Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 20 of 22
Found at i:9732685 original size:22 final size:22
Alignment explanation
Indices: 9732644--9732709 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
9732634 ACGCATTTAC
** *
9732644 TACAAACAAGTCACACAATGTA
1 TACAAACAAGTCATGCAATGCA
* *
9732666 TACAAACAAGTCATGTAATGCC
1 TACAAACAAGTCATGCAATGCA
9732688 TACAAACAAGTCATGCAATGCA
1 TACAAACAAGTCATGCAATGCA
9732710 CAACTCATGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.45, C:0.23, G:0.12, T:0.20
Consensus pattern (22 bp):
TACAAACAAGTCATGCAATGCA
Found at i:9733105 original size:38 final size:38
Alignment explanation
Indices: 9733063--9733153 Score: 128
Period size: 38 Copynumber: 2.4 Consensus size: 38
9733053 TCGATGGCAG
*
9733063 TGGAGAGCTAGATGGCGAGATATATATCCTGATGGTGT
1 TGGAGAGCTAGATGACGAGATATATATCCTGATGGTGT
* * * *
9733101 TGGAGAGTTAGACGATGAGATATGTATCCTGATGGTGT
1 TGGAGAGCTAGATGACGAGATATATATCCTGATGGTGT
*
9733139 TGAAGAGCTAGATGA
1 TGGAGAGCTAGATGA
9733154 AGGGATAGCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (38 bp):
TGGAGAGCTAGATGACGAGATATATATCCTGATGGTGT
Found at i:9744287 original size:28 final size:28
Alignment explanation
Indices: 9744243--9744556 Score: 319
Period size: 29 Copynumber: 11.0 Consensus size: 28
9744233 AACATATATA
*
9744243 TTTT-TTGTTTAAATTAAGACAAACATG
1 TTTTCTTGTCTAAATTAAGACAAACATG
* ** * *
9744270 TTTTCTTGTGTAGGTTAACACAAAACATAT
1 TTTTCTTGTCTAAATTAAGAC-AAACAT-G
* * *
9744300 TTTTCTTATCTAAATTAGGAAAAACATG
1 TTTTCTTGTCTAAATTAAGACAAACATG
* *
9744328 TTTTCTT-ACTTAAATTAAGACAAACATA
1 TTTTCTTGTC-TAAATTAAGACAAACATG
*
9744356 TTTT-TGTGTCCAAATTAAGACAAAACATG
1 TTTTCT-TGTCTAAATTAAGAC-AAACATG
* * * *
9744385 TTTTATTGTCTAAATGAAAACAAACATT
1 TTTTCTTGTCTAAATTAAGACAAACATG
* *
9744413 TTTTCTTGTCTAAACTAAAACAAAACATG
1 TTTTCTTGTCTAAATTAAGAC-AAACATG
*
9744442 TTTTCTTGTCGAAATTAAGACAAACATG
1 TTTTCTTGTCTAAATTAAGACAAACATG
* *
9744470 TCTTCTTGTCTAAGTTAAGACAAAACATG
1 TTTTCTTGTCTAAATTAAGAC-AAACATG
9744499 TTTTCTTGTCTAAATTAAGACACAACATG
1 TTTTCTTGTCTAAATTAAGACA-AACATG
* * *
9744528 TTTTTTTATCTAAATTAGGACAAACATG
1 TTTTCTTGTCTAAATTAAGACAAACATG
9744556 T
1 T
9744557 AAAAGTTACC
Statistics
Matches: 237, Mismatches: 39, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
27 6 0.03
28 106 0.45
29 110 0.46
30 15 0.06
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (28 bp):
TTTTCTTGTCTAAATTAAGACAAACATG
Found at i:9744379 original size:86 final size:83
Alignment explanation
Indices: 9744243--9744556 Score: 289
Period size: 86 Copynumber: 3.7 Consensus size: 83
9744233 AACATATATA
* ** * *
9744243 TTTT-TTGTTTAAATTAAGACAAACATGTTTTCTTGTGT-AGGTTAACACAAAACATATTTTTCT
1 TTTTCTTGTCTAAATTAAGACAAACATG-TTT-TTGTGTCAAATTAAGACAAAACAT-GTTTTCT
*
9744306 TATCTAAATTAGGAAAAACATG
63 TGTCTAAATTA-GAAAAACATG
* * *
9744328 TTTTCTT-ACTTAAATTAAGACAAACATATTTTTGTGTCCAAATTAAGACAAAACATGTTTTATT
1 TTTTCTTGTC-TAAATTAAGACAAACATGTTTTTGTGT-CAAATTAAGACAAAACATGTTTTCTT
* * *
9744392 GTCTAAATGAAAACAAACATT
64 GTCTAAATTAGAA-AAACATG
* * *
9744413 TTTTCTTGTCTAAACTAAAACAAAACATGTTTTCT-TGTCGAAATTAAGAC-AAACATGTCTTCT
1 TTTTCTTGTCTAAATTAAGAC-AAACATGTTTT-TGTGTC-AAATTAAGACAAAACATGTTTTCT
*
9744476 TGTCTAAGTTAAGACAAAACATG
63 TGTCTAAATT-AGA-AAAACATG
* * *
9744499 TTTTCTTGTCTAAATTAAGACACAACATGTTTTTTTATCTAAATTAGGAC-AAACATGT
1 TTTTCTTGTCTAAATTAAGACA-AACATGTTTTTGTGTC-AAATTAAGACAAAACATGT
9744557 AAAAGTTACC
Statistics
Matches: 189, Mismatches: 27, Indels: 25
0.78 0.11 0.10
Matches are distributed among these distances:
84 8 0.04
85 65 0.34
86 114 0.60
87 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (83 bp):
TTTTCTTGTCTAAATTAAGACAAACATGTTTTTGTGTCAAATTAAGACAAAACATGTTTTCTTGT
CTAAATTAGAAAAACATG
Found at i:9744382 original size:57 final size:57
Alignment explanation
Indices: 9744199--9744556 Score: 343
Period size: 57 Copynumber: 6.2 Consensus size: 57
9744189 TCTGATATTG
* * * *
9744199 AGACAACA-ATGTTTTTTTGTTTAGAA-TAAGACAAAACATATATATTTTTTGTTTAAATTA
1 AGACAAAACATGTTTTCTTGTCTA-AATTAAGAC-AAAC--ATAT-TTTTTTGTCTAAATTA
* ** * *
9744259 AGAC-AAACATGTTTTCTTGTGTAGGTTAACACAAAACATATTTTTCTTATCTAAATTA
1 AGACAAAACATGTTTTCTTGTCTAAATTAAGAC-AAACATATTTTT-TTGTCTAAATTA
* * * *
9744317 GGA-AAAACATGTTTTCTT-ACTTAAATTAAGACAAACATATTTTTGTGTCCAAATTA
1 AGACAAAACATGTTTTCTTGTC-TAAATTAAGACAAACATATTTTTTTGTCTAAATTA
* * * *
9744373 AGACAAAACATGTTTTATTGTCTAAATGAAAACAAACAT-TTTTTCTTGTCTAAACTA
1 AGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATATTTTT-TTGTCTAAATTA
* * * * * *
9744430 AAACAAAACATGTTTTCTTGTCGAAATTAAGACAAACATGTCTTCTTGTCTAAGTTA
1 AGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATATTTTTTTGTCTAAATTA
* *
9744487 AGACAAAACATGTTTTCTTGTCTAAATTAAGACACAACATGTTTTTTTATCTAAATTA
1 AGACAAAACATGTTTTCTTGTCTAAATTAAGACA-AACATATTTTTTTGTCTAAATTA
*
9744545 GGAC-AAACATGT
1 AGACAAAACATGT
9744557 AAAAGTTACC
Statistics
Matches: 247, Mismatches: 41, Indels: 23
0.79 0.13 0.07
Matches are distributed among these distances:
56 16 0.06
57 138 0.56
58 64 0.26
59 2 0.01
60 27 0.11
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.38
Consensus pattern (57 bp):
AGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATATTTTTTTGTCTAAATTA
Found at i:9746576 original size:18 final size:18
Alignment explanation
Indices: 9746553--9746590 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
9746543 AGCTTGTATG
9746553 TTCATTGGTCCACACACA
1 TTCATTGGTCCACACACA
9746571 TTCATTGGTCCACACACA
1 TTCATTGGTCCACACACA
9746589 TT
1 TT
9746591 TGTGTGCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (18 bp):
TTCATTGGTCCACACACA
Found at i:9748969 original size:30 final size:30
Alignment explanation
Indices: 9748935--9749166 Score: 182
Period size: 30 Copynumber: 7.8 Consensus size: 30
9748925 AATGTTGTAG
*
9748935 AGGTTATGCTTAAGCCTTTAAAACGTAGTA
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTA
* *** * * * **
9748965 AGGTTATACTTGTTCC-TTGAAAGGAAAAA
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTA
* * *
9748994 AGGTTATTCTTAAGCCTTTAAATAGTAATA
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTA
* * * * * *
9749024 AGGTTATGCTTGATCCTTGAAAGA-CAGAA
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTA
* *
9749053 AGGTTATGCTTAAGCCTCTAAAAAGTAGTG
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTA
* *
9749083 AGGTTATGCTTAAGCCTTTCAAATGTAGTA
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTA
** * *
9749113 AGGTTACACTTGATCCTTTAAAAAGTAGTA
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTA
* *
9749143 AAGTTATGCTTAATCC-TTAAAAAG
1 AGGTTATGCTTAAGCCTTTAAAAAG
9749167 GCAAGGATTA
Statistics
Matches: 152, Mismatches: 48, Indels: 5
0.74 0.23 0.02
Matches are distributed among these distances:
29 49 0.32
30 103 0.68
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (30 bp):
AGGTTATGCTTAAGCCTTTAAAAAGTAGTA
Found at i:9749011 original size:29 final size:28
Alignment explanation
Indices: 9748979--9749069 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
9748969 TATACTTGTT
*
9748979 CCTTGAAAGGAAAAAAGGTTATTCTTAAG
1 CCTTGAAA-GAAAAAAGGTTATGCTTAAG
* * * * *
9749008 CCTTTAAATAGTAATAAGGTTATGCTTGAT
1 CC-TTGAA-AGAAAAAAGGTTATGCTTAAG
*
9749038 CCTTGAAAGACAGAAAGGTTATGCTTAAG
1 CCTTGAAAGA-AAAAAGGTTATGCTTAAG
9749067 CCT
1 CCT
9749070 CTAAAAAGTA
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
28 2 0.04
29 23 0.49
30 21 0.45
31 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (28 bp):
CCTTGAAAGAAAAAAGGTTATGCTTAAG
Found at i:9749090 original size:59 final size:59
Alignment explanation
Indices: 9748935--9749160 Score: 229
Period size: 59 Copynumber: 3.8 Consensus size: 59
9748925 AATGTTGTAG
* * *
9748935 AGGTTATGCTTAAGCCTTTAAAACGTAGTAAGGTTATACTTGTTCCTTGAAAGGAAAAA
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTAAGGTTATGCTTGATCCTTGAAAGGAAAAA
* * * *
9748994 AGGTTATTCTTAAGCCTTTAAATAGTAATAAGGTTATGCTTGATCCTTGAAA-GACAGAA
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTAAGGTTATGCTTGATCCTTGAAAGGA-AAAA
* * * * * * * **
9749053 AGGTTATGCTTAAGCCTCTAAAAAGTAGTGAGGTTATGCTTAAGCCTTTCAAATGTAGTA
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTAAGGTTATGCTTGATCC-TTGAAAGGAAAAA
** * * * *
9749113 AGGTTACACTTGATCCTTTAAAAAGTAGTAAAGTTATGCTTAATCCTT
1 AGGTTATGCTTAAGCCTTTAAAAAGTAGTAAGGTTATGCTTGATCCTT
9749161 AAAAAGGCAA
Statistics
Matches: 139, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
58 2 0.01
59 90 0.65
60 46 0.33
61 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (59 bp):
AGGTTATGCTTAAGCCTTTAAAAAGTAGTAAGGTTATGCTTGATCCTTGAAAGGAAAAA
Found at i:9749095 original size:89 final size:89
Alignment explanation
Indices: 9748994--9749166 Score: 226
Period size: 89 Copynumber: 1.9 Consensus size: 89
9748984 AAAGGAAAAA
* ** *
9748994 AGGTTATTCTTAAGCCTTT-AAATAGTAATAAGGTTATGCTTGATCCTTGAAAGA-CAG-AAAGG
1 AGGTTATGCTTAAGCCTTTCAAAT-GTAATAAGGTTACACTTGATCCTTGAAAAAGCAGTAAA-G
9749056 TTATGCTTAAGCCTCTAAAAAGTAGTG
64 TTATGCTTAAGCCT-TAAAAAGTAGTG
* * *
9749083 AGGTTATGCTTAAGCCTTTCAAATGTAGTAAGGTTACACTTGATCCTTTAAAAAGTAGTAAAGTT
1 AGGTTATGCTTAAGCCTTTCAAATGTAATAAGGTTACACTTGATCCTTGAAAAAGCAGTAAAGTT
*
9749148 ATGCTTAATCCTTAAAAAG
66 ATGCTTAAGCCTTAAAAAG
9749167 GCAAGGATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
89 50 0.68
90 20 0.27
91 3 0.04
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (89 bp):
AGGTTATGCTTAAGCCTTTCAAATGTAATAAGGTTACACTTGATCCTTGAAAAAGCAGTAAAGTT
ATGCTTAAGCCTTAAAAAGTAGTG
Found at i:9750364 original size:244 final size:245
Alignment explanation
Indices: 9749928--9750400 Score: 626
Period size: 244 Copynumber: 1.9 Consensus size: 245
9749918 AAGTGTTCAA
* * * * * **
9749928 GTTTAACGACTTTGGAGTAAAGATTCTTGTTAGCTACAAAATGGCTATGAACTTCGTTGCAATGA
1 GTTTAACAACTTTGGAGTAAAAATCCTTGTTAGCTACAAAATGGCCATGAACTTCATTGCAACAA
** * * * *
9749993 CTCATTGTGACAAGGCCAAAAAGAGATCAAGAATCAAGTGTGCTAGAGTAAGGAGGAACAAGTTC
66 CTCACCGTGACAAGGCCAAAAAGAGATCAAGAATCAAGTATGCTAGAGTAAAGAGGAACAAATGC
* * ** * ** * *
9750058 TTGAATATTGAAAGCTCTCTTGACACATAAAATGAAAATGGGTGGATTCTATTACAAAAATCTTT
131 TTGAAGATTGAAAACTCTCTCAACACACAAAATGAAAATAAGTGAATTCTATTACAAAAATCTCT
** *
9750123 TTGTGCTTTTAATTTTAAGAACTTTGCTT-ATTTGGTATCAATTGTGTAG
196 TCATGCTTTTAATTTTAAAAACTTTGCTTGATTTGGTATCAATTGTGTAG
* * *
9750172 GTTTAACAACCTTT-GAGTAAAAATCCTTGTTGGCTCCAAGATGGCCATGAACTTCATTGCAACA
1 GTTTAACAA-CTTTGGAGTAAAAATCCTTGTTAGCTACAAAATGGCCATGAACTTCATTGCAACA
* * * *
9750236 ACTCACCGTGACAAGGCCAAAAGGAGATGAGGAATTAAGTATGCTAGAGTAAAGAGGAACAAATG
65 ACTCACCGTGACAAGGCCAAAAAGAGATCAAGAATCAAGTATGCTAGAGTAAAGAGGAACAAATG
*
9750301 CTTGAAGATTGAAAACTCTCTCAACACACAAAATGAAAATAAGTGAATTCTATTACCAAAATCTC
130 CTTGAAGATTGAAAACTCTCTCAACACACAAAATGAAAATAAGTGAATTCTATTACAAAAATCTC
9750366 TTCATGCTTTTAATTTTAAAAACTTTGCTTGATTT
195 TTCATGCTTTTAATTTTAAAAACTTTGCTTGATTT
9750401 CTTGAGATTA
Statistics
Matches: 194, Mismatches: 33, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
244 186 0.96
245 8 0.04
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (245 bp):
GTTTAACAACTTTGGAGTAAAAATCCTTGTTAGCTACAAAATGGCCATGAACTTCATTGCAACAA
CTCACCGTGACAAGGCCAAAAAGAGATCAAGAATCAAGTATGCTAGAGTAAAGAGGAACAAATGC
TTGAAGATTGAAAACTCTCTCAACACACAAAATGAAAATAAGTGAATTCTATTACAAAAATCTCT
TCATGCTTTTAATTTTAAAAACTTTGCTTGATTTGGTATCAATTGTGTAG
Found at i:9754846 original size:76 final size:75
Alignment explanation
Indices: 9754691--9754851 Score: 200
Period size: 76 Copynumber: 2.1 Consensus size: 75
9754681 AATGCCATCT
* * *
9754691 ATTTTAATTTTTGGTGATTCATAAAAATAAATATTGTTTCCTACTTTGAAGCGAATTCCTAAAAT
1 ATTTTAATTTTAGGTGATTCATAAAAATAAATATAGTTTCCTACTTTAAAGCGAATTCCTAAAAT
*
9754756 TAAGAATAGG
66 TAAGAATAGC
* ** *
9754766 ATTTTAATTTTAGGTGATTCATAAAGTATAGGAA-ATAGTTT-CTACTTTAAATTGAATTCTTAA
1 ATTTTAATTTTAGGTGATTCATAAA-AATA--AATATAGTTTCCTACTTTAAAGCGAATTCCTAA
*
9754829 AATTAAGGATAGC
63 AATTAAGAATAGC
9754842 ATTTTAATTT
1 ATTTTAATTT
9754852 GGAAATTCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
75 24 0.32
76 42 0.57
77 6 0.08
78 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.42
Consensus pattern (75 bp):
ATTTTAATTTTAGGTGATTCATAAAAATAAATATAGTTTCCTACTTTAAAGCGAATTCCTAAAAT
TAAGAATAGC
Found at i:9757042 original size:44 final size:42
Alignment explanation
Indices: 9756967--9757084 Score: 103
Period size: 44 Copynumber: 2.8 Consensus size: 42
9756957 TATTGTGAAC
* * *** * *
9756967 ATGGATTGAAAAGGTCTCCACATTTTGATGATGGGTGTTGTGAT
1 ATGGATTGAGAAGGTCTCCATATTCCCATGAT-GGCGTTGT-AA
*
9757011 ATGGATTGAGAAGGTCTCCATATTCCCATGATTGCGTTGTAA
1 ATGGATTGAGAAGGTCTCCATATTCCCATGATGGCGTTGTAA
* * *
9757053 AGCGGATTGAGTATGTCTCCAT-TTCCCATGAT
1 A-TGGATTGAGAAGGTCTCCATATTCCCATGAT
9757085 TCTGTGGTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 12 0.19
43 23 0.37
44 27 0.44
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (42 bp):
ATGGATTGAGAAGGTCTCCATATTCCCATGATGGCGTTGTAA
Found at i:9757095 original size:42 final size:42
Alignment explanation
Indices: 9757012--9757169 Score: 183
Period size: 42 Copynumber: 3.7 Consensus size: 42
9757002 TGTTGTGATA
*
9757012 TGGATTGAGAAGGTCTCCATATTCCCATGATTGC-GTTGTAAAG
1 TGGATTGAGTAGGTCTCCAT-TTCCCATGATT-CTGTTGTAAAG
* * *
9757055 CGGATTGAGTATGTCTCCATTTCCCATGATTCTGTGGTAAAG
1 TGGATTGAGTAGGTCTCCATTTCCCATGATTCTGTTGTAAAG
* * * * *
9757097 TGAATTAAGTAGGTCTCCACTCCCCATGATTTTGTTGTAAAG
1 TGGATTGAGTAGGTCTCCATTTCCCATGATTCTGTTGTAAAG
* * *
9757139 TGGATTGAGTAAGTTTGCATTTCCCATGATT
1 TGGATTGAGTAGGTCTCCATTTCCCATGATT
9757170 TTGTATATTG
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.01
42 77 0.81
43 17 0.18
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (42 bp):
TGGATTGAGTAGGTCTCCATTTCCCATGATTCTGTTGTAAAG
Found at i:9763733 original size:20 final size:20
Alignment explanation
Indices: 9763698--9763735 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9763688 ATTTTATTGA
*
9763698 TATTTTATTCATAAATATAT
1 TATTTTATTCAAAAATATAT
*
9763718 TATTTTATTTAAAAATAT
1 TATTTTATTCAAAAATAT
9763736 TCTTTGTACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTTATTCAAAAATATAT
Found at i:9763735 original size:18 final size:19
Alignment explanation
Indices: 9763698--9763736 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
9763688 ATTTTATTGA
*
9763698 TATTTTATTCATAAATATAT
1 TATTTTATT-ATAAAAATAT
9763718 TATTTTATT-TAAAAATAT
1 TATTTTATTATAAAAATAT
9763736 T
1 T
9763737 CTTTGTACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTTATTATAAAAATAT
Found at i:9769847 original size:68 final size:67
Alignment explanation
Indices: 9769731--9769938 Score: 254
Period size: 68 Copynumber: 3.1 Consensus size: 67
9769721 AAACATATCG
* * * *
9769731 AATGCCATAATGCTAGGTATATGATGTAAATTTCATATATTATGTGAGATGATAAAGAATGCATG
1 AATGCCTTGATGCTAGGTATATGATGTAAATTTCATATACTATATGAGATGATAAA-AATGCATG
9769796 ATA
65 ATA
* * * *
9769799 AATGCCTTGATGCTAGGTATATCATGTAAACTCCATATACTATATGAGATCATTAAAAATGCATG
1 AATGCCTTGATGCTAGGTATATGATGTAAATTTCATATACTATATGAGATGA-TAAAAATGCATG
9769864 ATA
65 ATA
* * * * * * *
9769867 AATGCCTTGATGCTATGTCTATGATGTAAATTTCATATACCACATGAGATGATGAATAGTACATG
1 AATGCCTTGATGCTAGGTATATGATGTAAATTTCATATACTATATGAGATGAT-AAAAATGCATG
9769932 ATA
65 ATA
9769935 AATG
1 AATG
9769939 ATATGATGCT
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 1 0.01
68 114 0.96
69 4 0.03
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (67 bp):
AATGCCTTGATGCTAGGTATATGATGTAAATTTCATATACTATATGAGATGATAAAAATGCATGA
TA
Found at i:9769946 original size:68 final size:68
Alignment explanation
Indices: 9769731--9769991 Score: 249
Period size: 68 Copynumber: 3.9 Consensus size: 68
9769721 AAACATATCG
* * * ** ** *
9769731 AATGCCATAATGCTAGGTATATGATGTAAATTTCATATATTATGTGAGATGATAAAGAATGCATG
1 AATGCCTTGATGCTAGGTATATGATGTAAATTCCATATACCACATGAGATGATAAAGAATACATG
9769796 ATA
66 ATA
* * * * * *
9769799 AATGCCTTGATGCTAGGTATATCATGTAAACTCCATATACTATATGAGATCATTAAA-AATGCAT
1 AATGCCTTGATGCTAGGTATATGATGTAAATTCCATATACCACATGAGATGA-TAAAGAATACAT
9769863 GATA
65 GATA
* * * * * *
9769867 AATGCCTTGATGCTATGTCTATGATGTAAATTTCATATACCACATGAGATGATGAATAGTACATG
1 AATGCCTTGATGCTAGGTATATGATGTAAATTCCATATACCACATGAGATGATAAAGAATACATG
9769932 ATA
66 ATA
* * * * * *
9769935 AATG-ATATGATGCTA-TTATGTGAAGTAGATTCCACATACCACATGAGATGATAAAGA
1 AATGCCT-TGATGCTAGGTATATGATGTAAATTCCATATACCACATGAGATGATAAAGA
9769992 GTACTTATTG
Statistics
Matches: 161, Mismatches: 29, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
67 37 0.23
68 120 0.75
69 4 0.02
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (68 bp):
AATGCCTTGATGCTAGGTATATGATGTAAATTCCATATACCACATGAGATGATAAAGAATACATG
ATA
Found at i:9770255 original size:31 final size:32
Alignment explanation
Indices: 9770202--9770265 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
9770192 ATAAAAGCCC
**
9770202 AAGGTGCAATGGGTTTGTACATTGCCGA-CCA
1 AAGGTGCAATGGGTTTAAACATTGCCGATCCA
*
9770233 AAGGTGCAATAGGG-TTAAACATTGTCGATCCA
1 AAGGTGCAAT-GGGTTTAAACATTGCCGATCCA
9770265 A
1 A
9770266 GGTTGATGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (32 bp):
AAGGTGCAATGGGTTTAAACATTGCCGATCCA
Found at i:9771822 original size:12 final size:12
Alignment explanation
Indices: 9771803--9771836 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9771793 TTAAGCTAGC
9771803 TAAAAAAGAAAT
1 TAAAAAAGAAAT
* *
9771815 TGAAAAAGATAT
1 TAAAAAAGAAAT
9771827 TAAAAAAGAA
1 TAAAAAAGAA
9771837 GGTAAGAAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (12 bp):
TAAAAAAGAAAT
Found at i:9777555 original size:727 final size:727
Alignment explanation
Indices: 9776143--9777599 Score: 2474
Period size: 727 Copynumber: 2.0 Consensus size: 727
9776133 CACAAGGCAA
**
9776143 TGATCAAGGTTGGTTACCATAACCCGTCATGTGGTGAAGTGGCTAACATGATAATGTTGTTGAAG
1 TGATCAAGGTTGGTTACCATAACCCGTCATGTGGTGAAGCAGCTAACATGATAATGTTGTTGAAG
* *
9776208 ATCAATTTCCCAATTTCAATTGATTTCCCGATCACAATTACATACAACAGGATTACTCGATCTTT
66 ATCAATTGCCCAATTTCAATTGATTTCCCGATCACAATTACATACAACAGGATTACTCGATCCTT
* *
9776273 TGTCATATCACTCAGGTATTTCATAGGAAGCATCTTTACAACCAAAAAATGATACCATACATTAT
131 TGTCATATCACTAAGGTATTTCATAGGAAGCATCTTTACAACCAAAAAATGATACCACACATTAT
**
9776338 AGCTGCTATCCATGGCATTACCTTTGAAAGAAATTGGAACAACCTTGGGCAATTTCCATTTAGTA
196 AGCTGCTATCCATGGCATTACCTTTGAAAGAAATTGGAACAACCTTGGGCAATAACCATTTAGTA
9776403 TCATAAATGCTAAAAGACCTCAGAACTTCATCTAAATTGATGTCACCATTCACTTATTAGCCTTA
261 TCATAAATGCTAAAAGACCTCAGAACTTCATCTAAATTGATGTCACCATTCACTTATTAGCCTTA
*
9776468 ATCATCATTCTTAATGTTAAGTGTATTGTAAAAATAATTAATAGTGGAGCATCAAAAGGTACCTA
326 ATCATCATTCTCAATGTTAAGTGTATTGTAAAAATAATTAATAGTGGAGCATCAAAAGGTACCTA
9776533 ATGGCCTCGAACGAATGCTCACCCATAGTCATATCCAACTGCATTGGCATAGAATTCTCAAACAA
391 ATGGCCTCGAACGAATGCTCACCCATAGTCATATCCAACTGCATTGGCATAGAATTCTCAAACAA
*
9776598 CAGGCATTACTACTGCTTCTAGTTAGGCATAAAATTTCTCCCACTAACTTGCATTGATAATATTG
456 CAGGCATTACTACTGCTTCTAGTTAGGCACAAAATTTCTCCCACTAACTTGCATTGATAATATTG
* * *
9776663 TAGATGTGGAGATAAAGTCCTGTTCAAACATCAGTGCCATATTCAGGAACTGGAACATTTTGCAA
521 TAAATGTGGAGATAAAGTCCTGTTCAAACATCAGTACCACATTCAGGAACTGGAACATTTTGCAA
* * * * *
9776728 TAGTGACTAGGTGTATCGTTTCTTAACTTTGTTTTAAAAAAATTTACTTCAACCAAAATTATTCC
586 TAGTGACTAGGAGTACCGTTTCTTAACTTTGTGTCAAAAAAATTTACTTCAACCAAAACTATTCC
*
9776793 CACTCCCATTAGCAAATGTCCTTTTTTTAGGTGCCATGATAATTATCATAATACCTAATCAAGAA
651 CACTCCCATTAGCAAAGGTCCTTTTTTTAGGTGCCATGATAATTATCATAATACCTAATCAAGAA
*
9776858 GCAACCCAATTT
716 GAAACCCAATTT
* *
9776870 TGATCAAGGTTGGTTAGCATAACCCGTCATGTGGTGAAGCAGCTGACATGATAATGTTGTTGAAG
1 TGATCAAGGTTGGTTACCATAACCCGTCATGTGGTGAAGCAGCTAACATGATAATGTTGTTGAAG
** * * *
9776935 ATCAATTGCCCAATTTCAATTGATTTTTCGGTCACAATTGCATACAAGAGGATTACTCGATCCTT
66 ATCAATTGCCCAATTTCAATTGATTTCCCGATCACAATTACATACAACAGGATTACTCGATCCTT
*
9777000 TGTCATATCACTAAGGTATTTCATAGGAAGCATCTTTACAACCAAAAAATGATACCACACATTGT
131 TGTCATATCACTAAGGTATTTCATAGGAAGCATCTTTACAACCAAAAAATGATACCACACATTAT
*
9777065 AGCTGCTATCCATGGCATTACCTTTGAAAGAAATTGGAACAGCCTTGGGCAATAACCATTTAGTA
196 AGCTGCTATCCATGGCATTACCTTTGAAAGAAATTGGAACAACCTTGGGCAATAACCATTTAGTA
9777130 TCATAAATGCTAAAAGACCTC-GAAACTTCATCTAAATTGATGTCACCATTCACTTATTAGCCTT
261 TCATAAATGCTAAAAGACCTCAG-AACTTCATCTAAATTGATGTCACCATTCACTTATTAGCCTT
* * *
9777194 AATCATCATTCTCAATGTTAGGTGTATTGTAAAATTAATTAATAGTGGAGCATCAAATGGTACCT
325 AATCATCATTCTCAATGTTAAGTGTATTGTAAAAATAATTAATAGTGGAGCATCAAAAGGTACCT
* *
9777259 AATGGCCTCGAACGAATGCTCACTCATAGTCATATCCAA-TGGCATTGGCATAGAATTCTCAAAG
390 AATGGCCTCGAACGAATGCTCACCCATAGTCATATCCAACT-GCATTGGCATAGAATTCTCAAAC
* *
9777323 AACAGGCATTACTACTGCTTTTAGTTAGGCACAAAATTTCTCCCAGTAACTTGCATTGATAATAT
454 AACAGGCATTACTACTGCTTCTAGTTAGGCACAAAATTTCTCCCACTAACTTGCATTGATAATAT
* * *
9777388 TGTAAATGTGGAGATAAAGTCTTTTTCAGACATC-GATACCACATTCAGGAACTGGAACATTTTG
519 TGTAAATGTGGAGATAAAGTCCTGTTCAAACATCAG-TACCACATTCAGGAACTGGAACATTTTG
9777452 CAATAGTGACTAGGAGTACCGTTTCTTAACTTTG-GTCAAAATAAATTTACTTCAACCAAAACTA
583 CAATAGTGACTAGGAGTACCGTTTCTTAACTTTGTGTCAAAA-AAATTTACTTCAACCAAAACTA
*
9777516 TTTCCACTCCCATTAGCAAAGGTCCTTCTTTTT-GGTGCCATGATAATTATCATAATACCTAATC
647 TTCCCACTCCCATTAGCAAAGGTCCTT-TTTTTAGGTGCCATGATAATTATCATAATACCTAATC
9777580 AAGAAGAAACCCAATTT
711 AAGAAGAAACCCAATTT
9777597 TGA
1 TGA
9777600 CCACAAATTC
Statistics
Matches: 685, Mismatches: 40, Indels: 10
0.93 0.05 0.01
Matches are distributed among these distances:
726 8 0.01
727 672 0.98
728 5 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (727 bp):
TGATCAAGGTTGGTTACCATAACCCGTCATGTGGTGAAGCAGCTAACATGATAATGTTGTTGAAG
ATCAATTGCCCAATTTCAATTGATTTCCCGATCACAATTACATACAACAGGATTACTCGATCCTT
TGTCATATCACTAAGGTATTTCATAGGAAGCATCTTTACAACCAAAAAATGATACCACACATTAT
AGCTGCTATCCATGGCATTACCTTTGAAAGAAATTGGAACAACCTTGGGCAATAACCATTTAGTA
TCATAAATGCTAAAAGACCTCAGAACTTCATCTAAATTGATGTCACCATTCACTTATTAGCCTTA
ATCATCATTCTCAATGTTAAGTGTATTGTAAAAATAATTAATAGTGGAGCATCAAAAGGTACCTA
ATGGCCTCGAACGAATGCTCACCCATAGTCATATCCAACTGCATTGGCATAGAATTCTCAAACAA
CAGGCATTACTACTGCTTCTAGTTAGGCACAAAATTTCTCCCACTAACTTGCATTGATAATATTG
TAAATGTGGAGATAAAGTCCTGTTCAAACATCAGTACCACATTCAGGAACTGGAACATTTTGCAA
TAGTGACTAGGAGTACCGTTTCTTAACTTTGTGTCAAAAAAATTTACTTCAACCAAAACTATTCC
CACTCCCATTAGCAAAGGTCCTTTTTTTAGGTGCCATGATAATTATCATAATACCTAATCAAGAA
GAAACCCAATTT
Found at i:9802132 original size:26 final size:26
Alignment explanation
Indices: 9802101--9802150 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
9802091 AATATTAAAA
*
9802101 TATTTT-AAAATTAACATTTAATATTT
1 TATTTTAAAAATTAA-AATTAATATTT
9802127 TATTTTAAAAATTAAAATTAATAT
1 TATTTTAAAAATTAAAATTAATAT
9802151 CATCTCGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TATTTTAAAAATTAAAATTAATATTT
Found at i:9803650 original size:19 final size:19
Alignment explanation
Indices: 9803628--9803667 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9803618 TATATGGGAT
*
9803628 ACCAACCTATATACGTATA
1 ACCAACCTATAAACGTATA
*
9803647 ACCAACCTGTAAACGTATA
1 ACCAACCTATAAACGTATA
9803666 AC
1 AC
9803668 TATCACACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.23
Consensus pattern (19 bp):
ACCAACCTATAAACGTATA
Found at i:9809960 original size:20 final size:20
Alignment explanation
Indices: 9809935--9809975 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9809925 TAATTAGTTT
9809935 ATTTTAAGTGATTTATTTTA
1 ATTTTAAGTGATTTATTTTA
* * *
9809955 ATTTTATGTTATTTCTTTTA
1 ATTTTAAGTGATTTATTTTA
9809975 A
1 A
9809976 CTTGGTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (20 bp):
ATTTTAAGTGATTTATTTTA
Found at i:9826408 original size:29 final size:28
Alignment explanation
Indices: 9826334--9826461 Score: 105
Period size: 28 Copynumber: 4.4 Consensus size: 28
9826324 CTTTAAAATG
* *
9826334 TTTGTCTTAATTTAGATAAGAAAATATG
1 TTTGTCTTAATTTAGATAAAAAAATATT
** *
9826362 TTCATATTAATTTAAGATAAAAAAATATTT
1 TTTGTCTTAATTT-AGATAAAAAAATA-TT
* * *
9826392 TTTGTCTTAATCTAGATAAGAAAACT-TA
1 TTTGTCTTAATTTAGATAA-AAAAATATT
* * *
9826420 TTCGTCTTAATTTAGACAAGATAAAATAAT
1 TTTGTCTTAATTTAGATAA-A-AAAATATT
9826450 TTTGTCTTAATT
1 TTTGTCTTAATT
9826462 AAAGATAGGA
Statistics
Matches: 77, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
28 29 0.38
29 22 0.29
30 26 0.34
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (28 bp):
TTTGTCTTAATTTAGATAAAAAAATATT
Found at i:9826430 original size:58 final size:58
Alignment explanation
Indices: 9826334--9826460 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 58
9826324 CTTTAAAATG
* * * *
9826334 TTTGTCTTAATTTAGATAAGAAAATATGTTCATATTAATTTAAGATAA-A-AAAATATTT
1 TTTGTCTTAATCTAGATAAGAAAATATATTCATATTAATTT-AGACAAGATAAAATA-AT
* *
9826392 TTTGTCTTAATCTAGATAAGAAAACT-TATTCGTCTTAATTTAGACAAGATAAAATAAT
1 TTTGTCTTAATCTAGATAAGAAAA-TATATTCATATTAATTTAGACAAGATAAAATAAT
9826450 TTTGTCTTAAT
1 TTTGTCTTAAT
9826461 TAAAGATAGG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
57 5 0.08
58 48 0.80
59 7 0.12
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (58 bp):
TTTGTCTTAATCTAGATAAGAAAATATATTCATATTAATTTAGACAAGATAAAATAAT
Found at i:9841761 original size:80 final size:78
Alignment explanation
Indices: 9841580--9841765 Score: 187
Period size: 80 Copynumber: 2.4 Consensus size: 78
9841570 TCCCAGTGTT
* * * * * *
9841580 GGGTAAGAATACCACATGCTTAAGCTTGTCCAGCATGCCATCATCCCTTTTTGTATGTTGGATTT
1 GGGTAAGAATACCACATGATTAAGCTTGGCCAACATGCCATCATCCCCTTATGTATGTTGGATCT
9841645 AGTCCTACTGTAG
66 AGTCCTACTGTAG
* * * * * *
9841658 GGGTAAGAATATCACAAGTTTAAGCTTGGCCAACGTGCCATCTTTTCCCCTTATGTATGTTGGCT
1 GGGTAAGAATACCACATGATTAAGCTTGGCCAACATGCCATC--ATCCCCTTATGTATGTTGGAT
* **
9841723 CTAGTCTTGGTGT-G
64 CTAGTCCTACTGTAG
*
9841737 GAGGTAAAAATACCACATGATTAAG-TTGG
1 G-GGTAAGAATACCACATGATTAAGCTTGG
9841766 GTATTGTACC
Statistics
Matches: 87, Mismatches: 18, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
78 36 0.41
79 6 0.07
80 45 0.52
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (78 bp):
GGGTAAGAATACCACATGATTAAGCTTGGCCAACATGCCATCATCCCCTTATGTATGTTGGATCT
AGTCCTACTGTAG
Found at i:9872721 original size:9 final size:9
Alignment explanation
Indices: 9872709--9872744 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
9872699 GGATGTGGGT
9872709 AATGTGGCA
1 AATGTGGCA
9872718 AATGTGGCA
1 AATGTGGCA
*
9872727 AATGTGCCA
1 AATGTGGCA
*
9872736 ATTGTGGCA
1 AATGTGGCA
9872745 GATTATGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (9 bp):
AATGTGGCA
Found at i:9875999 original size:20 final size:20
Alignment explanation
Indices: 9875948--9876004 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
9875938 CTTGAAGAAC
* *
9875948 ATCTATGGATAAATGACCAA
1 ATCTATCGATAGATGACCAA
* * *
9875968 ATCTATCAATAGATGGCCCA
1 ATCTATCGATAGATGACCAA
*
9875988 ATCTATTGATAGATGAC
1 ATCTATCGATAGATGAC
9876005 TCCATCCATT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (20 bp):
ATCTATCGATAGATGACCAA
Found at i:9877236 original size:80 final size:80
Alignment explanation
Indices: 9877119--9877311 Score: 212
Period size: 80 Copynumber: 2.4 Consensus size: 80
9877109 CTGATCTCAA
* * * *
9877119 TGTGGGGGTAAGAATACCACTA-GGTTAAGCTTGGCCAACATGCCATCTTTTTCCCTTT-TGTAT
1 TGTGGGAGTAAAAATACCA-AAGGGTTAAGCTTGGCCAACATGCCATC-GTTTCCCTTTATGTAT
* * *
9877182 GTTGGCTCTAGTCTTAG
64 ATTAGCTCTAGTCATAG
* *
9877199 TTTGGGAGTAAAAATACCAAAGGGTTAAGCTTGGCCAACGTGCCATCGTTTCCCTTTATGTATAT
1 TGTGGGAGTAAAAATACCAAAGGGTTAAGCTTGGCCAACATGCCATCGTTTCCCTTTATGTATAT
* *
9877264 TAGTTCTAGTCATGG
66 TAGCTCTAGTCATAG
* ** *
9877279 TGTGGGGGTAAGTATACCACAGGGTTAAG-TTGG
1 TGTGGGAGTAAAAATACCAAAGGGTTAAGCTTGG
9877312 GCATTGTACC
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
79 14 0.15
80 81 0.85
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (80 bp):
TGTGGGAGTAAAAATACCAAAGGGTTAAGCTTGGCCAACATGCCATCGTTTCCCTTTATGTATAT
TAGCTCTAGTCATAG
Found at i:9879247 original size:19 final size:19
Alignment explanation
Indices: 9879223--9879259 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
9879213 TTAGCTTTGG
9879223 TTTATTTACATAA-TTTATT
1 TTTATTTA-ATAACTTTATT
9879242 TTTATTTAATAACTTTAT
1 TTTATTTAATAACTTTAT
9879260 GGAATTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTTAATAACTTTATT
Found at i:9882244 original size:76 final size:76
Alignment explanation
Indices: 9882113--9882272 Score: 230
Period size: 76 Copynumber: 2.1 Consensus size: 76
9882103 TGCCATTTAT
* ** *
9882113 TTTAGTTTTGGGTAATTCATAAAGAATAGGGAATTGTTTTCAACTTAAAGTGAATTCCTAAAATT
1 TTTAATTTTGGGTAATTCATAAAGAATAGAAAATTATTTTCAACTTAAAGTGAATTCCTAAAATT
9882178 ATGGTTAACAC
66 ATGGTTAACAC
* * * *
9882189 TTTAATTTTGGGTGATTCGTAAAGAATAGAAAATTATTTTCTACTTGAAGTGAATTCCTAAAATT
1 TTTAATTTTGGGTAATTCATAAAGAATAGAAAATTATTTTCAACTTAAAGTGAATTCCTAAAATT
* *
9882254 ATGGTTAGCAT
66 ATGGTTAACAC
9882265 TTTAATTT
1 TTTAATTT
9882273 GGAATATTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.41
Consensus pattern (76 bp):
TTTAATTTTGGGTAATTCATAAAGAATAGAAAATTATTTTCAACTTAAAGTGAATTCCTAAAATT
ATGGTTAACAC
Found at i:9897111 original size:13 final size:13
Alignment explanation
Indices: 9897093--9897117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9897083 AGTGGTGACT
9897093 TTGATGAAATATA
1 TTGATGAAATATA
9897106 TTGATGAAATAT
1 TTGATGAAATAT
9897118 TCAATTGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGATGAAATATA
Found at i:9897512 original size:18 final size:18
Alignment explanation
Indices: 9897486--9897528 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
9897476 CCACAAGATA
* *
9897486 ATATTTAAATATACATGT
1 ATATATAAATATACATAT
* *
9897504 ATATATAAATGTATATAT
1 ATATATAAATATACATAT
9897522 ATATATA
1 ATATATA
9897529 TGTATACCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (18 bp):
ATATATAAATATACATAT
Found at i:9897524 original size:16 final size:16
Alignment explanation
Indices: 9897503--9897534 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9897493 AATATACATG
9897503 TATATATAAATGTATA
1 TATATATAAATGTATA
*
9897519 TATATATATATGTATA
1 TATATATAAATGTATA
9897535 CCATGGCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TATATATAAATGTATA
Found at i:9899410 original size:3 final size:3
Alignment explanation
Indices: 9899402--9899445 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
9899392 TAAATATCAT
* *
9899402 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAT TAC TAA TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
9899446 GAGATAAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (3 bp):
TAC
Found at i:9900987 original size:22 final size:22
Alignment explanation
Indices: 9900962--9901003 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9900952 AGGGTGATGG
* *
9900962 GGTATTGGGTAAATGGGTAATA
1 GGTAGTGGGTAAATGCGTAATA
9900984 GGTAGTGGGTAAATGCGTAA
1 GGTAGTGGGTAAATGCGTAA
9901004 GTGGGCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.02, G:0.38, T:0.29
Consensus pattern (22 bp):
GGTAGTGGGTAAATGCGTAATA
Found at i:9901023 original size:15 final size:14
Alignment explanation
Indices: 9900975--9901025 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
9900965 ATTGGGTAAA
9900975 TGGGTAATAGGTAG
1 TGGGTAATAGGTAG
9900989 TGGGTAA-ATGCGTAAG
1 TGGGTAATA-G-GT-AG
9901005 TGGGCTAATAGGTAG
1 TGGG-TAATAGGTAG
9901020 TGGGTA
1 TGGGTA
9901026 GTCCAAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 10 0.31
15 8 0.25
16 8 0.25
17 4 0.12
18 1 0.03
ACGTcount: A:0.27, C:0.04, G:0.41, T:0.27
Consensus pattern (14 bp):
TGGGTAATAGGTAG
Found at i:9901312 original size:9 final size:10
Alignment explanation
Indices: 9901291--9901315 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9901281 AAAAAATTTA
9901291 TTTTTGAATT
1 TTTTTGAATT
9901301 TTTTTGAATT
1 TTTTTGAATT
9901311 TTTTT
1 TTTTT
9901316 TGAAATGTAC
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTGAATT
Found at i:9901313 original size:11 final size:11
Alignment explanation
Indices: 9901285--9901319 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
9901275 TTTTTAAAAA
9901285 AATTTATTTTTG
1 AATTT-TTTTTG
9901297 AA-TTTTTTTG
1 AATTTTTTTTG
9901307 AATTTTTTTTG
1 AATTTTTTTTG
9901318 AA
1 AA
9901320 ATGTACCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.36
11 12 0.55
12 2 0.09
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:9901888 original size:21 final size:21
Alignment explanation
Indices: 9901859--9901932 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
9901849 TTGACTTTCG
*
9901859 ATGATGGCA-CTAGTCCATGTC
1 ATGAAGGCATCTA-TCCATGTC
**
9901880 ATGAAGGCATCTATCTTTGTC
1 ATGAAGGCATCTATCCATGTC
* ** *
9901901 ATGAAGGCATCAATCTTTGTT
1 ATGAAGGCATCTATCCATGTC
9901922 ATGAAGGCATC
1 ATGAAGGCATC
9901933 AGTCTTTGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 44 0.94
22 3 0.06
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (21 bp):
ATGAAGGCATCTATCCATGTC
Found at i:9901933 original size:21 final size:21
Alignment explanation
Indices: 9901876--9901947 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
9901866 CACTAGTCCA
*
9901876 TGTCATGAAGGCATCTATCTT
1 TGTCATGAAGGCATCAATCTT
9901897 TGTCATGAAGGCATCAATCTT
1 TGTCATGAAGGCATCAATCTT
* *
9901918 TGTTATGAAGGCATCAGTCTT
1 TGTCATGAAGGCATCAATCTT
9901939 TGTCATGAA
1 TGTCATGAA
9901948 TTGCATGAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (21 bp):
TGTCATGAAGGCATCAATCTT
Found at i:9903926 original size:3 final size:3
Alignment explanation
Indices: 9903906--9903990 Score: 89
Period size: 3 Copynumber: 28.3 Consensus size: 3
9903896 CTCTAATAGC
* * *
9903906 AGT AGT AAT AGT ACT AGT AGT AGT AGT AGT AGT AGT AGT AGT GGT AGT
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT
* * * * * *
9903954 AGT AAT AGT AGT AGC AGC GGC AGT AGT AGT AAT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
9903991 ACTATATTTA
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.35, C:0.05, G:0.31, T:0.29
Consensus pattern (3 bp):
AGT
Found at i:9903990 original size:12 final size:12
Alignment explanation
Indices: 9903899--9903967 Score: 72
Period size: 12 Copynumber: 6.0 Consensus size: 12
9903889 ACCCCATCTC
*
9903899 TAATAGCAGTAG
1 TAATAGTAGTAG
*
9903911 TAATAGTACTAG
1 TAATAGTAGTAG
9903923 ---TAGTAGTAG
1 TAATAGTAGTAG
*
9903932 TAGTAGTAGTAG
1 TAATAGTAGTAG
* *
9903944 TAGTGGTAGTAG
1 TAATAGTAGTAG
9903956 TAATAGTAGTAG
1 TAATAGTAGTAG
9903968 CAGCGGCAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.17
12 40 0.83
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (12 bp):
TAATAGTAGTAG
Found at i:9909229 original size:21 final size:20
Alignment explanation
Indices: 9909205--9909251 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
9909195 TTAAAGTAAT
*
9909205 TTAAAGCAAAATAACATAAAA
1 TTAAACCAAAATAAC-TAAAA
*
9909226 TTAAACCAAAATAACTTAAA
1 TTAAACCAAAATAACTAAAA
9909246 TTAAAC
1 TTAAAC
9909252 TAATCAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (20 bp):
TTAAACCAAAATAACTAAAA
Found at i:9915836 original size:35 final size:37
Alignment explanation
Indices: 9915796--9915898 Score: 113
Period size: 35 Copynumber: 2.9 Consensus size: 37
9915786 TGGTTATTGG
* * *
9915796 TTGATCTCGTTAAGAAGCAAGTGTAAGGGTTAAT-GC
1 TTGATCTCGTTAAAAAGTAAGTGTAAGGGTTAATCAC
* * *
9915832 -TGATCCCATTAAAAAGTAAGTGTAAAGGTT-ATCAC
1 TTGATCTCGTTAAAAAGTAAGTGTAAGGGTTAATCAC
* *
9915867 TTGATCTCGTGAAAAAGTTAGTGTAAGGGTTA
1 TTGATCTCGTTAAAAAGTAAGTGTAAGGGTTA
9915899 TCGTTTGATC
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
34 2 0.04
35 26 0.49
36 25 0.47
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (37 bp):
TTGATCTCGTTAAAAAGTAAGTGTAAGGGTTAATCAC
Found at i:9915907 original size:36 final size:35
Alignment explanation
Indices: 9915795--9915917 Score: 113
Period size: 36 Copynumber: 3.5 Consensus size: 35
9915785 ATGGTTATTG
* *
9915795 GTTGATCTCGTTAAGAAGCAAGTGTAAGGGTTAAT-
1 GTTGATCTCGTTAAAAAGTAAGTGTAAGGGTT-ATC
* * * *
9915830 GCTGATCCCATTAAAAAGTAAGTGTAAAGGTTATC
1 GTTGATCTCGTTAAAAAGTAAGTGTAAGGGTTATC
* * *
9915865 ACTTGATCTCGTGAAAAAGTTAGTGTAAGGGTTATC
1 -GTTGATCTCGTTAAAAAGTAAGTGTAAGGGTTATC
* *
9915901 GTTTGATCCCATTAAAA
1 G-TTGATCTCGTTAAAA
9915918 CACAAGAATC
Statistics
Matches: 68, Mismatches: 17, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
34 2 0.03
35 26 0.38
36 40 0.59
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (35 bp):
GTTGATCTCGTTAAAAAGTAAGTGTAAGGGTTATC
Found at i:9918279 original size:19 final size:20
Alignment explanation
Indices: 9918235--9918281 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
9918225 CTTGCCACAA
*
9918235 TTGGTGTCTTTCACAATGTC
1 TTGGTGTCTTTCACAATGCC
*
9918255 TAGGTGT-TTTCACAATGCC
1 TTGGTGTCTTTCACAATGCC
9918274 TTGGTGTC
1 TTGGTGTC
9918282 AACTTATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGGTGTCTTTCACAATGCC
Found at i:9921356 original size:73 final size:73
Alignment explanation
Indices: 9921273--9921479 Score: 297
Period size: 73 Copynumber: 2.8 Consensus size: 73
9921263 ACTTTCAAAA
* * *
9921273 GTGAGTTTTTAGTTAGCTAACCATTCTTCTTAGTCGATTAAGCCTTCTCTGTCTCACAATCAAAT
1 GTGAGCTTTTAGCTGGCTAACCATTCTTCTTAGTCGATTAAGCCTTCTCTGTCTCACAATCAAAT
* **
9921338 TTTTTATT
66 TTTTGACC
* *
9921346 GTGAGCTTTTAGCTGGTTAACCATTCTTCTTAGTCGATTAAGCCTTTTCTGTCTCACAATCAAAT
1 GTGAGCTTTTAGCTGGCTAACCATTCTTCTTAGTCGATTAAGCCTTCTCTGTCTCACAATCAAAT
9921411 TTTTGACC
66 TTTTGACC
* * * * *
9921419 GTGAGCTTTTAGCTGGCTAACCACTCTTCTTAGTCGATTATGTCTTCTATGACTCACAATC
1 GTGAGCTTTTAGCTGGCTAACCATTCTTCTTAGTCGATTAAGCCTTCTCTGTCTCACAATC
9921480 TGCTTTACTC
Statistics
Matches: 119, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 119 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (73 bp):
GTGAGCTTTTAGCTGGCTAACCATTCTTCTTAGTCGATTAAGCCTTCTCTGTCTCACAATCAAAT
TTTTGACC
Found at i:9922437 original size:23 final size:24
Alignment explanation
Indices: 9922382--9922438 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
9922372 TCTCTTTGTC
*
9922382 AAGAATTTGCTAAAGTAATGCAAA
1 AAGAATTTGATAAAGTAATGCAAA
*
9922406 AAGAATTTGATAAAGTAAT-CAAG
1 AAGAATTTGATAAAGTAATGCAAA
*
9922429 GAGAATTTGA
1 AAGAATTTGA
9922439 AATGAGCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.26
Consensus pattern (24 bp):
AAGAATTTGATAAAGTAATGCAAA
Found at i:9925208 original size:35 final size:36
Alignment explanation
Indices: 9925143--9925213 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 36
9925133 AAAGATTATC
* * *
9925143 GCTTGATCTCGTTAAAAAGCAAGTATAAGGGGTATT
1 GCTTGATCCCATTAAAAAGCAAGTACAAGGGGTATT
* *
9925179 GCTTGATCCCATT-AAAAGCAAGTGCAAGGGTTATT
1 GCTTGATCCCATTAAAAAGCAAGTACAAGGGGTATT
9925214 AGTGTAAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (36 bp):
GCTTGATCCCATTAAAAAGCAAGTACAAGGGGTATT
Found at i:9930456 original size:43 final size:43
Alignment explanation
Indices: 9930395--9930477 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
9930385 CTCCAAAGAG
* *
9930395 ACAAGAAAAATTGATATCTGAAG-AGGCAAGAATCGATTCTCAA
1 ACAAGAAAAACTGATATCTCAAGAAGG-AAGAATCGATTCTCAA
*
9930438 ACAAGAAAAACTGATATCTCAAGAATGAAGAATCGATTCT
1 ACAAGAAAAACTGATATCTCAAGAAGGAAGAATCGATTCT
9930478 TAAAAACTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 34 0.94
44 2 0.06
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (43 bp):
ACAAGAAAAACTGATATCTCAAGAAGGAAGAATCGATTCTCAA
Found at i:9931085 original size:28 final size:28
Alignment explanation
Indices: 9930966--9931102 Score: 91
Period size: 28 Copynumber: 4.8 Consensus size: 28
9930956 ATGTTATTAA
* *
9930966 GGTTATGCTTGATCCTTGAAAAGGC-TAA
1 GGTTATGCTTAATCCTTGAAAAGGCAT-G
* * *
9930994 GGTTATG-TCTAATCCTTG-TAAGGTAAAAG
1 GGTTATGCT-TAATCCTTGAAAAGG--CATG
* * * * *
9931023 GGTTAAGCTTAAGCCTTTAAAAAGTAGTG
1 GGTTATGCTTAATCCTTGAAAAGGCA-TG
*
9931052 AGGTTATGCTTGATCCTTGAAAAGGCATG
1 -GGTTATGCTTAATCCTTGAAAAGGCATG
*
9931081 GGTTATGCTTAATCCATGAAAA
1 GGTTATGCTTAATCCTTGAAAA
9931103 ACAGCCATTT
Statistics
Matches: 81, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
27 5 0.06
28 36 0.44
29 16 0.20
30 24 0.30
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.32
Consensus pattern (28 bp):
GGTTATGCTTAATCCTTGAAAAGGCATG
Found at i:9936805 original size:54 final size:55
Alignment explanation
Indices: 9936704--9936889 Score: 161
Period size: 54 Copynumber: 3.5 Consensus size: 55
9936694 ATTCAGTGGA
* * * * *
9936704 AAATGCTTTTCTAAC-AAAAAATTCT-ATTGAAAATTTCTTGCGGAATTCCGTTAG
1 AAATGCTTTTCTAACTAGAAAATTCTGTTTG-AAATTTCTTGCGAAATTCCATGAG
* *
9936758 AAATGCTTTT-TAACTAGAAAATTCTGTTTGAAATTTCTTAG-TAAATTCCATGGG
1 AAATGCTTTTCTAACTAGAAAATTCTGTTTGAAATTTCTT-GCGAAATTCCATGAG
* * * * * *
9936812 AAATACTTTTCTAA-TAGAAAATTCAGTTGGAAATTT-TTGACAAAATTTCATGGG
1 AAATGCTTTTCTAACTAGAAAATTCTGTTTGAAATTTCTTG-CGAAATTCCATGAG
* *
9936866 AAATGCTTTTCCAA-TGGAAAATTC
1 AAATGCTTTTCTAACTAGAAAATTC
9936890 CATTGGCAAT
Statistics
Matches: 111, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
52 1 0.01
53 6 0.05
54 97 0.87
55 7 0.06
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (55 bp):
AAATGCTTTTCTAACTAGAAAATTCTGTTTGAAATTTCTTGCGAAATTCCATGAG
Found at i:9936901 original size:54 final size:54
Alignment explanation
Indices: 9936800--9936938 Score: 181
Period size: 54 Copynumber: 2.6 Consensus size: 54
9936790 ATTTCTTAGT
* * * ***
9936800 AAATTCCATGGGAAATACTTTTCTAATAGAAAATTCAGTTGGAAATTTTTGACA
1 AAATTCCATGGGAAATGCTTTTCCAATGGAAAATTCAGTTGGAAATTTCCAACA
* *
9936854 AAATTTCATGGGAAATGCTTTTCCAATGGAAAATTCCA-TTGGCAATTTCCAACA
1 AAATTCCATGGGAAATGCTTTTCCAATGGAAAATT-CAGTTGGAAATTTCCAACA
*
9936908 GAATTCCATGGGAAATGCTTTTCCAATGGAA
1 AAATTCCATGGGAAATGCTTTTCCAATGGAA
9936939 TTTTACGGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 72 0.97
55 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (54 bp):
AAATTCCATGGGAAATGCTTTTCCAATGGAAAATTCAGTTGGAAATTTCCAACA
Found at i:9937828 original size:12 final size:12
Alignment explanation
Indices: 9937807--9937840 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
9937797 TTGTTTTCAT
9937807 ATTG-TTTATTC
1 ATTGATTTATTC
9937818 ATTGATTTATTC
1 ATTGATTTATTC
*
9937830 ATTAATTTATT
1 ATTGATTTATT
9937841 TTTGGCACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (12 bp):
ATTGATTTATTC
Found at i:9938175 original size:5 final size:5
Alignment explanation
Indices: 9938165--9938189 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9938155 TCATTTAATG
9938165 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
9938190 TTCAATTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:9942675 original size:23 final size:21
Alignment explanation
Indices: 9942649--9942693 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
9942639 AGAAAAAAAC
*
9942649 AGAAAGCTATTAACATTTGCACA
1 AGAAAGCTATGAA-ATTT-CACA
*
9942672 AGAAAGTTATGAAATTTCACA
1 AGAAAGCTATGAAATTTCACA
9942693 A
1 A
9942694 TGGAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 11 0.55
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (21 bp):
AGAAAGCTATGAAATTTCACA
Found at i:9949069 original size:20 final size:19
Alignment explanation
Indices: 9949037--9949074 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
9949027 TGTTAAGTGA
9949037 TTAATTTAAGTTATTTTAG
1 TTAATTTAAGTTATTTTAG
*
9949056 TTAATTTTAGGTTATTTTA
1 TTAA-TTTAAGTTATTTTA
9949075 TTTTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (19 bp):
TTAATTTAAGTTATTTTAG
Found at i:9949760 original size:12 final size:13
Alignment explanation
Indices: 9949745--9949780 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
9949735 AGAGATTTTT
9949745 GAGGCAGCAAGA-
1 GAGGCAGCAAGAG
9949757 GAGGCAGCAA-AG
1 GAGGCAGCAAGAG
9949769 GAGGCAGCAAGA
1 GAGGCAGCAAGA
9949781 AATTATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (13 bp):
GAGGCAGCAAGAG
Found at i:9955160 original size:21 final size:22
Alignment explanation
Indices: 9955131--9955174 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
9955121 AAGTGATTAA
9955131 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
9955152 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
9955174 T
1 T
9955175 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:9955844 original size:12 final size:13
Alignment explanation
Indices: 9955829--9955862 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
9955819 GATTTTTGAG
9955829 GGCAGCAAGA-GA
1 GGCAGCAAGAGGA
9955841 GGCAGCAA-AGGA
1 GGCAGCAAGAGGA
9955853 GGCAGCAAGA
1 GGCAGCAAGA
9955863 AACTATTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.41, C:0.18, G:0.41, T:0.00
Consensus pattern (13 bp):
GGCAGCAAGAGGA
Found at i:9958478 original size:28 final size:28
Alignment explanation
Indices: 9958447--9958586 Score: 145
Period size: 29 Copynumber: 4.8 Consensus size: 28
9958437 CAATATTTTA
* * *
9958447 TCTTATCTAAATTGAGACAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
9958475 TCTTGTTTAGATTAAGACAAAAAAAATGCTTT
1 TCTTGTCTAAATTAAGAC---AAACATG-TTT
* *
9958507 TCTTGTCTTGAATTAAGACAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
*
9958536 TCTTGTCTAAATTAAGATCAAACATGGTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
9958565 TCTTGTCTAAATTAAGACAAAC
1 TCTTGTCTAAATTAAGACAAAC
9958587 CTATTAAAGT
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
28 28 0.30
29 36 0.39
30 5 0.05
31 6 0.06
32 9 0.10
33 9 0.10
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:9958541 original size:29 final size:28
Alignment explanation
Indices: 9958426--9958591 Score: 136
Period size: 29 Copynumber: 5.6 Consensus size: 28
9958416 TCTTACTTTT
*
9958426 AATTAAGAC-AACAATATTTTATCTTATCTA
1 AATTAAGACAAAC-ATA-TTT-TCTTGTCTA
* * * *
9958456 AATTGAGACAAATATGTTTTCTTGTTTA
1 AATTAAGACAAACATATTTTCTTGTCTA
* * * *
9958484 GATTAAGACAAAAAAAATGCTTTTCTTGTCTTG
1 AATTAAGAC---AAACAT-ATTTTCTTGTC-TA
9958517 AATTAAGACAAACATATTTTCTTGTCTA
1 AATTAAGACAAACATATTTTCTTGTCTA
**
9958545 AATTAAGATCAAACATGGTTTCTTGTCTA
1 AATTAAGA-CAAACATATTTTCTTGTCTA
*
9958574 AATTAAGACAAACCTATT
1 AATTAAGACAAACATATT
9958592 AAAGTTGCCA
Statistics
Matches: 109, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
28 30 0.28
29 39 0.36
30 15 0.14
31 7 0.06
32 9 0.08
33 9 0.08
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
AATTAAGACAAACATATTTTCTTGTCTA
Found at i:9959064 original size:39 final size:39
Alignment explanation
Indices: 9959010--9959091 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
9959000 TTGAGTATTT
* *
9959010 AGATGTGATGTGTAGCTAATTCATCAATCCATTGGGTCC
1 AGATGTGATGTGTAGCTAATTCATCAATCCACTAGGTCC
9959049 AGATGTGATGTGTAGCTAATTCATCAATCCACTAGGTCC
1 AGATGTGATGTGTAGCTAATTCATCAATCCACTAGGTCC
9959088 AGAT
1 AGAT
9959092 TAATTACCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (39 bp):
AGATGTGATGTGTAGCTAATTCATCAATCCACTAGGTCC
Found at i:9960441 original size:73 final size:74
Alignment explanation
Indices: 9960268--9960452 Score: 212
Period size: 73 Copynumber: 2.5 Consensus size: 74
9960258 TCTTAGTTTA
* * * * * ** *
9960268 CTAACCATTCTTCCTAGTCGATTAAGTCTTCTTTGTCTTGTAATTGAATTATTTAGAAATGATCT
1 CTAACCATACTTCTTAGTCGATTAAGTCTTCTCTATCTTGCAATCAAATTATTTAGAAATGAGCT
9960333 CTTAATTGG
66 CTTAATTGG
* * *
9960342 CTAACCATGCTTCTTAGTCGACTAAGTCTTCTCTATCTTGCAATCAAATT-TTT-GACCATGAGC
1 CTAACCATACTTCTTAGTCGATTAAGTCTTCTCTATCTTGCAATCAAATTATTTAGA-AATGAGC
* *
9960405 TTTTAGTTGG
65 TCTTAATTGG
* *
9960415 CTAACCATACTTTTTAGTCGATTAAGTCTTTTCTATCT
1 CTAACCATACTTCTTAGTCGATTAAGTCTTCTCTATCT
9960453 CACAATCTAC
Statistics
Matches: 94, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
72 2 0.02
73 50 0.53
74 42 0.45
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.43
Consensus pattern (74 bp):
CTAACCATACTTCTTAGTCGATTAAGTCTTCTCTATCTTGCAATCAAATTATTTAGAAATGAGCT
CTTAATTGG
Found at i:9960862 original size:17 final size:17
Alignment explanation
Indices: 9960842--9960876 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9960832 TGAGGAATTT
*
9960842 CTCCCCCTGAGTGTATG
1 CTCCCCCTGAATGTATG
*
9960859 CTCCCCCTTAATGTATG
1 CTCCCCCTGAATGTATG
9960876 C
1 C
9960877 ATGATCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.37, G:0.17, T:0.31
Consensus pattern (17 bp):
CTCCCCCTGAATGTATG
Found at i:9965045 original size:21 final size:20
Alignment explanation
Indices: 9965019--9965163 Score: 130
Period size: 21 Copynumber: 6.9 Consensus size: 20
9965009 TATTACTTCG
9965019 ATGATCTTTGAACTTGTTTGA
1 ATGAT-TTTGAACTTGTTTGA
9965040 ATGATCTTTGAACTTGTTTGA
1 ATGAT-TTTGAACTTGTTTGA
*
9965061 ATGATCTTTGAACTTATTTGA
1 ATGAT-TTTGAACTTGTTTGA
* *
9965082 ATGA-TTTGCAAAATTGCTTGA
1 ATGATTTTG--AACTTGTTTGA
* *
9965103 ATGAGTTTTGAAATTGCTTGA
1 ATGA-TTTTGAACTTGTTTGA
* *
9965124 ATTAATTTTGAACTTGGTTGA
1 A-TGATTTTGAACTTGTTTGA
* *
9965145 ATAGTTTTTAAACTTGTTT
1 AT-GATTTTGAACTTGTTT
9965164 AAATAAGTTT
Statistics
Matches: 107, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
19 4 0.04
20 1 0.01
21 96 0.90
22 2 0.02
23 4 0.04
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.47
Consensus pattern (20 bp):
ATGATTTTGAACTTGTTTGA
Found at i:9965168 original size:21 final size:23
Alignment explanation
Indices: 9965129--9965180 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
9965119 CTTGAATTAA
* *
9965129 TTTTGAACTTGGTTGAAT-AG-T
1 TTTTAAACTTGGTTAAATAAGTT
*
9965150 TTTTAAACTTGTTTAAATAAGTT
1 TTTTAAACTTGGTTAAATAAGTT
9965173 TTTTAAAC
1 TTTTAAAC
9965181 CTCACTTGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
22 2 0.08
23 9 0.35
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (23 bp):
TTTTAAACTTGGTTAAATAAGTT
Found at i:9965342 original size:20 final size:20
Alignment explanation
Indices: 9965319--9965357 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9965309 TGGTTCTAGC
*
9965319 CAAAATCTATGGATAGATTG
1 CAAAAACTATGGATAGATTG
*
9965339 CAAAAACTATTGATAGATT
1 CAAAAACTATGGATAGATT
9965358 TTGGGATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (20 bp):
CAAAAACTATGGATAGATTG
Found at i:9965975 original size:12 final size:12
Alignment explanation
Indices: 9965958--9965982 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9965948 GTATTTTTTT
9965958 AAATTAATAAAA
1 AAATTAATAAAA
9965970 AAATTAATAAAA
1 AAATTAATAAAA
9965982 A
1 A
9965983 TTATATAATA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATTAATAAAA
Found at i:9979423 original size:19 final size:16
Alignment explanation
Indices: 9979387--9979428 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 16
9979377 CTACAAAAAC
9979387 ATAAAACTTGACTTAA
1 ATAAAACTTGACTTAA
9979403 ATAATAACTTAGACTTAAA
1 ATAA-AACTT-GACTT-AA
9979422 ATAAAAC
1 ATAAAAC
9979429 ATCATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.17
17 5 0.22
18 8 0.35
19 6 0.26
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.29
Consensus pattern (16 bp):
ATAAAACTTGACTTAA
Found at i:9988355 original size:16 final size:16
Alignment explanation
Indices: 9988330--9988368 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
9988320 TGTGAAATTG
9988330 AGAAAAAAAAA-AAGAA
1 AGAAAAAAAAAGAA-AA
*
9988346 AGAAAGAAAAAGAAAA
1 AGAAAAAAAAAGAAAA
9988362 AGAAAAA
1 AGAAAAA
9988369 GGATGAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAAGAAAA
Found at i:9988357 original size:6 final size:6
Alignment explanation
Indices: 9988330--9988369 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
9988320 TGTGAAATTG
*
9988330 AGAAAA AAAAAA AGAAAGAA AGAAAA AGAAAA AGAAAA AG
1 AGAAAA AGAAAA AG-AA-AA AGAAAA AGAAAA AGAAAA AG
9988370 GATGAAGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 22 0.73
7 4 0.13
8 4 0.13
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:9989082 original size:21 final size:20
Alignment explanation
Indices: 9989053--9989093 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
9989043 AATTAAGTTG
9989053 TTTTAATTTAATTTAACTTTA
1 TTTTAATTTAATTT-ACTTTA
*
9989074 TTTTGATTTAATTTACTTTA
1 TTTTAATTTAATTTACTTTA
9989094 AGAAAAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTAATTTAATTTACTTTA
Found at i:9991586 original size:31 final size:31
Alignment explanation
Indices: 9991548--9991621 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
9991538 GTAACAAAAT
*
9991548 ATTATCAATATTATAACCAACTATCGTTAGC
1 ATTATCAATATTATAACCAACTATCATTAGC
*
9991579 ATTATCAATACTATAACCAACTATCATTAGC
1 ATTATCAATATTATAACCAACTATCATTAGC
*
9991610 A-TATCAACATTA
1 ATTATCAATATTA
9991622 GTAGATCATA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 9 0.23
31 30 0.77
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (31 bp):
ATTATCAATATTATAACCAACTATCATTAGC
Found at i:10002160 original size:40 final size:40
Alignment explanation
Indices: 10002112--10002189 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
10002102 TGTGAAGGAC
*
10002112 ACCAATCTTGGCAAGGTTGAAAATCCCACTAAGGTGAATT
1 ACCAATCTTGGCAAGGTTGAAAACCCCACTAAGGTGAATT
**
10002152 ACCAATCTTGGTGAGGTTGAAAACCCCACTAAGGTGAA
1 ACCAATCTTGGCAAGGTTGAAAACCCCACTAAGGTGAA
10002190 AAAATAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.23
Consensus pattern (40 bp):
ACCAATCTTGGCAAGGTTGAAAACCCCACTAAGGTGAATT
Found at i:10006470 original size:31 final size:31
Alignment explanation
Indices: 10006435--10006501 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
10006425 ATGTCTATCC
10006435 CAAAATAACACTAAAAAGTCGAATATACATT
1 CAAAATAACACTAAAAAGTCGAATATACATT
**
10006466 CAAAATTCCACTAAAAAGTCGAATATACATT
1 CAAAATAACACTAAAAAGTCGAATATACATT
10006497 CAAAA
1 CAAAA
10006502 ATCTGAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.54, C:0.18, G:0.06, T:0.22
Consensus pattern (31 bp):
CAAAATAACACTAAAAAGTCGAATATACATT
Found at i:10009970 original size:35 final size:34
Alignment explanation
Indices: 10009931--10010115 Score: 203
Period size: 35 Copynumber: 5.3 Consensus size: 34
10009921 TTAATTGTTT
10009931 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
1 AATTTAATCAATTAG-CCCAATAACTTAATTAAAC
* * *
10009966 AATTTAATTAATTATGCCTAATAACTAAATTAAAC
1 AATTTAATCAATTA-GCCCAATAACTTAATTAAAC
* *
10010001 AATTTGATCAATTAAGCCCAATAACTTGATTAAAC
1 AATTTAATCAATT-AGCCCAATAACTTAATTAAAC
* *
10010036 AAATTTAATCAATTAGGCCCAATAATTTGATTAAAC
1 -AATTTAATCAATTA-GCCCAATAACTTAATTAAAC
* * * *
10010072 AATTTAATGAATTAG-GC-ACAACTTAACTAAAC
1 AATTTAATCAATTAGCCCAATAACTTAATTAAAC
10010104 AATTTTAATCAA
1 AA-TTTAATCAA
10010116 GTGCTTGAAA
Statistics
Matches: 128, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
32 13 0.10
33 9 0.07
34 1 0.01
35 72 0.56
36 33 0.26
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (34 bp):
AATTTAATCAATTAGCCCAATAACTTAATTAAAC
Found at i:10010075 original size:71 final size:71
Alignment explanation
Indices: 10009931--10010085 Score: 206
Period size: 71 Copynumber: 2.2 Consensus size: 71
10009921 TTAATTGTTT
* * *
10009931 AATTTAATCAATT-AGACCCAATAACTTAATTAAACAATTTAATTAATTATGCCTAATAACTAAA
1 AATTTAATCAATTAAGACCCAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTAAA
10009995 TTAAAC
66 TTAAAC
* * * **
10010001 AATTTGATCAATTAAG-CCCAATAACTTGATTAAACAAATTTAATCAATTAGGCCCAATAATTTG
1 AATTTAATCAATTAAGACCCAATAACTTAATTAAAC-AATTTAATCAATTAGGCCCAATAACTAA
10010065 ATTAAAC
65 ATTAAAC
*
10010072 AATTTAATGAATTA
1 AATTTAATCAATTA
10010086 GGCACAACTT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
70 30 0.41
71 43 0.59
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (71 bp):
AATTTAATCAATTAAGACCCAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTAAA
TTAAAC
Found at i:10013736 original size:35 final size:35
Alignment explanation
Indices: 10013697--10013795 Score: 132
Period size: 35 Copynumber: 2.9 Consensus size: 35
10013687 TTAATTCAAA
10013697 TAATTAGGCCCAATAACTTAATTAAACAATTTAAT
1 TAATTAGGCCCAATAACTTAATTAAACAATTTAAT
* * *
10013732 TAATTAGGCCCAATGACGTACTTAAACAATTTAAT
1 TAATTAGGCCCAATAACTTAATTAAACAATTTAAT
* *
10013767 TAATTAGG---GACAACTTAATTAAACAATTT
1 TAATTAGGCCCAATAACTTAATTAAACAATTT
10013796 TAATCAAGNN
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
32 16 0.29
35 40 0.71
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.33
Consensus pattern (35 bp):
TAATTAGGCCCAATAACTTAATTAAACAATTTAAT
Found at i:10018341 original size:17 final size:18
Alignment explanation
Indices: 10018308--10018342 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10018298 CTAATTGTAG
10018308 AGTCCTAATCATTATTAGA
1 AGTCCTAAT-ATTATTAGA
10018327 AGTCCTAAT-TTATTAG
1 AGTCCTAATATTATTAG
10018343 TATATTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (18 bp):
AGTCCTAATATTATTAGA
Found at i:10020510 original size:36 final size:36
Alignment explanation
Indices: 10020411--10020629 Score: 231
Period size: 36 Copynumber: 6.3 Consensus size: 36
10020401 TTAATTGTTT
* * * *
10020411 ATTTTAATCAATTAAGCCCAATAACTCAATTAAATA
1 ATTTTAATCAATTAGGCCCAATGACTTAATTAAACA
* ** *
10020447 A-TTTAAT-AA-TAAGCCCAACAATTTAATTAAACA
1 ATTTTAATCAATTAGGCCCAATGACTTAATTAAACA
*
10020480 ATTTTAATCAATTAGGCCTAATGACTTAATTAAACA
1 ATTTTAATCAATTAGGCCCAATGACTTAATTAAACA
* *
10020516 ATTTTAATCAACTATGCCCAATGACTTAATTAAACA
1 ATTTTAATCAATTAGGCCCAATGACTTAATTAAACA
* *
10020552 A-TGTAA-CTAATTAGGCTCAATGACTTAATTAAACA
1 ATTTTAATC-AATTAGGCCCAATGACTTAATTAAACA
* *
10020587 A-TTTAATTAATTAGGCAC-A--ACTTAATTAAACA
1 ATTTTAATCAATTAGGCCCAATGACTTAATTAAACA
10020619 ATTTTAATCAA
1 ATTTTAATCAA
10020630 GTACTTGAGA
Statistics
Matches: 157, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
32 14 0.09
33 29 0.18
34 10 0.06
35 50 0.32
36 54 0.34
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (36 bp):
ATTTTAATCAATTAGGCCCAATGACTTAATTAAACA
Found at i:10023003 original size:77 final size:75
Alignment explanation
Indices: 10022876--10023019 Score: 225
Period size: 77 Copynumber: 1.9 Consensus size: 75
10022866 AATGTCATAT
*
10022876 ATTTTAATTTTGGGTGATTCATAAAAAATAAAAAATTATTTCCTACTTTAAAACTAATTCCTAAA
1 ATTTTAATTTTGGGTGATTCATAAAAAATAAAAAATTATTTCCTACTTTAAAA-AAATT-CTAAA
10022941 ATTAAGGATTGA
64 ATTAAGGATTGA
* ** *
10022953 ATTTTAATTTTGGGTGATTCATAAAGAATAGCAAATTGTTTCCTACTTTAAAAAAATTCTAAAAT
1 ATTTTAATTTTGGGTGATTCATAAAAAATAAAAAATTATTTCCTACTTTAAAAAAATTCTAAAAT
10023018 TA
66 TA
10023020 TGGACAATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 9 0.15
76 4 0.06
77 49 0.79
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.40
Consensus pattern (75 bp):
ATTTTAATTTTGGGTGATTCATAAAAAATAAAAAATTATTTCCTACTTTAAAAAAATTCTAAAAT
TAAGGATTGA
Found at i:10030229 original size:19 final size:18
Alignment explanation
Indices: 10030201--10030236 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
10030191 CCATAACAAA
10030201 GAAAAAAAAAAAAGAAAG
1 GAAAAAAAAAAAAGAAAG
10030219 GAAAGAAAAAAAAAGAAA
1 GAAA-AAAAAAAAAGAAA
10030237 CATACAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAAAAGAAAG
Found at i:10030245 original size:22 final size:21
Alignment explanation
Indices: 10030195--10030246 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
10030185 GTCCATCCAT
*
10030195 AACAAAGAAAAAAAAAAAAGA
1 AACAAAGAAAAAAAAAAAACA
*
10030216 AAGGAAAGAAAAAAAAAGAAACA
1 AA-CAAAGAAAAAAAAA-AAACA
*
10030239 TACAAAGA
1 AACAAAGA
10030247 GAAGGCCTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 18 0.72
23 5 0.20
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (21 bp):
AACAAAGAAAAAAAAAAAACA
Found at i:10036662 original size:11 final size:11
Alignment explanation
Indices: 10036646--10036675 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
10036636 ATTTTATTTA
10036646 TTTCTTTTCTT
1 TTTCTTTTCTT
10036657 TTTCTTTTCTT
1 TTTCTTTTCTT
10036668 TTT-TTTTC
1 TTTCTTTTC
10036676 AAAACTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:10036667 original size:16 final size:15
Alignment explanation
Indices: 10036646--10036675 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
10036636 ATTTTATTTA
10036646 TTTCTTTTCTTTTTCT
1 TTTCTTTT-TTTTTCT
10036662 TTTCTTTTTTTTTC
1 TTTCTTTTTTTTTC
10036676 AAAACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTTTTTTTCT
Found at i:10044676 original size:87 final size:87
Alignment explanation
Indices: 10044530--10044710 Score: 301
Period size: 87 Copynumber: 2.1 Consensus size: 87
10044520 TTAAGGTCAT
10044530 TTGATAATCAGTTACTAGGATTCTATTTTTATTCATTATTTGCTCTTTCCCTCTTAACTGATTAA
1 TTGATAATCAGTTACTAGGATTCTATTTTTATTCATTATTTGCTCTTTCCCTCTTAACTGATTAA
*
10044595 CTCTTCATTAAACTTAGATCTC
66 CTCTTCATTAAACTTAGATCCC
* * *
10044617 TTGATAATCAGTTACTAGGGTT-TAATTTTTGTTCATTGTTTGCTCTTTCCCTCTTAACTGATTA
1 TTGATAATCAGTTACTAGGATTCT-ATTTTTATTCATTATTTGCTCTTTCCCTCTTAACTGATTA
*
10044681 ACTCTTCATTAAACTTAGCTCCC
65 ACTCTTCATTAAACTTAGATCCC
10044704 TTGATAA
1 TTGATAA
10044711 ATAATTCCTA
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
86 1 0.01
87 87 0.99
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.46
Consensus pattern (87 bp):
TTGATAATCAGTTACTAGGATTCTATTTTTATTCATTATTTGCTCTTTCCCTCTTAACTGATTAA
CTCTTCATTAAACTTAGATCCC
Found at i:10048601 original size:33 final size:32
Alignment explanation
Indices: 10048564--10048630 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
10048554 CAATGTATGG
10048564 CTTGTAAGTGTTAAATAAATATTTGTATATGAA
1 CTTGTAAGTGTTAAATAAATA-TTGTATATGAA
* *
10048597 CTTGTAAGTGTTAAGTAAATATTGTTTATGAA
1 CTTGTAAGTGTTAAATAAATATTGTATATGAA
10048629 CT
1 CT
10048631 AAGTACCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.43
Consensus pattern (32 bp):
CTTGTAAGTGTTAAATAAATATTGTATATGAA
Found at i:10055481 original size:13 final size:12
Alignment explanation
Indices: 10055463--10055492 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10055453 CAAACAAAAC
*
10055463 AAAAAAAATTTA
1 AAAAAAAAATTA
10055475 AAAAAAAAATTA
1 AAAAAAAAATTA
10055487 AAAAAA
1 AAAAAA
10055493 GGGTTCACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:10060589 original size:16 final size:16
Alignment explanation
Indices: 10060564--10060597 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
10060554 TTAGTTTAAA
*
10060564 TTTTAGTTAATTAATT
1 TTTTAATTAATTAATT
10060580 TTTTAATTAATTAATT
1 TTTTAATTAATTAATT
10060596 TT
1 TT
10060598 GATTGTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTAATTAATTAATT
Found at i:10061664 original size:19 final size:19
Alignment explanation
Indices: 10061628--10061671 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
10061618 TTCGAAACTC
*
10061628 TTATTTTTTTTCTTTTTAG
1 TTATTTTTTTTCTATTTAG
*
10061647 TTATTTTTATTT-TATTTAT
1 TTATTTTT-TTTCTATTTAG
10061666 TTATTT
1 TTATTT
10061672 ACATTAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (19 bp):
TTATTTTTTTTCTATTTAG
Found at i:10068439 original size:14 final size:14
Alignment explanation
Indices: 10068404--10068439 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
10068394 TTTTTCCTCA
*
10068404 TTTCTCTATTTTTC
1 TTTCTCTTTTTTTC
*
10068418 CTTCTCTTTTTTTC
1 TTTCTCTTTTTTTC
10068432 TTTCTCTT
1 TTTCTCTT
10068440 GGGTGAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTCTCTTTTTTTC
Found at i:10069709 original size:174 final size:174
Alignment explanation
Indices: 10069419--10069772 Score: 564
Period size: 174 Copynumber: 2.0 Consensus size: 174
10069409 TATTATTATT
* * ** * * * *
10069419 TAATTATCATTTTCTTGTGTATGAAATATTTTATTTCAAAATATTTCTTTCGCCTATCACTTCTC
1 TAATTATCATTTTCTCGCGTACAAAATAGTTTATTCCAAAATATTCCTTTCGCCTATCACTACTC
* * * *
10069484 TTTCGCACTTAGATTTACATCCATCTGCCCTCTATCTCATCGATGATATTGTATTGGCTCTTATA
66 TTTCGCACTTAGATTTACATCCATCTACACTCCATCCCATCGATGATATTGTATTGGCTCTTATA
10069549 CGAGGGTATGGGGTGTTACAATAATACTATATACATACTGGCAG
131 CGAGGGTATGGGGTGTTACAATAATACTATATACATACTGGCAG
10069593 TAATTATCATTTTCTCGCGTACAAAATAGTTTATTCCAAAATATTCCTTTCGCCTATCACTACTC
1 TAATTATCATTTTCTCGCGTACAAAATAGTTTATTCCAAAATATTCCTTTCGCCTATCACTACTC
* *
10069658 TTTCGCACTTAGATTTACATCCATCTACAGTCCGTCCCATCGATGATATTGTATTGGCTCTTATA
66 TTTCGCACTTAGATTTACATCCATCTACACTCCATCCCATCGATGATATTGTATTGGCTCTTATA
* *
10069723 CGAGGGTATGGGTTGTTACAATAATACTATATATATACTGGCAG
131 CGAGGGTATGGGGTGTTACAATAATACTATATACATACTGGCAG
10069767 TAATTA
1 TAATTA
10069773 AATCCAAAAT
Statistics
Matches: 164, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
174 164 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (174 bp):
TAATTATCATTTTCTCGCGTACAAAATAGTTTATTCCAAAATATTCCTTTCGCCTATCACTACTC
TTTCGCACTTAGATTTACATCCATCTACACTCCATCCCATCGATGATATTGTATTGGCTCTTATA
CGAGGGTATGGGGTGTTACAATAATACTATATACATACTGGCAG
Found at i:10071666 original size:27 final size:26
Alignment explanation
Indices: 10071609--10071663 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
10071599 TTAAGAAGCC
* * *
10071609 CAATTAACTTAATTATTTAATTTAAT
1 CAATTAACTTAATAACTTAATTTAAA
10071635 CAATTAAGCTTAATAACTTAA-TTAAA
1 CAATTAA-CTTAATAACTTAATTTAAA
10071661 CAA
1 CAA
10071664 ATTTAATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (26 bp):
CAATTAACTTAATAACTTAATTTAAA
Found at i:10071713 original size:36 final size:36
Alignment explanation
Indices: 10071627--10071714 Score: 158
Period size: 36 Copynumber: 2.4 Consensus size: 36
10071617 TTAATTATTT
* *
10071627 AATTTAATCAATTAAGCTTAATAACTTAATTAAACA
1 AATTTAATCAATTAGGCCTAATAACTTAATTAAACA
10071663 AATTTAATCAATTAGGCCTAATAACTTAATTAAACA
1 AATTTAATCAATTAGGCCTAATAACTTAATTAAACA
10071699 AATTTAATCAATTAGG
1 AATTTAATCAATTAGG
10071715 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (36 bp):
AATTTAATCAATTAGGCCTAATAACTTAATTAAACA
Found at i:10073932 original size:17 final size:17
Alignment explanation
Indices: 10073910--10073942 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10073900 CTCCATTACT
10073910 AATCTTAAACATATCTC
1 AATCTTAAACATATCTC
*
10073927 AATCTTAATCATATCT
1 AATCTTAAACATATCT
10073943 ATTTTGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (17 bp):
AATCTTAAACATATCTC
Found at i:10096690 original size:5 final size:5
Alignment explanation
Indices: 10096654--10096689 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
10096644 TTTTTAGTCA
* *
10096654 TTTAT TTTAT TTTAT TTTAT TTTAT TGTAT TGTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
10096690 GGGTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:10107355 original size:73 final size:72
Alignment explanation
Indices: 10107170--10107364 Score: 196
Period size: 73 Copynumber: 2.7 Consensus size: 72
10107160 TAAACAGAAT
* * * * *
10107170 GCTCTTAGTCGACTAATCATTATCACTTAGCCGACTAAGTCGTCTCTGTCTCTGAACCCAATTTC
1 GCTCTTAGTCGACTAA-CATTCTCTCTTAGTCGACTAAGTCGTTTCTGTCTCTAAACCCAATTTC
10107235 TAGCAGTA
65 TAGCAGTA
* * ** * * **
10107243 GCCTGTTAGTCGCCTAACAAAACT-TCTTAGTTGATTAAGTCGTTTCTGTCTCTAAACCCGGTTT
1 G-CTCTTAGTCGACTAAC-ATTCTCTCTTAGTCGACTAAGTCGTTTCTGTCTCTAAACCCAATTT
10107307 CTAGCAGTAA
64 CTAGCAGT-A
* *
10107317 GCTCTTAGTTGACTAACATTCTCTCTTGGTCGACTAAGT-GTTCTCTGT
1 GCTCTTAGTCGACTAACATTCTCTCTTAGTCGACTAAGTCGTT-TCTGT
10107365 TCCATGATTT
Statistics
Matches: 96, Mismatches: 21, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
72 6 0.06
73 73 0.76
74 17 0.18
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (72 bp):
GCTCTTAGTCGACTAACATTCTCTCTTAGTCGACTAAGTCGTTTCTGTCTCTAAACCCAATTTCT
AGCAGTA
Found at i:10115541 original size:22 final size:22
Alignment explanation
Indices: 10115513--10115571 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
10115503 AGACAGAATA
*
10115513 CTCTTAGTAGACTAATCACTAT
1 CTCTTAGTCGACTAATCACTAT
*
10115535 CTCTTAGTCGACTAATCATTAT
1 CTCTTAGTCGACTAATCACTAT
*
10115557 CACTTAGTCGACTAA
1 CTCTTAGTCGACTAA
10115572 GTCATCTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (22 bp):
CTCTTAGTCGACTAATCACTAT
Found at i:10115719 original size:73 final size:72
Alignment explanation
Indices: 10115535--10115719 Score: 176
Period size: 73 Copynumber: 2.5 Consensus size: 72
10115525 TAATCACTAT
*
10115535 CTCTTAGTCGACTAATCATTATCACTTAGTCGACTAAGTCATCTCTGTCTCTGAACTCAATTTCT
1 CTCTTAGTCGACTAA-CA-TATCTCTTAGTCGACTAAGTCATCTCTGTCTCTGAACTCAATTTCT
*
10115600 AACAGTAGC
64 AACAATAGC
* * * * * * * *
10115609 CTCTTAGTTGACTAACAAAACTTCTTAGTCAATTAAGTCATTTCTGTCTCTGAAC-CTGATTTTT
1 CTCTTAGTCGACTAACATATC-TCTTAGTCGACTAAGTCATCTCTGTCTCTGAACTC-AATTTCT
**
10115673 GGCAATAAG-
64 AACAAT-AGC
* *
10115682 CTCTTAGTCGACTAACACTGTCTCTTGGTCGACTAAGT
1 CTCTTAGTCGACTAACA-TATCTCTTAGTCGACTAAGT
10115720 GTTCTCTATT
Statistics
Matches: 88, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
72 3 0.03
73 68 0.77
74 17 0.19
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (72 bp):
CTCTTAGTCGACTAACATATCTCTTAGTCGACTAAGTCATCTCTGTCTCTGAACTCAATTTCTAA
CAATAGC
Found at i:10126944 original size:19 final size:18
Alignment explanation
Indices: 10126915--10126952 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
10126905 TCTATAATTA
*
10126915 TTTAGTTAATTAATTATT
1 TTTAGTTAATTAATCATT
10126933 TTTAGTTTAATTAATCATT
1 TTTAG-TTAATTAATCATT
10126952 T
1 T
10126953 GAAATTGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTAGTTAATTAATCATT
Found at i:10129704 original size:3 final size:3
Alignment explanation
Indices: 10129696--10129720 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10129686 CTAACTATAC
10129696 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
10129721 TTCTTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:10133249 original size:30 final size:30
Alignment explanation
Indices: 10133215--10133272 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
10133205 TGGTTGCATG
*
10133215 TCCTT-AAAAATGTAGTGTAAAGGTTATAGC
1 TCCTTGAAAAA-GTAGTGCAAAGGTTATAGC
* *
10133245 TCCTTGAAAAAGTGGTGCCAAGGTTATA
1 TCCTTGAAAAAGTAGTGCAAAGGTTATA
10133273 CTTCCAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (30 bp):
TCCTTGAAAAAGTAGTGCAAAGGTTATAGC
Found at i:10144975 original size:188 final size:188
Alignment explanation
Indices: 10144658--10145031 Score: 748
Period size: 188 Copynumber: 2.0 Consensus size: 188
10144648 GCAATAGATC
10144658 TTATAGATTGAAGTATATGGGACACTTGAGGATAACATGTCGGTGCTTGTTAAAGAACAAGTTCA
1 TTATAGATTGAAGTATATGGGACACTTGAGGATAACATGTCGGTGCTTGTTAAAGAACAAGTTCA
10144723 CTGAACATGACTAAAACCTGTTAAAATTACAAGACACTAAGCAAGGAAGGGTAGAGAGCAGTGGA
66 CTGAACATGACTAAAACCTGTTAAAATTACAAGACACTAAGCAAGGAAGGGTAGAGAGCAGTGGA
10144788 CAATGCAAGAGTATTTATAGTGGTTGGGTCCCCTTGACCTACATCCACTACCTTGAGG
131 CAATGCAAGAGTATTTATAGTGGTTGGGTCCCCTTGACCTACATCCACTACCTTGAGG
10144846 TTATAGATTGAAGTATATGGGACACTTGAGGATAACATGTCGGTGCTTGTTAAAGAACAAGTTCA
1 TTATAGATTGAAGTATATGGGACACTTGAGGATAACATGTCGGTGCTTGTTAAAGAACAAGTTCA
10144911 CTGAACATGACTAAAACCTGTTAAAATTACAAGACACTAAGCAAGGAAGGGTAGAGAGCAGTGGA
66 CTGAACATGACTAAAACCTGTTAAAATTACAAGACACTAAGCAAGGAAGGGTAGAGAGCAGTGGA
10144976 CAATGCAAGAGTATTTATAGTGGTTGGGTCCCCTTGACCTACATCCACTACCTTGA
131 CAATGCAAGAGTATTTATAGTGGTTGGGTCCCCTTGACCTACATCCACTACCTTGA
10145032 TCTCTCAATA
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 186 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (188 bp):
TTATAGATTGAAGTATATGGGACACTTGAGGATAACATGTCGGTGCTTGTTAAAGAACAAGTTCA
CTGAACATGACTAAAACCTGTTAAAATTACAAGACACTAAGCAAGGAAGGGTAGAGAGCAGTGGA
CAATGCAAGAGTATTTATAGTGGTTGGGTCCCCTTGACCTACATCCACTACCTTGAGG
Found at i:10158022 original size:18 final size:17
Alignment explanation
Indices: 10157993--10158027 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10157983 TATTTTCTAG
*
10157993 CTTTTGAAAATATCCAA
1 CTTTTGAAAATAACCAA
10158010 CTTTTGAAAAATAACCAA
1 CTTTTG-AAAATAACCAA
10158028 AGTCAATAAA
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:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (17 bp):
CTTTTGAAAATAACCAA
Found at i:10161117 original size:25 final size:25
Alignment explanation
Indices: 10161087--10161141 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
10161077 CGCAACTACG
*
10161087 TATATCAACTTGTGGCCTAACCACA
1 TATATCAACCTGTGGCCTAACCACA
**
10161112 TATATCAACCTGTGGCCTTGCCACA
1 TATATCAACCTGTGGCCTAACCACA
10161137 TATAT
1 TATAT
10161142 ATCACAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (25 bp):
TATATCAACCTGTGGCCTAACCACA
Found at i:10161726 original size:21 final size:22
Alignment explanation
Indices: 10161700--10161740 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10161690 AGAAAATTGG
* *
10161700 CAATGTTTA-TTTATCGAATAT
1 CAATGTATAGTTTATAGAATAT
10161721 CAATGTATAGTTTATAGAAT
1 CAATGTATAGTTTATAGAAT
10161741 TTGAAATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (22 bp):
CAATGTATAGTTTATAGAATAT
Found at i:10164549 original size:8 final size:8
Alignment explanation
Indices: 10164529--10164584 Score: 69
Period size: 8 Copynumber: 7.0 Consensus size: 8
10164519 AGATTCGGCT
10164529 AGGAAGCAA
1 AGGAAG-AA
10164538 AGGAAGAA
1 AGGAAGAA
10164546 AGGAAGAA
1 AGGAAGAA
**
10164554 AAAAAGAA
1 AGGAAGAA
*
10164562 AAG-AGAA
1 AGGAAGAA
10164569 AGGAAGAA
1 AGGAAGAA
10164577 AGGAAGAA
1 AGGAAGAA
10164585 GGGGAGAGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
7 6 0.14
8 30 0.71
9 6 0.14
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (8 bp):
AGGAAGAA
Found at i:10168716 original size:24 final size:24
Alignment explanation
Indices: 10168676--10168721 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
10168666 ACTAGAAAAG
*
10168676 GAAAAAGAGATATAAGCTAAACAA
1 GAAAAAGAGATATAAGCAAAACAA
*
10168700 GAAAATGAGA-ATGAAGCAAAAC
1 GAAAAAGAGATAT-AAGCAAAAC
10168722 TATAAGCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.61, C:0.09, G:0.20, T:0.11
Consensus pattern (24 bp):
GAAAAAGAGATATAAGCAAAACAA
Found at i:10168993 original size:26 final size:26
Alignment explanation
Indices: 10168957--10169008 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
10168947 TCTAGTAAAG
10168957 GTAAAAAGACAATGGAAATGAAGACT
1 GTAAAAAGACAATGGAAATGAAGACT
10168983 GTAAAAAGACAATGGAAATGAAGACT
1 GTAAAAAGACAATGGAAATGAAGACT
10169009 AACTCTCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (26 bp):
GTAAAAAGACAATGGAAATGAAGACT
Found at i:10184635 original size:6 final size:6
Alignment explanation
Indices: 10184619--10184657 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
10184609 CCTGTTAGAA
*
10184619 ATATAG GTATAG ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATA
10184658 GATTAGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:10192693 original size:22 final size:22
Alignment explanation
Indices: 10192659--10192704 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
10192649 TTGAGAAAGT
10192659 TTGCATCTTCAAAAAT-GAATTA
1 TTGCATCTTC-AAAATGGAATTA
10192681 TTGCAT-TTACAAAATGGAATTA
1 TTGCATCTT-CAAAATGGAATTA
10192703 TT
1 TT
10192705 TACGTTGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
TTGCATCTTCAAAATGGAATTA
Found at i:10192975 original size:21 final size:21
Alignment explanation
Indices: 10192944--10193030 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
10192934 AAAAATAGTC
* *
10192944 AAAATTACTTGAATGAGTTTT
1 AAAATTGCTTGAATAAGTTTT
*
10192965 AGAATTGCTTGAATAAGTTTT
1 AAAATTGCTTGAATAAGTTTT
10192986 AAAATTGCTTGAATAAGTTTT
1 AAAATTGCTTGAATAAGTTTT
* * * * *
10193007 GAACTTGTTTAAATATGTTTT
1 AAAATTGCTTGAATAAGTTTT
10193028 AAA
1 AAA
10193031 CCTCTACATT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (21 bp):
AAAATTGCTTGAATAAGTTTT
Found at i:10192991 original size:42 final size:42
Alignment explanation
Indices: 10192944--10193030 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
10192934 AAAAATAGTC
* *
10192944 AAAATTACTTGAATGAGTTTTAGAA-TTGCTTGAATAAGTTTT
1 AAAATTACTTGAATAAGTTTT-GAACTTGCTTAAATAAGTTTT
* * *
10192986 AAAATTGCTTGAATAAGTTTTGAACTTGTTTAAATATGTTTT
1 AAAATTACTTGAATAAGTTTTGAACTTGCTTAAATAAGTTTT
10193028 AAA
1 AAA
10193031 CCTCTACATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 3 0.08
42 36 0.92
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (42 bp):
AAAATTACTTGAATAAGTTTTGAACTTGCTTAAATAAGTTTT
Found at i:10193199 original size:21 final size:21
Alignment explanation
Indices: 10193173--10193220 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
10193163 TCTAGATGCT
10193173 AAGTATGGATACCTACCTTAA
1 AAGTATGGATACCTACCTTAA
* * *
10193194 AGGTATGGATACTTGCCTTAA
1 AAGTATGGATACCTACCTTAA
10193215 AAGTAT
1 AAGTAT
10193221 CAATACCAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (21 bp):
AAGTATGGATACCTACCTTAA
Found at i:10194703 original size:74 final size:71
Alignment explanation
Indices: 10194573--10194764 Score: 163
Period size: 72 Copynumber: 2.6 Consensus size: 71
10194563 TCCAATGTGT
* * ** * *
10194573 TTTGCTTGGTCAAGTCTCGATA-TTAAAAGGCCAACTCTTGATACTTTCGGGTTTTTTTTTTTTA
1 TTTGCTTGGTCAAGTCTCAATACTT-CAAGG-CATGTCTTGATACTTTCGGG--TTTTTTGTCTA
**
10194637 TTAAATGAGC
62 CCAAATGAGC
* **
10194647 TTTGCTTGGTCAAGTCTCAATACTTCAAGGTCATGTTTTGATACTTT-TTGTCTTTTTGTCTACC
1 TTTGCTTGGTCAAGTCTCAATACTTCAAGG-CATGTCTTGATACTTTCGGGT-TTTTTGTCTACC
* *
10194711 ATATTAGC
64 AAATGAGC
* * *
10194719 TTTGCCTAGTCAAGTTTCAATACTTCAAAGGCATGTCTTGATACTT
1 TTTGCTTGGTCAAGTCTCAATACTTC-AAGGCATGTCTTGATACTT
10194765 AACACTTGAG
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
71 1 0.01
72 51 0.53
73 5 0.05
74 38 0.39
75 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (71 bp):
TTTGCTTGGTCAAGTCTCAATACTTCAAGGCATGTCTTGATACTTTCGGGTTTTTTGTCTACCAA
ATGAGC
Found at i:10195156 original size:28 final size:28
Alignment explanation
Indices: 10195112--10195196 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
10195102 AGTATTTAAA
10195112 GGTTGTGCTTGAACCTTGAAAAGGCATT
1 GGTTGTGCTTGAACCTTGAAAAGGCATT
* *
10195140 GGTTGTGCTTGATCCTTGAAAAGGCAAT
1 GGTTGTGCTTGAACCTTGAAAAGGCATT
* * * *
10195168 GGTTATCCTTGAACCTTTAAAAGACATT
1 GGTTGTGCTTGAACCTTGAAAAGGCATT
10195196 G
1 G
10195197 TATTGAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (28 bp):
GGTTGTGCTTGAACCTTGAAAAGGCATT
Found at i:10195719 original size:28 final size:29
Alignment explanation
Indices: 10195685--10195744 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
10195675 TAGATATTCA
*
10195685 ATATATCTTG-ATAGCTATTGTGGATATT
1 ATATATCTTGTATAGCTAATGTGGATATT
*
10195713 ATATATCTTGTTTAGCTAATGTGGATATT
1 ATATATCTTGTATAGCTAATGTGGATATT
10195742 ATA
1 ATA
10195745 AATATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (29 bp):
ATATATCTTGTATAGCTAATGTGGATATT
Done.