Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 130 of 207
Found at i:39793424 original size:6 final size:6
Alignment explanation
Indices: 39793398--39793467 Score: 63
Period size: 6 Copynumber: 11.5 Consensus size: 6
39793388 AAGATTAATC
* *
39793398 AAAAT- AAAATA AATGAATA AAAATA AAAATA AAAATA AAAAT- GAAACA
1 AAAATA AAAATA AA--AATA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
39793446 AAATTA AAAATA GGAAATA AAA
1 AAAATA AAAATA -AAAATA AAA
39793468 GTTATTTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
5 8 0.15
6 33 0.63
7 5 0.10
8 6 0.12
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:39793434 original size:18 final size:17
Alignment explanation
Indices: 39793398--39793467 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 17
39793388 AAGATTAATC
39793398 AAAATAAAATAAATGAATA
1 AAAATAAAATAAA--AATA
39793417 AAAATAAAAATAAAAATA
1 AAAAT-AAAATAAAAATA
* * *
39793435 AAAATGAAACAAAATTA
1 AAAATAAAATAAAAATA
39793452 AAAATAGGAAATAAAA
1 AAAATA--AAATAAAA
39793468 GTTATTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 14 0.33
18 9 0.21
19 12 0.28
20 8 0.19
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:39793467 original size:29 final size:27
Alignment explanation
Indices: 39793398--39793467 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 27
39793388 AAGATTAATC
39793398 AAAAT-AAAAT-AAATGAATAAAAATA
1 AAAATAAAAATAAAATGAATAAAAATA
39793423 AAAATAAAAATAAAAATGAA-ACAAAATTA
1 AAAATAAAAAT-AAAATGAATA-AAAA-TA
*
39793452 AAAATAGGAAATAAAA
1 AAAATA-AAAATAAAA
39793468 GTTATTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
25 5 0.13
26 5 0.13
27 1 0.03
28 11 0.29
29 12 0.32
30 4 0.11
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (27 bp):
AAAATAAAAATAAAATGAATAAAAATA
Found at i:39799165 original size:23 final size:23
Alignment explanation
Indices: 39799135--39799186 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
39799125 CAAATTAGAA
39799135 GTAATTCATGGTAGACATCCCTT
1 GTAATTCATGGTAGACATCCCTT
39799158 GTAATTCATGGTAGACATCCCTT
1 GTAATTCATGGTAGACATCCCTT
*
39799181 GAAATT
1 GTAATT
39799187 TTTTAAAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (23 bp):
GTAATTCATGGTAGACATCCCTT
Found at i:39802617 original size:275 final size:275
Alignment explanation
Indices: 39802122--39802672 Score: 1048
Period size: 275 Copynumber: 2.0 Consensus size: 275
39802112 AATTTGCAAA
*
39802122 ATAATAAAAATGGTGCGAAAGAAGGGATTTGTACTTGGGTTTCAAGGAACTTTTCACTAACACTT
1 ATAATAAAAATGGTGCAAAAGAAGGGATTTGTACTTGGGTTTCAAGGAACTTTTCACTAACACTT
39802187 AACTATCCAACTAATACCTCATTTATTTCCTAAAATGCATAGATAGTCTCAAAATTTAGGGCATG
66 AACTATCCAACTAATACCTCATTTATTTCCTAAAATGCATAGATAGTCTCAAAATTTAGGGCATG
*
39802252 ACCACTTTTTCTCGATTCACAAACCCAATTCGACTAACCCCAGATTTTAGGAATGTAACAATTAT
131 ACCACTTTTTCTCAATTCACAAACCCAATTCGACTAACCCCAGATTTTAGGAATGTAACAATTAT
39802317 CGTGTGTGAATATGATGTGCGGATTGTGAAAGTATACACATTGAAACAAGTAATAAAGTGATAAG
196 CGTGTGTGAATATGATGTGCGGATTGTGAAAGTATACACATTGAAACAAGTAATAAAGTGATAAG
39802382 TGAGATCGTCTCCAT
261 TGAGATCGTCTCCAT
39802397 ATAATAAAAATGGTGCAAAAGAAGGGATTTGTACTTGGGTTTCAAGGAACTTTTCACTAACACTT
1 ATAATAAAAATGGTGCAAAAGAAGGGATTTGTACTTGGGTTTCAAGGAACTTTTCACTAACACTT
39802462 AACTATCCAACTAATACCTCATTTATTTCCTAAAATGCATAGATAGTCTCAAAATTTAGGGCATG
66 AACTATCCAACTAATACCTCATTTATTTCCTAAAATGCATAGATAGTCTCAAAATTTAGGGCATG
* *
39802527 ACCACTTTTTCTCAATTCACAAACCCAATTCGACTAACCCCAGATTTTAGGAATGTTACAATTGT
131 ACCACTTTTTCTCAATTCACAAACCCAATTCGACTAACCCCAGATTTTAGGAATGTAACAATTAT
* *
39802592 CGTGTGTGAATGTGATGTTCGGATTGTGAAAGTATACACATTGAAACAAGTAATAAAGTGATAAG
196 CGTGTGTGAATATGATGTGCGGATTGTGAAAGTATACACATTGAAACAAGTAATAAAGTGATAAG
39802657 TGAGATCGTCTCCAT
261 TGAGATCGTCTCCAT
39802672 A
1 A
39802673 GGGATTAGAG
Statistics
Matches: 270, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
275 270 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (275 bp):
ATAATAAAAATGGTGCAAAAGAAGGGATTTGTACTTGGGTTTCAAGGAACTTTTCACTAACACTT
AACTATCCAACTAATACCTCATTTATTTCCTAAAATGCATAGATAGTCTCAAAATTTAGGGCATG
ACCACTTTTTCTCAATTCACAAACCCAATTCGACTAACCCCAGATTTTAGGAATGTAACAATTAT
CGTGTGTGAATATGATGTGCGGATTGTGAAAGTATACACATTGAAACAAGTAATAAAGTGATAAG
TGAGATCGTCTCCAT
Found at i:39803671 original size:31 final size:31
Alignment explanation
Indices: 39803635--39803698 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
39803625 AAGATTGACC
39803635 TTTTAGGGTAGGTCCATCAGCCTATAATCCT
1 TTTTAGGGTAGGTCCATCAGCCTATAATCCT
39803666 TTTTAGGGTAGGTCCATCAGCCTATAATCCT
1 TTTTAGGGTAGGTCCATCAGCCTATAATCCT
39803697 TT
1 TT
39803699 CTCTCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (31 bp):
TTTTAGGGTAGGTCCATCAGCCTATAATCCT
Found at i:39807654 original size:30 final size:30
Alignment explanation
Indices: 39807620--39807694 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
39807610 GGTTGATACC
* * *
39807620 TCCCTTTTCGTAATTCCATAATCGAAGTTA
1 TCCCTTTTCATAATTCCATAACCGAAGCTA
* * *
39807650 TCCCTTTTCATAGTTCGATAGCCGAAGCTA
1 TCCCTTTTCATAATTCCATAACCGAAGCTA
39807680 TCCCTTTTCATAATT
1 TCCCTTTTCATAATT
39807695 TTATGGTCGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (30 bp):
TCCCTTTTCATAATTCCATAACCGAAGCTA
Found at i:39807713 original size:60 final size:60
Alignment explanation
Indices: 39807649--39807849 Score: 167
Period size: 60 Copynumber: 3.4 Consensus size: 60
39807639 AATCGAAGTT
* * *
39807649 ATCCCTTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTTTATGGTCGTCACC
1 ATCCCTTTTCATAGATCGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCATCACC
* * * ** * * * * *
39807709 ATCCCTCTTCATTGTTCGACGGCC--ATCATCATCCCTTTTCATAATTTGATAGCCA-AAGCT
1 ATCCCTTTTCATAGATCGATAGCCGAAGC-T-ATCCCTTTTCATAATTTGATGGTCATCA-CC
* * * ** * *
39807769 ATCCCTTTTCATAGATCGGTAGCCGAAGCCATCTCTTTTCATAGCTCGGTGGTCATCACC
1 ATCCCTTTTCATAGATCGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCATCACC
39807829 ATCCCTTTTCATA-ATCGATAG
1 ATCCCTTTTCATAGATCGATAG
39807850 ACGTATCCCT
Statistics
Matches: 106, Mismatches: 29, Indels: 13
0.72 0.20 0.09
Matches are distributed among these distances:
58 2 0.02
59 9 0.08
60 92 0.87
61 1 0.01
62 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.35
Consensus pattern (60 bp):
ATCCCTTTTCATAGATCGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCATCACC
Found at i:39807792 original size:30 final size:30
Alignment explanation
Indices: 39807738--39807845 Score: 96
Period size: 30 Copynumber: 3.6 Consensus size: 30
39807728 CGGCCATCAT
* *
39807738 CATCCCTTTTCATA-ATTTGATAGCCAAAGC
1 CATCCCTTTTCATAGA-TCGGTAGCCAAAGC
* *
39807768 TATCCCTTTTCATAGATCGGTAGCCGAAGC
1 CATCCCTTTTCATAGATCGGTAGCCAAAGC
* * * * *
39807798 CATCTCTTTTCATAGCTCGGTGGTCATCA-C
1 CATCCCTTTTCATAGATCGGTAGCCA-AAGC
39807828 CATCCCTTTTCATA-ATCG
1 CATCCCTTTTCATAGATCG
39807846 ATAGACGTAT
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
29 3 0.05
30 58 0.92
31 2 0.03
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (30 bp):
CATCCCTTTTCATAGATCGGTAGCCAAAGC
Found at i:39807801 original size:90 final size:89
Alignment explanation
Indices: 39807649--39807849 Score: 210
Period size: 90 Copynumber: 2.2 Consensus size: 89
39807639 AATCGAAGTT
* * ** * *
39807649 ATCCCTTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTTTATGGTCGTCACCATCCC
1 ATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATAATGGTA-GGCCGTAACCATCCC
* * *
39807714 TCTTCATTGTTCGACGGCCATCATC
65 TCTTCATAGCTCGACGGCCATCACC
*
39807739 ATCCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTCATAGATCGGTA-GCCG-AAGCCATC
1 ATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATA-AT-GGTAGGCCGTAA-CCATC
* * ** *
39807802 TCTTTTCATAGCTCGGTGGTCATCACC
63 CCTCTTCATAGCTCGACGGCCATCACC
39807829 ATCCCTTTTCATAA-TCGATAG
1 ATCCCTTTTCATAATTCGATAG
39807850 ACGTATCCCT
Statistics
Matches: 92, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
89 7 0.08
90 81 0.88
91 2 0.02
92 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.35
Consensus pattern (89 bp):
ATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATAATGGTAGGCCGTAACCATCCCT
CTTCATAGCTCGACGGCCATCACC
Found at i:39815332 original size:30 final size:30
Alignment explanation
Indices: 39815293--39815371 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
39815283 ACCCGAAGCT
* * *
39815293 ATCCGTTTTCATACTTTTATAGTTGTCACC
1 ATCCCTTTTCATACTTTGATAGTCGTCACC
** * *
39815323 ATCCCTTTTCATTGTTCGATGGTCGTCACC
1 ATCCCTTTTCATACTTTGATAGTCGTCACC
*
39815353 ATCCTTTTTCATACTTTGA
1 ATCCCTTTTCATACTTTGA
39815372 CAGCCGAAGC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.18, C:0.25, G:0.11, T:0.46
Consensus pattern (30 bp):
ATCCCTTTTCATACTTTGATAGTCGTCACC
Found at i:39815392 original size:30 final size:30
Alignment explanation
Indices: 39815351--39815425 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
39815341 ATGGTCGTCA
* * **
39815351 CCATCCTTTTTCATACTTTGACAGCCGAAG
1 CCATCCCTTTTCATACATCAACAGCCGAAG
* * *
39815381 CTATCCCTTTTCATAGATCAATAGCCGAAG
1 CCATCCCTTTTCATACATCAACAGCCGAAG
39815411 CCATCCCTTTTCATA
1 CCATCCCTTTTCATA
39815426 GCTAGATGGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.25, C:0.31, G:0.11, T:0.33
Consensus pattern (30 bp):
CCATCCCTTTTCATACATCAACAGCCGAAG
Found at i:39828596 original size:25 final size:25
Alignment explanation
Indices: 39828562--39828612 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
39828552 GAGGAAGAGG
*
39828562 GTGACTGGCTCGAGTAGCAAAAATT
1 GTGAATGGCTCGAGTAGCAAAAATT
* *
39828587 GTGAATGGCTCGGGTATCAAAAATT
1 GTGAATGGCTCGAGTAGCAAAAATT
39828612 G
1 G
39828613 ACTTAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.25
Consensus pattern (25 bp):
GTGAATGGCTCGAGTAGCAAAAATT
Found at i:39831155 original size:32 final size:30
Alignment explanation
Indices: 39831102--39831168 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 30
39831092 GTATCATCTC
*
39831102 ATATATATATATCAAACTTATAATATAACAT
1 ATATATATATATCAAACTTATAAAATAA-AT
39831133 A-ATATATATTAT-AAACAATTATAAAATAAAT
1 ATATATATA-TATCAAAC--TTATAAAATAAAT
39831164 ATATA
1 ATATA
39831169 AGGAGATAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
30 11 0.35
31 7 0.23
32 13 0.42
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (30 bp):
ATATATATATATCAAACTTATAAAATAAAT
Found at i:39831168 original size:30 final size:29
Alignment explanation
Indices: 39831101--39831168 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
39831091 TGTATCATCT
*
39831101 CATATATATATATCAAACTTATAATATAA
1 CATATATATATATCAAACTTATAAAATAA
39831130 CATAATATATATTAT-AAACAATTATAAAATAA
1 CAT-ATATATA-TATCAAAC--TTATAAAATAA
39831162 -ATATATA
1 CATATATA
39831169 AGGAGATAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
29 3 0.09
30 16 0.47
31 5 0.15
32 10 0.29
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (29 bp):
CATATATATATATCAAACTTATAAAATAA
Found at i:39840273 original size:47 final size:47
Alignment explanation
Indices: 39840198--39840717 Score: 817
Period size: 47 Copynumber: 11.1 Consensus size: 47
39840188 GAAATGATAG
*
39840198 TAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
39840245 TAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
39840292 TAAGGCCTAATGGCCGATGTGATGAATTTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
39840339 TAAGGCCAAATGGCCGATGTGATGAATTTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
39840386 TAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
39840433 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
39840480 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
39840527 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
39840574 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
39840621 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
39840667 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
39840714 TAAG
1 TAAG
39840718 TCCCGAAGGG
Statistics
Matches: 446, Mismatches: 26, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
46 40 0.09
47 406 0.91
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:39840892 original size:37 final size:37
Alignment explanation
Indices: 39840836--39840914 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
39840826 CCGAGCTCTA
* * *
39840836 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
39840873 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
39840910 AAGAC
1 AAGAC
39840915 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:39849767 original size:11 final size:11
Alignment explanation
Indices: 39849751--39849793 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
39849741 CCCAAGAGAG
39849751 AAAAAGAAAAT
1 AAAAAGAAAAT
* *
39849762 AAAAAGGAAAG
1 AAAAAGAAAAT
39849773 AAAAAGAAAAT
1 AAAAAGAAAAT
* *
39849784 TAAAACAAAA
1 AAAAAGAAAA
39849794 GCCTACATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (11 bp):
AAAAAGAAAAT
Found at i:39849794 original size:22 final size:22
Alignment explanation
Indices: 39849749--39849794 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
39849739 GGCCCAAGAG
**
39849749 AGAAAAAGAAAATAAAAAGGAA
1 AGAAAAAGAAAATAAAAACAAA
*
39849771 AGAAAAAGAAAATTAAAACAAA
1 AGAAAAAGAAAATAAAAACAAA
39849793 AG
1 AG
39849795 CCTACATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (22 bp):
AGAAAAAGAAAATAAAAACAAA
Found at i:39850336 original size:42 final size:42
Alignment explanation
Indices: 39850182--39850484 Score: 403
Period size: 42 Copynumber: 7.3 Consensus size: 42
39850172 CTTCATATAC
* * **
39850182 AATGCAATGAAAAGTAAATAGACCT-CACAGTTGGGCCTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTGGGCCTCTA
*
39850223 AATGCAATGAAAGGTAAATGGACTTCCACACCTGGGCCTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
39850265 AATG-ATTGAAACGTAAATGGACCTCCACACTTGGGCCTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
39850306 AATGCAATTAAAGGTACATGGACCTCCACACCTAGGCCTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
39850348 AATGCAATGAAACGTAAATGGGCCTCCACACCTGAGCCTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
39850390 AATGCAATGAAAGATAAATGGACCTCAACACCTGGGACTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
39850432 AATGCAATGAAAAGTAAATGGACCTCCACACCTTGGCCTATA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTGGGCCTCTA
*
39850474 ACTGCAATGAA
1 AATGCAATGAA
39850485 TGTTTTCCTT
Statistics
Matches: 226, Mismatches: 34, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
41 59 0.26
42 167 0.74
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
AATGCAATGAAAGGTAAATGGACCTCCACACCTGGGCCTCTA
Found at i:39850917 original size:15 final size:14
Alignment explanation
Indices: 39850889--39850946 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 14
39850879 TCTCTCCCTT
39850889 TTTCTCTTTTTTTTG
1 TTTCT-TTTTTTTTG
39850904 TTTCTTTTTGTTTTG
1 TTTCTTTTT-TTTTG
39850919 TTGT-TTTTCTTTTT-
1 TT-TCTTTT-TTTTTG
39850933 TCTTCTTTTTTTTT
1 T-TTCTTTTTTTTT
39850947 ATGTAGGCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.29
15 25 0.66
16 2 0.05
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTCTTTTTTTTTG
Found at i:39856905 original size:18 final size:18
Alignment explanation
Indices: 39856870--39856907 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39856860 GCAATAAGTG
*
39856870 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
39856888 ACGTTTTGAAAGA-GAATA
1 ACGTTTTGAAA-ATGAATA
39856906 AC
1 AC
39856908 ATTTGAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:39861544 original size:12 final size:12
Alignment explanation
Indices: 39861529--39861553 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39861519 ACCATTGTAG
39861529 TTATCATTTCCA
1 TTATCATTTCCA
39861541 TTATCATTTCCA
1 TTATCATTTCCA
39861553 T
1 T
39861554 CTATTCCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATCATTTCCA
Found at i:39866105 original size:20 final size:18
Alignment explanation
Indices: 39866080--39866131 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
39866070 ACCTGAAAAT
39866080 AAATCAAAGTTTTCTTTAAA
1 AAATCAAAGTTTTC-TT-AA
* *
39866100 AAATCACTATTTTTCTTAA
1 AAATCA-AAGTTTTCTTAA
39866119 AAATCAAAGTTTT
1 AAATCAAAGTTTT
39866132 ATTTCGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 5 0.19
19 8 0.30
20 8 0.30
21 6 0.22
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (18 bp):
AAATCAAAGTTTTCTTAA
Found at i:39866477 original size:3 final size:3
Alignment explanation
Indices: 39866469--39866497 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39866459 ACTAGAATGC
39866469 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
39866498 TTACCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:39874375 original size:19 final size:21
Alignment explanation
Indices: 39874338--39874383 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
39874328 TAAATATTAG
*
39874338 ATTAAATTTAATATTAAATATT
1 ATTAAATTTAATA-TAAATACT
39874360 ATTAAA-TTAATA-AAATACT
1 ATTAAATTTAATATAAATACT
39874379 ATTAA
1 ATTAA
39874384 GATAAGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.48
21 6 0.26
22 6 0.26
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAAATTTAATATAAATACT
Found at i:39874387 original size:58 final size:58
Alignment explanation
Indices: 39874300--39874426 Score: 184
Period size: 58 Copynumber: 2.2 Consensus size: 58
39874290 ATTACTTTTA
* * *
39874300 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATAT
1 TATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAA-AC
* * *
39874359 TATTAAATTAATAAAATAC-TATTAAGATAAGTATTAAATTTAATTTAATATTAAAAC
1 TATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAAC
39874416 TATTAAATTAA
1 TATTAAATTAA
39874427 CATTTTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
57 12 0.19
58 32 0.52
59 18 0.29
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (58 bp):
TATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAAC
Found at i:39874738 original size:19 final size:20
Alignment explanation
Indices: 39874714--39874756 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
39874704 TTCAACCAGT
*
39874714 TTTTGGGTT-TCGGTCTCAA
1 TTTTGGGTTCTCGGGCTCAA
39874733 TTTTGGGTTCTCGGGCTCAA
1 TTTTGGGTTCTCGGGCTCAA
39874753 TTTT
1 TTTT
39874757 CGATATCCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.49
Consensus pattern (20 bp):
TTTTGGGTTCTCGGGCTCAA
Found at i:39892699 original size:43 final size:43
Alignment explanation
Indices: 39892625--39892709 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
39892615 CATTGGCGTC
* ** *
39892625 GTATATGATTACGTGTAAGACCTTGTCTGGGATAGTGGCATTT
1 GTATATGATTACATGTAAGACCACGTCTGGGACAGTGGCATTT
* * *
39892668 GTATTTGATTACATGTAAGACCACGTGTGGGACATTGGCATT
1 GTATATGATTACATGTAAGACCACGTCTGGGACAGTGGCATT
39892710 GTACGAGCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (43 bp):
GTATATGATTACATGTAAGACCACGTCTGGGACAGTGGCATTT
Found at i:39893056 original size:19 final size:19
Alignment explanation
Indices: 39893032--39893085 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
39893022 AATCTTCAAG
39893032 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
39893051 GATATGTAACCTTAGATAT
1 GATATGCAATCTTAGATAT
*
39893070 GATAAGCAATCTTAGA
1 GATATGCAATCTTAGA
39893086 AGATATGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:39898447 original size:24 final size:24
Alignment explanation
Indices: 39898390--39898441 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39898380 TTTTTAGAAG
* **
39898390 ATTTAGTATTTATTATTATAATAT
1 ATTTAGCATTTATTAGAATAATAT
39898414 ATTTAGCATTTATTAGAATAATAT
1 ATTTAGCATTTATTAGAATAATAT
39898438 ATTT
1 ATTT
39898442 GACATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGAATAATAT
Found at i:39898452 original size:24 final size:24
Alignment explanation
Indices: 39898407--39898453 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39898397 ATTTATTATT
*
39898407 ATAATATATTTAGCATTTATTAGA
1 ATAATATATTTAGCATTGATTAGA
39898431 ATAATATATTT-GACATTGATTAG
1 ATAATATATTTAG-CATTGATTAG
39898454 TGTTAGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGA
Found at i:39898677 original size:24 final size:24
Alignment explanation
Indices: 39898650--39898695 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
39898640 TTCAGTTTTC
39898650 AACAAATTTCTAAATAATTTTAAA
1 AACAAATTTCTAAATAATTTTAAA
* *
39898674 AACAGATTTTTAAATAATTTTA
1 AACAAATTTCTAAATAATTTTA
39898696 GAAATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (24 bp):
AACAAATTTCTAAATAATTTTAAA
Found at i:39899107 original size:27 final size:27
Alignment explanation
Indices: 39899075--39899133 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
39899065 AAATAATAAA
39899075 ATTTAA-TTTAATATTAAGATAAATATT
1 ATTTAACTTT-ATATTAAGATAAATATT
* **
39899102 ATTTAACTTTATTTTAATTTAAATATT
1 ATTTAACTTTATATTAAGATAAATATT
39899129 ATTTA
1 ATTTA
39899134 TTTTTAGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
ATTTAACTTTATATTAAGATAAATATT
Found at i:39899363 original size:15 final size:15
Alignment explanation
Indices: 39899340--39899370 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39899330 AATGTTACAC
*
39899340 ACAATAATATTTAAT
1 ACAAAAATATTTAAT
39899355 ACAAAAATATTTAAT
1 ACAAAAATATTTAAT
39899370 A
1 A
39899371 ATTGATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
ACAAAAATATTTAAT
Found at i:39899543 original size:22 final size:21
Alignment explanation
Indices: 39899505--39899545 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
39899495 TATTATTTGT
*
39899505 ACATTTTTGTAATTTAAATGG
1 ACATTTTTGTAAATTAAATGG
39899526 ACATTTTTGTAAAATTAAAT
1 ACATTTTTGT-AAATTAAAT
39899546 TACTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (21 bp):
ACATTTTTGTAAATTAAATGG
Found at i:39899857 original size:39 final size:39
Alignment explanation
Indices: 39899728--39899881 Score: 141
Period size: 40 Copynumber: 3.8 Consensus size: 39
39899718 AGCGGCACTT
** * *
39899728 TTAGCGGCGTTTGGACAAAAAATGCCGGTAAAAATCAAGCA
1 TTAGCGGCGTTTTTA-AAAAAATGCCGCTAAAAAT-GAGCA
* ** * *
39899769 TTAGCGGCGCTTTCT--GGAAATCGCCACTAAAGATTGAGCA
1 TTAGCGGCG-TTTTTAAAAAAAT-GCCGCTAAA-AATGAGCA
*
39899809 TTAGTGGCGTTTTTAAAAAAATGCCGCTAAAAATGAGCA
1 TTAGCGGCGTTTTTAAAAAAATGCCGCTAAAAATGAGCA
*
39899848 TTAGCGGCGTTTTTCAAAAAAATGCCGCAAAAAA
1 TTAGCGGCGTTTTT-AAAAAAATGCCGCTAAAAA
39899882 CCTTAGCCCA
Statistics
Matches: 91, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
39 28 0.31
40 45 0.49
41 15 0.16
42 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (39 bp):
TTAGCGGCGTTTTTAAAAAAATGCCGCTAAAAATGAGCA
Found at i:39899961 original size:32 final size:32
Alignment explanation
Indices: 39899924--39900029 Score: 131
Period size: 32 Copynumber: 3.0 Consensus size: 32
39899914 CGTGGCTTTA
39899924 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCCT
1 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCCT
39899956 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTGGGTCTTT
1 GCGGCGTTTTTGGAAAAGCGCCGCTAATG-C-----C--T
39899996 AGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCT
1 -GCGGCGTTTTTGGAAAAGCGCCGCTAATGCCT
39900029 G
1 G
39900030 GGTCTTTAGC
Statistics
Matches: 65, Mismatches: 0, Indels: 18
0.78 0.00 0.22
Matches are distributed among these distances:
32 30 0.46
33 2 0.03
35 1 0.02
38 1 0.02
40 2 0.03
41 29 0.45
ACGTcount: A:0.18, C:0.24, G:0.32, T:0.26
Consensus pattern (32 bp):
GCGGCGTTTTTGGAAAAGCGCCGCTAATGCCT
Found at i:39900013 original size:41 final size:41
Alignment explanation
Indices: 39899956--39900064 Score: 193
Period size: 41 Copynumber: 2.7 Consensus size: 41
39899946 GCTAATGCCT
39899956 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTGGGTCTTTA
1 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTGGGTCTTTA
39899997 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTGGGTCTTTA
1 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTGGGTCTTTA
*
39900038 GCGGCGTTTTT-GATAAAGCGCCTCTAA
1 GCGGCGTTTTTGGA-AAAGCGCCGCTAA
39900065 AAACATTTTA
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
40 2 0.03
41 64 0.97
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTGGGTCTTTA
Found at i:39900307 original size:22 final size:22
Alignment explanation
Indices: 39900282--39900359 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 22
39900272 GAGTTACTGT
39900282 TTTAAGGTTTAGGGAGTATGGA
1 TTTAAGGTTTAGGGAGTATGGA
* * * *
39900304 TTTAAGGATTATGGATTAGGGA
1 TTTAAGGTTTAGGGAGTATGGA
* *
39900326 -TTATGGTTTAAGG-GT-TGAGA
1 TTTAAGGTTTAGGGAGTATG-GA
39900346 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
39900360 GGTTAGTGGT
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 21 0.49
22 18 0.42
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (22 bp):
TTTAAGGTTTAGGGAGTATGGA
Found at i:39900339 original size:15 final size:14
Alignment explanation
Indices: 39900287--39900335 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
39900277 ACTGTTTTAA
*
39900287 GGTTTAGGGAGTAT
1 GGTTTAGGGATTAT
*
39900301 GGATTTAAGGATTAT
1 GG-TTTAGGGATTAT
*
39900316 GGATTAGGGATTAT
1 GGTTTAGGGATTAT
39900330 GGTTTA
1 GGTTTA
39900336 AGGGTTGAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.39
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:39900374 original size:15 final size:15
Alignment explanation
Indices: 39900354--39900387 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39900344 GATTTAAGGT
*
39900354 TTAGGGGGTTAGTGG
1 TTAGGGGGTTAGGGG
*
39900369 TTAGGGGTTTAGGGG
1 TTAGGGGGTTAGGGG
39900384 TTAG
1 TTAG
39900388 ATGTTATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.50, T:0.35
Consensus pattern (15 bp):
TTAGGGGGTTAGGGG
Found at i:39900393 original size:22 final size:21
Alignment explanation
Indices: 39900330--39900393 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
39900320 TAGGGATTAT
*
39900330 GGTTTAAGGGTTGAGAT-TTAA
1 GGTTTAGGGGTT-AGATGTTAA
*
39900351 GGTTTAGGGGGTTAG-TGGTTAGG
1 GGTTTA-GGGGTTAGAT-GTTA-A
39900374 GGTTTAGGGGTTAGATGTTA
1 GGTTTAGGGGTTAGATGTTA
39900394 TAGGGTTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 1 0.03
21 8 0.22
22 20 0.56
23 7 0.19
ACGTcount: A:0.20, C:0.00, G:0.42, T:0.38
Consensus pattern (21 bp):
GGTTTAGGGGTTAGATGTTAA
Found at i:39900495 original size:13 final size:12
Alignment explanation
Indices: 39900460--39900503 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
39900450 TGGGTTTAGA
39900460 TTAA-TTATTTT
1 TTAATTTATTTT
39900471 TTAATTTATTTT
1 TTAATTTATTTT
* *
39900483 TTAATATGTTTT
1 TTAATTTATTTT
39900495 TTAATTTAT
1 TTAATTTAT
39900504 ATATTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 4 0.14
12 24 0.86
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (12 bp):
TTAATTTATTTT
Found at i:39900510 original size:24 final size:23
Alignment explanation
Indices: 39900459--39900510 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
39900449 TTGGGTTTAG
*
39900459 ATTAATTATTTTTTAATTTATTT
1 ATTAATTATTTTTTAATTTATAT
* *
39900482 TTTAATATGTTTTTTAATTTATAT
1 ATTAAT-TATTTTTTAATTTATAT
39900506 ATTAA
1 ATTAA
39900511 ATAATTTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTAATTATTTTTTAATTTATAT
Found at i:39900735 original size:21 final size:21
Alignment explanation
Indices: 39900711--39900751 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
39900701 GATTTAAGGT
39900711 TTAGGGATTAAGAGTTAGGGG
1 TTAGGGATTAAGAGTTAGGGG
*
39900732 TTAGGGGTTAAGAGTTAGGG
1 TTAGGGATTAAGAGTTAGGG
39900752 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.44, T:0.29
Consensus pattern (21 bp):
TTAGGGATTAAGAGTTAGGGG
Found at i:39900760 original size:21 final size:20
Alignment explanation
Indices: 39900708--39900761 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 20
39900698 TAGGATTTAA
39900708 GGTTTAGGGATTAAGAGTTAG
1 GGTTTAGGG-TTAAGAGTTAG
*
39900729 GGGTTAGGGGTTAAGAGTTAG
1 GGTTTA-GGGTTAAGAGTTAG
39900750 GGATTTAGGGTT
1 GG-TTTAGGGTT
39900762 TTAAGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (20 bp):
GGTTTAGGGTTAAGAGTTAG
Found at i:39905356 original size:43 final size:43
Alignment explanation
Indices: 39905325--39905597 Score: 395
Period size: 43 Copynumber: 6.4 Consensus size: 43
39905315 CGTTTGCGAA
* * * ***
39905325 AAAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTTTATAAA
1 AAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGG
* * *
39905368 AAAAGCACCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GT
1 AAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGG
*
39905410 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGG
*
39905453 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGG
*
39905496 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGG
* * * *
39905539 AAAAGCGCCGCAAAAGATCATGGTCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGG
39905582 AAAAGCGCCGCTAAAG
1 AAAAGCGCCGCTAAAG
39905598 TCAGCGACGC
Statistics
Matches: 213, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
42 38 0.18
43 175 0.82
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGG
Found at i:39905693 original size:21 final size:21
Alignment explanation
Indices: 39905667--39905710 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
39905657 TTCAGCGGCG
* *
39905667 CTAAAAAGTGCCGCTAAAGGC
1 CTAAAAAGCGCCGCTAAAAGC
39905688 CTAAAAAGCGCCGCTAAAAGC
1 CTAAAAAGCGCCGCTAAAAGC
39905709 CT
1 CT
39905711 GTTTTGGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (21 bp):
CTAAAAAGCGCCGCTAAAAGC
Found at i:39909053 original size:129 final size:131
Alignment explanation
Indices: 39908771--39909115 Score: 408
Period size: 129 Copynumber: 2.6 Consensus size: 131
39908761 GCTGTCATCA
* * * * * * *
39908771 TAAATCAACGAGCCTTAATAACACTAGTTGTGAACTTAAATCAATGAGCTGTTCAAAATAGCGAT
1 TAAATCAGCGAGCCTTAATAATATTAGTTGTGATCTTAAATCAATGAGCTGTTTAGAGTAGCGAT
* * * ** *
39908836 AGAAAATTAGCTAACTCATAAAAGATTTTTCATGATATTAAATAAATTGAACTTAGGTTGTGATC
66 AGAAAATCAACTAACTCAGAAAAGATAATTCATGATAGTAAATAAATTGAACTTAGGTTGTGATC
39908901 G
131 G
* * *
39908902 TAAATCAGCGAGCCTTAATAATATTAGTTGTGATCTTAAATCAGTGAGCTGTTTAGTGTACCGAT
1 TAAATCAGCGAGCCTTAATAATATTAGTTGTGATCTTAAATCAATGAGCTGTTTAGAGTAGCGAT
** * * *
39908967 AGTGAATCATCTAACTCAGAAAA-A-AATTCATGATAGTAAATCAAA-TGATCTTTGGTTGTGAT
66 AGAAAATCAACTAACTCAGAAAAGATAATTCATGATAGTAAAT-AAATTGAACTTAGGTTGTGAT
39909029 CG
130 CG
* * * * * * *
39909031 TAAATCAGTGAGCCTTAATAATATCAATTGTAATCTTAAATAAATGAGCTATTTGGAGTAGCGAT
1 TAAATCAGCGAGCCTTAATAATATTAGTTGTGATCTTAAATCAATGAGCTGTTTAGAGTAGCGAT
39909096 AGAAAATCAACTAACTCAGA
66 AGAAAATCAACTAACTCAGA
39909116 CAAGGTCGTT
Statistics
Matches: 180, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
129 103 0.57
130 4 0.02
131 73 0.41
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.32
Consensus pattern (131 bp):
TAAATCAGCGAGCCTTAATAATATTAGTTGTGATCTTAAATCAATGAGCTGTTTAGAGTAGCGAT
AGAAAATCAACTAACTCAGAAAAGATAATTCATGATAGTAAATAAATTGAACTTAGGTTGTGATC
G
Found at i:39910491 original size:18 final size:18
Alignment explanation
Indices: 39910468--39910504 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39910458 GATAGTTTGA
*
39910468 TATTCGATTTATTCAAAT
1 TATTCGAGTTATTCAAAT
*
39910486 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCAAAT
39910504 T
1 T
39910505 TGATAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (18 bp):
TATTCGAGTTATTCAAAT
Found at i:39915884 original size:23 final size:23
Alignment explanation
Indices: 39915857--39915978 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
39915847 AGTGTAATTG
*
39915857 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
39915880 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
39915903 ATCAGTGGTAGTTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
39915926 TTCAGTGGTAGCTAT-GGCTACGT
1 ATCAGTGGTAGCT-TCGGCTACAT
39915949 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39915972 ATCAGTG
1 ATCAGTG
39915979 TGGCACTTAT
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
22 1 0.01
23 84 0.98
24 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:39915909 original size:46 final size:46
Alignment explanation
Indices: 39915857--39915978 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
39915847 AGTGTAATTG
*
39915857 ATCAGTGGTAGCTTCAGCTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* * *
39915903 ATCAGTGGTAGTTTCGGCTACATTTCAGTGGTAGCTATGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
39915949 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
39915979 TGGCACTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:39919676 original size:30 final size:30
Alignment explanation
Indices: 39919640--39919699 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
39919630 TACAAGATTG
39919640 CCCTAATTCACCACTATATAAACCCCTCTC
1 CCCTAATTCACCACTATATAAACCCCTCTC
39919670 CCCTAATTCACCACTATATAAACCCCTCTC
1 CCCTAATTCACCACTATATAAACCCCTCTC
39919700 TACTATCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.43, G:0.00, T:0.27
Consensus pattern (30 bp):
CCCTAATTCACCACTATATAAACCCCTCTC
Found at i:39940810 original size:8 final size:8
Alignment explanation
Indices: 39940797--39940831 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
39940787 CTCCTTTTTA
39940797 TTAAATAT
1 TTAAATAT
39940805 TTAAATAT
1 TTAAATAT
*
39940813 CTAATATAT
1 TTAA-ATAT
39940822 TTAAATAT
1 TTAAATAT
39940830 TT
1 TT
39940832 GGCTAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (8 bp):
TTAAATAT
Found at i:39942308 original size:114 final size:114
Alignment explanation
Indices: 39942016--39942692 Score: 898
Period size: 114 Copynumber: 5.9 Consensus size: 114
39942006 AACGCGTTGC
* * **
39942016 AAAATACCTAAGCCCAATGACGCCGTTTTCCAAGCTTTCGGGGATTTAGCGGCATTTTTAA-TAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGT-A
*
39942080 AGCGCCGCTAATGCTCAGGGCTTTAGCAGG-GTTTTTGATAAAGCGCCACAAA
65 AGCGCCGCTAATGCTCAAGGCTTTAGC-GGCGTTTTTGATAAAGCGCCAC--A
* * *
39942132 AAAAAACCTAAGCCCAATGACGCCGTTTTCTGAGCTTTGGGGGATTTAGCGGCGTTTTTAAGTAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGTAA
* *
39942197 GCGCCGCTAATGCTCAAGGCTTTAGCAGCGTTTTTGATAAAGCGCCTCA
66 GCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTTGATAAAGCGCCACA
* * * **
39942246 AAAAAACCTAAGCCTAACGACGCGGTTTTCTAAGCTTTCGGGGATTTAGCGGCATTTTTAAGTTC
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGTAA
* * * *
39942311 GTGCCACTAATGCCCAAGGCTTTAGCGGCATTTTTGATAAAGCGCCACA
66 GCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTTGATAAAGCGCCACA
*
39942360 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGTAA
* *
39942425 GCGCCGCTAAAAATGCTCAGGGCTTTAGCGGTGTTTTTGATAAAGCGCCACA
66 GCGCCGCT---AATGCTCAAGGCTTTAGCGGCGTTTTTGATAAAGCGCCACA
* * * *
39942477 GAAAAACCTCAGCCCAACGACGCCGTTTTCTGAGCTTTTGGGGATTTAGCGGCATTTTTAAGTAC
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGTAA
* * *
39942542 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGA-AAAGCACCGC-
66 GCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTT-GATAAAGCGCCACA
* * * **
39942590 AAAAAACCTAAGCCCAACGACGCCATTTTCTTAGCTTTCGAGGATTTAGTAGCATTTTTTAA-TA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCA-TTTTTAAGT-
*
39942654 AAGCGCCGCTAATGCTC-AGTGCTTTAGTGGCGTTTTTGA
64 AAGCGCCGCTAATGCTCAAG-GCTTTAGCGGCGTTTTTGA
39942693 GGATGCGCCG
Statistics
Matches: 499, Mismatches: 53, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
113 50 0.10
114 239 0.48
115 3 0.01
116 101 0.20
117 106 0.21
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (114 bp):
AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGTAA
GCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTTGATAAAGCGCCACA
Found at i:39942532 original size:231 final size:228
Alignment explanation
Indices: 39942016--39942692 Score: 941
Period size: 231 Copynumber: 2.9 Consensus size: 228
39942006 AACGCGTTGC
* * *
39942016 AAAATACCTAAGCCCAATGACGCCGTTTTCCAAGCTTTCGGGGATTTAGCGGCATTTTTAA-TAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCATTTTTAAGT-A
*
39942080 AGCGCCGCTAATGCTCAGGGCTTTAGCAGG-GTTTTTGATAAAGCGCCACAAAAAAAAACCTAAG
65 CGCGCCGCTAATGCTCAGGGCTTTAGC-GGCGTTTTTGATAAAGCGCCAC--AAAAAAACCTAAG
* *
39942144 CCCAATGACGCCGTTTTCTGAGCTTTGGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATG
127 CCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATG
* * *
39942209 CTCAAGGCTTTAGCAGCGTTTTTGATAAAGCGCCTCA
192 CTCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCACA
* * *
39942246 AAAAAACCTAAGCCTAACGACGCGGTTTTCTAAGCTTTCGGGGATTTAGCGGCATTTTTAAGTTC
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCATTTTTAAGTAC
* * * * *
39942311 GTGCCACTAATGCCCAAGGCTTTAGCGGCATTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCA
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCA
39942376 ACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAAAAATGC
131 ACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCT---AATGC
*
39942441 TCAGGGCTTTAGCGGTGTTTTTGATAAAGCGCCACA
193 TCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCACA
* * * *
39942477 GAAAAACCTCAGCCCAACGACGCCGTTTTCTGAGCTTTTGGGGATTTAGCGGCATTTTTAAGTAC
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCATTTTTAAGTAC
* *
39942542 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGA-AAAGCACCGC-AAAAAACCTAAGCCC
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT-GATAAAGCGCCACAAAAAAACCTAAGCCC
* * * ** *
39942605 AACGACGCCATTTTCTTAGCTTTCGAGGATTTAGTAGCATTTTTTAA-TAAAGCGCCGCTAATGC
130 AACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC-GTTTTTAAGT-AAGCGCCGCTAATGC
* *
39942669 TCAGTGCTTTAGTGGCGTTTTTGA
193 TCAGGGCTTTAGCGGCGTTTTTGA
39942693 GGATGCGCCG
Statistics
Matches: 398, Mismatches: 41, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
228 98 0.25
229 2 0.01
230 145 0.36
231 151 0.38
232 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (228 bp):
AAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCATTTTTAAGTAC
GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCA
ACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCA
GGGCTTTAGCGGCGTTTTTGATAAAGCGCCACA
Found at i:39943329 original size:14 final size:14
Alignment explanation
Indices: 39943310--39943379 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
39943300 TTAATGTGAT
* *
39943310 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
39943324 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
**
39943338 TT-AGGGATTAGATG
1 TTAAGGG-TTAGGGG
* *
39943352 TTAAGAGTTAGGGA
1 TTAAGGGTTAGGGG
*
39943366 TTTAGGGTTTAGGG
1 TTAAGGG-TTAGGG
39943380 ATTCGGTGTT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
13 4 0.09
14 30 0.70
15 9 0.21
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:39943466 original size:7 final size:7
Alignment explanation
Indices: 39943452--39943485 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
39943442 TAAAGTTTAA
39943452 GGGTTAG
1 GGGTTAG
*
39943459 GTGTTAG
1 GGGTTAG
39943466 GGGTTAG
1 GGGTTAG
*
39943473 GGGTTAA
1 GGGTTAG
39943480 GGGTTA
1 GGGTTA
39943486 AGGATTTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (7 bp):
GGGTTAG
Found at i:39943471 original size:14 final size:14
Alignment explanation
Indices: 39943448--39943485 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
39943438 TAAATAAAGT
*
39943448 TTAAGGGTTAGGTG
1 TTAAGGGTTAGGGG
*
39943462 TTAGGGGTTAGGGG
1 TTAAGGGTTAGGGG
39943476 TTAAGGGTTA
1 TTAAGGGTTA
39943486 AGGATTTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:39943616 original size:90 final size:89
Alignment explanation
Indices: 39943469--39943731 Score: 359
Period size: 90 Copynumber: 3.0 Consensus size: 89
39943459 GTGTTAGGGG
* * * *
39943469 TTAGGGGTTAAGGGTTAAGGATTTAGGTCG-GGTTATGGTTTAGGGTTTAGTTTAATTAGTGCTT
1 TTAGGGGTTAAGGGTTAGGGATTTAGGTTGAGGTTAGGGTTTAGGGTTTAGATTAATTAGTGCTT
*
39943533 TTGAATTTATATATTAAATAAAGT
66 TTTAATTTATATATTAAATAAAGT
* * *
39943557 TTAGGGGTTAGGGGTTAGGGATTCGAGGTTGAGTTTAGGGTTTAGGGTTTAGATTAATTAGTG-T
1 TTAGGGGTTAAGGGTTAGGGATT-TAGGTTGAGGTTAGGGTTTAGGGTTTAGATTAATTAGTGCT
39943621 TTGTTAATTTATATATTAAATAAAGT
65 TT-TTAATTTATATATTAAATAAAGT
* * * * * * *
39943647 TTAGGAGTTATGGGTTAGGGATTTAGGGTCAGGTTAGGGTTTAAGATTTAGATTAATTAGTACTT
1 TTAGGGGTTAAGGGTTAGGGATTTAGGTTGAGGTTAGGGTTTAGGGTTTAGATTAATTAGTGCTT
39943712 TTTAATTTATATATTAAATA
66 TTTAATTTATATATTAAATA
39943732 GGTTCTTTAT
Statistics
Matches: 154, Mismatches: 17, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
88 21 0.14
89 59 0.38
90 74 0.48
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.43
Consensus pattern (89 bp):
TTAGGGGTTAAGGGTTAGGGATTTAGGTTGAGGTTAGGGTTTAGGGTTTAGATTAATTAGTGCTT
TTTAATTTATATATTAAATAAAGT
Found at i:39944212 original size:84 final size:84
Alignment explanation
Indices: 39944124--39944310 Score: 207
Period size: 84 Copynumber: 2.2 Consensus size: 84
39944114 TTTATCTTAA
* * * * **
39944124 GGAATGAAATATTTTTGTGCCGTTTTTAATAAAAACGCCGCAAG-GATTTATTAAAATTTGCCAG
1 GGAATAAAATATTATAGTGCCGTTTTTAAGAAAAACGCCGCAAGAG-TGAATTAAAATTTGCCA-
*
39944188 A-GCGACGCCGTTTCTCTACT
64 ATACGACGCCGTTTCTCTACT
* * * * **
39944208 GGAATAAAATCTTATAGTGGCGTTTTTTAGGAAAACGCCGCAAGAGTGAATTAATGTTTGCCAAT
1 GGAATAAAATATTATAGTGCCGTTTTTAAGAAAAACGCCGCAAGAGTGAATTAAAATTTGCCAAT
*
39944273 ACGGCGCCGTTTCTCTACT
66 ACGACGCCGTTTCTCTACT
*
39944292 GGAATAAAATCTTATAGTG
1 GGAATAAAATATTATAGTG
39944311 GCATTTTTTA
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
83 1 0.01
84 85 0.98
85 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (84 bp):
GGAATAAAATATTATAGTGCCGTTTTTAAGAAAAACGCCGCAAGAGTGAATTAAAATTTGCCAAT
ACGACGCCGTTTCTCTACT
Found at i:39944311 original size:84 final size:78
Alignment explanation
Indices: 39944193--39944350 Score: 235
Period size: 84 Copynumber: 1.9 Consensus size: 78
39944183 GCCAGAGCGA
*
39944193 CGCCGTTTCTCTACTGGAATAAAATCTTATAGTGGCGTTTTTTAGGAAAACGCCGCAAGAGTGAA
1 CGCCGTTTCTCTACTGGAATAAAATCTTATAGTGGCATTTTTT-----AA-GCCGCAAGAGTGAA
39944258 TTAATGTTTGCCAATACGG
60 TTAATGTTTGCCAATACGG
*
39944277 CGCCGTTTCTCTACTGGAATAAAATCTTATAGTGGCATTTTTTAAGCCGCAATAGTGAATTAATG
1 CGCCGTTTCTCTACTGGAATAAAATCTTATAGTGGCATTTTTTAAGCCGCAAGAGTGAATTAATG
*
39944342 TTTGTCAAT
66 TTTGCCAAT
39944351 GAGGCACTGT
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
78 27 0.38
79 2 0.03
84 42 0.59
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (78 bp):
CGCCGTTTCTCTACTGGAATAAAATCTTATAGTGGCATTTTTTAAGCCGCAAGAGTGAATTAATG
TTTGCCAATACGG
Found at i:39945852 original size:12 final size:12
Alignment explanation
Indices: 39945835--39945863 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
39945825 ATACTTACAT
39945835 AACTTATATATA
1 AACTTATATATA
39945847 AACTTATATATA
1 AACTTATATATA
39945859 AACTT
1 AACTT
39945864 GCATAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
AACTTATATATA
Found at i:39945877 original size:9 final size:9
Alignment explanation
Indices: 39945859--39946202 Score: 148
Period size: 9 Copynumber: 39.8 Consensus size: 9
39945849 CTTATATATA
*
39945859 AACTTGCAT
1 AACTTACAT
39945868 AACTTACAT
1 AACTTACAT
*
39945877 AA-TAACATAAT
1 AACTTAC---AT
39945888 AACTTACAT
1 AACTTACAT
*
39945897 AA--TACAC
1 AACTTACAT
39945904 AACTTACAT
1 AACTTACAT
*
39945913 AACTTAAAT
1 AACTTACAT
39945922 AACTTACAT
1 AACTTACAT
*
39945931 -A-GTACAT
1 AACTTACAT
**
39945938 AACTTTGAT
1 AACTTACAT
*
39945947 AACTAACAT
1 AACTTACAT
* *
39945956 TA--TACAC
1 AACTTACAT
39945963 AACTTACAT
1 AACTTACAT
39945972 AA--TACAT
1 AACTTACAT
**
39945979 TTCTTACAT
1 AACTTACAT
39945988 AACTTACAT
1 AACTTACAT
*
39945997 AA--TACAC
1 AACTTACAT
39946004 AACTTA-ATT
1 AACTTACA-T
*
39946013 AATATTATACAT
1 -A-ACT-TACAT
*
39946025 AACATACAT
1 AACTTACAT
39946034 AA--TACAT
1 AACTTACAT
*
39946041 AA--TACAC
1 AACTTACAT
39946048 AACTTA-ATT
1 AACTTACA-T
*
39946057 AATATTATACAT
1 -A-ACT-TACAT
*
39946069 AACATACAT
1 AACTTACAT
*
39946078 AA-TACACAT
1 AACT-TACAT
39946087 AACTTACAT
1 AACTTACAT
*
39946096 -A-GTACAT
1 AACTTACAT
*
39946103 AACTAACAT
1 AACTTACAT
*
39946112 AA--TACAC
1 AACTTACAT
*
39946119 AACTTACGT
1 AACTTACAT
*
39946128 AACTTAAAT
1 AACTTACAT
39946137 AACTTACAT
1 AACTTACAT
*
39946146 AGCTTACAT
1 AACTTACAT
39946155 AA--TACAT
1 AACTTACAT
39946162 AACTTACAT
1 AACTTACAT
39946171 AACTT-CTAT
1 AACTTAC-AT
39946180 AA--TACAT
1 AACTTACAT
39946187 AACTTACAT
1 AACTTACAT
*
39946196 AATTTAC
1 AACTTAC
39946203 CTAATACATA
Statistics
Matches: 248, Mismatches: 49, Indels: 76
0.66 0.13 0.20
Matches are distributed among these distances:
7 61 0.25
8 11 0.04
9 150 0.60
10 5 0.02
11 10 0.04
12 9 0.04
13 2 0.01
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:39945916 original size:25 final size:25
Alignment explanation
Indices: 39945859--39946210 Score: 105
Period size: 25 Copynumber: 14.0 Consensus size: 25
39945849 CTTATATATA
*
39945859 AACTTGCATAACTTACATAATA-AC
1 AACTTACATAACTTACATAATACAC
39945883 -A--TA-ATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
*
39945904 AACTTACATAACTTAAATAACTTACA-
1 AACTTACATAACTTACATAA--TACAC
* * **
39945930 TA-GTACATAACTTTGATAACTA-AC
1 AACTTACATAACTTACATAA-TACAC
* * *
39945954 -ATTATACACAACTTACATAATACAT
1 AACT-TACATAACTTACATAATACAC
**
39945979 TTCTTACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
* *
39946004 AACTTA-ATTAATATTATACATAACATACAT
1 AACTTACA-T-A-ACT-TACAT-A-ATACAC
*
39946034 AA--TACATAA-TACACAACTTAATTA-A-
1 AACTTACATAACT-TAC-A--TAA-TACAC
* * *
39946059 TATTATACATAACATACATAATACAC
1 AACT-TACATAACTTACATAATACAC
*
39946085 ATAACTTACAT-A-GTACATAACTA-AC
1 --AACTTACATAACTTACATAA-TACAC
* * * * *
39946110 ATA-ATACACAACTTACGTAACTTAAAT
1 A-ACTTACATAACTTACATAA--TACAC
* *
39946137 AACTTACATAGCTTACATAATACAT
1 AACTTACATAACTTACATAATACAC
*
39946162 AACTTACATAACTT-CTATAATACAT
1 AACTTACATAACTTAC-ATAATACAC
* *
39946187 AACTTACATAATTTACCTAATACA
1 AACTTACATAACTTACATAATACA
39946211 TAAATATATA
Statistics
Matches: 247, Mismatches: 41, Indels: 79
0.67 0.11 0.22
Matches are distributed among these distances:
20 15 0.06
21 3 0.01
22 1 0.00
23 8 0.03
24 12 0.05
25 134 0.54
26 14 0.06
27 31 0.13
28 20 0.08
29 2 0.01
30 7 0.03
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:39945967 original size:41 final size:41
Alignment explanation
Indices: 39945922--39946198 Score: 165
Period size: 41 Copynumber: 6.9 Consensus size: 41
39945912 TAACTTAAAT
* ** *
39945922 AACTTACATAGTACATAACTTTGATAACTAACATTATACAC
1 AACTTACATAATACATAACTTACATAACTAACATAATACAC
** *
39945963 AACTTACATAATACATTTCTTACATAACTTACATAATACAC
1 AACTTACATAATACATAACTTACATAACTAACATAATACAC
* *
39946004 AACTTAATTAATATTATACATAACATACATAA-T-ACATAATACAC
1 AACTT-A--CATA--ATACATAACTTACATAACTAACATAATACAC
*
39946048 AACTTA-AT--TA-AT-ATTATACATAAC-ATACATAATACAC
1 AACTTACATAATACATAACT-TACATAACTA-ACATAATACAC
* *
39946085 -A-TAAC-T--TACAT-A-GTACATAACTAACATAATACAC
1 AACTTACATAATACATAACTTACATAACTAACATAATACAC
* * * * *
39946119 AACTTACGTAACTTAAATAACTTACATAGCTTACATAATACAT
1 AACTTACATAA--TACATAACTTACATAACTAACATAATACAC
* *
39946162 AACTTACATAACTTCTATAA--TACATAACTTACATAAT
1 AACTTACATAA-TAC-ATAACTTACATAACTAACATAAT
39946199 TTACCTAATA
Statistics
Matches: 188, Mismatches: 26, Indels: 44
0.73 0.10 0.17
Matches are distributed among these distances:
34 20 0.11
35 16 0.09
36 9 0.05
37 12 0.06
40 2 0.01
41 59 0.31
42 3 0.02
43 33 0.18
44 19 0.10
45 1 0.01
46 14 0.07
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (41 bp):
AACTTACATAATACATAACTTACATAACTAACATAATACAC
Found at i:39946002 original size:16 final size:16
Alignment explanation
Indices: 39945983--39946198 Score: 117
Period size: 16 Copynumber: 13.1 Consensus size: 16
39945973 ATACATTTCT
39945983 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
39945999 TACACAACTTAATTAATATTA
1 TACATAACTT-A--CATA--A
*
39946020 TACATAACATACATAA
1 TACATAACTTACATAA
*
39946036 TACATAA--TACA-CA
1 TACATAACTTACATAA
*
39946049 -ACTTAA-TTA-ATATTA
1 TACATAACTTACATA--A
*
39946064 TACATAACATACATAA
1 TACATAACTTACATAA
*
39946080 TACACATAACTTACATAG
1 T--ACATAACTTACATAA
*
39946098 TACATAACTAACATAA
1 TACATAACTTACATAA
* *
39946114 TACACAACTTACGTAA
1 TACATAACTTACATAA
* *
39946130 CTTAAATAACTTACATAGCT
1 --TACATAACTTACATA--A
39946150 TACATAA--TACATAA
1 TACATAACTTACATAA
39946164 CTTACATAACTT-CTATAA
1 --TACATAACTTAC-ATAA
39946182 TACATAACTTACATAA
1 TACATAACTTACATAA
39946198 T
1 T
39946199 TTACCTAATA
Statistics
Matches: 153, Mismatches: 23, Indels: 48
0.68 0.10 0.21
Matches are distributed among these distances:
12 6 0.04
13 3 0.02
14 4 0.03
15 1 0.01
16 78 0.51
17 5 0.03
18 43 0.28
19 3 0.02
20 1 0.01
21 9 0.06
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.31
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:39946050 original size:44 final size:44
Alignment explanation
Indices: 39945983--39946083 Score: 184
Period size: 44 Copynumber: 2.2 Consensus size: 44
39945973 ATACATTTCT
39945983 TACATAACTTACATAATACACAACTTAATTAATATTATACATAACA
1 TACATAA--TACATAATACACAACTTAATTAATATTATACATAACA
39946029 TACATAATACATAATACACAACTTAATTAATATTATACATAACA
1 TACATAATACATAATACACAACTTAATTAATATTATACATAACA
39946073 TACATAATACA
1 TACATAATACA
39946084 CATAACTTAC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 48 0.87
46 7 0.13
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (44 bp):
TACATAATACATAATACACAACTTAATTAATATTATACATAACA
Found at i:39946425 original size:25 final size:26
Alignment explanation
Indices: 39946395--39946458 Score: 103
Period size: 25 Copynumber: 2.5 Consensus size: 26
39946385 CATAATAACT
39946395 TACATAACTTAATAACTCATA-TATA
1 TACATAACTTAATAACTCATATTATA
* *
39946420 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTCATATTATA
39946446 TACATAACTTAAT
1 TACATAACTTAAT
39946459 CATTGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.39
Consensus pattern (26 bp):
TACATAACTTAATAACTCATATTATA
Found at i:39948198 original size:43 final size:43
Alignment explanation
Indices: 39948142--39948367 Score: 294
Period size: 43 Copynumber: 5.3 Consensus size: 43
39948132 CATCAGACAA
*
39948142 TAGCGGCGTTTGTGAGGGAAGCGCCGCTAAAGAACATGAACTT
1 TAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGAACATGAACTT
* **
39948185 TAGCGGCGTTTGTGAGAAAAGCGCCTTTAAAGAACATG-ACATT
1 TAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGAACATGAAC-TT
* * *
39948228 TAGCGGCGTTTGTGAAAGAGGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGAACATGAACTT
* * * *
39948271 TAGCGGCGTTTGTGAGAGAGGCGCCACTAAAAAACATGACCTT
1 TAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGAACATGAACTT
* **
39948314 TAGCGGCGTTTGTGAGA-AATGCGCCGCTAAAAAACATGTTCTT
1 TAGCGGCGTTTGTGAGAGAA-GCGCCGCTAAAGAACATGAACTT
39948357 TAGCGGCGTTT
1 TAGCGGCGTTT
39948368 ATTTCTATAA
Statistics
Matches: 163, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
42 3 0.02
43 159 0.98
44 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGAACATGAACTT
Found at i:39951360 original size:26 final size:26
Alignment explanation
Indices: 39951331--39951380 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
39951321 TGAGAATAGC
39951331 TTTTAAAAAATACTGTGAAAAAATAA
1 TTTTAAAAAATACTGTGAAAAAATAA
* * *
39951357 TTTTGAAAAATACTTTTAAAAAAT
1 TTTTAAAAAATACTGTGAAAAAAT
39951381 TTAGATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (26 bp):
TTTTAAAAAATACTGTGAAAAAATAA
Found at i:39951365 original size:13 final size:13
Alignment explanation
Indices: 39951331--39951380 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
39951321 TGAGAATAGC
*
39951331 TTTTAAAAAATAC
1 TTTTAAAAAATAA
* *
39951344 TGTGAAAAAATAA
1 TTTTAAAAAATAA
* *
39951357 TTTTGAAAAATAC
1 TTTTAAAAAATAA
39951370 TTTTAAAAAAT
1 TTTTAAAAAAT
39951381 TTAGATTAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (13 bp):
TTTTAAAAAATAA
Found at i:39954408 original size:25 final size:26
Alignment explanation
Indices: 39954348--39954408 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
39954338 TTCATATTGT
39954348 TTCA-TGTTTT-TTTTTTATTTTTAA
1 TTCATTGTTTTATTTTTTATTTTTAA
* ***
39954372 TTAATAAATTTATTTTTTA-TTTTAA
1 TTCATTGTTTTATTTTTTATTTTTAA
39954397 TTCATTGTTTTA
1 TTCATTGTTTTA
39954409 ATTAATAACT
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
24 3 0.11
25 17 0.63
26 7 0.26
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (26 bp):
TTCATTGTTTTATTTTTTATTTTTAA
Found at i:39958251 original size:17 final size:18
Alignment explanation
Indices: 39958225--39958258 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39958215 CTAATGAACA
*
39958225 AATAATCAAT-CAATACC
1 AATAAGCAATACAATACC
39958242 AATAAGCAATACAATAC
1 AATAAGCAATACAATAC
39958259 ACATGAGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (18 bp):
AATAAGCAATACAATACC
Found at i:39959868 original size:12 final size:12
Alignment explanation
Indices: 39959846--39959882 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39959836 ACGTTTATTG
39959846 TTTTTTA-TTAT
1 TTTTTTATTTAT
39959857 TTTTTTATTTAT
1 TTTTTTATTTAT
39959869 TTTATTT-TTTAT
1 TTT-TTTATTTAT
39959881 TT
1 TT
39959883 CAATCAGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 7 0.29
12 14 0.58
13 3 0.12
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:39960306 original size:41 final size:44
Alignment explanation
Indices: 39960205--39960322 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 44
39960195 CTGTAACCCA
*
39960205 TCTTCAATCTGCTCCACTGCAATTTCAAGGAAGTGAGATCTGCTG
1 TCTTCAATCTGCTCCACTGCAACTTCAAGG-AGTGAGATCTGCTG
* * *
39960250 TCTTCAGTCTACTCCATTGCAACTTCAAGG-G-GAGA-CTGCTG
1 TCTTCAATCTGCTCCACTGCAACTTCAAGGAGTGAGATCTGCTG
* * *
39960291 TCTTTAATCCGCTCCACTGCAACTTCAGGGAG
1 TCTTCAATCTGCTCCACTGCAACTTCAAGGAG
39960323 ATAGAATTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 30 0.48
42 5 0.08
43 1 0.02
45 26 0.42
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (44 bp):
TCTTCAATCTGCTCCACTGCAACTTCAAGGAGTGAGATCTGCTG
Found at i:39960401 original size:41 final size:42
Alignment explanation
Indices: 39960301--39960402 Score: 127
Period size: 44 Copynumber: 2.4 Consensus size: 42
39960291 TCTTTAATCC
*
39960301 GCTCCACTGCAACTTCAGGGAGATAGAATTGTAGGATGTAATAT
1 GCTCCACTGCAACTTCAGGGAGATAGAATTGTA-CATG-AATAT
* *
39960345 GCTCCACTGCAACTTCAGGGAGATAAGATTTGT-CATG-ATTT
1 GCTCCACTGCAACTTCAGGGAGAT-AGAATTGTACATGAATAT
*
39960386 GCTCTACTGCAACTTCA
1 GCTCCACTGCAACTTCA
39960403 TAGACATAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
41 19 0.36
43 3 0.06
44 24 0.45
45 7 0.13
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (42 bp):
GCTCCACTGCAACTTCAGGGAGATAGAATTGTACATGAATAT
Found at i:39960538 original size:42 final size:44
Alignment explanation
Indices: 39960447--39960553 Score: 121
Period size: 42 Copynumber: 2.5 Consensus size: 44
39960437 ATTCCACTAA
* * * *
39960447 AACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGT
1 AACTTCAGGGAGATAAGATTC-CTATCTTCAATCCGCTCCACTGC
*
39960492 AACTTCAGGGAGATAAGACTT-C-A-CTTCAATCCGCTCCATTGC
1 AACTTCAGGGAGATAAGA-TTCCTATCTTCAATCCGCTCCACTGC
*
39960534 AACTTCAGGGAGATAGGATT
1 AACTTCAGGGAGATAAGATT
39960554 ATTGGCTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
41 2 0.04
42 32 0.58
43 1 0.02
44 1 0.02
45 17 0.31
46 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (44 bp):
AACTTCAGGGAGATAAGATTCCTATCTTCAATCCGCTCCACTGC
Found at i:39960594 original size:223 final size:225
Alignment explanation
Indices: 39960131--39960781 Score: 631
Period size: 223 Copynumber: 2.9 Consensus size: 225
39960121 ATTTGTCCCG
* * * *
39960131 CTGCAACTTCAGGGAGATAAGATTCACTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATC
1 CTGCAAATTCAGGGAGATAAGATTCGCCATGATCTGCTCTACTGCAACTTCAGAGACATAAGATC
* *** * ** ** * * * *
39960196 TGTAACCCAT--CTTCAATCTGCTCCACTGCAATTTCAAGGAAGTGAGA-TCTGCTGTCTTCAGT
66 TGTGATTTATAACTTTAATCTATTCCACTAAAACTTCAAGGAAATAAGATTC-GCTATCTTCAGT
* * * * * * *
39960258 CTACTCCATTGCAACTTCAAGGG-GA-GACT-GCTGT--CTTTAATCCGCTCCACTGCAACTTCA
130 CTAATCCACTACAACTTC-AGGGAGATAAATCACT-TCACTTCAATCCGCTCCACTGCAACTTCA
* *
39960318 GGGAGATAGAATTGTAGGATGTAATATGCTCCA
193 GGGAGATAGGATTATAGGATGTAATATGCTCCA
* * * * *
39960351 CTGCAACTTCAGGGAGATAAGATTTGTCATGATTTGCTCTACTGCAACTTCATAGACATAAGATC
1 CTGCAAATTCAGGGAGATAAGATTCGCCATGATCTGCTCTACTGCAACTTCAGAGACATAAGATC
* * *
39960416 TGTGATTTGTAACTTTAATTTATTCCACTAAAACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
66 TGTGATTTATAACTTTAATCTATTCCACTAAAACTTCAAGGAAATAAGATTCGCTATCTTCAGTC
** ** * *
39960481 TGCTCCACTGTAACTTCAGGGAGAT-AA-GACTTCACTTCAATCCGCTCCATTGCAACTTCAGGG
131 TAATCCACTACAACTTCAGGGAGATAAATCACTTCACTTCAATCCGCTCCACTGCAACTTCAGGG
* * * * *
39960544 AGATAGGATTATTGGCTTTAATTTG-TTCA
196 AGATAGGATTATAGGATGTAATATGCTCCA
* * * * *
39960573 GGTGTAAATTCAGGGAGATAAGATTCGCCATGATCTGCTCTATTGCAATTTCAGAGAGATAAGAT
1 -CTGCAAATTCAGGGAGATAAGATTCGCCATGATCTGCTCTACTGCAACTTCAGAGACATAAGAT
* * * ** * * *
39960638 TTGTGATTTATAGCTTTAATCTGTTCCACTGCAATTTTAAGGAAATAAGATTCGCTATCTTTAGT
65 CTGTGATTTATAACTTTAATCTATTCCACTAAAACTTCAAGGAAATAAGATTCGCTATCTTCAGT
*
39960703 CTAATCCACTACAACTTCAGGGAGATAAAACTTCACTTCACTTCAATCTGCTCCACTGCAACTTC
130 CTAATCCACTACAACTTCAGGGAGAT-AAA--TCACTTCACTTCAATCCGCTCCACTGCAACTTC
39960768 AGGGAGATAGGATT
192 AGGGAGATAGGATT
39960782 CGCCATGATC
Statistics
Matches: 352, Mismatches: 65, Indels: 20
0.81 0.15 0.05
Matches are distributed among these distances:
220 63 0.18
221 5 0.01
222 61 0.17
223 178 0.51
225 2 0.01
228 43 0.12
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (225 bp):
CTGCAAATTCAGGGAGATAAGATTCGCCATGATCTGCTCTACTGCAACTTCAGAGACATAAGATC
TGTGATTTATAACTTTAATCTATTCCACTAAAACTTCAAGGAAATAAGATTCGCTATCTTCAGTC
TAATCCACTACAACTTCAGGGAGATAAATCACTTCACTTCAATCCGCTCCACTGCAACTTCAGGG
AGATAGGATTATAGGATGTAATATGCTCCA
Found at i:39960782 original size:92 final size:90
Alignment explanation
Indices: 39960653--39961000 Score: 253
Period size: 92 Copynumber: 3.9 Consensus size: 90
39960643 ATTTATAGCT
* * * * *
39960653 TTAATCTGTTCCACTGCAATTTTAAGGAAATAAGATTCGCTATCTTTAGTCTAATCCACTACAAC
1 TTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAATCTACTCCACTACAAC
39960718 TTCAGGGAGATAAAACTTCACTTCAC
66 TTCAGGGAGATAAAACTTCACTT-AC
* * * * * * * * *
39960744 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTCGC---C-ATGATCTGCTCTATTGCAA
1 TT-AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAATCTACTCCACTACAA
* * * *
39960805 CTTCAGAGAGATAAGATCTGTGATTTATAGC
65 CTTCAGGGAGATAA-AACT-TCA-CT-TA-C
* * * * *
39960836 ATTAATCTATTCCACTGCAATTTCAGGGAAATAAGATTCGCTATCTTCAATCTACTCTACTGCAA
1 -TTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAATCTACTCCACTACAA
* *
39960901 TTTCAGGGAGATAAGACTTCAC-T--
65 CTTCAGGGAGATAAAACTTCACTTAC
* * * * ** ** * *
39960924 TTAATCTGATCCATTGCAACTTCAGGGAGATAGGATT-ATTGGCTTTAATCTGCTCCACTATAAC
1 TTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAATCTACTCCACTACAAC
39960988 TTCAGGGAGATAA
66 TTCAGGGAGATAA
39961001 GATTCTCCAT
Statistics
Matches: 196, Mismatches: 50, Indels: 27
0.72 0.18 0.10
Matches are distributed among these distances:
86 30 0.15
87 31 0.16
88 24 0.12
89 4 0.02
90 2 0.01
91 5 0.03
92 67 0.34
93 2 0.01
94 2 0.01
95 3 0.02
96 26 0.13
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (90 bp):
TTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAATCTACTCCACTACAAC
TTCAGGGAGATAAAACTTCACTTAC
Found at i:39960849 original size:407 final size:405
Alignment explanation
Indices: 39960344--39961183 Score: 1220
Period size: 407 Copynumber: 2.1 Consensus size: 405
39960334 GGATGTAATA
* * * * *
39960344 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATGATTTGCTCTACTGCAACTTCATAGACA
1 TGCTCCACTGCAACTTCAGGGAGATAGGATTCGCCATGATCTGCTCTACTGCAACTTCAGAGACA
* * *
39960409 TAAGATCTGTGATTTGTAACTTTAATTTATTCCACTAAAACTTCAGGGAAATAAGATTCGCTATC
66 TAAGATCTGTGATTTATAACATTAATCTATTCCACTAAAACTTCAGGGAAATAAGATTCGCTATC
* * * *
39960474 TTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTCACTTCAATCCGCTCCATTGCAACTT
131 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCCGATCCATTGCAACTT
* * * *
39960539 CAGGGAGATAGGATTATTGGCTTTAATTTG-TTCAGGTGTAAATTCAGGGAGATAAGATTCGCCA
196 CAGGGAGATAGGATTATTGGCTTTAATCTGCTCCA-CTATAAATTCAGGGAGATAAGATTCGCCA
* * * * *
39960603 TGATCTGCTCTATTGCAATTTCAGAGAGATAAGATTTGTGATTTATAGCTTTAATCTGTTCCACT
260 TGATCTACTCTACTACAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCCACT
* * *
39960668 GCAATTTTAAGGAAATAAGATTCGCTATCTTTAGTCTAATCCACTACAACTTCAGGGAGATAAAA
325 GCAATTTCAAAGAAATAAGATTCGCTATCTTCAGTCTAATCCACTACAACTTCAGGGAGATAAAA
*
39960733 CTTCACTTCACTTCAATC
390 CTTCACTTCA-ATCAA-C
* *
39960751 TGCTCCACTGCAACTTCAGGGAGATAGGATTCGCCATGATCTGCTCTATTGCAACTTCAGAGAGA
1 TGCTCCACTGCAACTTCAGGGAGATAGGATTCGCCATGATCTGCTCTACTGCAACTTCAGAGACA
* ** *
39960816 TAAGATCTGTGATTTATAGCATTAATCTATTCCACTGCAATTTCAGGGAAATAAGATTCGCTATC
66 TAAGATCTGTGATTTATAACATTAATCTATTCCACTAAAACTTCAGGGAAATAAGATTCGCTATC
* * * *
39960881 TTCAATCTACTCTACTGCAATTTCAGGGAGATAAGACTTCACTTTAATCTGATCCATTGCAACTT
131 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCCGATCCATTGCAACTT
* *
39960946 CAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTATAACTTCAGGGAGATAAGATTCTCCAT
196 CAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTATAAATTCAGGGAGATAAGATTCGCCAT
*
39961011 GATCTACTCTACTACAACTTCAGAGAGATAATATCTGTGATTTATAGCTTTAATCTGTTCCACTG
261 GATCTACTCTACTACAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCCACTG
* ** * *
39961076 CAATTTCAAAGAAATAAGATTCGGTATCTTCAGTCTGTTCCACTGCAACTTCAGGGAGATAAGAC
326 CAATTTCAAAGAAATAAGATTCGCTATCTTCAGTCTAATCCACTACAACTTCAGGGAGATAAAAC
*
39961141 TTCACTTCAATCCAC
391 TTCACTTCAATCAAC
*
39961156 T-CT--ACTGCAACTTCAGGGATATAGGATT
1 TGCTCCACTGCAACTTCAGGGAGATAGGATT
39961184 ATTGGCTCTA
Statistics
Matches: 387, Mismatches: 45, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
402 24 0.06
404 2 0.01
405 2 0.01
406 3 0.01
407 353 0.91
408 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (405 bp):
TGCTCCACTGCAACTTCAGGGAGATAGGATTCGCCATGATCTGCTCTACTGCAACTTCAGAGACA
TAAGATCTGTGATTTATAACATTAATCTATTCCACTAAAACTTCAGGGAAATAAGATTCGCTATC
TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCCGATCCATTGCAACTT
CAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTATAAATTCAGGGAGATAAGATTCGCCAT
GATCTACTCTACTACAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCCACTG
CAATTTCAAAGAAATAAGATTCGCTATCTTCAGTCTAATCCACTACAACTTCAGGGAGATAAAAC
TTCACTTCAATCAAC
Found at i:39960908 original size:184 final size:179
Alignment explanation
Indices: 39960581--39960960 Score: 571
Period size: 184 Copynumber: 2.1 Consensus size: 179
39960571 CAGGTGTAAA
* * *
39960581 TTCAGGGAGATAAGATTCGCCATGATCTGCTCTATTGCAATTTCAGAGAGATAAGATTTGTGATT
1 TTCAGGGAGATAGGATTCGCCATGATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTGATT
* * * * *
39960646 TATAGCTTTAATCTGTTCCACTGCAATTTTAAGGAAATAAGATTCGCTATCTTTAGTCTAATCCA
66 TATAGCATTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTTCAATCTAATCCA
*
39960711 CTACAACTTCAGGGAGATAAAACTTCACTTCACTTCAATCTGCTCCACTGCAAC
131 CTACAACTTCAGGGAGATAAAACTTCAC-T---TT-AATCTGATCCACTGCAAC
39960765 TTCAGGGAGATAGGATTCGCCATGATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTGATT
1 TTCAGGGAGATAGGATTCGCCATGATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTGATT
* * *
39960830 TATAGCATTAATCTATTCCACTGCAATTTCAGGGAAATAAGATTCGCTATCTTCAATCTACTCTA
66 TATAGCATTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTTCAATCTAATCCA
* * * *
39960895 CTGCAATTTCAGGGAGATAAGACTTCACTTTAATCTGATCCATTGCAAC
131 CTACAACTTCAGGGAGATAAAACTTCACTTTAATCTGATCCACTGCAAC
39960944 TTCAGGGAGATAGGATT
1 TTCAGGGAGATAGGATT
39960961 ATTGGCTTTA
Statistics
Matches: 180, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
179 33 0.18
180 2 0.01
183 1 0.01
184 144 0.80
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (179 bp):
TTCAGGGAGATAGGATTCGCCATGATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTGATT
TATAGCATTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTTCAATCTAATCCA
CTACAACTTCAGGGAGATAAAACTTCACTTTAATCTGATCCACTGCAAC
Found at i:39960948 original size:42 final size:43
Alignment explanation
Indices: 39960837--39961449 Score: 132
Period size: 45 Copynumber: 13.8 Consensus size: 43
39960827 ATTTATAGCA
* * *
39960837 TTAATCT-ATTCCACTGCAATTTCAGGGAAATAAGAT-TCGCTATCT
1 TTAATCTGA-TCCACTGCAACTTCAGGGAGATAAGATAT-TC-A-CT
* * * *
39960882 TCAATCT-ACTCTACTGCAATTTCAGGGAGATAAGA-CTTCACT
1 TTAATCTGA-TCCACTGCAACTTCAGGGAGATAAGATATTCACT
* * **
39960924 TTAATCTGATCCATTGCAACTTCAGGGAGATAGGATTATTGGCT
1 TTAATCTGATCCACTGCAACTTCAGGGAGATAAGA-TATTCACT
* **
39960968 TTAATCTGCTCCACTATAACTTCAGGGAGATAAGAT-TCTC-C-
1 TTAATCTGATCCACTGCAACTTCAGGGAGATAAGATAT-TCACT
* * * * * * *
39961009 ATGATCT-ACTCTACTACAACTTCAGAGAGATAATATCTGTGATTTATAGCT
1 TTAATCTGA-TCCACTGCAACTTCAGGGAGATAAGA----T-A-TT-CA-CT
* * ** *
39961060 TTAATCTGTTCCACTGCAATTTCAAAGAAATAAG--ATTCGGTATCT
1 TTAATCTGATCCACTGCAACTTCAGGGAGATAAGATATTC---A-CT
* * * *
39961105 TCAGTCTGTTCCACTGCAACTTCAGGGAGATAAGA-CTTCACT
1 TTAATCTGATCCACTGCAACTTCAGGGAGATAAGATATTCACT
* * * * * **
39961147 TCAATC-CACTCTACTGCAACTTCAGGGATATAGGATTATTGGCT
1 TTAATCTGA-TCCACTGCAACTTCAGGGAGATAAGA-TATTCACT
* * * * *
39961191 CTAATCTGCTCCATTACAACTTTAGGGAGATAAGAT-TTGC-C-
1 TTAATCTGATCCACTGCAACTTCAGGGAGATAAGATATT-CACT
* * * * * * *
39961232 ATGATCTGTTCTAATGCAACTTCAGAGAGATAAGATTTGTGATTTATAGCT
1 TTAATCTGATCCACTGCAACTTCAGGGAGATAAGA----T-A-TT-CA-CT
* * * *
39961283 TTAATCT-ATTTCATTGCAACTTCAAGGAAATAAGAT-TTGCTATCT
1 TTAATCTGA-TCCACTGCAACTTCAGGGAGATAAGATATT-C-A-CT
* * * * *
39961328 TCAGTCT-ACTCCATTGCAACTTTAGGGAGATAAGA-CTTCACT
1 TTAATCTGA-TCCACTGCAACTTCAGGGAGATAAGATATTCACT
* * * ** **
39961370 TCAATCCGCTCCACTAAAACTTCAGGGAGAT-AGAATTATTGGCT
1 TTAATCTGATCCACTGCAACTTCAGGGAGATAAG-A-TATTCACT
* * *
39961414 TTAATCTGCTCCACTACAACTTTAGGGAGATAAGAT
1 TTAATCTGATCCACTGCAACTTCAGGGAGATAAGAT
39961450 TCGCCATCTT
Statistics
Matches: 415, Mismatches: 108, Indels: 92
0.67 0.18 0.15
Matches are distributed among these distances:
41 56 0.13
42 91 0.22
43 10 0.02
44 99 0.24
45 100 0.24
46 3 0.01
47 2 0.00
48 3 0.01
50 2 0.00
51 49 0.12
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (43 bp):
TTAATCTGATCCACTGCAACTTCAGGGAGATAAGATATTCACT
Found at i:39960994 original size:223 final size:222
Alignment explanation
Indices: 39960706--39961456 Score: 1018
Period size: 223 Copynumber: 3.4 Consensus size: 222
39960696 CTTTAGTCTA
* ** ** * *
39960706 ATCCACTACAACTTCAGGGAGATAAAACTTCACTTCACTTCAATCTGCTCCACTGCAACTTCAGG
1 ATCCACTGCAACTTCAGGGAGATAGGA-TT-A-TTGGCTTTAATCTGCTCCACTACAACTTCAGG
* *
39960771 GAGATAGGATTCGCCATGATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTGATTTATAGC
63 GAGATAAGATTCGCCATGATCTGCTCTAATGCAACTTCAGAGAGATAAGATCTGTGATTTATAGC
* * * *
39960836 ATTAATCTATTCCACTGCAATTTCAGGGAAATAAGATTCGCTATCTTCAATCTACTCTACTGCAA
128 TTTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAA
*
39960901 TTTCAGGGAGATAAGACTTCACTTTAATCTG
193 TTTCAGGGAGATAAGACTTCACTTCAATC-G
* *
39960932 ATCCATTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTATAACTTCAGGGAG
1 ATCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTACAACTTCAGGGAG
* * * * *
39960997 ATAAGATTCTCCATGATCTACTCTACTACAACTTCAGAGAGATAATATCTGTGATTTATAGCTTT
66 ATAAGATTCGCCATGATCTGCTCTAATGCAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTT
* * * ** *
39961062 AATCTGTTCCACTGCAATTTCAAAGAAATAAGATTCGGTATCTTCAGTCTGTTCCACTGCAACTT
131 AATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAATTT
*
39961127 CAGGGAGATAAGACTTCACTTCAATCC
196 CAGGGAGATAAGACTTCACTTCAATCG
* * * * *
39961154 ACTCTACTGCAACTTCAGGGATATAGGATTATTGGCTCTAATCTGCTCCATTACAACTTTAGGGA
1 A-TCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTACAACTTCAGGGA
* * *
39961219 GATAAGATTTGCCATGATCTGTTCTAATGCAACTTCAGAGAGATAAGATTTGTGATTTATAGCTT
65 GATAAGATTCGCCATGATCTGCTCTAATGCAACTTCAGAGAGATAAGATCTGTGATTTATAGCTT
* * * * *
39961284 TAATCTATTTCATTGCAACTTCAAGGAAATAAGATTTGCTATCTTCAGTCTACTCCATTGCAACT
130 TAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAA-T
39961349 TT-AGGGAGATAAGACTTCACTTCAATCCG
194 TTCAGGGAGATAAGACTTCACTTCAAT-CG
* ** * *
39961378 CTCCACTAAAACTTCAGGGAGATAGAATTATTGGCTTTAATCTGCTCCACTACAACTTTAGGGAG
1 ATCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTACAACTTCAGGGAG
39961443 ATAAGATTCGCCAT
66 ATAAGATTCGCCAT
39961457 CTTCTTCAAT
Statistics
Matches: 459, Mismatches: 63, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
222 1 0.00
223 429 0.93
224 4 0.01
225 2 0.00
226 23 0.05
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (222 bp):
ATCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTACAACTTCAGGGAG
ATAAGATTCGCCATGATCTGCTCTAATGCAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTT
AATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAATTT
CAGGGAGATAAGACTTCACTTCAATCG
Found at i:39962744 original size:50 final size:45
Alignment explanation
Indices: 39962679--39962806 Score: 148
Period size: 45 Copynumber: 2.7 Consensus size: 45
39962669 CCCCTTTCGT
* *
39962679 CTCAAGGCGCCCTTTGCGGGTTTTCACCTTGGCCTCTTTTTTTTTTAGGA
1 CTCAAAGCGCCCTTTGCGGGTTTTCACCTTGG-----TTTCTTTTTAGGA
* * *
39962729 CTCAAAGCGCTCTTTGTGAGTTTTCACCTTGGTTTCTTTTTAGGA
1 CTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGTTTCTTTTTAGGA
* *
39962774 CTTAAAGCACCCTTTGCGGGTTTTCACCTTGGT
1 CTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGT
39962807 CCTTTCTCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
45 40 0.59
50 28 0.41
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.41
Consensus pattern (45 bp):
CTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGTTTCTTTTTAGGA
Found at i:39963819 original size:11 final size:11
Alignment explanation
Indices: 39963767--39963819 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
39963757 GGCCTCTCCT
*
39963767 TTTTCTTTTCC
1 TTTTCTTTTCA
*
39963778 TTTTCTTTTCT
1 TTTTCTTTTCA
**
39963789 TTTTC-CATCA
1 TTTTCTTTTCA
39963799 TTTTCATTTTCA
1 TTTTC-TTTTCA
39963811 TTTTCTTTT
1 TTTTCTTTT
39963820 TAAAATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.56
12 8 0.24
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTCTTTTCA
Found at i:39968664 original size:17 final size:18
Alignment explanation
Indices: 39968638--39968671 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39968628 CTAATGAACA
*
39968638 AATAATCAAT-CAATACC
1 AATAAGCAATACAATACC
39968655 AATAAGCAATACAATAC
1 AATAAGCAATACAATAC
39968672 ACATGAGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (18 bp):
AATAAGCAATACAATACC
Found at i:39969184 original size:21 final size:21
Alignment explanation
Indices: 39969146--39969185 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39969136 ATAAGAGTGA
* *
39969146 TAATTAATAATAATAATAAAT
1 TAATTAATAACAAAAATAAAT
*
39969167 TAATTAATAGCAAAAATAA
1 TAATTAATAACAAAAATAA
39969186 CAAACAGGAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
TAATTAATAACAAAAATAAAT
Found at i:39971047 original size:11 final size:12
Alignment explanation
Indices: 39971016--39971066 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 12
39971006 TAGCTTTTGG
39971016 TTTTTCTCTTTAC
1 TTTTTCT-TTTAC
39971029 TTTCTTCTTTTA-
1 TTT-TTCTTTTAC
39971041 TTTTTCTTTT--
1 TTTTTCTTTTAC
*
39971051 TGTTTCTTTTAC
1 TTTTTCTTTTAC
39971063 TTTT
1 TTTT
39971067 GCTACCGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 9 0.27
11 7 0.21
12 6 0.18
13 7 0.21
14 4 0.12
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTTAC
Found at i:39990399 original size:26 final size:27
Alignment explanation
Indices: 39990311--39990398 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
39990301 GGGTATAATA
*
39990311 GTCATTTTACCCTTC-GGAGGTATTTCG
1 GTCATTTTACCTTTCAGGA-GTATTTCG
* * *
39990338 ATCATTTTACCCTTTGAGG-GTATTTCT
1 GTCATTTTA-CCTTTCAGGAGTATTTCG
39990365 GTCATTTTACCTTTCAGGAGTATTTCG
1 GTCATTTTACCTTTCAGGAGTATTTCG
39990392 GTCATTT
1 GTCATTT
39990399 AACAACCTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
26 8 0.16
27 37 0.73
28 4 0.08
29 2 0.04
ACGTcount: A:0.17, C:0.19, G:0.18, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCTTTCAGGAGTATTTCG
Found at i:39999401 original size:72 final size:72
Alignment explanation
Indices: 39999294--39999451 Score: 212
Period size: 72 Copynumber: 2.2 Consensus size: 72
39999284 TTAGCGATGT
*
39999294 TTTTTAA-AAAGCGCTGCAAAAAACCTAAGCCCAACGATGCCGTTTTCTAAGCTTTCAGAGATTT
1 TTTTTAAGAAAGCGCTGCAAAAAAACTAAGCCCAACGATGCCGTTTTCTAAGCTTTCAGAGATTT
39999358 AGCGGCG
66 AGCGGCG
* * * * * *
39999365 TTTTTGAGAAAGCG-TCGCAAAAAAATTAAGCCCAACGATGCCGTTTTGTGAGCTTTCGGGGATT
1 TTTTTAAGAAAGCGCT-GCAAAAAAACTAAGCCCAACGATGCCGTTTTCTAAGCTTTCAGAGATT
* *
39999429 TAGTGGCA
65 TAGCGGCG
39999437 TTTTTAAGAAAGCGC
1 TTTTTAAGAAAGCGC
39999452 CGCTAATGCT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 7 0.09
72 67 0.91
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (72 bp):
TTTTTAAGAAAGCGCTGCAAAAAAACTAAGCCCAACGATGCCGTTTTCTAAGCTTTCAGAGATTT
AGCGGCG
Found at i:39999499 original size:113 final size:114
Alignment explanation
Indices: 39999355--39999568 Score: 306
Period size: 114 Copynumber: 1.9 Consensus size: 114
39999345 CTTTCAGAGA
* * * * * *
39999355 TTTAGCGGCGTTTTTGAGAAAGCGTCGCAAAAAAATTAAGCC-CAACGATGCCGTTTTGTGAGCT
1 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAAACTAAACCAAAACAATGCCGTTTTGTGAGCT
*
39999419 TTCGGGGA-TTTAGTGGCATTTTTAAGAAAGCGCCGCTAATGCTCAAGGC
66 TTCGGGGATTTTA-CGGCATTTTTAAGAAAGCGCCGCTAATGCTCAAGGC
* *
39999468 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAACCAAAATAATGCCGTTTTGTGAGCT
1 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAAACTAAACCAAAACAATGCCGTTTTGTGAGCT
* *
39999533 TTCGGGGATTTTACGGCGTTTTTAAGGAAGCGCCGC
66 TTCGGGGATTTTACGGCATTTTTAAGAAAGCGCCGC
39999569 AAAAAACTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
113 37 0.42
114 47 0.53
115 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (114 bp):
TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAAACTAAACCAAAACAATGCCGTTTTGTGAGCT
TTCGGGGATTTTACGGCATTTTTAAGAAAGCGCCGCTAATGCTCAAGGC
Found at i:39999597 original size:73 final size:74
Alignment explanation
Indices: 39999468--39999627 Score: 225
Period size: 73 Copynumber: 2.2 Consensus size: 74
39999458 TGCTCAAGGC
* * *
39999468 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAACCAAAATAATGCCGTTTTGTGAGCT
1 TTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAACCTAAACCAAAACAACGCCGTTTTGTGAGCT
*
39999533 TTCGGGGAT
66 TTCGGAGAT
* * * * *
39999542 TTTA-CGGCGTTTTTAAGGAAGCGCCGCAAAAAACTTAAGCCAAAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAACCTAAACCAAAACAACGCCGTTTTGTGAGCT
39999606 TTCGGAGA-
66 TTCGGAGAT
39999614 TTTAGCGGCATTTT
1 TTTAGCGGCATTTT
39999628 ATTAAAAACG
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
72 4 0.05
73 67 0.89
74 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (74 bp):
TTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAACCTAAACCAAAACAACGCCGTTTTGTGAGCT
TTCGGAGAT
Found at i:39999643 original size:187 final size:187
Alignment explanation
Indices: 39999292--40000078 Score: 906
Period size: 187 Copynumber: 4.2 Consensus size: 187
39999282 CATTAGCGAT
* * * * * * * * *
39999292 GTTTTTTAAAAAGCGCTGCAAAAAACCTAAGCC-CAACGATGCCGTTTTCTAAGCTTTCAGAGAT
1 GTTTTTGAGAAAGCGCCGCAAAAAACCTAAACCAAAACAATGCCGTTTTGTGAGCTTTCAGGGAT
* * ** * *
39999356 TTAGCGGCGTTTTTGAGAAAGCGTCGCAAAAAAATTAAGCC-CAACGATGCCGTTTTGTGAGCTT
66 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTT
*
39999420 TCGGGGATTTAGTGGCA-TTTTTAAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGC
131 TCGGGGATTTAGCGGCATTTTTTAAGAAA-CGCCGCTAATGCTCAAGGCTTTAGCGGC
* * *
39999477 ATTTTTGAGAAAGCGCCGCAAAAAACCTAAACCAAAATAATGCCGTTTTGTGAGCTTTCGGGGAT
1 GTTTTTGAGAAAGCGCCGCAAAAAACCTAAACCAAAACAATGCCGTTTTGTGAGCTTTCAGGGA-
* *
39999542 TTTA-CGGCGTTTTTAAGGAAGCGCCGCAAAAAACTTAAGCCAAAACGACGCCGTTTTGTGAGCT
65 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
*
39999606 TTCGGAGATTTAGCGGCATTTTATTAA-AAACGCCGCTAATGCTCAAGGCTTTAGCGGC
130 TTCGGGGATTTAGCGGCATTTT-TTAAGAAACGCCGCTAATGCTCAAGGCTTTAGCGGC
* * * *
39999664 TTTTTTGAGAAAGCGCTGCAAAAAACCT-AAGCAAAAAAGATGCCGTTTTGTGAGCTTTCAGGGA
1 GTTTTTGAGAAAGCGCCGCAAAAAACCTAAACCAAAACA-ATGCCGTTTTGTGAGCTTTCAGGGA
* * * * *
39999728 TTTAGCGGCGTTGTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAAAGACGCTGTTTTGTGAGCT
65 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
* * * * *
39999793 TTCGGGGTTTTAGCGGC-GTTTTTAAGTAAGCGCCGCTAATGCTCAAGGATTTAGCGGT
130 TTCGGGGATTTAGCGGCATTTTTTAAG-AAACGCCGCTAATGCTCAAGGCTTTAGCGGC
* * * * ** *
39999851 GTTTTTGAGAAAACGCCGAAAAAAACCTAAGCCAAAACAACGATGTTTTGTGAGCTTTCGGGGAT
1 GTTTTTGAGAAAGCGCCGCAAAAAACCTAAACCAAAACAATGCCGTTTTGTGAGCTTTCAGGGAT
* * * *
39999916 TTAGCGGCGTTTTTATGGAAGCGCCGCTGATACGCTGCAAAAAACCTAAGCCAAAACGATGCCAT
66 TTAGCGGCGTTTTTA-AGAA----AGC-G---C-C-GCAAAAAACCTAAGCCAAAACGACGCCGT
* * * *
39999981 TTTGTGAGCTTTCGGGGTTTTAGCTGCA-TTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAG
120 TTTGTGAGCTTTCGGGGATTTAGCGGCATTTTTTAAGAAA-CGCCGCTAATGCTCAAGGCTTTAG
40000045 CGGC
184 CGGC
40000049 GTTTTTGAGAAAGCGCCGCAAAAAACCTAA
1 GTTTTTGAGAAAGCGCCGCAAAAAACCTAA
40000079 GCGCTTTCGG
Statistics
Matches: 513, Mismatches: 66, Indels: 33
0.84 0.11 0.05
Matches are distributed among these distances:
185 32 0.06
186 71 0.14
187 273 0.53
188 16 0.03
189 4 0.01
192 2 0.00
193 1 0.00
196 1 0.00
197 3 0.01
198 110 0.21
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (187 bp):
GTTTTTGAGAAAGCGCCGCAAAAAACCTAAACCAAAACAATGCCGTTTTGTGAGCTTTCAGGGAT
TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTT
TCGGGGATTTAGCGGCATTTTTTAAGAAACGCCGCTAATGCTCAAGGCTTTAGCGGC
Found at i:39999774 original size:73 final size:73
Alignment explanation
Indices: 39999655--39999826 Score: 245
Period size: 73 Copynumber: 2.4 Consensus size: 73
39999645 TGCTCAAGGC
* ** *
39999655 TTTAGCGGCTTTTTTGAGAAAGCGCTGCAAAAAACCTAAGCAAAAAAGATGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCAAAAAAGACGCCGTTTTGTGAGCT
39999720 TTCAGGGA
66 TTCAGGGA
* * *
39999728 TTTAGCGGCGTTGTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAAAGACGCTGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCAAAAAAGACGCCGTTTTGTGAGCT
* *
39999793 TTCGGGGT
66 TTCAGGGA
* *
39999801 TTTAGCGGCGTTTTTAAGTAAGCGCC
1 TTTAGCGGCGTTTTTGAGAAAGCGCC
39999827 GCTAATGCTC
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 87 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCAAAAAAGACGCCGTTTTGTGAGCT
TTCAGGGA
Found at i:39999925 original size:114 final size:114
Alignment explanation
Indices: 39999725--39999943 Score: 343
Period size: 114 Copynumber: 1.9 Consensus size: 114
39999715 GAGCTTTCAG
* *
39999725 GGATTTAGCGGCGTTGTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAAAGACGCTGTTTTGTGA
1 GGATTTAGCGGCGTTGTTGAGAAAACGCCACAAAAAACCTAAGCCAAAAAGACGATGTTTTGTGA
* *
39999790 GCTTTCGGGGTTTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAA
66 GCTTTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAA
* *
39999839 GGATTTAGCGGTGTTTTTGAGAAAACGCCGA-AAAAAACCTAAGCCAAAACA-ACGATGTTTTGT
1 GGATTTAGCGGCGTTGTTGAGAAAACGCC-ACAAAAAACCTAAGCCAAAA-AGACGATGTTTTGT
*
39999902 GAGCTTTCGGGGATTTAGCGGCGTTTTTATGGAAGCGCCGCT
64 GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCT
39999944 GATACGCTGC
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
114 94 0.98
115 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (114 bp):
GGATTTAGCGGCGTTGTTGAGAAAACGCCACAAAAAACCTAAGCCAAAAAGACGATGTTTTGTGA
GCTTTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAA
Found at i:39999964 original size:84 final size:84
Alignment explanation
Indices: 39999870--40000027 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 84
39999860 AAAACGCCGA
** * *
39999870 AAAAAACCTAAGCCAAAACAACGATGTTTTGTGAGCTTTCGGGGATTTAGCGGCGTTTTT-ATGG
1 AAAAAACCTAAGCCAAAACAACGACATTTTGTGAGCTTTCGGGGATTTAGCGGCATTTTTGA-GA
39999934 AAGCGCCGCTGATACGCTGC
65 AAGCGCCGCTGATACGCTGC
* * * * *
39999954 AAAAAACCTAAGCCAAAACGATGCCATTTTGTGAGCTTTCGGGGTTTTAGCTGCATTTTTGAGAA
1 AAAAAACCTAAGCCAAAACAACGACATTTTGTGAGCTTTCGGGGATTTAGCGGCATTTTTGAGAA
40000019 AGCGCCGCT
66 AGCGCCGCT
40000028 AATGCTCAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 63 0.98
85 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (84 bp):
AAAAAACCTAAGCCAAAACAACGACATTTTGTGAGCTTTCGGGGATTTAGCGGCATTTTTGAGAA
AGCGCCGCTGATACGCTGC
Found at i:40000393 original size:22 final size:21
Alignment explanation
Indices: 40000368--40000415 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
40000358 GTGTTACCAT
*
40000368 TTTAAGGTTTATAGATTATGGG
1 TTTAAGGGTTATAGATTAT-GG
* * *
40000390 TTTAGGGGTTATGGTTTATGG
1 TTTAAGGGTTATAGATTATGG
40000411 TTTAA
1 TTTAA
40000416 AGGCTGGGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (21 bp):
TTTAAGGGTTATAGATTATGG
Found at i:40000482 original size:21 final size:20
Alignment explanation
Indices: 40000457--40000496 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
40000447 CATGTTAAGG
40000457 GTTTATGGTTTTAGGGTTTAT
1 GTTTATGGTTTT-GGGTTTAT
40000478 GTTTATGGTTTTGGGTTTA
1 GTTTATGGTTTTGGGTTTA
40000497 GATTAACTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.12, C:0.00, G:0.30, T:0.57
Consensus pattern (20 bp):
GTTTATGGTTTTGGGTTTAT
Found at i:40000803 original size:21 final size:20
Alignment explanation
Indices: 40000762--40000823 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
40000752 TAGGGATTAT
* *
40000762 GGTTTAAGGGTTGAGATTTAA
1 GGTTTAGGGGTT-AGAGTTAA
40000783 GGTTTAGGGGTTAGTAGTTAA
1 GGTTTAGGGGTTAG-AGTTAA
*
40000804 GGGTTAGGGGTTAAGAGTTA
1 GGTTTAGGGGTT-AGAGTTA
40000824 GGGATTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.06
21 32 0.89
22 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.39, T:0.35
Consensus pattern (20 bp):
GGTTTAGGGGTTAGAGTTAA
Found at i:40001513 original size:16 final size:16
Alignment explanation
Indices: 40001492--40001560 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
40001482 TTTGGTTCGC
40001492 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40001508 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40001524 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
*
40001541 TCTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40001557 TGTA
1 TGTA
40001561 ATATCCACTG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 35 0.70
17 15 0.30
ACGTcount: A:0.25, C:0.01, G:0.36, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40001538 original size:33 final size:32
Alignment explanation
Indices: 40001492--40001560 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
40001482 TTTGGTTCGC
*
40001492 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTCTATTGGATTAGAGG
40001524 TGTATTGGGATTAGAGGTCTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTCTATTGGATTAGAGG
40001557 TGTA
1 TGTA
40001561 ATATCCACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.36, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTCTATTGGATTAGAGG
Found at i:40001808 original size:16 final size:16
Alignment explanation
Indices: 40001771--40001825 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
40001761 TTAATCATAT
*
40001771 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
40001787 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
40001802 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
40001820 -TAAAAT
1 TTAAAAT
40001826 TCTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:40001818 original size:18 final size:18
Alignment explanation
Indices: 40001777--40001825 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
40001767 ATATTTAAAC
40001777 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
40001795 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
40001811 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
40001826 TCTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:40001962 original size:156 final size:156
Alignment explanation
Indices: 40001678--40002005 Score: 611
Period size: 156 Copynumber: 2.1 Consensus size: 156
40001668 TAGAATACCC
* *
40001678 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
*
40001743 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATCTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
40001808 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
40001834 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
*
40001899 TTATCAGTAATAAATATCTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATCTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
40001964 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
*
40001990 TTAGCAGAAATTTGTT
1 TTAGCAGAAAATTGTT
40002006 ATTGTTATTT
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 167 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
TTATCAGTAATAAATATCTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTATAA
Found at i:40001968 original size:18 final size:17
Alignment explanation
Indices: 40001947--40001981 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40001937 TTATTATTAA
*
40001947 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40001965 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40001982 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40008865 original size:43 final size:44
Alignment explanation
Indices: 40008801--40009068 Score: 171
Period size: 43 Copynumber: 6.2 Consensus size: 44
40008791 TCATTCTTTA
* * * *
40008801 TAGCGGCGTTT-TCGG-TAGAAGCGCTGGTAAAGGTCATTACCTT
1 TAGCGGCGTTTGTCGGAT-GAAGCGCTGCTAAAGGCCATGATCTT
* *
40008844 TAGCGGCGTTTGT-GGATGAAGCGCCGCTAAAGGCCACGATCTT
1 TAGCGGCGTTTGTCGGATGAAGCGCTGCTAAAGGCCATGATCTT
* * *
40008887 TAGCTGCGTTTGTGGGA-GAGGCGCTGCTAAAGGCCATGATCTT
1 TAGCGGCGTTTGTCGGATGAAGCGCTGCTAAAGGCCATGATCTT
* * * * * *
40008930 TAGCAGTGTTTGT-GTA-AAAGCGCCGCTAGAGGTCC-TGATCTT
1 TAGCGGCGTTTGTCGGATGAAGCGCTGCTAAAGG-CCATGATCTT
* * ** * *
40008972 TAGCGACGTTTAT-GGAAAAAGCGCCGCTAAAGGTACC--GATCTA
1 TAGCGGCGTTTGTCGGATGAAGCGCTGCTAAAGG--CCATGATCTT
* * * * * *
40009015 TAGCGGTGTTTGTGGGA-GATGCGCCGCTAAAGGTCATGATCTA
1 TAGCGGCGTTTGTCGGATGAAGCGCTGCTAAAGGCCATGATCTT
*
40009058 TAGTGGCGTTT
1 TAGCGGCGTTT
40009069 ATTTCTAAAA
Statistics
Matches: 183, Mismatches: 33, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
42 32 0.17
43 140 0.77
44 10 0.05
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (44 bp):
TAGCGGCGTTTGTCGGATGAAGCGCTGCTAAAGGCCATGATCTT
Found at i:40008896 original size:86 final size:85
Alignment explanation
Indices: 40008801--40009004 Score: 205
Period size: 86 Copynumber: 2.4 Consensus size: 85
40008791 TCATTCTTTA
* * * * * *
40008801 TAGCGGCGTTT-TCGGTAGAAGCGCTGGTAAAGGTCATTACCTTTAGCGGCGTTTGTGGATGAAG
1 TAGCGGCGTTTGT-GGGAGAAGCGCTGCTAAAGGCCATGACCTTTAGCAGCGTTTGTGGA-AAAG
40008865 CGCCGCTAAAGG-CCACGATCTT
64 CGCCGCTAAAGGTCC-CGATCTT
* * * * *
40008887 TAGCTGCGTTTGTGGGAGAGGCGCTGCTAAAGGCCATGATCTTTAGCAGTGTTTGTGTAAAAGCG
1 TAGCGGCGTTTGTGGGAGAAGCGCTGCTAAAGGCCATGACCTTTAGCAGCGTTTGTGGAAAAGCG
* *
40008952 CCGCTAGAGGTCCTGATCTT
66 CCGCTAAAGGTCCCGATCTT
* * * * *
40008972 TAGCGACGTTTATGGAAAAAGCGCCGCTAAAGG
1 TAGCGGCGTTTGTGGGAGAAGCGCTGCTAAAGG
40009005 TACCGATCTA
Statistics
Matches: 96, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
85 46 0.48
86 49 0.51
87 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (85 bp):
TAGCGGCGTTTGTGGGAGAAGCGCTGCTAAAGGCCATGACCTTTAGCAGCGTTTGTGGAAAAGCG
CCGCTAAAGGTCCCGATCTT
Found at i:40009001 original size:85 final size:84
Alignment explanation
Indices: 40008862--40009070 Score: 199
Period size: 85 Copynumber: 2.4 Consensus size: 84
40008852 TTTGTGGATG
* * * * * *
40008862 AAGCGCCGCTAAAGG-CCACGATCTTTAGCTGCGTTTGTGGGAGAGGCGCTGCTAAAGG-CCATG
1 AAGCGCCGCTAAAGGTCC-TGATCTTTAGC-GCGTTTATGGAAAAAGCGCCGCTAAAGGACC--G
* *
40008925 ATCTTTAGCAGTGTTTGT-GTAA
62 ATCTATAGCAGTGTTTGTGGGAA
*
40008947 AAGCGCCGCTAGAGGTCCTGATCTTTAGCGACGTTTATGGAAAAAGCGCCGCTAAAGGTACCGAT
1 AAGCGCCGCTAAAGGTCCTGATCTTTAGCG-CGTTTATGGAAAAAGCGCCGCTAAAGG-ACCGAT
* *
40009012 CTATAGCGGTGTTTGTGGGAG
64 CTATAGCAGTGTTTGTGGGAA
* * * *
40009033 ATGCGCCGCTAAAGGTCATGATCTATAGTGGCGTTTAT
1 AAGCGCCGCTAAAGGTCCTGATCTTTAG-CGCGTTTAT
40009071 TTCTAAAAAC
Statistics
Matches: 102, Mismatches: 16, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
84 1 0.01
85 63 0.62
86 35 0.34
87 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (84 bp):
AAGCGCCGCTAAAGGTCCTGATCTTTAGCGCGTTTATGGAAAAAGCGCCGCTAAAGGACCGATCT
ATAGCAGTGTTTGTGGGAA
Found at i:40017001 original size:16 final size:15
Alignment explanation
Indices: 40016971--40017018 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
40016961 ACCTGAAAAG
*
40016971 AAAATAAAGAAATAA
1 AAAATAAATAAATAA
40016986 AAAATAAATTAAATAA
1 AAAATAAA-TAAATAA
40017002 GAATAA-AAATAAATAA
1 -AA-AATAAATAAATAA
40017018 A
1 A
40017019 CCAAATTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 9 0.31
16 13 0.45
17 5 0.17
18 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAATAA
Found at i:40019888 original size:41 final size:41
Alignment explanation
Indices: 40019843--40019940 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
40019833 TCAGAACACT
* ** **
40019843 GGCATTAAGTCTGCTAGACATAAAGTCTGAAATATTTCGTC
1 GGCATTAAGCCTGCTAGACATAAAGTCCAAAATATTTCACC
*
40019884 GGCATTAAGCCTGCTAGACGTAAAGTCCAAAATATTTCACC
1 GGCATTAAGCCTGCTAGACATAAAGTCCAAAATATTTCACC
40019925 GGCATTAAGCCTGCTA
1 GGCATTAAGCCTGCTA
40019941 AGCACAGAGC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (41 bp):
GGCATTAAGCCTGCTAGACATAAAGTCCAAAATATTTCACC
Found at i:40020335 original size:65 final size:61
Alignment explanation
Indices: 40020152--40020338 Score: 148
Period size: 65 Copynumber: 3.0 Consensus size: 61
40020142 ACATGTATAA
* * * *
40020152 TTATATAT-AA-TTACTAACATTAAGTTCAGCTCAAAGAAACTTGTAGCT-TACATTCGAACCTC
1 TTATATATAAATTTA-TAACATTAAGTTAAACTCAAAG-AA-TTGTA-TTATACATTCGAACCAC
* * * * * **
40020214 TTATATATATATTTCATAACATTACA-TTGAATTCAAAGACATTGCATCATTTATTCGAACCAC
1 TTATATATAAATTT-ATAACATTA-AGTTAAACTCAAAGA-ATTGTATTATACATTCGAACCAC
40020277 ATATATATATACAATTTATAACATTAAGTTAAACTCAAAGAATTTGTATTATACATTCGAAC
1 -T-TATATATA-AATTTATAACATTAAGTTAAACTCAAAGAA-TTGTATTATACATTCGAAC
40020339 ATAATCATAT
Statistics
Matches: 97, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
62 8 0.08
63 17 0.18
64 23 0.24
65 45 0.46
66 4 0.04
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.36
Consensus pattern (61 bp):
TTATATATAAATTTATAACATTAAGTTAAACTCAAAGAATTGTATTATACATTCGAACCAC
Found at i:40028277 original size:41 final size:41
Alignment explanation
Indices: 40028232--40028329 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
40028222 CAGAACACTA
* **
40028232 GCATTAAGTCTGCTAGACATAAAGTCTGAAATATTTCACCG
1 GCATTAAGCCTGCTAGACATAAAGTCCAAAATATTTCACCG
* *
40028273 GCATTAAGCCTGCTAGACGTAAAGTCCAAAATATTTTACCG
1 GCATTAAGCCTGCTAGACATAAAGTCCAAAATATTTCACCG
40028314 GCATTAAGCCTGCTAG
1 GCATTAAGCCTGCTAG
40028330 GCACAGAGCC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (41 bp):
GCATTAAGCCTGCTAGACATAAAGTCCAAAATATTTCACCG
Found at i:40035523 original size:15 final size:15
Alignment explanation
Indices: 40035503--40035533 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40035493 GCTCTATAAA
*
40035503 TATTACAGAACTATT
1 TATTACAGAACAATT
40035518 TATTACAGAACAATT
1 TATTACAGAACAATT
40035533 T
1 T
40035534 CTCTCAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (15 bp):
TATTACAGAACAATT
Found at i:40035605 original size:27 final size:27
Alignment explanation
Indices: 40035542--40035605 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
40035532 TTCTCTCAAT
* * *
40035542 GTTCGTCATATGCACTATTTCTTTAGA
1 GTTCGTCATATGCACCATTCCTTCAGA
* *
40035569 GTTCGCCATATGTACCATTCCTTCAGA
1 GTTCGTCATATGCACCATTCCTTCAGA
*
40035596 GTTCATCATA
1 GTTCGTCATA
40035606 CCATTTAGTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (27 bp):
GTTCGTCATATGCACCATTCCTTCAGA
Found at i:40035802 original size:27 final size:26
Alignment explanation
Indices: 40035772--40035951 Score: 82
Period size: 26 Copynumber: 6.8 Consensus size: 26
40035762 TAGATCACCG
*
40035772 CAAAGGCTTCCATTTCATTAAT-TGCCA
1 CAAAGGCTTACATTTCA--AATATGCCA
* *
40035799 CAAAGCCTTACATTTCAGATATGCCA
1 CAAAGGCTTACATTTCAAATATGCCA
* * **
40035825 CAAAGGCTTTCATTTCAGATACACCA
1 CAAAGGCTTACATTTCAAATATGCCA
* ***
40035851 CAAAGGGTTTTGTTTCATAGAT-TGCCA
1 CAAAGGCTTACATTTCA-A-ATATGCCA
* *
40035878 CAAAGACTT-CTATTTCAAATACGCCA
1 CAAAGGCTTAC-ATTTCAAATATGCCA
* ** *
40035904 TGAAA-GCTTATGTTTCATAGAT-TGCTA
1 -CAAAGGCTTACATTTCA-A-ATATGCCA
* *
40035931 CAAAGGCTTCCATTTCTAATA
1 CAAAGGCTTACATTTCAAATA
40035952 CACTACAAAG
Statistics
Matches: 113, Mismatches: 29, Indels: 23
0.68 0.18 0.14
Matches are distributed among these distances:
25 6 0.05
26 58 0.51
27 45 0.40
28 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.32
Consensus pattern (26 bp):
CAAAGGCTTACATTTCAAATATGCCA
Found at i:40035838 original size:26 final size:26
Alignment explanation
Indices: 40035772--40035882 Score: 91
Period size: 26 Copynumber: 4.2 Consensus size: 26
40035762 TAGATCACCG
* *
40035772 CAAAGGCTTCCATTTCA-TTAATTGCCA
1 CAAAGGCTTTCATTTCAGAT-A-TGCCA
* *
40035799 CAAAGCCTTACATTTCAGATATGCCA
1 CAAAGGCTTTCATTTCAGATATGCCA
**
40035825 CAAAGGCTTTCATTTCAGATACACCA
1 CAAAGGCTTTCATTTCAGATATGCCA
* **
40035851 CAAAGGGTTTTGTTTCATAGAT-TGCCA
1 CAAAGGCTTTCATTTC--AGATATGCCA
40035878 CAAAG
1 CAAAG
40035883 ACTTCTATTT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
26 40 0.58
27 24 0.35
28 5 0.07
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (26 bp):
CAAAGGCTTTCATTTCAGATATGCCA
Found at i:40035877 original size:53 final size:52
Alignment explanation
Indices: 40035815--40035961 Score: 154
Period size: 53 Copynumber: 2.8 Consensus size: 52
40035805 CTTACATTTC
* *
40035815 AGATATGCCACAAAGGCTTTCATTTCAGATACACCACAAAGGGTTTTGTTTCAT
1 AGAT-TGCCACAAAGGCTTTCATTTCA-ATACACCACAAAGGCTTATGTTTCAT
* * *
40035869 AGATTGCCACAAAGAC-TTCTATTTCAAATACGCCATGAAA-GCTTATGTTTCAT
1 AGATTGCCACAAAGGCTTTC-ATTTC-AATACACCA-CAAAGGCTTATGTTTCAT
* * *
40035922 AGATTGCTACAAAGGCTTCCATTTCTAATACACTACAAAG
1 AGATTGCCACAAAGGCTTTCATTTC-AATACACCACAAAG
40035962 ACTTCCATCT
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
52 6 0.08
53 60 0.79
54 10 0.13
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (52 bp):
AGATTGCCACAAAGGCTTTCATTTCAATACACCACAAAGGCTTATGTTTCAT
Found at i:40041622 original size:27 final size:27
Alignment explanation
Indices: 40041589--40041643 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
40041579 TTCTCAAAGA
*
40041589 TAGATCTCAGATCCGGGCATTATCAAT
1 TAGATCTCAAATCCGGGCATTATCAAT
* *
40041616 TAGATCTCAAATCTGGGTATTATCAAT
1 TAGATCTCAAATCCGGGCATTATCAAT
40041643 T
1 T
40041644 GAAAGTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (27 bp):
TAGATCTCAAATCCGGGCATTATCAAT
Done.