTGTAATTCTATAAGTTTGTAATATATT
127 TTGGTTATTCGGTAACCTCCGAGTAACTAAACAAGTGTGGTAATTCTATAAGTTTGTAATATATA
* * * *
56636878 TTAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATTATATTTACATGAATAAAAC
192 TAAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATGTTTAC-TTAATAAAAC
* *** *
56636943 ATAATTTGGCCAACAATAATATTAAAATGAAATAAAATAAAAGAAATTTATATTCTATATTTTC-
256 ATAATTTGACCAACAATAATATTAAAATGAAATAAAAT-AAA-TTTTTTATATTATATA-TTTCA
* *
56637007 GAATCT-CATTGACTTTTT-AGCTCATTTTAAGTTACCAAAACTC--TACTCTTTCAAAAATTTG
318 GAATCTCCA-TAACTTTTTGA-CTCATTTTAAGTTATCAAAACTCTATACTCTTTCAAAAATTTG
* * * *
56637068 GTGGTTTTAATAATATTAATTTATAGTTGAAATGTAATTTTAAAATAAGAAAATTTTTGTTTAAT
381 GTGGTTTTAATAATATTAATTTAGAGTTGAAATGTAATTCTAAAACAA-AAAA-TTTTGTTTGAT
* * * ** * * * *
56637133 CAAAAAGAGTAACCAAATGCCAAAAATTTGGGGGTAAAAAAATTTAAAATCGTCACAACTTGCCT
444 CAAAAAGAGTAACCAAAAGCCTAAGATTCAGGGCTTAAAACATTCAAAATCGTCACAACTTGCCT
* * * * *
56637198 AGAATTTCAAAGTTTTCTGTTTCAAGTACGCTAATTTCGGTGCTAGGTTCTTTTAACACAGAACT
509 AGAATTTCAAAGTTTTCTGTTTCAAGTAGGCTACTTT-GGAGCTTGGTTCTTTTAACACAGAACA
* * * * *
56637263 TATTTTGGCTTGCAAAACATACCAATGGAAAGATCGCATTTCATACAACAGATATCATCTCACGT
573 CATTTTGGCTTGGAAAACATACCAATGGAAAGATCACATTTCATACAATAGAAATCATCTCACGT
* * * * *
56637328 TCGAA-TAGAATGACCAACAATAAAAGGTTTTAAAACGCCTTAAATTTAGTTACCCAAACCTG
638 TC-AACTAGAATGA-AAACAATAAAAGGTTTTGAAA-GCCTTTAATTTAGTTACCCAAATCTA
* * ** * ** *
56637390 TTGAAAGCCTTCAATTTGAGATTTCAACTTATATTTCAAATTAG-GGTTTGGTTTGGGGTTTTAT
1 TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTAGATTTTTGGTTT-GGGTTTTAG
* ** * * *
56637454 ATTCGATTTCAATTTGGGGATTCAATTTCAAGTTTGGCATGTGGTTTCGATTCAAAGTCTTTTTG
65 ATTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTG
* * *
56637519 GTTGTTCGGTAACCTCCGGAGTAACTAAACAAGTGTTGAAATTCTATAAGTTTGTAATATATATA
130 GTTATTCGGTAACCTCC-GAGTAACTAAACAAGTGTGGTAATTCTATAAGTTTG-----TA-ATA
* * * *
56637584 TATATAAATATATAAATTTAACAAAAAAAATTAAAAATTAATTTAGTATGATGTTTATATTAATA
188 TATATAAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATGTTTA-CTTAATA
* * **** * *
56637649 AAACATAATTTGGA-AAACAATAATATTAAAATGAAATAATATAAAAAAATTGTATTCTATATTT
252 AAACATAATTT-GACCAACAATAATATTAAAATGAAATAAAATAAATTTTTTATATTATATATTT
** * *
56637713 CAGAATCT-CATAGACTTTTTGGTTCATTTTAAGTTATCAAAACTTTATGCTCTTTCAAAAATTT
316 CAGAATCTCCATA-ACTTTTTGACTCATTTTAAGTTATCAAAACTCTATACTCTTTCAAAAATTT
* * *
56637777 GATTGTTTTAATAGTATTAATTTAGAGTTGAAATGTAATTCTAAAA-AAAAAATTTT-TTT-ATC
380 GGTGGTTTTAATAATATTAATTTAGAGTTGAAATGTAATTCTAAAACAAAAAATTTTGTTTGATC
* * * * * *
56637839 AAATAGAGTAACTAAAAGCCTAATATTC-GGTGCTTAAAACTTTAAAAATCATCACAACTTGCCT
445 AAAAAGAGTAACCAAAAGCCTAAGATTCAGG-GCTTAAAACATTCAAAATCGTCACAACTTGCCT
* * * ***
56637903 AGAATTTGAAAGTTTTCTATTTCAAGTAGGCTACTTTCGGAGCATGGTTCTTTTAACACAGAGTT
509 AGAATTTCAAAGTTTTCTGTTTCAAGTAGGCTACTTT-GGAGCTTGGTTCTTTTAACACAGAACA
* * * * ** * *
56637968 CATTTTGACTTGGAAAACATGCCAATGAAAAGATCTCATTTTGTACAATAGAAATAATCTCATGT
573 CATTTTGGCTTGGAAAACATACCAATGGAAAGATCACATTTCATACAATAGAAATCATCTCACGT
* * * * *
56638033 TCGACTAGAATGAGCAACAATAGAAGGTTTTAGAAAG-TTTTAAATTTATTTACCCAAATCTA
638 TCAACTAGAATGA-AAACAATAAAAGGTTTT-GAAAGCCTTT-AATTTAGTTACCCAAATCTA
* * * *
56638095 TTGAAAGCCTTAAATTTAATATTTTGACTTAGGTTTCAATTTAGGGTTTTT-GTTTGGGGTTTTA
1 TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTA-GATTTTTGGTTT-GGGTTTTA
** ** * * * * * * * *
56638159 GATTCGATTTTGATCAGGTGATTCAATTTTAGTTTTGATTTATGGTTTCGATTTGAAG-GCATTT
64 GATTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTT
* * * * * * *
56638223 GATTTTTCGATAACTTCTTGAGTAACTAAACAAGGGTTGTAATTCTATAAGTTTGTAATATATAT
129 GGTTATTCGGTAACCTC-CGAGTAACTAAACAAGTGTGGTAATTCTATAAGTTTGTAATATATAT
* *
56638288 AAATATATAAATTCAAC-AAAATATTT-AAAATTTATTTAATATGATGTTTACATTAATAAAA
193 AAATATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATGTTTAC-TTAATAAAA
56638349 TTGTTGGTTT
Statistics
Matches: 2491, Mismatches: 397, Indels: 257
0.79 0.13 0.08
Matches are distributed among these distances:
664 58 0.02
665 7 0.00
666 117 0.05
667 74 0.03
668 173 0.07
669 5 0.00
670 1 0.00
671 65 0.03
672 98 0.04
673 73 0.03
674 13 0.01
675 8 0.00
676 2 0.00
677 13 0.01
678 5 0.00
679 2 0.00
680 11 0.00
681 1 0.00
682 2 0.00
683 6 0.00
684 36 0.01
686 1 0.00
690 1 0.00
691 2 0.00
692 12 0.00
693 389 0.16
694 3 0.00
695 1 0.00
697 31 0.01
698 18 0.01
699 63 0.03
700 65 0.03
701 1 0.00
702 5 0.00
703 174 0.07
704 58 0.02
705 609 0.24
706 63 0.03
707 12 0.00
708 53 0.02
709 7 0.00
710 152 0.06
711 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (697 bp):
TTGAAAGCCTTAAATTTGAGATTTCGACTTAGGTTTCAATTTAGATTTTTGGTTTGGGTTTTAGA
TTCGATTTCAATTTGGGGATTCAATTTCAATTTTGGTTTGTGGTTTCGATTCGAAGCCCTTTTGG
TTATTCGGTAACCTCCGAGTAACTAAACAAGTGTGGTAATTCTATAAGTTTGTAATATATATAAA
TATATAAATTCAACAAAAAAATTTAAAAATTAATTTAATATGATGTTTACTTAATAAAACATAAT
TTGACCAACAATAATATTAAAATGAAATAAAATAAATTTTTTATATTATATATTTCAGAATCTCC
ATAACTTTTTGACTCATTTTAAGTTATCAAAACTCTATACTCTTTCAAAAATTTGGTGGTTTTAA
TAATATTAATTTAGAGTTGAAATGTAATTCTAAAACAAAAAATTTTGTTTGATCAAAAAGAGTAA
CCAAAAGCCTAAGATTCAGGGCTTAAAACATTCAAAATCGTCACAACTTGCCTAGAATTTCAAAG
TTTTCTGTTTCAAGTAGGCTACTTTGGAGCTTGGTTCTTTTAACACAGAACACATTTTGGCTTGG
AAAACATACCAATGGAAAGATCACATTTCATACAATAGAAATCATCTCACGTTCAACTAGAATGA
AAACAATAAAAGGTTTTGAAAGCCTTTAATTTAGTTACCCAAATCTA
Found at i:56642064 original size:39 final size:39
Alignment explanation
Indices: 56642010--56642164 Score: 177
Period size: 39 Copynumber: 4.0 Consensus size: 39
56642000 GATGTAGTTC
56642010 GGTACCCCTGAATGCACTTATGTGCCCCTGTTGTACTTT
1 GGTACCCCTGAATGCACTTATGTGCCCCTGTTGTACTTT
* ** * *
56642049 GGTACCCCTGGATGCACTTACT-TGCCATTGTTCTACTTC
1 GGTACCCCTGAATGCACTTA-TGTGCCCCTGTTGTACTTT
* *
56642088 GGTACCCCTGGATGCACTTATGTGCCCCTATTGTACTTT
1 GGTACCCCTGAATGCACTTATGTGCCCCTGTTGTACTTT
* * ** * *
56642127 AGTACCCCTAAACACACTTACGTGCCCTTGTTGTACTT
1 GGTACCCCTGAATGCACTTATGTGCCCCTGTTGTACTT
56642165 CAGTACTCCT
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
38 1 0.01
39 94 0.98
40 1 0.01
ACGTcount: A:0.17, C:0.30, G:0.18, T:0.35
Consensus pattern (39 bp):
GGTACCCCTGAATGCACTTATGTGCCCCTGTTGTACTTT
Found at i:56642115 original size:20 final size:20
Alignment explanation
Indices: 56642014--56642116 Score: 54
Period size: 20 Copynumber: 5.2 Consensus size: 20
56642004 TAGTTCGGTA
*
56642014 CCCCTGAATGCACTTATGTG
1 CCCCTGGATGCACTTATGTG
* * *
56642034 CCCCT-GTTGTACTT-TGGTA
1 CCCCTGGATGCACTTAT-GTG
56642053 CCCCTGGATGCACTTACT-TG
1 CCCCTGGATGCACTTA-TGTG
* * * ** *
56642073 -CCATTG-TTCTACTTCGGTA
1 CCCCTGGATGC-ACTTATGTG
56642092 CCCCTGGATGCACTTATGTG
1 CCCCTGGATGCACTTATGTG
56642112 CCCCT
1 CCCCT
56642117 ATTGTACTTT
Statistics
Matches: 56, Mismatches: 19, Indels: 16
0.62 0.21 0.18
Matches are distributed among these distances:
18 3 0.05
19 22 0.39
20 28 0.50
21 2 0.04
22 1 0.02
ACGTcount: A:0.15, C:0.32, G:0.19, T:0.34
Consensus pattern (20 bp):
CCCCTGGATGCACTTATGTG
Found at i:56642145 original size:78 final size:78
Alignment explanation
Indices: 56642007--56642184 Score: 232
Period size: 78 Copynumber: 2.3 Consensus size: 78
56641997 ATTGATGTAG
* * * ** ** *
56642007 TTCGGTACCCCTGAATGCACTTATGTGCCCCTGTTGTACTTTGGTACCCCTGGATGCACTTACTT
1 TTCGGTACCCCTGGATGCACTTATGTGCCCCTATTGTACTTTAGTACCCCTAAACACACTTACGT
56642072 GCCATTGTTCTAC
66 GCCATTGTTCTAC
56642085 TTCGGTACCCCTGGATGCACTTATGTGCCCCTATTGTACTTTAGTACCCCTAAACACACTTACGT
1 TTCGGTACCCCTGGATGCACTTATGTGCCCCTATTGTACTTTAGTACCCCTAAACACACTTACGT
* *
56642150 GCCCTTGTTGTAC
66 GCCATTGTTCTAC
* *
56642163 TTCAGTACTCCT-GATAGCACTT
1 TTCGGTACCCCTGGAT-GCACTT
56642185 TCGTGTCTTG
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
77 3 0.03
78 84 0.97
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (78 bp):
TTCGGTACCCCTGGATGCACTTATGTGCCCCTATTGTACTTTAGTACCCCTAAACACACTTACGT
GCCATTGTTCTAC
Found at i:56642170 original size:39 final size:39
Alignment explanation
Indices: 56642002--56642189 Score: 171
Period size: 39 Copynumber: 4.8 Consensus size: 39
56641992 AGAAAATTGA
* * * *
56642002 TGTAGTTCGGTACCCCTGAATGCACTTATGTGCCCCTGT
1 TGTACTTCAGTACCCCTGGATGCACTTACGTGCCCCTGT
** * **
56642041 TGTACTTTGGTACCCCTGGATGCACTTACTTGCCATTGT
1 TGTACTTCAGTACCCCTGGATGCACTTACGTGCCCCTGT
* * * *
56642080 TCTACTTCGGTACCCCTGGATGCACTTATGTGCCCCTAT
1 TGTACTTCAGTACCCCTGGATGCACTTACGTGCCCCTGT
* ** ** *
56642119 TGTACTTTAGTACCCCTAAACACACTTACGTGCCCTTGT
1 TGTACTTCAGTACCCCTGGATGCACTTACGTGCCCCTGT
* *
56642158 TGTACTTCAGTACTCCT-GATAGCACTTTCGTG
1 TGTACTTCAGTACCCCTGGAT-GCACTTACGTG
56642190 TCTTGTTCAC
Statistics
Matches: 118, Mismatches: 30, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
38 1 0.01
39 117 0.99
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.35
Consensus pattern (39 bp):
TGTACTTCAGTACCCCTGGATGCACTTACGTGCCCCTGT
Done.