Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007909.1 Hibiscus syriacus cultivar Beakdansim tig00110303_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3382237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 17
Found at i:2061003 original size:39 final size:39
Alignment explanation
Indices: 2060954--2061054 Score: 111
Period size: 39 Copynumber: 2.6 Consensus size: 39
2060944 AGGAAAAGGG
*
2060954 GAAAGAAGAAGGGACACCGCAAA-GG-AAAAAAGAAGAGGA
1 GAAAGGAGAAGGGACACCGCAAAGGGAAAAAAAGAA-A-GA
2060993 GAAAGGAGAAGGGACACCG-AAGAGGGAAAAAAAGAAAGA
1 GAAAGGAGAAGGGACACCGCAA-AGGGAAAAAAAGAAAGA
* *
2061032 -AAATGAGGAGGGAACACCGCAAA
1 GAAAGGAGAAGGG-ACACCGCAAA
2061055 AGAGGAGGAC
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
38 12 0.22
39 28 0.52
40 5 0.09
41 9 0.17
ACGTcount: A:0.54, C:0.11, G:0.34, T:0.01
Consensus pattern (39 bp):
GAAAGGAGAAGGGACACCGCAAAGGGAAAAAAAGAAAGA
Found at i:2061570 original size:12 final size:12
Alignment explanation
Indices: 2061550--2061580 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2061540 TAATCTCGGG
*
2061550 TTTGTTTTTTCA
1 TTTGATTTTTCA
2061562 TTTGATTTTTCA
1 TTTGATTTTTCA
2061574 TTTGATT
1 TTTGATT
2061581 ATCAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.06, G:0.10, T:0.71
Consensus pattern (12 bp):
TTTGATTTTTCA
Found at i:2063423 original size:85 final size:85
Alignment explanation
Indices: 2063226--2063414 Score: 247
Period size: 85 Copynumber: 2.2 Consensus size: 85
2063216 AATGACGTGT
** * * * *
2063226 GCTTCAATGACACACAATATAAGTCATACATGCATGTCATAAATTTATGACACACAAATGTATGT
1 GCTTCAATGATGCGCAATGTAAGTCATACATGCATGACATAAATTTATAACACACAAATGTATGT
2063291 CAAGCAGATTTATGACAGGG
66 CAAGCAGATTTATGACAGGG
* * *
2063311 TCTTCAATGATGCTCAATGTAAGTCATACATGCATGACATAAATTTATAACACACAAATGTGTGT
1 GCTTCAATGATGCGCAATGTAAGTCATACATGCATGACATAAATTTATAACACACAAATGTATGT
* *
2063376 C-ATCTTA-ATTTATGACGGGG
66 CAAGC--AGATTTATGACAGGG
2063396 GCTTCAATGATGCGCAATG
1 GCTTCAATGATGCGCAATG
2063415 AGCATCATAA
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
84 2 0.02
85 87 0.97
86 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (85 bp):
GCTTCAATGATGCGCAATGTAAGTCATACATGCATGACATAAATTTATAACACACAAATGTATGT
CAAGCAGATTTATGACAGGG
Found at i:2063437 original size:85 final size:85
Alignment explanation
Indices: 2063226--2063439 Score: 211
Period size: 85 Copynumber: 2.5 Consensus size: 85
2063216 AATGACGTGT
** * * * * *
2063226 GCTTCAATGACACACAATATAAGTCATACATGCATGTCATAAATTTATGACACACAAATGTATGT
1 GCTTCAATGATGCGCAATGTAAGTCATAAATGCACGTCATAAATTTATAACACACAAATGTATGT
2063291 CAAGCAGATTTATGACAGGG
66 CAAGCAGATTTATGACAGGG
* * * * * *
2063311 TCTTCAATGATGCTCAATGTAAGTCATACATGCATGACATAAATTTATAACACACAAATGTGTGT
1 GCTTCAATGATGCGCAATGTAAGTCATAAATGCACGTCATAAATTTATAACACACAAATGTATGT
* *
2063376 C-ATCTTA-ATTTATGACGGGG
66 CAAGC--AGATTTATGACAGGG
**
2063396 GCTTCAATGATGCGCAATG--AGCATCATAAATGTGCGTCATAAAT
1 GCTTCAATGATGCGCAATGTAAG--TCATAAATGCACGTCATAAAT
2063440 GCGTGTCAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
83 2 0.02
84 2 0.02
85 103 0.95
86 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (85 bp):
GCTTCAATGATGCGCAATGTAAGTCATAAATGCACGTCATAAATTTATAACACACAAATGTATGT
CAAGCAGATTTATGACAGGG
Found at i:2069714 original size:19 final size:19
Alignment explanation
Indices: 2069690--2069741 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
2069680 AATAGCATGA
2069690 GTGCATCGATGCATGTCTT
1 GTGCATCGATGCATGTCTT
2069709 GTGCATCGATGCATGTCTT
1 GTGCATCGATGCATGTCTT
2069728 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2069742 CAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (19 bp):
GTGCATCGATGCATGTCTT
Found at i:2069806 original size:84 final size:83
Alignment explanation
Indices: 2069644--2069806 Score: 231
Period size: 84 Copynumber: 2.0 Consensus size: 83
2069634 GTGCACTAAG
* * *
2069644 TGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCATGAGTGCATCGATGCATGTCTT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCACGAGTGCATCGATGCATGTCAT
*
2069709 GTGCATCGATGCATGTCT
66 GTGAATCGATGCATGTCT
* *
2069727 TGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAT-CCCCGAGTGCATCGATGCATGGT
1 TGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATACCACGAGTGCATCGATGCAT-GT
2069791 -ATGTGAATCGATGCAT
63 CATGTGAATCGATGCAT
2069807 AAAATGCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
83 29 0.41
84 36 0.51
85 6 0.08
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (83 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCACGAGTGCATCGATGCATGTCAT
GTGAATCGATGCATGTCT
Found at i:2072104 original size:23 final size:23
Alignment explanation
Indices: 2072073--2072125 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2072063 CGATTCCCTA
*
2072073 AAAGAGGGAACCAGTTCCCATTC
1 AAAGGGGGAACCAGTTCCCATTC
* * *
2072096 AAAGGGGGAATCGGTTCCCCTTC
1 AAAGGGGGAACCAGTTCCCATTC
2072119 -AAGGGGG
1 AAAGGGGG
2072126 TATCGATTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.28, C:0.23, G:0.32, T:0.17
Consensus pattern (23 bp):
AAAGGGGGAACCAGTTCCCATTC
Found at i:2072125 original size:22 final size:23
Alignment explanation
Indices: 2072086--2072136 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
2072076 GAGGGAACCA
2072086 GTTCCCATTCAAAGGGGGAATCG
1 GTTCCCATTCAAAGGGGGAATCG
* *
2072109 GTTCCCCTTC-AAGGGGGTATCG
1 GTTCCCATTCAAAGGGGGAATCG
*
2072131 ATTCCC
1 GTTCCC
2072137 TCTGCACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GTTCCCATTCAAAGGGGGAATCG
Found at i:2077459 original size:64 final size:63
Alignment explanation
Indices: 2077389--2077571 Score: 244
Period size: 65 Copynumber: 2.8 Consensus size: 63
2077379 CGTTGGAACA
* *
2077389 CTTAGTGCATCGGTGCA-GTAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTCA-AAATAG
1 CTTAGTGCATCGATGCATGT-A-TGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAA-AC
2077452 C
63 C
* * *
2077453 CTTAGTGCATTGATGCATGTCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACC
1 CTTAGTGCATCGATGCATGT-ATGTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAACC
*
2077518 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGATGTT
1 CTTAGTGCATCGATGCAT-GTATGTGCATCGATGCATAAAATGCATTCGATGTT
2077572 CAATTTATTC
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
64 46 0.44
65 54 0.51
66 5 0.05
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32
Consensus pattern (63 bp):
CTTAGTGCATCGATGCATGTATGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAACC
Found at i:2077610 original size:65 final size:62
Alignment explanation
Indices: 2077411--2077619 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 62
2077401 GTGCAGTAAG
* * * *
2077411 TGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTTAGTGCATTGATGCATGTCT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTC-AATTAACCTTGGTGCATTGATGCATG-GT
* * * *
2077475 TGTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACCCTGAGTGCATCGATGCATGGT
1 TGTGCATCGATGCATAAAATGCATTCGATG-TTTCAAT-TAACCTTG-GTGCATTGATGCATGGT
* * *
2077539 ATGTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCATTGGTGAATTGATGCATGGA
1 -TGTGCATCGATGCATAAAATGCATTCGATGTTTCAA-TTA-ACCTTGGTGCATTGATGCATGG-
2077603 T
62 T
*
2077604 TGGTGCATCGGTGCAT
1 T-GTGCATCGATGCAT
2077620 TCCTTTGAAA
Statistics
Matches: 120, Mismatches: 16, Indels: 17
0.78 0.10 0.11
Matches are distributed among these distances:
63 4 0.03
64 51 0.43
65 65 0.54
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (62 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTCAATTAACCTTGGTGCATTGATGCATGGT
Found at i:2077901 original size:24 final size:24
Alignment explanation
Indices: 2077874--2077927 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
2077864 ACAAAGCCAA
*
2077874 ACAGAGAAGAAAGTGTGTCAAAAG
1 ACAGAGAAGAAAATGTGTCAAAAG
**
2077898 ACAGAG-AGAAAATGTGTCGGAAG
1 ACAGAGAAGAAAATGTGTCAAAAG
2077921 ACAGAGA
1 ACAGAGA
2077928 CCATTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.09, G:0.31, T:0.11
Consensus pattern (24 bp):
ACAGAGAAGAAAATGTGTCAAAAG
Found at i:2080221 original size:18 final size:19
Alignment explanation
Indices: 2080184--2080221 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2080174 AGACTCTGAT
2080184 CTTGTTATAACTTTACTGC
1 CTTGTTATAACTTTACTGC
2080203 CTTGTT-TAACCTTTA-TGC
1 CTTGTTATAA-CTTTACTGC
2080221 C
1 C
2080222 AATCCAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.18, C:0.24, G:0.11, T:0.47
Consensus pattern (19 bp):
CTTGTTATAACTTTACTGC
Found at i:2083970 original size:37 final size:37
Alignment explanation
Indices: 2083929--2084047 Score: 98
Period size: 38 Copynumber: 3.2 Consensus size: 37
2083919 GTAATTGTAG
2083929 TTCATATATTTTTAATTAAATCTAAAATGTTATTTCA
1 TTCATATATTTTTAATTAAATCTAAAATGTTATTTCA
* * ** ** * * * *
2083966 TTCATAAATAATAAAATTTTGAT-GAAAACGTAATAAT-A
1 TTCATATAT-TTTTAA-TTAAATCTAAAATGTTAT-TTCA
2084004 GTTCATATATTTTTAATTAAATCTAAAATGTTATTTCA
1 -TTCATATATTTTTAATTAAATCTAAAATGTTATTTCA
2084042 TTCATA
1 TTCATA
2084048 AATAATAAAA
Statistics
Matches: 56, Mismatches: 20, Indels: 12
0.64 0.23 0.14
Matches are distributed among these distances:
37 19 0.34
38 24 0.43
39 13 0.23
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (37 bp):
TTCATATATTTTTAATTAAATCTAAAATGTTATTTCA
Found at i:2083999 original size:76 final size:76
Alignment explanation
Indices: 2083904--2084058 Score: 292
Period size: 76 Copynumber: 2.0 Consensus size: 76
2083894 TCGTTTTTGT
**
2083904 AATTTTGATGAAAACGTAATTGTAGTTCATATATTTTTAATTAAATCTAAAATGTTATTTCATTC
1 AATTTTGATGAAAACGTAATAATAGTTCATATATTTTTAATTAAATCTAAAATGTTATTTCATTC
2083969 ATAAATAATAA
66 ATAAATAATAA
2083980 AATTTTGATGAAAACGTAATAATAGTTCATATATTTTTAATTAAATCTAAAATGTTATTTCATTC
1 AATTTTGATGAAAACGTAATAATAGTTCATATATTTTTAATTAAATCTAAAATGTTATTTCATTC
2084045 ATAAATAATAA
66 ATAAATAATAA
2084056 AAT
1 AAT
2084059 AGATCCGATG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (76 bp):
AATTTTGATGAAAACGTAATAATAGTTCATATATTTTTAATTAAATCTAAAATGTTATTTCATTC
ATAAATAATAA
Found at i:2092291 original size:18 final size:18
Alignment explanation
Indices: 2092268--2092327 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
2092258 AATCACCAAG
*
2092268 TACGGATCCACCC-GCAAC
1 TACGGATCC-CCCTACAAC
2092286 TACGGATCCCCCTACAAC
1 TACGGATCCCCCTACAAC
* * *
2092304 TACGGATCCGCCGACAAG
1 TACGGATCCCCCTACAAC
2092322 TACGGA
1 TACGGA
2092328 ACCACCTGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
17 3 0.08
18 34 0.92
ACGTcount: A:0.28, C:0.38, G:0.20, T:0.13
Consensus pattern (18 bp):
TACGGATCCCCCTACAAC
Found at i:2095729 original size:82 final size:82
Alignment explanation
Indices: 2095592--2095756 Score: 330
Period size: 82 Copynumber: 2.0 Consensus size: 82
2095582 TCTTCTCATT
2095592 CTCCCCAAAAGATGAAACTTTAGATGTTTCATTCCTATGTCATGTTAATACTAGAACTACCGTCC
1 CTCCCCAAAAGATGAAACTTTAGATGTTTCATTCCTATGTCATGTTAATACTAGAACTACCGTCC
2095657 TTCAACATCTTTTTAAA
66 TTCAACATCTTTTTAAA
2095674 CTCCCCAAAAGATGAAACTTTAGATGTTTCATTCCTATGTCATGTTAATACTAGAACTACCGTCC
1 CTCCCCAAAAGATGAAACTTTAGATGTTTCATTCCTATGTCATGTTAATACTAGAACTACCGTCC
2095739 TTCAACATCTTTTTAAA
66 TTCAACATCTTTTTAAA
2095756 C
1 C
2095757 CATTCGAGAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.35
Consensus pattern (82 bp):
CTCCCCAAAAGATGAAACTTTAGATGTTTCATTCCTATGTCATGTTAATACTAGAACTACCGTCC
TTCAACATCTTTTTAAA
Found at i:2105307 original size:34 final size:36
Alignment explanation
Indices: 2105230--2105307 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 36
2105220 AAATGATAAT
* *
2105230 AAACAAAA-TTAACCAAAGTATATTAACAAAAAGTC
1 AAACAAAATTTAACCAAAATAAATTAACAAAAAGTC
2105265 AAAC-AAATTTAA-CAAAATAAATTAA-AATAAA-TC
1 AAACAAAATTTAACCAAAATAAATTAACAA-AAAGTC
*
2105298 CAACAAAATT
1 AAACAAAATT
2105308 AATGAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 7 0.19
34 22 0.59
35 8 0.22
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.22
Consensus pattern (36 bp):
AAACAAAATTTAACCAAAATAAATTAACAAAAAGTC
Found at i:2105360 original size:13 final size:14
Alignment explanation
Indices: 2105342--2105371 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2105332 GATAAATAAA
2105342 AAAAAAT-TACAAT
1 AAAAAATATACAAT
2105355 AAAAAATATACAAT
1 AAAAAATATACAAT
2105369 AAA
1 AAA
2105372 TAACTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAAAATATACAAT
Found at i:2105373 original size:18 final size:18
Alignment explanation
Indices: 2105352--2105402 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
2105342 AAAAAATTAC
2105352 AATAAAAAATATAC-AATA
1 AATAAAAAA-ATACAAATA
**
2105370 AATAACTAAATACAAATA
1 AATAAAAAAATACAAATA
*
2105388 TATAAAAAAA-ACAAA
1 AATAAAAAAATACAAA
2105403 ATCTATCGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.20
Consensus pattern (18 bp):
AATAAAAAAATACAAATA
Found at i:2107693 original size:12 final size:12
Alignment explanation
Indices: 2107676--2107711 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
2107666 TTTGATGTTT
2107676 TCTCTTTGATTC
1 TCTCTTTGATTC
2107688 TCTCTTTGATTC
1 TCTCTTTGATTC
2107700 TCTC-TTGATTC
1 TCTCTTTGATTC
2107711 T
1 T
2107712 AGTTGCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (12 bp):
TCTCTTTGATTC
Found at i:2108382 original size:12 final size:12
Alignment explanation
Indices: 2108359--2108388 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2108349 TTTTGAAAAT
2108359 ACTACT-TTAAC
1 ACTACTCTTAAC
2108370 ACTACTCTTAAC
1 ACTACTCTTAAC
2108382 ACTACTC
1 ACTACTC
2108389 CTCTATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (12 bp):
ACTACTCTTAAC
Found at i:2112738 original size:18 final size:18
Alignment explanation
Indices: 2112715--2112756 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
2112705 AATCTTTTGT
2112715 TTCTTCCTTTGATGATGG
1 TTCTTCCTTTGATGATGG
2112733 TTCTTCCTTTGATGATGG
1 TTCTTCCTTTGATGATGG
2112751 TTCTTC
1 TTCTTC
2112757 AACGTCATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (18 bp):
TTCTTCCTTTGATGATGG
Found at i:2114610 original size:22 final size:21
Alignment explanation
Indices: 2114568--2114607 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2114558 GAGTTTATTT
2114568 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
2114589 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2114608 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2116306 original size:12 final size:12
Alignment explanation
Indices: 2116289--2116324 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
2116279 TTTGATGTTT
2116289 TCTCTTTGATTC
1 TCTCTTTGATTC
2116301 TCTCTTTGATTC
1 TCTCTTTGATTC
2116313 TCTC-TTGATTC
1 TCTCTTTGATTC
2116324 T
1 T
2116325 AGTTGCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (12 bp):
TCTCTTTGATTC
Found at i:2117256 original size:17 final size:18
Alignment explanation
Indices: 2117227--2117274 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
2117217 GCAAAAAAAA
*
2117227 TTAATTAAA-TAAAATA-
1 TTAAATAAATTAAAATAC
*
2117243 TTAAA-AAATTTAAATAC
1 TTAAATAAATTAAAATAC
2117260 TTAAATAAATTAAAA
1 TTAAATAAATTAAAA
2117275 ACAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 5 0.19
18 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAATAAATTAAAATAC
Found at i:2118277 original size:35 final size:32
Alignment explanation
Indices: 2118212--2118282 Score: 79
Period size: 35 Copynumber: 2.1 Consensus size: 32
2118202 ATTAAATTTT
* *
2118212 AAATATTTTGAAGTTAAAATAAATATTTTAAA
1 AAATATTTAGAAGTTAAAATAAATAATTTAAA
* *
2118244 AAATAATTTAGAAGGTTAATATGAAATAATTTAAG
1 AAAT-ATTTAGAA-GTTAAAAT-AAATAATTTAAA
2118279 AAAT
1 AAAT
2118283 TAAAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 4 0.12
33 7 0.22
34 7 0.22
35 14 0.44
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (32 bp):
AAATATTTAGAAGTTAAAATAAATAATTTAAA
Found at i:2123211 original size:14 final size:15
Alignment explanation
Indices: 2123176--2123208 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2123166 ATCAACAAAT
2123176 ATAATTTTTTTATAA
1 ATAATTTTTTTATAA
2123191 ATAATTTTTATT-TAA
1 ATAATTTTT-TTATAA
2123206 ATA
1 ATA
2123209 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAATTTTTTTATAA
Found at i:2124636 original size:16 final size:15
Alignment explanation
Indices: 2124615--2124661 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
2124605 TTGTAAATTA
*
2124615 TAAATATAAAATTATT
1 TAAATATAAAA-TAAT
2124631 TAAATATTCAAAA-AAT
1 TAAATA-T-AAAATAAT
2124647 TAAATATAAAATAAT
1 TAAATATAAAATAAT
2124662 AAAAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.15
15 4 0.15
16 14 0.52
17 1 0.04
18 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAATATAAAATAAT
Found at i:2125341 original size:24 final size:24
Alignment explanation
Indices: 2125288--2125342 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
2125278 AATATCTTAT
**
2125288 TTTTAAAATATTTGAATAATTTTA
1 TTTTAAAATATTAAAATAATTTTA
*
2125312 TATTTAAAAT-TTAAAATAATATTTG
1 T-TTTAAAATATTAAAATAAT-TTTA
2125337 TTTTAA
1 TTTTAA
2125343 TTCAATAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTTAAAATATTAAAATAATTTTA
Found at i:2125733 original size:20 final size:20
Alignment explanation
Indices: 2125708--2125936 Score: 184
Period size: 20 Copynumber: 11.2 Consensus size: 20
2125698 AATGACCAAC
*
2125708 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
2125728 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
2125748 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
2125768 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
2125789 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
2125810 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
2125831 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
2125852 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2125872 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2125894 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2125914 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2125932 AAAAT
1 AAAAT
2125937 GAGTAAATTC
Statistics
Matches: 173, Mismatches: 23, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
18 4 0.02
20 126 0.73
21 13 0.08
22 30 0.17
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:2125816 original size:42 final size:42
Alignment explanation
Indices: 2125765--2125936 Score: 212
Period size: 42 Copynumber: 4.2 Consensus size: 42
2125755 CAACGGTCAA
*
2125765 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
* * *
2125807 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
* ***
2125849 CAGAAAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
2125889 CCAAG--AATCGCAACGCG--ATTCCAAGAATCGCAACGCGATT
1 --AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
2125929 AAGAAAAT
1 AAGAAAAT
2125937 GAGTAAATTC
Statistics
Matches: 112, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
38 3 0.03
39 3 0.03
40 44 0.39
41 3 0.03
42 59 0.53
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
Found at i:2125819 original size:62 final size:59
Alignment explanation
Indices: 2125710--2125936 Score: 230
Period size: 62 Copynumber: 3.7 Consensus size: 59
2125700 TGACCAACAA
* * * * *
2125710 AATCGCAACGCGATT-TAGAAAATCGCAACGTTGA-AAAGAAAATCGCAACG-G-TCAAAAG
1 AATCGCAACGCGATTCCA-AGAATCGCAACG-CGATTAAGAAAATCGCAACGCGATC-CAAG
* *
2125768 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAGAGAATCGCAACGCGATCTTCCAA
1 --AATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA---TCCAA
2125833 G
59 G
* *
2125834 AATCGCAATGCGATT-CAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-TCCAAG
2125894 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAAT
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAAT
2125937 GAGTAAATTC
Statistics
Matches: 143, Mismatches: 13, Indels: 22
0.80 0.07 0.12
Matches are distributed among these distances:
60 57 0.40
61 6 0.04
62 62 0.43
63 2 0.01
64 11 0.08
66 3 0.02
67 2 0.01
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (59 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATCCAAG
Found at i:2125920 original size:60 final size:61
Alignment explanation
Indices: 2125770--2125936 Score: 248
Period size: 60 Copynumber: 2.7 Consensus size: 61
2125760 GTCAAAAGAA
* *
2125770 AATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAGAGAATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-CTTCCAAG
* *
2125834 AATCGCAATGCGATT-CAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGA-TTCCAAG
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTAAGAAAATCGCAACGCGACTTCCAAG
2125894 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAAT
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAAT
2125937 GAGTAAATTC
Statistics
Matches: 95, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
60 45 0.47
61 4 0.04
62 35 0.37
64 11 0.12
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (61 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGACTTCCAAG
Found at i:2126043 original size:6 final size:6
Alignment explanation
Indices: 2126032--2126090 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
2126022 GACACGTATT
2126032 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2126078 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
2126091 GGACCCGAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.38
6 33 0.62
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2126095 original size:15 final size:15
Alignment explanation
Indices: 2126036--2126098 Score: 72
Period size: 15 Copynumber: 3.9 Consensus size: 15
2126026 CGTATTACCA
2126036 CGACCACGACCACGACC
1 CGACC-CGACC-CGACC
2126053 ACGACCACGACCACGACC
1 -CGACC-CGACC-CGACC
2126071 CGACCCGACCCGACC
1 CGACCCGACCCGACC
*
2126086 CGACCGGACCCGA
1 CGACCCGACCCGA
2126099 GACGAGACGG
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
15 17 0.39
16 5 0.11
17 5 0.11
18 17 0.39
ACGTcount: A:0.27, C:0.52, G:0.21, T:0.00
Consensus pattern (15 bp):
CGACCCGACCCGACC
Found at i:2126599 original size:6 final size:6
Alignment explanation
Indices: 2126578--2126637 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
2126568 CGCCGTCTCG
2126578 GGTCG- GGTCG- GGTCGT GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2126623 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
2126638 AATACGTGTC
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
5 15 0.28
6 38 0.72
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:2126765 original size:20 final size:20
Alignment explanation
Indices: 2126740--2126878 Score: 174
Period size: 20 Copynumber: 6.8 Consensus size: 20
2126730 CTCATTTTCT
*
2126740 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
2126760 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
2126780 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2126800 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
2126820 GAAGATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTT-G
*
2126842 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2126862 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
2126879 CTTCTTTTCA
Statistics
Matches: 104, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.02
20 66 0.63
21 9 0.09
22 27 0.26
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:2126792 original size:40 final size:40
Alignment explanation
Indices: 2126733--2126940 Score: 176
Period size: 42 Copynumber: 5.1 Consensus size: 40
2126723 GAATTTACTC
*
2126733 ATTTTCTGAATCGCATTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
2126773 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
* * *
2126813 ATTCTT-GGAAGATCGCGTTGCGATT-TTATGAATCGCATTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* **** *
2126855 ATTCTT-GGAAGATCGCGTTGCGA-TCTTCTTTTCAACGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTTGGAATC-GCGTTGCG
* * *
2126897 CTTTTCTAAATCGCGTTGCGGTT-TT-GATATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
2126936 ATTTT
1 ATTTT
2126941 GTTGGTCATT
Statistics
Matches: 140, Mismatches: 19, Indels: 19
0.79 0.11 0.11
Matches are distributed among these distances:
39 11 0.08
40 58 0.41
41 12 0.09
42 59 0.42
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (40 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:2126846 original size:42 final size:42
Alignment explanation
Indices: 2126742--2126878 Score: 192
Period size: 42 Copynumber: 3.3 Consensus size: 42
2126732 CATTTTCTGA
* *
2126742 ATCGCATTGCGATTCTTGGAATCGCGTTGCGATT-TTCTG-A-
1 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTT-GGAAG
2126782 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAAG
* *
2126824 ATCGCGTTGCGATT-TTATGAATCGCATTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTCTTGGAAG
2126866 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
2126879 CTTCTTTTCA
Statistics
Matches: 89, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
40 34 0.38
41 5 0.06
42 50 0.56
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (42 bp):
ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAAG
Found at i:2126846 original size:62 final size:60
Alignment explanation
Indices: 2126740--2126878 Score: 215
Period size: 62 Copynumber: 2.2 Consensus size: 60
2126730 CTCATTTTCT
* * *
2126740 GAATCGCATTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTG
2126800 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTG
2126862 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
2126879 CTTCTTTTCA
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
60 20 0.28
61 1 0.01
62 37 0.51
63 1 0.01
64 13 0.18
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (60 bp):
GAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTG
Found at i:2126894 original size:62 final size:61
Alignment explanation
Indices: 2126740--2126939 Score: 198
Period size: 62 Copynumber: 3.3 Consensus size: 61
2126730 CTCATTTTCT
* *
2126740 GAATCGCATTGCGA-TTCTTGGAA-TCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTCTTGGAAGAC-CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
* *
2126800 GAATCGCGTTGCGA-TTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTTCTTGGAAGA-C-CGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
*** * * *
2126862 GAAGATCGCGTTGCGATCTTCTTTTCA-A-CGTTGCGCTTTTCTAAATCGCGTTGCGGTT-TT-
1 G-A-ATCGCGTTGCGAT-TTCTTGGAAGACCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
2126922 GATATCGCGTTGCGATTT
1 GA-ATCGCGTTGCGATTT
2126940 TGTTGGTCAT
Statistics
Matches: 121, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
58 2 0.02
59 14 0.12
60 23 0.19
61 2 0.02
62 60 0.50
63 1 0.01
64 12 0.10
65 1 0.01
66 6 0.05
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.38
Consensus pattern (61 bp):
GAATCGCGTTGCGATTTCTTGGAAGACCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
Found at i:2126913 original size:20 final size:20
Alignment explanation
Indices: 2126890--2126940 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2126880 TTCTTTTCAA
* *
2126890 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
* *
2126910 CGTTGCGGTTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
2126929 CGTTGCGATTTT
1 CGTTGCGATTTT
2126941 GTTGGTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:2135726 original size:21 final size:22
Alignment explanation
Indices: 2135693--2135734 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2135683 GGTTAAAATA
2135693 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
2135715 AAAAA-AATAATTAAATAAAA
1 AAAAATAAGAATTAAATAAAA
2135735 AAATTAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:2138305 original size:11 final size:10
Alignment explanation
Indices: 2138289--2138341 Score: 61
Period size: 11 Copynumber: 4.9 Consensus size: 10
2138279 AAAGTTCGCT
2138289 AAAAAAATAGA
1 AAAAAAATA-A
2138300 AAAAAAATAA
1 AAAAAAATAA
2138310 AACAAAAATAA
1 AA-AAAAATAA
*
2138321 AAAAAACAAAA
1 AAAAAA-ATAA
2138332 AACAAAAATA
1 AA-AAAAATA
2138342 TAACGAAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 7 0.19
11 26 0.70
12 4 0.11
ACGTcount: A:0.85, C:0.06, G:0.02, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:2138317 original size:22 final size:22
Alignment explanation
Indices: 2138291--2138341 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
2138281 AGTTCGCTAA
*
2138291 AAAAATAGAAAAAAA-ATAAAAC
1 AAAAATA-AAAAAAACAAAAAAC
2138313 AAAAATAAAAAAAACAAAAAAC
1 AAAAATAAAAAAAACAAAAAAC
2138335 AAAAATA
1 AAAAATA
2138342 TAACGAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.84, C:0.06, G:0.02, T:0.08
Consensus pattern (22 bp):
AAAAATAAAAAAAACAAAAAAC
Found at i:2138326 original size:15 final size:15
Alignment explanation
Indices: 2138288--2138332 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2138278 TAAAGTTCGC
*
2138288 TAAAAAAATAGAAAAA
1 TAAAAAAA-ACAAAAA
*
2138304 -AAATAAAACAAAAA
1 TAAAAAAAACAAAAA
2138318 TAAAAAAAACAAAAA
1 TAAAAAAAACAAAAA
2138333 ACAAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.84, C:0.04, G:0.02, T:0.09
Consensus pattern (15 bp):
TAAAAAAAACAAAAA
Found at i:2142195 original size:15 final size:15
Alignment explanation
Indices: 2142175--2142204 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2142165 TTCCTCTTGT
2142175 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
2142190 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
2142205 CCTTTTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.27, G:0.27, T:0.40
Consensus pattern (15 bp):
TCTTCCTGATGTGCG
Found at i:2143885 original size:17 final size:17
Alignment explanation
Indices: 2143865--2143914 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
2143855 AAGATATATT
2143865 AAAATAAAATTAATAAA
1 AAAATAAAATTAATAAA
* * *
2143882 AAAAGAAAAATAATATA
1 AAAATAAAATTAATAAA
*
2143899 ATAATAAATATTAATA
1 AAAATAAA-ATTAATA
2143915 GTAATAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAATAAAATTAATAAA
Found at i:2143978 original size:18 final size:18
Alignment explanation
Indices: 2143957--2144004 Score: 87
Period size: 18 Copynumber: 2.6 Consensus size: 18
2143947 GTTGCGGTTA
2143957 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
2143975 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
2143993 AAATAAACAAAT
1 AAATAAA-AAAT
2144005 TAAAGAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:2144678 original size:19 final size:19
Alignment explanation
Indices: 2144622--2144684 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
2144612 CTATTTAAAC
**
2144622 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
2144642 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
2144662 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
2144681 TAAA
1 TAAA
2144685 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:2152534 original size:22 final size:23
Alignment explanation
Indices: 2152506--2152558 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
2152496 GGACGAAATT
*
2152506 ACTGTAGCAAGGGTATCGGTA-C
1 ACTGTAGCAAGGGTATCGATACC
2152528 ACTGTAGC-AGGGTATCGATACC
1 ACTGTAGCAAGGGTATCGATACC
*
2152550 CCTGTAGCA
1 ACTGTAGCA
2152559 TTCTGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (23 bp):
ACTGTAGCAAGGGTATCGATACC
Found at i:2152626 original size:22 final size:22
Alignment explanation
Indices: 2152598--2152640 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2152588 TCACGAGTAT
* *
2152598 ATTACTGTTTACGATACTGTTC
1 ATTACTGTTCACAATACTGTTC
2152620 ATTACTGTTCACAATACTGTT
1 ATTACTGTTCACAATACTGTT
2152641 TATACCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (22 bp):
ATTACTGTTCACAATACTGTTC
Found at i:2154096 original size:59 final size:59
Alignment explanation
Indices: 2154026--2154143 Score: 173
Period size: 59 Copynumber: 2.0 Consensus size: 59
2154016 GAACATTTCT
* * * **
2154026 CATTTTTATTATTAATCTGAGTTGTCTATTTTTATTCATCCAACAATTTAAAAAAAATA
1 CATTTTCATTATGAATCTGAGTCGTCTATTTTTACCCATCCAACAATTTAAAAAAAATA
* *
2154085 CATTTTCATTATGAATTTGAGTCGTCTATTTTTACCCATTCAACAATTTAAAAAAAATA
1 CATTTTCATTATGAATCTGAGTCGTCTATTTTTACCCATCCAACAATTTAAAAAAAATA
2154144 TAAAAGTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (59 bp):
CATTTTCATTATGAATCTGAGTCGTCTATTTTTACCCATCCAACAATTTAAAAAAAATA
Found at i:2156605 original size:18 final size:18
Alignment explanation
Indices: 2156582--2156616 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2156572 AAATTGTTTG
*
2156582 GATTTTTTTCATATTTAT
1 GATTTTCTTCATATTTAT
*
2156600 GATTTTCTTGATATTTA
1 GATTTTCTTCATATTTA
2156617 GGGTTTAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.09, T:0.63
Consensus pattern (18 bp):
GATTTTCTTCATATTTAT
Found at i:2159926 original size:37 final size:37
Alignment explanation
Indices: 2159884--2159988 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
2159874 CCTTTTCGTC
2159884 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
2159921 TTACTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
2159958 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
2159989 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:2160581 original size:18 final size:18
Alignment explanation
Indices: 2160558--2160668 Score: 67
Period size: 18 Copynumber: 6.2 Consensus size: 18
2160548 TCTTTGCATT
2160558 TTTATTATTATTATTATA
1 TTTATTATTATTATTATA
*
2160576 TTTATTATTATTTTTACTA
1 TTTATTATTATTATTA-TA
*
2160595 TTATATT-TTCCTT-TT-TA
1 TT-TATTATT-ATTATTATA
2160612 TTCTACTTATT-TATATTATA
1 TT-TA-TTATTAT-TATTATA
*
2160632 TATGTA-TATT-TTTTTATA
1 T-T-TATTATTATTATTATA
2160650 -TT-TTATTATTATTATA
1 TTTATTATTATTATTATA
2160666 TTT
1 TTT
2160669 TTTTTACTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 25
0.71 0.06 0.24
Matches are distributed among these distances:
15 5 0.07
16 8 0.11
17 9 0.12
18 24 0.32
19 17 0.23
20 9 0.12
21 3 0.04
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTATTATTATTATTATA
Found at i:2160656 original size:28 final size:27
Alignment explanation
Indices: 2160619--2160672 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
2160609 TTATTCTACT
2160619 TATTTATATTATATATGTATATTTTTTTA
1 TATTTATATTAT-TAT-TATATTTTTTTA
2160648 TATTT-TATTATTATTATATTTTTTT
1 TATTTATATTATTATTATATTTTTTT
2160673 TACTTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 11 0.44
27 3 0.12
28 6 0.24
29 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (27 bp):
TATTTATATTATTATTATATTTTTTTA
Found at i:2160712 original size:12 final size:11
Alignment explanation
Indices: 2160690--2160719 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
2160680 TCTTTCTTTT
2160690 TATTATTCTTG
1 TATTATTCTTG
2160701 TATTATTACTTG
1 TATTATT-CTTG
2160713 TATTATT
1 TATTATT
2160720 TTTAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:2160964 original size:2 final size:2
Alignment explanation
Indices: 2160959--2160987 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2160949 ATTTTACTAT
2160959 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2160988 TCTACACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2165424 original size:16 final size:16
Alignment explanation
Indices: 2165403--2165455 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
2165393 CAATCAGAAC
*
2165403 AAAAAGGGCAAAAACA
1 AAAAAGGACAAAAACA
*
2165419 AAAAA-GAAAAGAAACA
1 AAAAAGGACAA-AAACA
*
2165435 AAAAAGAACAAAAATCA
1 AAAAAGGACAAAAA-CA
2165452 AAAA
1 AAAA
2165456 GAAAAAGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.10
16 18 0.60
17 9 0.30
ACGTcount: A:0.77, C:0.09, G:0.11, T:0.02
Consensus pattern (16 bp):
AAAAAGGACAAAAACA
Found at i:2165471 original size:32 final size:31
Alignment explanation
Indices: 2165400--2165460 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
2165390 ATTCAATCAG
**
2165400 AACAAAAAGGGCAAAAACAAAAAAGAAAAGA
1 AACAAAAAGAACAAAAACAAAAAAGAAAAGA
2165431 AACAAAAAAGAACAAAAATC-AAAAAGAAAA
1 AAC-AAAAAGAACAAAAA-CAAAAAAGAAAA
2165461 AGGGACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 3 0.12
32 22 0.85
33 1 0.04
ACGTcount: A:0.77, C:0.10, G:0.11, T:0.02
Consensus pattern (31 bp):
AACAAAAAGAACAAAAACAAAAAAGAAAAGA
Found at i:2166093 original size:22 final size:22
Alignment explanation
Indices: 2166065--2166119 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2166055 GCTACCCCAT
2166065 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
2166087 CAAACCTTTGAGCATCGAATGC
1 CAAACCTTTGAGCATCAAATGC
2166109 CAAACCTTTGA
1 CAAACCTTTGA
2166120 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:2167141 original size:106 final size:106
Alignment explanation
Indices: 2167013--2167646 Score: 811
Period size: 106 Copynumber: 6.0 Consensus size: 106
2167003 ATATCGTGCC
* *
2167013 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAATAAACAACTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACAAAGGGACCG-CTGGTTGTCAATAAACAACTTCC
*
2167077 CAATTTCAGAGCCAATTTAAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2167119 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2167184 AATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2167225 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2167290 AATTTCAGAGCCAATTTCAACTTCACATCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2167331 ACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
2167396 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
2167437 AC-CCAAGACAACACAAGCTCAACTTCACGACAAAGGGGCGGCTGATTGTCAA-CAA-AA-TT-T
1 ACTCC-AGACAACACAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAATAAACAACTTCC
* *
2167497 C-ATTT-AGAGTCAATTTCAACTTCACAGCGAATGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
2167537 ACTCGAGACAACACAAGTTCAACTCCACAACAAAGGGA-CGACTGGTTGTCAACAAATAATTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACAAAGGGACCG-CTGGTTGTCAATAAACAACTTCC
** * * *
2167601 CGGTTCCATAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
2167643 ACTC
1 ACTC
2167647 AGAACAATGC
Statistics
Matches: 465, Mismatches: 52, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
99 1 0.00
100 72 0.15
101 7 0.02
102 3 0.01
103 4 0.01
104 3 0.01
105 6 0.01
106 367 0.79
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACAACAAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:2168248 original size:37 final size:37
Alignment explanation
Indices: 2168191--2168287 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
2168181 CCTTTTCGTC
*
2168191 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATATGATAGAATT
* * *
2168228 TTGCTATGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATATGATAGAATT
*
2168265 CTACTATGATTTAAACTCCTAAA
1 CTACTATGATTCAAACTCCTAAA
2168288 GATAGGATCC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATATGATAGAATT
Found at i:2168886 original size:24 final size:23
Alignment explanation
Indices: 2168859--2168966 Score: 88
Period size: 22 Copynumber: 4.9 Consensus size: 23
2168849 CTTTGCATTT
2168859 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTA-TA
* *
2168883 TTATTTTTACTATTATATTT-TCC
1 TTATTATTACTATTATATTTAT-A
*
2168906 TT-TTATT-CTACT-TATTTATA
1 TTATTATTACTATTATATTTATA
2168926 TTATATATGTA-TATT-T-TTTATA
1 TTAT-TAT-TACTATTATATTTATA
*
2168948 TT-TTATTATTATTATATTT
1 TTATTATTACTATTATATTT
2168967 TTTTACTTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
19 2 0.03
20 14 0.20
21 8 0.12
22 19 0.28
23 7 0.10
24 19 0.28
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATTATTACTATTATATTTATA
Found at i:2168970 original size:27 final size:28
Alignment explanation
Indices: 2168918--2168969 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
2168908 TTATTCTACT
2168918 TATTTATATTATATATGTATATTTTTTA
1 TATTTATATTATATATGTATATTTTTTA
2168946 TATTT-TATTAT-TAT-TATATTTTTT
1 TATTTATATTATATATGTATATTTTTT
2168970 TACTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TATTTATATTATATATGTATATTTTTTA
Found at i:2169003 original size:11 final size:11
Alignment explanation
Indices: 2168983--2169028 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
2168973 TTTCTCTTTC
2168983 TTTT-TATTAT
1 TTTTGTATTAT
2168993 TTTTGTATTAT
1 TTTTGTATTAT
*
2169004 TACTTGTATTAT
1 T-TTTGTATTAT
*
2169016 TTTTATATTAT
1 TTTTGTATTAT
2169027 TT
1 TT
2169029 ATTTTGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 4 0.13
11 17 0.55
12 10 0.32
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTGTATTAT
Found at i:2169038 original size:23 final size:23
Alignment explanation
Indices: 2168984--2169027 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2168974 TTCTCTTTCT
*
2168984 TTTTATTATTTTTGTATTATTAC
1 TTTTATTATTTTTATATTATTAC
*
2169007 TTGTATTATTTTTATATTATT
1 TTTTATTATTTTTATATTATT
2169028 TATTTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (23 bp):
TTTTATTATTTTTATATTATTAC
Found at i:2169194 original size:23 final size:22
Alignment explanation
Indices: 2169131--2169198 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
2169121 AAGTGTTATA
* *
2169131 TTTTATAATATTATACATATATT
1 TTTTATTATATTATA-TTATATT
*
2169154 TTTCTATTA-ATT-TTTTATATT
1 TTT-TATTATATTATATTATATT
2169175 TTTTATTATCATTATATTATATT
1 TTTTATTAT-ATTATATTATATT
2169198 T
1 T
2169199 ATTTTCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 5 0.14
21 9 0.24
22 4 0.11
23 15 0.41
24 4 0.11
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTATTATATTATATTATATT
Found at i:2169264 original size:2 final size:2
Alignment explanation
Indices: 2169257--2169289 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2169247 TTATTATTAT
2169257 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2169290 TCTACACAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2169457 original size:2 final size:2
Alignment explanation
Indices: 2169445--2169489 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2169435 GTGTTGTTAC
*
2169445 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2169487 TA T
1 TA T
2169490 TGTAATTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2169643 original size:13 final size:12
Alignment explanation
Indices: 2169616--2169686 Score: 65
Period size: 13 Copynumber: 5.9 Consensus size: 12
2169606 TACTTTGTTA
* *
2169616 TTATTATTTTGT
1 TTATTTTTTTAT
2169628 TTATTTGTTTTAT
1 TTATTT-TTTTAT
*
2169641 TTATTTTCTT-T
1 TTATTTTTTTAT
*
2169652 TTCTTTTTTTAT
1 TTATTTTTTTAT
*
2169664 ATATATTTTTTA-
1 TTAT-TTTTTTAT
2169676 TTATTTTTTTA
1 TTATTTTTTTA
2169687 CTTACTATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
11 16 0.33
12 14 0.29
13 18 0.38
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (12 bp):
TTATTTTTTTAT
Found at i:2171744 original size:36 final size:36
Alignment explanation
Indices: 2171702--2171777 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2171692 TTATAGCTAA
*
2171702 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2171738 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2171774 AAAA
1 AAAA
2171778 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2174508 original size:21 final size:20
Alignment explanation
Indices: 2174483--2174524 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
2174473 TAAGTAACTA
2174483 TTTATATA-TTGTTTCTATATT
1 TTTATATACTT-TTTC-ATATT
*
2174504 TTTATTTACTTTTTCATATT
1 TTTATATACTTTTTCATATT
2174524 T
1 T
2174525 ACAGGTGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 11 0.58
22 2 0.11
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTATATACTTTTTCATATT
Found at i:2177888 original size:24 final size:24
Alignment explanation
Indices: 2177856--2177903 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2177846 GAGATTGTAC
* *
2177856 TGAATATAAATTAACGAACATAAA
1 TGAACATAAATGAACGAACATAAA
2177880 TGAACATAAATGAACGAACATAAA
1 TGAACATAAATGAACGAACATAAA
2177904 CGAGAACGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.21
Consensus pattern (24 bp):
TGAACATAAATGAACGAACATAAA
Found at i:2178227 original size:21 final size:20
Alignment explanation
Indices: 2178200--2178250 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2178190 TTAAGATTTA
*
2178200 AGCTTTAGATTTTAGGGTTTG
1 AGCTTTAGA-TTTAGAGTTTG
2178221 AAG-TTTAGGATTTAGAGTTTG
1 -AGCTTTA-GATTTAGAGTTTG
2178242 AGCTTTAGA
1 AGCTTTAGA
2178251 GTAAGGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 18 0.69
22 4 0.15
ACGTcount: A:0.25, C:0.04, G:0.27, T:0.43
Consensus pattern (20 bp):
AGCTTTAGATTTAGAGTTTG
Found at i:2178452 original size:2 final size:2
Alignment explanation
Indices: 2178439--2178479 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2178429 AGTTTTACAT
*
2178439 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2178480 GATCCACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2179438 original size:51 final size:51
Alignment explanation
Indices: 2179343--2179452 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 51
2179333 AGTAAAACGT
* * ** *
2179343 GCCCCCTGCCCCGCGCTATATGTTGATTTGGCGCCACGTGGGGTATAGCAC
1 GCCCCCTGCCCCGCGCTATACGCTGACATGGCGACACGTGGGGTATAGCAC
*
2179394 GCCCCCTGCCCCGCGCTATACGCTGACATGG-GTTACACGT-GGGTATAGCGC
1 GCCCCCTGCCCCGCGCTATACGCTGACATGGCG--ACACGTGGGGTATAGCAC
*
2179445 GGCCCCTG
1 GCCCCCTG
2179453 ATCCGTGCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 1 0.02
51 44 0.88
52 5 0.10
ACGTcount: A:0.14, C:0.35, G:0.30, T:0.21
Consensus pattern (51 bp):
GCCCCCTGCCCCGCGCTATACGCTGACATGGCGACACGTGGGGTATAGCAC
Found at i:2179661 original size:12 final size:10
Alignment explanation
Indices: 2179629--2179653 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2179619 TTCATCACAC
2179629 CAAATTCTCT
1 CAAATTCTCT
2179639 CAAATTCTCT
1 CAAATTCTCT
2179649 CAAAT
1 CAAAT
2179654 ATTCTCTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2179737 original size:17 final size:18
Alignment explanation
Indices: 2179700--2179740 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2179690 ATATTATGTA
*
2179700 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
2179718 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
2179735 TTTACT
1 TTTACT
2179741 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:2181428 original size:18 final size:18
Alignment explanation
Indices: 2181389--2181438 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
2181379 GCCACCTCAG
** *
2181389 CCATTTATGATGCTGCAG
1 CCATTTATGATGCCACAA
2181407 CCATTTATGATGCCACAA
1 CCATTTATGATGCCACAA
*
2181425 CCATATATGATGCC
1 CCATTTATGATGCC
2181439 TCCATCGCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (18 bp):
CCATTTATGATGCCACAA
Found at i:2184996 original size:24 final size:23
Alignment explanation
Indices: 2184925--2184997 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 23
2184915 AATAGTAAGT
* *
2184925 AAAAAATAATAAAATATATATATAA
1 AAAAAAGAAAAAAATA-ATA-ATAA
2184950 AAAAAAGAAAAAGAA-AATAAATAA
1 AAAAAAGAAAAA-AATAAT-AATAA
* *
2184974 AACAAATAAACAAAATAATAATAA
1 AAAAAAGAAA-AAAATAATAATAA
2184998 CAAAGTACGA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 21 0.52
25 17 0.43
26 2 0.05
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (23 bp):
AAAAAAGAAAAAAATAATAATAA
Found at i:2185555 original size:12 final size:11
Alignment explanation
Indices: 2185527--2185567 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2185517 TAACAAAATA
* *
2185527 AATAATATAAA
1 AATAATACAAG
2185538 AATAATACAAG
1 AATAATACAAG
2185549 TAATAATACAAG
1 -AATAATACAAG
2185561 AATAATA
1 AATAATA
2185568 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:2185672 original size:12 final size:12
Alignment explanation
Indices: 2185651--2185696 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2185641 AGAATAAAAG
*
2185651 GTAAATATAATA
1 GTAAAAATAATA
2185663 GTAAAAATAATA
1 GTAAAAATAATA
* *
2185675 ATAAATATAATA
1 GTAAAAATAATA
*
2185687 GTAATAATAA
1 GTAAAAATAA
2185697 AAATGCAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (12 bp):
GTAAAAATAATA
Found at i:2186001 original size:30 final size:28
Alignment explanation
Indices: 2185979--2186033 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
2185969 CGGTGATCGG
2185979 TATATTTACCGATCTAACACCGGTCAGAT
1 TATATTTACCGATCTAACACCGGT-AGAT
* *
2186008 TATATTTCCCGATCTAACACCCGTAG
1 TATATTTACCGATCTAACACCGGTAG
2186034 CAGTAAAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (28 bp):
TATATTTACCGATCTAACACCGGTAGAT
Found at i:2189873 original size:35 final size:34
Alignment explanation
Indices: 2189788--2189874 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2189778 ATTTGGTATT
*
2189788 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
2189822 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
2189860 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2189875 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:2190473 original size:18 final size:18
Alignment explanation
Indices: 2190447--2190504 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
2190437 AAAGGCGATG
*
2190447 GCGGCATCATATATGGTT
1 GCGGCATCATAAATGGTT
*
2190465 GCGGTATCATAAATGGCTT
1 GCGGCATCATAAATGG-TT
*
2190484 -CGGCATCATAAATGGCT
1 GCGGCATCATAAATGGTT
2190501 GCGG
1 GCGG
2190505 TGGCTACTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 1 0.03
18 31 0.91
19 2 0.06
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (18 bp):
GCGGCATCATAAATGGTT
Found at i:2192223 original size:17 final size:18
Alignment explanation
Indices: 2192180--2192220 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2192170 AAAAAATATT
2192180 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
2192197 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
2192215 ATTAAA
1 AGTAAA
2192221 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:2192281 original size:10 final size:10
Alignment explanation
Indices: 2192262--2192292 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2192252 CTTAAACAGA
*
2192262 GAGAGTATTT
1 GAGAGAATTT
2192272 GAGAGAATTT
1 GAGAGAATTT
2192282 GAGAGAATTT
1 GAGAGAATTT
2192292 G
1 G
2192293 GTGTGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:2194752 original size:21 final size:21
Alignment explanation
Indices: 2194726--2194765 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2194716 TGTAGCCCTG
* *
2194726 GTATCAATATTGAGGGTAACA
1 GTATCAATACTGAGAGTAACA
2194747 GTATCAATACTGAGAGTAA
1 GTATCAATACTGAGAGTAA
2194766 ATTTTGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (21 bp):
GTATCAATACTGAGAGTAACA
Found at i:2195159 original size:24 final size:24
Alignment explanation
Indices: 2195127--2195178 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
2195117 CAAGTACTAC
2195127 GTAAACACTTATAATCAAAGACAT
1 GTAAACACTTATAATCAAAGACAT
*
2195151 GTAAACACTTATAATCAAATACAT
1 GTAAACACTTATAATCAAAGACAT
2195175 GTAA
1 GTAA
2195179 GTTTCCCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (24 bp):
GTAAACACTTATAATCAAAGACAT
Found at i:2197283 original size:29 final size:28
Alignment explanation
Indices: 2197247--2197304 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
2197237 CCTAAATTAA
2197247 TTTGTGTCATTGCTTACATCAATTTAGT
1 TTTGTGTCATTGCTTACATCAATTTAGT
**
2197275 TTTGATGTCATTTTTTACATCAATTTAGT
1 TTTG-TGTCATTGCTTACATCAATTTAGT
2197304 T
1 T
2197305 AGGTGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (28 bp):
TTTGTGTCATTGCTTACATCAATTTAGT
Found at i:2201289 original size:2 final size:2
Alignment explanation
Indices: 2201282--2201310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2201272 GTTTGACGAC
2201282 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2201311 TGAAGTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2215530 original size:21 final size:21
Alignment explanation
Indices: 2215492--2215540 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2215482 AGTGTCCAAC
2215492 AATAATAAAATCAATAGAAA-
1 AATAATAAAATCAATAGAAAT
**
2215512 AATTAATAAAATCGGTAGAAAT
1 AA-TAATAAAATCAATAGAAAT
2215534 AATAATA
1 AATAATA
2215541 TTCCAGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.24
Consensus pattern (21 bp):
AATAATAAAATCAATAGAAAT
Found at i:2217451 original size:3 final size:3
Alignment explanation
Indices: 2217443--2217470 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2217433 TTTCTATTTA
2217443 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2217471 ATATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2219107 original size:61 final size:58
Alignment explanation
Indices: 2218954--2219100 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 58
2218944 GTAATTATTG
** * * *
2218954 TTTAGTCCTTTAAATTT-ATGTTTTATTATTTTAGTCCTTTGAGTTTTTGTTTGTGCTAT
1 TTTAGTCCTTT-AATTTCATGTTTT-TTATTTTAGTCCTTCAAGTTTCTATTTGTGATAT
* *
2219013 TTATA-TCCCTTTAGTTTC-TGTGTTTTCTATTTTAGTACCTTCAAGTTTCTATTTTTGATAT
1 TT-TAGT-CCTTTAATTTCATGT-TTTT-TATTTTAGT-CCTTCAAGTTTCTATTTGTGATAT
2219074 TTTAGTCCTTTAATTTCATGTTTTTTA
1 TTTAGTCCTTTAATTTCATGTTTTTTA
2219101 CCTTTTAAGA
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
59 13 0.18
60 35 0.49
61 24 0.33
ACGTcount: A:0.18, C:0.12, G:0.11, T:0.60
Consensus pattern (58 bp):
TTTAGTCCTTTAATTTCATGTTTTTTATTTTAGTCCTTCAAGTTTCTATTTGTGATAT
Found at i:2221225 original size:31 final size:32
Alignment explanation
Indices: 2221190--2221250 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
2221180 TTTTACATGT
*
2221190 ACTAACTTGTTT-TTCTCTTTTGTTTGTGTAC
1 ACTAACTTATTTCTTCTCTTTTGTTTGTGTAC
2221221 ACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 ACTAACTTATTTCTTCTCTTTTGTTTGTGT
2221251 CATTTTGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.59
Consensus pattern (32 bp):
ACTAACTTATTTCTTCTCTTTTGTTTGTGTAC
Found at i:2222010 original size:21 final size:20
Alignment explanation
Indices: 2221965--2222010 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2221955 TTGGGATCAA
*
2221965 CATTTTTGCGTTTGCATTTG
1 CATTTTTGCGTTTGCATATG
*
2221985 CATTTTTGCATTTTGCATATG
1 CATTTTTGC-GTTTGCATATG
*
2222006 TATTT
1 CATTT
2222011 CAATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57
Consensus pattern (20 bp):
CATTTTTGCGTTTGCATATG
Found at i:2222689 original size:20 final size:20
Alignment explanation
Indices: 2222661--2222699 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2222651 ATTCATTCTT
2222661 TTTGAGACCTTGAAACATTC
1 TTTGAGACCTTGAAACATTC
*
2222681 TTTGCGACCTTGAAACATT
1 TTTGAGACCTTGAAACATT
2222700 GCATTTATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
TTTGAGACCTTGAAACATTC
Found at i:2224228 original size:24 final size:23
Alignment explanation
Indices: 2224175--2224231 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
2224165 TGAAAGGGGT
2224175 AATATTTTCAAAATCTTTGATTA
1 AATATTTTCAAAATCTTTGATTA
* *
2224198 AACATTTTTAAAACTCTTTTGA-TA
1 AATATTTTCAAAA-TC-TTTGATTA
*
2224222 GATATTTTCA
1 AATATTTTCA
2224232 GACTTTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 11 0.41
24 11 0.41
25 5 0.19
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (23 bp):
AATATTTTCAAAATCTTTGATTA
Found at i:2224899 original size:38 final size:35
Alignment explanation
Indices: 2224845--2224942 Score: 99
Period size: 35 Copynumber: 2.7 Consensus size: 35
2224835 GTTTCTCTCG
* *
2224845 AAACAAAATGTTGTCTCGCTAT-AGACAACTTCTTTTGAA
1 AAAC-AAATTTTGTCTCGCT-TGAGAC-ACTT-TTCT-AA
* *
2224884 AAACAAATTTTGTCTCACTTGAGACAGTTTTCTAA
1 AAACAAATTTTGTCTCGCTTGAGACACTTTTCTAA
*
2224919 AAACAAATTTTGTCTCGTTTGAGA
1 AAACAAATTTTGTCTCGCTTGAGA
2224943 TAATTTCTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
35 24 0.46
36 3 0.06
37 4 0.08
38 17 0.33
39 4 0.08
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (35 bp):
AAACAAATTTTGTCTCGCTTGAGACACTTTTCTAA
Found at i:2224928 original size:35 final size:35
Alignment explanation
Indices: 2224882--2224985 Score: 109
Period size: 35 Copynumber: 2.9 Consensus size: 35
2224872 ACTTCTTTTG
*
2224882 AAAAACAAATTTTGTCTCACTTGAGACAGTTTTCT
1 AAAAACAAATTTTGTCTCACTTGAGACAATTTTCT
** * *
2224917 AAAAACAAATTTTGTCTCGTTTGAGATAATTTCTTT
1 AAAAACAAATTTTGTCTCACTTGAGACAATTT-TCT
* * ** *
2224953 CAAAATAAATTTCATCTCACTTGAGACATTTTT
1 AAAAACAAATTTTGTCTCACTTGAGACAATTTT
2224986 TTTTCTTTGA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
35 29 0.53
36 26 0.47
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (35 bp):
AAAAACAAATTTTGTCTCACTTGAGACAATTTTCT
Found at i:2226157 original size:129 final size:128
Alignment explanation
Indices: 2225953--2226413 Score: 498
Period size: 129 Copynumber: 3.5 Consensus size: 128
2225943 CCAGTCATCC
* * *
2225953 TCATCACGTAGGAACCGTGTCATCCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATCACCC-GACCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
* *
2226018 CTTAGATAACCAGTCGTCCTCATCAAGTAGAAACCATGTTATCACCTTTAGATGGCTAGAACTCT
65 CTTAGATAACCAGTCGTCCTCATCAAGTAG-AACCGTGTTATCACCTTTAGATGGCAAGAACTCT
* * * * *
2226083 TCATCACGTATGAGCCGTGTCATCACTCGACCAGACCTCCTCATCAAGTAGGAGCCTTGTCACCC
1 TCATCACGTATGAGCCGTGTCATCACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
* * * * *
2226148 CTAGATAACCAGTCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGACCATAACTCT
66 TTAGATAACCAGTCGTCCTCATCAAGTA-GAACCGTGTTATCACCTTTAGATGGCAAGAACTCT
* ** * * *
2226212 TCATCAAGTATGAGGTGTGTCATCA-TCGACCTGATCTCCTCATCACGTGGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATCACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
* * * **
2226276 TTTGATAACCAGAAC-TCTTCATCACA-TATGAGTCGTGTTATCACCTTCGTAAAGATGGCCAAG
66 TTAGATAACCAG-TCGTCCTCATCA-AGTA-GAACCGTGTTATCACCTT--T--AGATGG-CAAG
2226339 AACTCT
123 AACTCT
** * * * * *
2226345 TCATCACGTATGAGTAGTGTCATC-CCCGACCAAATCTCCTCATCATGTAGGAACCGAGTCACCC
1 TCATCACGTATGAGCCGTGTCATCACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
2226409 TTAGA
66 TTAGA
2226414 CGACCCGAAC
Statistics
Matches: 276, Mismatches: 46, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
128 69 0.25
129 112 0.41
130 26 0.09
132 5 0.02
133 64 0.23
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (128 bp):
TCATCACGTATGAGCCGTGTCATCACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
TTAGATAACCAGTCGTCCTCATCAAGTAGAACCGTGTTATCACCTTTAGATGGCAAGAACTCT
Found at i:2226620 original size:3 final size:3
Alignment explanation
Indices: 2226612--2226652 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
2226602 TTTCTATTTA
2226612 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT A
2226653 ATATATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2228219 original size:29 final size:29
Alignment explanation
Indices: 2228129--2228209 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
2228119 GTAATTATTG
2228129 TTTAGTCCTTTAAATTTATGTTTTATTAT
1 TTTAGTCCTTTAAATTTATGTTTTATTAT
2228158 TTTAGTCCTTTAAATTTATGTTTTATTAT
1 TTTAGTCCTTTAAATTTATGTTTTATTAT
* *
2228187 TTTAGTCCTTTGAATTTTTGTTT
1 TTTAGTCCTTTAAATTTATGTTT
2228210 GAGCTATTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (29 bp):
TTTAGTCCTTTAAATTTATGTTTTATTAT
Found at i:2232311 original size:29 final size:29
Alignment explanation
Indices: 2232268--2232379 Score: 84
Period size: 29 Copynumber: 3.8 Consensus size: 29
2232258 TATTGTTTAC
*
2232268 ATTTTAAATTGATCCTTAAACTTTTGAAT
1 ATTTTAAATTCATCCTTAAACTTTTGAAT
* *
2232297 ATTTTAATTTCATCCTTAAA-TTATGAATTTT
1 ATTTTAAATTCATCCTTAAACTTTTGAA---T
* * *
2232328 TTTTCTAAATT-AGTCCTTAAACTTTTAAAC
1 ATTT-TAAATTCA-TCCTTAAACTTTTGAAT
* * *
2232358 ATTCTAATTTCATCCTCAAACT
1 ATTTTAAATTCATCCTTAAACT
2232380 ATGACTCTCA
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
28 6 0.09
29 32 0.50
30 3 0.05
31 5 0.08
32 13 0.20
33 5 0.08
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (29 bp):
ATTTTAAATTCATCCTTAAACTTTTGAAT
Found at i:2232347 original size:61 final size:60
Alignment explanation
Indices: 2232267--2232436 Score: 173
Period size: 61 Copynumber: 2.8 Consensus size: 60
2232257 TTATTGTTTA
* * * * *
2232267 CATTTTAAATTGATCCTTAAACTTTTGAATATTTTAATTTCATCCTTAAATTATGAATTTT
1 CATTCTAAATTGATCCTTAAACTTTTGAATATTTTAATTTCATCCTCAAACTATG-ACTCT
** * * *
2232328 TTTTCTAAATT-AGTCCTTAAACTTTTAAACATTCTAATTTCATCCTCAAACTATGACTCT
1 CATTCTAAATTGA-TCCTTAAACTTTTGAATATTTTAATTTCATCCTCAAACTATGACTCT
* ** * *
2232388 CATTCTAAATTGTTCCCCAAACTTTTGAATCTTTCAATTTCATCC-CAAA
1 CATTCTAAATTGATCCTTAAACTTTTGAATATTTTAATTTCATCCTCAAA
2232437 AGTCATCCAA
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
59 4 0.05
60 38 0.44
61 45 0.52
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (60 bp):
CATTCTAAATTGATCCTTAAACTTTTGAATATTTTAATTTCATCCTCAAACTATGACTCT
Found at i:2233370 original size:2 final size:2
Alignment explanation
Indices: 2233365--2233422 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2233355 TTATTAAAAA
2233365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2233407 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2233423 CATACAAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2234926 original size:2 final size:2
Alignment explanation
Indices: 2234919--2234954 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2234909 TATTTTTAAA
*
2234919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2234955 TTTATAGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2240388 original size:19 final size:19
Alignment explanation
Indices: 2240364--2240436 Score: 74
Period size: 19 Copynumber: 3.6 Consensus size: 19
2240354 ACCTAATTTT
2240364 GGTATCAATACCATATAAG
1 GGTATCAATACCATATAAG
*
2240383 GGTATCAGTACCATAGTATAG
1 GGTATCAATACCATA-TA-AG
*
2240404 TGGTATCAATACCTATGGTAAG
1 -GGTATCAATACC-AT-ATAAG
*
2240426 GGTATCGATAC
1 GGTATCAATAC
2240437 TGGCCACATC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 14 0.31
20 2 0.04
21 12 0.27
22 13 0.29
23 4 0.09
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (19 bp):
GGTATCAATACCATATAAG
Found at i:2240509 original size:22 final size:22
Alignment explanation
Indices: 2240479--2240520 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2240469 CTGGTAGGGG
* *
2240479 GTATTGATATCATAATAGGGTA
1 GTATCGATACCATAATAGGGTA
*
2240501 GTATCGATACCATAGTAGGG
1 GTATCGATACCATAATAGGG
2240521 GTATCAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (22 bp):
GTATCGATACCATAATAGGGTA
Found at i:2241088 original size:45 final size:45
Alignment explanation
Indices: 2241024--2241301 Score: 239
Period size: 45 Copynumber: 6.2 Consensus size: 45
2241014 ATAAAAGAAT
* * *
2241024 AATGCATATGGGTGCATTATTGGCATGAAATG-ATGCCAGAGTTGA
1 AATGCATATGGGTGCATTATT-ACATGAAAAGTATGCTAGAGTTGA
*
2241069 AATGCATATGGGTGCATTATCTACAT-AAAAGTATACTAGAGTTGA
1 AATGCATATGGGTGCATTAT-TACATGAAAAGTATGCTAGAGTTGA
*
2241114 AATGCATATGGGTGCATTATCAACA-GAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTGCATTAT-TACATGAAAAGTATGCTAGAGTTGA
* * * * *
2241159 AATGTATATGGGTACCTTATCAACA-GAAAAGTATACTATG-GTTGA
1 AATGCATATGGGTGCATTAT-TACATGAAAAGTATGCTA-GAGTTGA
* * * * * * *
2241204 GATGTATATGGATACATTATCAACAT-AAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTAT-TACATGAAAAGTATGCTAGAGTTGA
* * * *
2241249 AATGCATATCGGTGCATTATCAACA-GAAAAG-ATGTTAGAGTTTAA
1 AATGCATATGGGTGCATTAT-TACATGAAAAGTATGCTAGAG-TTGA
2241294 AATGCATA
1 AATGCATA
2241302 ATGATGTATT
Statistics
Matches: 202, Mismatches: 23, Indels: 16
0.84 0.10 0.07
Matches are distributed among these distances:
44 10 0.05
45 190 0.94
46 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTACATGAAAAGTATGCTAGAGTTGA
Found at i:2241099 original size:79 final size:79
Alignment explanation
Indices: 2240936--2241081 Score: 238
Period size: 79 Copynumber: 1.8 Consensus size: 79
2240926 AAAACGAATC
* * * * *
2240936 TAAAATAATAATGCATATGGGTGTATTATTGGCATGAAAGGATGTCATAGTTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGTTGAAATGCATATGG
2241001 GTACACAGTCAGCA
66 GTACACAGTCAGCA
*
2241015 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCAGAGTTGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGTTGAAATGCATATGG
2241080 GT
66 GT
2241082 GCATTATCTA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGTTGAAATGCATATGG
GTACACAGTCAGCA
Found at i:2241179 original size:90 final size:90
Alignment explanation
Indices: 2241024--2241301 Score: 319
Period size: 90 Copynumber: 3.1 Consensus size: 90
2241014 ATAAAAGAAT
*** * *
2241024 AATGCATATGGGTGCATTATTGGCATGAAATG-ATGCCAGAGTTGAAATGCATATGGGTGCATTA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTA
* *
2241088 TCTACATAAAAGTATACTAGAGTTGA
65 TCAACAGAAAAGTATACTAGAGTTGA
* * *
2241114 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGGTACCTTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTAT
2241179 CAACAGAAAAGTATACTATG-GTTGA
66 CAACAGAAAAGTATACTA-GAGTTGA
* * * * * * * *
2241204 GATGTATATGGATACATTATCAACATAAAAGTATACTATAGTTGAAATGCATATCGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTAT
** *
2241269 CAACAGAAAAG-ATGTTAGAGTTTAA
66 CAACAGAAAAGTATACTAGAG-TTGA
2241294 AATGCATA
1 AATGCATA
2241302 ATGATGTATT
Statistics
Matches: 158, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
88 1 0.01
89 10 0.06
90 146 0.92
91 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (90 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTAT
CAACAGAAAAGTATACTAGAGTTGA
Found at i:2242506 original size:14 final size:14
Alignment explanation
Indices: 2242487--2242528 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
2242477 ACATACTTAA
2242487 AGTTTATTTTTTAT
1 AGTTTATTTTTTAT
*
2242501 AGTTTAATTGTTTAT
1 AGTTT-ATTTTTTAT
*
2242516 ATTTTATTTTTTA
1 AGTTTATTTTTTA
2242529 GAATTTAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (14 bp):
AGTTTATTTTTTAT
Found at i:2242597 original size:26 final size:26
Alignment explanation
Indices: 2242567--2242621 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
2242557 GTTTAAGTAG
*
2242567 TAAGATTTTAGGATTGAAGATTAAAA
1 TAAGATTTTAGGATTGAAGACTAAAA
* *
2242593 TAAGATTTTAGGATTTAAGGCTAAAA
1 TAAGATTTTAGGATTGAAGACTAAAA
2242619 TAA
1 TAA
2242622 ATATATTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (26 bp):
TAAGATTTTAGGATTGAAGACTAAAA
Found at i:2242998 original size:28 final size:28
Alignment explanation
Indices: 2242958--2243017 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
2242948 AAATAAGAAT
2242958 CTCTGTCATTATGATACGTTTTTCTATG
1 CTCTGTCATTATGATACGTTTTTCTATG
2242986 CTCTGTCATTATGATACGTTTTTCTATG
1 CTCTGTCATTATGATACGTTTTTCTATG
2243014 CTCT
1 CTCT
2243018 TGTGGCACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.50
Consensus pattern (28 bp):
CTCTGTCATTATGATACGTTTTTCTATG
Found at i:2245763 original size:31 final size:32
Alignment explanation
Indices: 2245716--2245777 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
2245706 GATTTTGAAA
* *
2245716 AAAAATTAAAAGTCTAAGTATTAAA-ACGAAT
1 AAAAATTAAAAGTCTAAATACTAAATACGAAT
* *
2245747 AAAAATTAATATTCTAAATACTAAATACGAA
1 AAAAATTAAAAGTCTAAATACTAAATACGAA
2245778 GTTTACCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.27
Consensus pattern (32 bp):
AAAAATTAAAAGTCTAAATACTAAATACGAAT
Found at i:2248885 original size:2 final size:2
Alignment explanation
Indices: 2248878--2248903 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2248868 GAAAACAAGG
2248878 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
2248904 CAAGGAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2250481 original size:18 final size:17
Alignment explanation
Indices: 2250460--2250493 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2250450 AATATTTTTA
*
2250460 ATAT-TTTAAAGAAAAT
1 ATATATTTAAACAAAAT
2250476 ATATATTTAAACAAAAT
1 ATATATTTAAACAAAAT
2250493 A
1 A
2250494 AAAAAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (17 bp):
ATATATTTAAACAAAAT
Done.