Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 96 of 290
Found at i:29398187 original size:52 final size:49
Alignment explanation
Indices: 29398114--29398371 Score: 143
Period size: 52 Copynumber: 5.1 Consensus size: 49
29398104 TTTTCTTTAA
* *
29398114 AAAAAATCAGAACTTTTTTTAAAAATCAAAACTTTATTTTAAAAT-AGTT
1 AAAAAATCAAAACTTTTTTTAAAAATCAAAACTTTACTTTAAAATGAG-T
* *
29398163 GAAAAAGATCAAAACTTTCTTTTAAAAATTTTAAAACTTTCCTTTAAAATGAGT
1 -AAAAA-ATCAAAACTTT-TTTTAAAAA--TCAAAACTTTACTTTAAAATGAGT
* ** * *
29398217 AAAAAAACAAATTTTTATTTTAAAAATCTAAACTTTCTCCTTTAAAA--A--
1 AAAAAATCAAAACTTT-TTTTAAAAATCAAAAC-TT-TACTTTAAAATGAGT
* ** * * * *
29398265 AAAGAATCACTA-TTTTTCTTAAAAATCAAAGCTTTTATTTTGAGAT-AGTT
1 AAAAAATCAAAACTTTTT-TTAAAAATCAAAAC-TTTACTTTAAAATGAG-T
* ** * * *
29398315 AAAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTCCTTTGAAATGACT
1 --AAAAAATCAAAACTTTTTTTAAAAATCAAAACTTTACTTTAAAATGAGT
29398366 AAAAAA
1 AAAAAA
29398372 ACATATTTTT
Statistics
Matches: 160, Mismatches: 32, Indels: 33
0.71 0.14 0.15
Matches are distributed among these distances:
46 8 0.05
47 19 0.12
48 7 0.04
49 6 0.04
50 11 0.07
51 23 0.14
52 57 0.36
53 9 0.06
54 18 0.11
55 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.37
Consensus pattern (49 bp):
AAAAAATCAAAACTTTTTTTAAAAATCAAAACTTTACTTTAAAATGAGT
Found at i:29398189 original size:22 final size:22
Alignment explanation
Indices: 29398164--29398211 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
29398154 AAAATAGTTG
*
29398164 AAAAAGATCAAAACTTTCTTTT
1 AAAAAGATCAAAACTTTCCTTT
** *
29398186 AAAAATTTTAAAACTTTCCTTT
1 AAAAAGATCAAAACTTTCCTTT
29398208 AAAA
1 AAAA
29398212 TGAGTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAAGATCAAAACTTTCCTTT
Found at i:29398372 original size:149 final size:149
Alignment explanation
Indices: 29398080--29398415 Score: 438
Period size: 149 Copynumber: 2.3 Consensus size: 149
29398070 ACGGTGGTCG
**
29398080 AATTTTCT-TTTTACAAAAT-TAAAATTT-TCTTT--AAAAAA-AATCAGAACTTTTTTTAAAAA
1 AATTTT-TATTTTA-AAAATCTAAAATTTCTCTTTAAAAAAAAGAATCACTA-TTTTTTTAAAAA
* * *
29398139 TCAAAACTTTATTTTAAAATAGTTGAAAAAGATCAAAACTTTCTTTTAAAAATTTTAAAACTTTC
63 TCAAAACTTTATTTTAAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAATTTTAAAACTTTC
*
29398204 CTTTAAAATGAGTAAAAAAACA
128 CTTTAAAATGACTAAAAAAACA
*
29398226 AATTTTTATTTTAAAAATCTAAACTTTCTCCTTTAAAAAAAAGAATCACTATTTTTCTTAAAAAT
1 AATTTTTATTTTAAAAATCTAAAATTTCT-CTTTAAAAAAAAGAATCACTATTTTT-TTAAAAAT
* * *
29398291 CAAAGCTTTTATTTTGAGATAGTTAAAAAAAATCAAAACTTT-ATTTAAAAA-TTT-AAACTTTC
64 CAAAAC-TTTATTTTAAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAATTTTAAAACTTTC
*
29398353 CTTTGAAATGACTAAAAAAACA
128 CTTTAAAATGACTAAAAAAACA
* *
29398375 TATTTTTATTTTTAAAATCTAAAATTTCTCTTTAAAAAAAA
1 AATTTTTATTTTAAAAATCTAAAATTTCTCTTTAAAAAAAA
29398416 ATCAAAACTT
Statistics
Matches: 167, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
145 6 0.04
146 18 0.11
147 1 0.01
148 16 0.10
149 54 0.32
150 14 0.08
151 27 0.16
152 31 0.19
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (149 bp):
AATTTTTATTTTAAAAATCTAAAATTTCTCTTTAAAAAAAAGAATCACTATTTTTTTAAAAATCA
AAACTTTATTTTAAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAATTTTAAAACTTTCCTT
TAAAATGACTAAAAAAACA
Found at i:29398770 original size:12 final size:12
Alignment explanation
Indices: 29398750--29398783 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29398740 TAATAACATT
*
29398750 TAATAATAATGG
1 TAATAATAATGA
*
29398762 TAGTAATAATGA
1 TAATAATAATGA
29398774 TAATAATAAT
1 TAATAATAAT
29398784 AATTTGCGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (12 bp):
TAATAATAATGA
Found at i:29399720 original size:10 final size:10
Alignment explanation
Indices: 29399707--29399741 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
29399697 CTTTTATCTT
*
29399707 TCTTTAATTA
1 TCTTTATTTA
29399717 TCTTTATTTA
1 TCTTTATTTA
*
29399727 TCTGTATTTA
1 TCTTTATTTA
29399737 TCTTT
1 TCTTT
29399742 TAGAATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (10 bp):
TCTTTATTTA
Found at i:29400509 original size:40 final size:38
Alignment explanation
Indices: 29400463--29400540 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 38
29400453 CGGAATTTCA
*
29400463 ATCAAAACTTTTAATTCTGTTTTTATTTTATTTTTTCCAG
1 ATCAAAACTTTTAATTCTGTTTTT-TTAT-TTTTTTCCAG
29400503 ATCAAAACTTTTAATTCTGTTTTTTTATTTTTTTCCAG
1 ATCAAAACTTTTAATTCTGTTTTTTTATTTTTTTCCAG
29400541 GTACGCAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 10 0.27
39 3 0.08
40 24 0.65
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (38 bp):
ATCAAAACTTTTAATTCTGTTTTTTTATTTTTTTCCAG
Found at i:29408516 original size:33 final size:33
Alignment explanation
Indices: 29408474--29408545 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
29408464 TTTACACATG
* *
29408474 TATATTTTTATTACCATACAATTATCTACTATT
1 TATATTTTTATTACCACACAATTATCTACCATT
29408507 TATATTTTTATTACCACACAATTATCTACCATT
1 TATATTTTTATTACCACACAATTATCTACCATT
29408540 TA-ATTT
1 TATATTT
29408546 ATTTAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
32 4 0.11
33 33 0.89
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (33 bp):
TATATTTTTATTACCACACAATTATCTACCATT
Found at i:29410934 original size:29 final size:29
Alignment explanation
Indices: 29410892--29410966 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
29410882 GAAATATTTT
*
29410892 CATGGCCCGAAGCCAAAACATCTGATATG
1 CATGGCCCAAAGCCAAAACATCTGATATG
*
29410921 CATGGCCCAAAGCCAAAACATTTGATATG
1 CATGGCCCAAAGCCAAAACATCTGATATG
*
29410950 CATGGCCCAAAGTCAAA
1 CATGGCCCAAAGCCAAA
29410967 TCAGTATAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (29 bp):
CATGGCCCAAAGCCAAAACATCTGATATG
Found at i:29415087 original size:6 final size:6
Alignment explanation
Indices: 29415072--29415140 Score: 97
Period size: 6 Copynumber: 11.5 Consensus size: 6
29415062 TTTGAGTCCC
29415072 TTTA-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-T
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
29415118 TTTATT TTCTCTT ATTTATT TTT
1 TTTATT TT-TATT -TTTATT TTT
29415141 GAAGACTTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
5 9 0.16
6 41 0.71
7 6 0.10
8 2 0.03
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:29416152 original size:4 final size:4
Alignment explanation
Indices: 29416145--29416215 Score: 133
Period size: 4 Copynumber: 17.8 Consensus size: 4
29416135 CTTAAAAAAA
*
29416145 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAA ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
29416193 ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATA
29416216 TTAGTAGTAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 65 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:29419471 original size:21 final size:23
Alignment explanation
Indices: 29419424--29419477 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
29419414 TATTCAAGAT
**
29419424 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
29419447 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
29419468 AAAAT-ATATA
1 AAAATAATATA
29419478 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:29419720 original size:29 final size:28
Alignment explanation
Indices: 29419652--29419750 Score: 71
Period size: 29 Copynumber: 3.4 Consensus size: 28
29419642 TATATATAAA
* * *
29419652 AAATAATAAT-GAAAATAATATTAGTATAT
1 AAATAATAATAG-AAA-AATATAAATAGAT
29419681 AAATAGA-AATA-AAAATATAATAAATAGA-
1 AAATA-ATAATAGAAAA-AT-ATAAATAGAT
*
29419709 AATATAATAATAGTAGAAATATAAATAGAT
1 AA-ATAATAATAG-AAAAATATAAATAGAT
29419739 AAATAATAATAG
1 AAATAATAATAG
29419751 TATTAGAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
27 1 0.02
28 8 0.14
29 40 0.70
30 5 0.09
31 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (28 bp):
AAATAATAATAGAAAAATATAAATAGAT
Found at i:29419727 original size:17 final size:15
Alignment explanation
Indices: 29419687--29419732 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
29419677 ATATAAATAG
*
29419687 AAATAAAAATATAAT
1 AAATAGAAATATAAT
29419702 AAATAGAAATATAAT
1 AAATAGAAATATAAT
29419717 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
29419733 ATAGATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:29419732 original size:14 final size:15
Alignment explanation
Indices: 29419712--29419752 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
29419702 AAATAGAAAT
29419712 ATAATAATAGTAGAA
1 ATAATAATAGTAGAA
*
29419727 AT-ATAAATAG-ATAA
1 ATAAT-AATAGTAGAA
29419741 ATAATAATAGTA
1 ATAATAATAGTA
29419753 TTAGAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (15 bp):
ATAATAATAGTAGAA
Found at i:29419747 original size:15 final size:14
Alignment explanation
Indices: 29419687--29419747 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 14
29419677 ATATAAATAG
*
29419687 AAATAAAAATATAAT
1 AAATAGAAA-ATAAT
29419702 AAATAGAAATATAAT
1 AAATAGAAA-ATAAT
29419717 -AATAGTAGAAAT-AT
1 AAATAG-A-AAATAAT
29419731 AAATAGATAAATAAT
1 AAATAGA-AAATAAT
29419746 AA
1 AA
29419748 TAGTATTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 12 0.30
15 26 0.65
16 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (14 bp):
AAATAGAAAATAAT
Found at i:29423091 original size:18 final size:18
Alignment explanation
Indices: 29423050--29423085 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29423040 ACAGTGGGTG
29423050 AAATTAGGTTTTCAAGTC
1 AAATTAGGTTTTCAAGTC
29423068 AAATTAGGTTTTCAAGTC
1 AAATTAGGTTTTCAAGTC
29423086 TTATTAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
AAATTAGGTTTTCAAGTC
Found at i:29429213 original size:23 final size:23
Alignment explanation
Indices: 29429183--29429230 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
29429173 CGATCACATA
29429183 ATTAAGAGATTAAGTGAGCAACC
1 ATTAAGAGATTAAGTGAGCAACC
29429206 ATTAAGAGATTAAGTGAGCAACC
1 ATTAAGAGATTAAGTGAGCAACC
29429229 AT
1 AT
29429231 CGCATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (23 bp):
ATTAAGAGATTAAGTGAGCAACC
Found at i:29436482 original size:16 final size:17
Alignment explanation
Indices: 29436448--29436482 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29436438 GTTTTGTCCA
*
29436448 TTTATGGTTTTGGACTT
1 TTTATGGTTTTGAACTT
29436465 TTTATGGTTTT-AACTT
1 TTTATGGTTTTGAACTT
29436481 TT
1 TT
29436483 CTAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.63
Consensus pattern (17 bp):
TTTATGGTTTTGAACTT
Found at i:29443555 original size:33 final size:33
Alignment explanation
Indices: 29443518--29443586 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
29443508 GGCTATAATG
29443518 TATACAAGTCGAAAAATCATTCTACCTATAGTC
1 TATACAAGTCGAAAAATCATTCTACCTATAGTC
*
29443551 TATACAAGTCGAAATATCATTCTACCTATAGTC
1 TATACAAGTCGAAAAATCATTCTACCTATAGTC
29443584 TAT
1 TAT
29443587 CCTATACATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (33 bp):
TATACAAGTCGAAAAATCATTCTACCTATAGTC
Found at i:29444892 original size:40 final size:39
Alignment explanation
Indices: 29444842--29445042 Score: 219
Period size: 39 Copynumber: 5.1 Consensus size: 39
29444832 CAAATCCAAT
* * **
29444842 CACCACCACAAAGCATACGGGACTTTAAGCTTGGATATAA
1 CACCAGCACAAAGCCTACGGGACTTT-AGCCCGGATATAA
* *
29444882 TACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAA
1 CACCAGCACAAAGCCTACGGGACTTTAGCCCGGATATAA
* *
29444921 CACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAA
1 CACCAGCAC-AAAGCCTACGGGACTTTAGCCCGGATATAA
* *
29444960 CACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAA
1 CACCAGCAC-AAAGCCTACGGGACTTTAGCCCGGATATAA
* * * *
29444999 CACCAACACGAATGCCTTCAGGAC-TTAGCCCGGATATAA
1 CACCAGCAC-AAAGCCTACGGGACTTTAGCCCGGATATAA
29445038 CACCA
1 CACCA
29445043 TTATAAAGTC
Statistics
Matches: 149, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 115 0.77
40 34 0.23
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (39 bp):
CACCAGCACAAAGCCTACGGGACTTTAGCCCGGATATAA
Found at i:29444928 original size:39 final size:39
Alignment explanation
Indices: 29444874--29445042 Score: 277
Period size: 39 Copynumber: 4.3 Consensus size: 39
29444864 CTTTAAGCTT
* * *
29444874 GGATATAATACCAGCAC-AAAGCCTGCGGGACTTTAGCCC
1 GGATATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCC
29444913 GGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCC
1 GGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCC
29444952 GGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCC
1 GGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCC
* *
29444991 GGATATAACACCAACACGAATGCCTTCAGGACTTAGCCC
1 GGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCC
29445030 GGATATAACACCA
1 GGATATAACACCA
29445043 TTATAAAGTC
Statistics
Matches: 124, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
39 112 0.90
40 12 0.10
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (39 bp):
GGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCC
Found at i:29445148 original size:28 final size:28
Alignment explanation
Indices: 29445115--29445196 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
29445105 ATTTAATCAT
* *
29445115 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* *
29445143 TCAATATCTCGCACATTAAGTGCCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* * *
29445171 TCAATATTTCGTACACTGAGTACCAT
1 TCAATATTTCGCACACTAAGTGCCAT
29445197 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGCCATTC
Found at i:29449354 original size:5 final size:5
Alignment explanation
Indices: 29449344--29449376 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
29449334 ACCTATGTGA
29449344 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
29449377 GAACACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:29453808 original size:14 final size:14
Alignment explanation
Indices: 29453789--29453815 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29453779 CAATTTGTGA
29453789 AAAATAAAATAAAT
1 AAAATAAAATAAAT
29453803 AAAATAAAATAAA
1 AAAATAAAATAAA
29453816 GAACACACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:29458304 original size:13 final size:14
Alignment explanation
Indices: 29458273--29458303 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29458263 TTGAAATAAC
*
29458273 AAAATGATAAAAAG
1 AAAATAATAAAAAG
29458287 AAAATAATAAAAAG
1 AAAATAATAAAAAG
29458301 AAA
1 AAA
29458304 TTAAAACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAATAATAAAAAG
Found at i:29459776 original size:88 final size:88
Alignment explanation
Indices: 29459558--29459827 Score: 353
Period size: 88 Copynumber: 3.1 Consensus size: 88
29459548 TTCAGGGAGA
** * ** *
29459558 TAAGGCTCACTGTCTTCGATCTGCTCTGCTACTGTTTAGGGAGATAAGATCTGTAATTTCCAACC
1 TAAGGCTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
* * *
29459623 TATTACCCCACTACTTA-GGGGT
66 TGTTACCCTACTGCTTAGGGGGT
* * * *
29459645 TAAGACTCACTGTTTTCAATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTTAGCC
1 TAAGGCTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
29459710 TGTTACCCTACTGCTTAGGGGGT
66 TGTTACCCTACTGCTTAGGGGGT
* ** * *
29459733 TAAGGCTCACCGTCTTCGATCCACTCCACTACTGCTTAGGGAGATAAAATCTATAATTTTTAGCC
1 TAAGGCTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
* *
29459798 TGTTTCCCTACTGCTTAGGAGGT
66 TGTTACCCTACTGCTTAGGGGGT
29459821 TAAGGCT
1 TAAGGCT
29459828 TACATCTTCG
Statistics
Matches: 158, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
87 69 0.44
88 89 0.56
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (88 bp):
TAAGGCTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
TGTTACCCTACTGCTTAGGGGGT
Found at i:29459906 original size:70 final size:70
Alignment explanation
Indices: 29459769--29459908 Score: 201
Period size: 70 Copynumber: 2.0 Consensus size: 70
29459759 CACTACTGCT
* * *
29459769 TAGGGAGATAAAATCTATAATTTTTAGCCTGTTTCCCTACTGCTTAGGAGGTTAAGGCTTACATC
1 TAGGGAGATAAAATCTATAATTTTCAGCCTGTTACCCTACTGCTTAGGAGGTTAAGGCTCACATC
29459834 TTCGA
66 TTCGA
* * * *
29459839 TAGGGAGATAAGATCTATAATTTTCA-CTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
1 TAGGGAGATAAAATCTATAATTTTCAGCCTGTTACCCTACTGCTTAGGAGGTTAAGGCTCA-CAT
29459903 CTTCGA
65 CTTCGA
29459909 GCTGCTTCGC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 30 0.48
70 32 0.52
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (70 bp):
TAGGGAGATAAAATCTATAATTTTCAGCCTGTTACCCTACTGCTTAGGAGGTTAAGGCTCACATC
TTCGA
Found at i:29459924 original size:44 final size:44
Alignment explanation
Indices: 29459874--29460106 Score: 160
Period size: 44 Copynumber: 5.3 Consensus size: 44
29459864 ACTTGTTACC
29459874 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGAGCTGCTTCG
1 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGAGCTGCTTCG
* * * * * * *
29459918 CTACTGCTTAGGGAGATAA-GAT--CTGTAATTTCTAGCCTG-TTACC
1 CTACTGCTTAGGGGGTTAAGGCTCACCGT--CTTCGAG-CTGCTT-CG
*
29459962 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTTCG
1 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGAGCTGCTTCG
* * * * * *
29460006 CTACTGCTTAGGGAGATT-A-GAT--CTGTAATTTCCAGCCTG-TTACC
1 CTACTGCTTAGGG-GGTTAAGGCTCACCGT--CTTCGAG-CTGCTT-CG
* * *
29460050 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCG
1 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGAGCTGCTTCG
*
29460094 CTACTGTTTAGGG
1 CTACTGCTTAGGG
29460107 AGATAAGATC
Statistics
Matches: 139, Mismatches: 32, Indels: 36
0.67 0.15 0.17
Matches are distributed among these distances:
41 6 0.04
43 20 0.14
44 90 0.65
45 17 0.12
47 6 0.04
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (44 bp):
CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGAGCTGCTTCG
Found at i:29459987 original size:88 final size:88
Alignment explanation
Indices: 29459839--29460367 Score: 739
Period size: 88 Copynumber: 6.1 Consensus size: 88
29459829 ACATCTTCGA
* *
29459839 TAGGGAGATAAGATCTATAATTT-TCA-CTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCG
1 TAGGGAGATAAGATCTGTAATTTCT-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCG
* *
29459902 TCTTCGAGCTGCTTCGCTACTGCT
65 TCTTCGATCTGCTCCGCTACTGCT
29459926 TAGGGAGATAAGATCTGTAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
1 TAGGGAGATAAGATCTGTAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
*
29459991 CTTCGATCTGCTTCGCTACTGCT
66 CTTCGATCTGCTCCGCTACTGCT
* *
29460014 TAGGGAGATTAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
1 TAGGGAGATAAGATCTGTAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
* *
29460079 CTTTGATCTGCTCCGCTACTGTT
66 CTTCGATCTGCTCCGCTACTGCT
* *
29460102 TAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGCACCGT
1 TAGGGAGATAAGATCTGTAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
** *
29460167 CTTTTATCTGCTCCGCTACTACT
66 CTTCGATCTGCTCCGCTACTGCT
* * **
29460190 TAAGGAGATTAGATCTGTAATTT-TCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATTG
1 TAGGGAGATAAGATCTGTAATTTCT-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCG
* **
29460254 TCTTCGATCTGCTCCACTACTATT
65 TCTTCGATCTGCTCCGCTACTGCT
* * * * *
29460278 TA--GA-A-GAGATCTGTATTTTCGAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGT
1 TAGGGAGATAAGATCTGTAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
* *
29460339 CTTCGATCTGCTCCACTACTGTT
66 CTTCGATCTGCTCCGCTACTGCT
29460362 TAGGGA
1 TAGGGA
29460368 AGATCTCGGT
Statistics
Matches: 407, Mismatches: 29, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
84 74 0.18
85 1 0.00
86 4 0.01
87 23 0.06
88 305 0.75
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (88 bp):
TAGGGAGATAAGATCTGTAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
CTTCGATCTGCTCCGCTACTGCT
Found at i:29460045 original size:245 final size:245
Alignment explanation
Indices: 29459594--29460345 Score: 913
Period size: 245 Copynumber: 3.0 Consensus size: 245
29459584 TGCTACTGTT
* * * * *
29459594 TAGGGAGATAAGATCTGTAATTTCCAACCTATTACCCCACTACTTA-GGGGTTAAGACTCACTGT
1 TAGGGAGATAAGATCTGTAATTTCC-ACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
* *
29459658 TTTCAATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTG
65 CTTCAATCTGCTCCGCTACTGCTTAAGGAGATAAGATCTGTAA-TTTTAGCCTGTTACCCTACTG
** * *
29459723 CTTAGGGGGTTAAGGCTCACCGTCTTCGATCCACTCCACTACTGCTTAGGGAGATAAAATCTATA
129 CTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
** * *
29459788 ATTTTTAGCCTGTTTCCCTACTGCTTAGGAGGTTAAGGCTTAC-ATCTTCGA
194 ATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTATCTTCGA
* * *
29459839 TAGGGAGATAAGATCTATAATTTTCACTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTC
1 TAGGGAGATAAGATCTGTAATTTCCACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTC
* * * *
29459904 TTCGAGCTGCTTCGCTACTGCTTAGGGAGATAAGATCTGTAATTTCTAGCCTGTTACCCTACTGC
66 TTCAATCTGCTCCGCTACTGCTTAAGGAGATAAGATCTGTAATTT-TAGCCTGTTACCCTACTGC
* * *
29459969 TTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTTCGCTACTGCTTAGGGAGATTAGATCTGTAA
130 TTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
*
29460034 TTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCGCTA
195 TTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTA----C--T-ATCT--T-CG--A
*
29460097 CTGTTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGC
1 -----TAGGGAGATAAGATCTGTAATTTCCA-CCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
** * *
29460162 ACCGTCTTTTATCTGCTCCGCTACTACTTAAGGAGATTAGATCTGTAATTTTCAGCCTGTTACCC
60 ACCGTCTTCAATCTGCTCCGCTACTGCTTAAGGAGATAAGATCTGTAATTTT-AGCCTGTTACCC
** ** *
29460227 TACTGCTTAGGGGGTTAAGGCTCATTGTCTTCGATCTGCTCCACTACTATTTA--GA-A-GAGAT
124 TACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT
* * *
29460288 CTGTATTTTCGAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGA
189 CTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTATCTTCGA
29460345 T
1 T
29460346 CTGCTCCACT
Statistics
Matches: 437, Mismatches: 48, Indels: 46
0.82 0.09 0.09
Matches are distributed among these distances:
243 1 0.00
244 19 0.04
245 189 0.43
248 1 0.00
249 1 0.00
250 2 0.00
251 1 0.00
253 7 0.02
254 1 0.00
255 1 0.00
256 3 0.01
258 1 0.00
260 48 0.11
261 1 0.00
262 2 0.00
263 25 0.06
264 134 0.31
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (245 bp):
TAGGGAGATAAGATCTGTAATTTCCACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTC
TTCAATCTGCTCCGCTACTGCTTAAGGAGATAAGATCTGTAATTTTAGCCTGTTACCCTACTGCT
TAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
TTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTATCTTCGA
Found at i:29460142 original size:44 final size:44
Alignment explanation
Indices: 29459918--29460150 Score: 167
Period size: 44 Copynumber: 5.3 Consensus size: 44
29459908 AGCTGCTTCG
*
29459918 CTACTGCTTAGGGAGATAAGATCTGTAATTTCTAGCCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACC
* * * * * * * *
29459962 CTACTGCTTAGGGGGTTAAGGCTCACCGT--CTTCGA-TCTGCTT-CG
1 CTACTGCTTAGGGAGATAA-GAT--CTGTAATTTCCAGCCTG-TTACC
*
29460006 CTACTGCTTAGGGAGATTAGATCTGTAATTTCCAGCCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACC
* * * * * * * *
29460050 CTACTGCTTAGGGGGTTAAGGCTCACCGT-CTTT-GA-TCTGCT-CC
1 CTACTGCTTAGGGAGATAA-GAT--CTGTAATTTCCAGCCTGTTACC
*
29460093 GCTACTGTTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACC
29460138 CTACTGCTTAGGG
1 CTACTGCTTAGGG
29460151 GGTTAAGGCG
Statistics
Matches: 137, Mismatches: 36, Indels: 32
0.67 0.18 0.16
Matches are distributed among these distances:
41 6 0.04
42 3 0.02
43 13 0.09
44 93 0.68
45 13 0.09
46 3 0.02
47 6 0.04
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (44 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACC
Found at i:29460186 original size:44 final size:44
Alignment explanation
Indices: 29459962--29460191 Score: 106
Period size: 44 Copynumber: 5.2 Consensus size: 44
29459952 GCCTGTTACC
* *
29459962 CTACTGCTTAGGGGGTTAAGGCTCACCGTC-TTCGATCTGCTTCG
1 CTACTGCTTAGGGGGTTAAGGCGCACCGTCTTTC-ATCTGCTCCG
* * * * *
29460006 CTACTGCTTAGGGAGATT-A---G-ATCTGTAATTTCCAGCCTGTTACC-
1 CTACTGCTTAGGG-GGTTAAGGCGCA-CCGT-CTTT-CA-TCTGCT-CCG
* *
29460050 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCG
1 CTACTGCTTAGGGGGTTAAGGCGCACCGTCTTTCATCTGCTCCG
* * * * * * *
29460094 CTACTGTTTAGGGAGATAA---G-ATCTGTAATTTCCAGCCTGTTACC-
1 CTACTGCTTAGGGGGTTAAGGCGCA-CCGT-CTTT-CA-TCTGCT-CCG
*
29460138 CTACTGCTTAGGGGGTTAAGGCGCACCGTCTTTTATCTGCTCCG
1 CTACTGCTTAGGGGGTTAAGGCGCACCGTCTTTCATCTGCTCCG
*
29460182 CTACTACTTA
1 CTACTGCTTA
29460192 AGGAGATTAG
Statistics
Matches: 131, Mismatches: 32, Indels: 46
0.63 0.15 0.22
Matches are distributed among these distances:
40 2 0.02
41 6 0.05
42 3 0.02
43 11 0.08
44 86 0.66
45 8 0.06
46 6 0.05
47 7 0.05
48 2 0.02
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.33
Consensus pattern (44 bp):
CTACTGCTTAGGGGGTTAAGGCGCACCGTCTTTCATCTGCTCCG
Found at i:29460812 original size:126 final size:127
Alignment explanation
Indices: 29460674--29460925 Score: 416
Period size: 126 Copynumber: 2.0 Consensus size: 127
29460664 AAGTGTGTGC
* * * * *
29460674 ACAACTCGAGTTGGATTTTAGGATTCACTCGTTCCAAAGGAATAAAATACTACATCCATCATGTT
1 ACAACTCAAGTTGGATCTTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCATGTT
*
29460739 AGGATACGATATTTTAAGCCT-AAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGAA
66 AGGACACGATATTTTAAGCCTCAAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGAA
*
29460800 ACAACTCAAGTTGGATCTTAAGATTCACTCGTTCTAAAGGAATAAAATACCACATCCAGCATGTT
1 ACAACTCAAGTTGGATCTTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCATGTT
* *
29460865 AGGACACGATATTTTAAGCCTCCAAAAATTGAGATCACCTCATGATTTCCAAAACATGCGA
66 AGGACACGATATTTTAAGCCTCAAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGA
29460926 CGAAAATTTT
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
126 79 0.68
127 37 0.32
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (127 bp):
ACAACTCAAGTTGGATCTTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCATGTT
AGGACACGATATTTTAAGCCTCAAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGAA
Found at i:29461609 original size:29 final size:29
Alignment explanation
Indices: 29461539--29461609 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
29461529 AGAGCCAAAT
29461539 TATACAT-AAATAAATTTAAAATAAATTA
1 TATACATAAAATAAATTTAAAATAAATTA
* ** *
29461567 TATATATATGATAAATTTAAGAATGAA-TA
1 TATACATAAAATAAATTTAA-AATAAATTA
*
29461596 TTTACATAAAATAA
1 TATACATAAAATAA
29461610 TATGAAAACA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
28 6 0.18
29 22 0.67
30 5 0.15
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (29 bp):
TATACATAAAATAAATTTAAAATAAATTA
Found at i:29463505 original size:177 final size:177
Alignment explanation
Indices: 29463128--29463933 Score: 1227
Period size: 177 Copynumber: 4.5 Consensus size: 177
29463118 AGACAAAGTA
* ** * *
29463128 GGTGGCTAAAATTTGCTCCATAATCGATACATGGAGATAAGACTCGCCATCTTCGACCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* * *
29463193 TAGCCGATACATGGCGATAAGATCTGTAATTTTTAGTTTGCTTCCTTGCTACCTCAGGAAGATAA
66 TAGCCGATACATGGAGATAAGATCTGTAA-TTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAA
*
29463258 GACTTGTACCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
130 GACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* * *
29463306 GGTGGCTAAAATCTGCTCCATAGTCGATACATAGAGATAAGATTCGCCATCTTCAATCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* **
29463371 TAGCCTATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTTATTGCTACCTCAGGAAGATAAG
66 TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
* * * *
29463436 ACTTGTATCTTTAACCTTCTCTTTTGCTACCTTAGAGAGATAAGGCT
131 ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* * * * *
29463483 GGTGGCTAAAATCTACTCCATAGCCAATACATGAAGATAAGATTCGCCATCTTCAATCTGCTCTA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* ** * *
29463548 TAGCCGATACATGGAGATAAGATCTGTAATTTCAATCTGCTTCCTTATTACCTTAGGAAGGTAAG
66 TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
* *
29463613 ACTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAAGCT
131 ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* *
29463660 GGTGGCTAAAATCTACTCCATAGCCGATACATGGATATAAGATTCGCCATCTTCGATCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* *
29463725 TTA-CCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTTAGAAAGATAA
66 -TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAA
* *
29463789 GACTTGTATCTCCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGACT
130 GACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* * *
29463837 AGTGGCTAAAATCTGCTCCATAGCCGATATATGGAGATAAGATTCACCATCTTCGATCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
29463902 TAGCCGATACATGGAGATAAGATCTGTAATTT
66 TAGCCGATACATGGAGATAAGATCTGTAATTT
29463934 TATCGACATC
Statistics
Matches: 570, Mismatches: 56, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
176 2 0.00
177 480 0.84
178 88 0.15
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (177 bp):
GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
Found at i:29463853 original size:44 final size:45
Alignment explanation
Indices: 29463760--29463854 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 45
29463750 GTAATTTCAG
* * * **
29463760 TCTGCT-TCCTTGCTACCTTAGAAAGATAAGACTTGTATCTCCAA
1 TCTGCTCTCCTTGCTACCTCAGAAAGATAAGACTAGTAGCTAAAA
* * *
29463804 CCTGCTCT-CTTGCTACCTCAGAGAGATAAGACTAGTGGCTAAAA
1 TCTGCTCTCCTTGCTACCTCAGAAAGATAAGACTAGTAGCTAAAA
29463848 TCTGCTC
1 TCTGCTC
29463855 CATAGCCGAT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
44 40 0.98
45 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (45 bp):
TCTGCTCTCCTTGCTACCTCAGAAAGATAAGACTAGTAGCTAAAA
Found at i:29468566 original size:21 final size:21
Alignment explanation
Indices: 29468541--29468584 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
29468531 GAAATGCAAG
*
29468541 AAAAGAAGATTTGCTCAAGAT
1 AAAAGAAGATTTGCTCAAAAT
*
29468562 AAAAGAATATTTGCTCAAAAT
1 AAAAGAAGATTTGCTCAAAAT
29468583 AA
1 AA
29468585 GACATAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (21 bp):
AAAAGAAGATTTGCTCAAAAT
Found at i:29481850 original size:14 final size:14
Alignment explanation
Indices: 29481825--29481855 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29481815 TTGAAATAAT
29481825 AAAATGATAAAAAG
1 AAAATGATAAAAAG
*
29481839 AAAATTATAAAAAG
1 AAAATGATAAAAAG
29481853 AAA
1 AAA
29481856 CTAAAACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (14 bp):
AAAATGATAAAAAG
Found at i:29498313 original size:17 final size:18
Alignment explanation
Indices: 29498291--29498324 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29498281 AGTCATATTG
29498291 AAATTGCG-AAATTAAAT
1 AAATTGCGAAAATTAAAT
29498308 AAATTGCGAAAATTAAA
1 AAATTGCGAAAATTAAA
29498325 ATGGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCGAAAATTAAAT
Found at i:29499072 original size:20 final size:20
Alignment explanation
Indices: 29499043--29499094 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
29499033 AATTAAATTC
29499043 TAAAAGATAAATACAA-ATAAA
1 TAAAA-ATAAATA-AATATAAA
*
29499064 TAAAAATAATTAAATATAAA
1 TAAAAATAAATAAATATAAA
*
29499084 TAAAATTAAAT
1 TAAAAATAAAT
29499095 CCTAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 20 0.74
21 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAAAATAAATAAATATAAA
Found at i:29499082 original size:16 final size:16
Alignment explanation
Indices: 29499049--29499094 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29499039 ATTCTAAAAG
29499049 ATAAATACAAA-TAAAT
1 ATAAATA-AAATTAAAT
*
29499065 A-AAA-ATAATTAAAT
1 ATAAATAAAATTAAAT
29499079 ATAAATAAAATTAAAT
1 ATAAATAAAATTAAAT
29499095 CCTAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.08
14 7 0.28
15 6 0.24
16 10 0.40
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAATAAAATTAAAT
Found at i:29500824 original size:21 final size:21
Alignment explanation
Indices: 29500798--29500846 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
29500788 AATAATTAAC
* *
29500798 TAATAAATCATTAAGATAAAA
1 TAATAAATAATTAAAATAAAA
29500819 TAATAAATAATTAAAATAAAA
1 TAATAAATAATTAAAATAAAA
29500840 TAATAAA
1 TAATAAA
29500847 GAAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
TAATAAATAATTAAAATAAAA
Found at i:29504579 original size:10 final size:10
Alignment explanation
Indices: 29504560--29504609 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
29504550 TTAAATTCTA
29504560 AAAGATAAAT
1 AAAGATAAAT
29504570 ACAA-ATAAAT
1 A-AAGATAAAT
*
29504580 AAAGATAATT
1 AAAGATAAAT
29504590 AAAGATAAAT
1 AAAGATAAAT
29504600 GAAA-ATAAAT
1 -AAAGATAAAT
29504610 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:29508053 original size:15 final size:16
Alignment explanation
Indices: 29508011--29508063 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
29508001 AAAAGTGACT
*
29508011 AAAATAGAAACAATCA
1 AAAATAGAAATAATCA
*
29508027 AAAATATG-AATAA-CC
1 AAAATA-GAAATAATCA
*
29508042 AAAATAGAAATAATCT
1 AAAATAGAAATAATCA
29508058 AAAATA
1 AAAATA
29508064 TTAGTAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 12 0.39
16 17 0.55
17 1 0.03
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAATAGAAATAATCA
Found at i:29515552 original size:22 final size:22
Alignment explanation
Indices: 29515517--29515559 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29515507 TATTAGTTAC
*
29515517 ATTTTAATTTTTAAT-AATTAT
1 ATTTTAAGTTTTAATGAATTAT
29515538 ATTTTACAGTTTTAATGAATTA
1 ATTTTA-AGTTTTAATGAATTA
29515560 GTTGAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
ATTTTAAGTTTTAATGAATTAT
Found at i:29530917 original size:16 final size:16
Alignment explanation
Indices: 29530885--29530915 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
29530875 TACAAATATT
29530885 TTAATTAATTATAAAA
1 TTAATTAATTATAAAA
29530901 TTAATT-ATTATAAAA
1 TTAATTAATTATAAAA
29530916 ATCCACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATTAATTATAAAA
Found at i:29539557 original size:25 final size:25
Alignment explanation
Indices: 29539523--29539573 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29539513 TTCCTTATAA
* **
29539523 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAAGAATTAAATTAGG
29539548 ACTTTAAATTAAGAATTAAATTAGG
1 ACTTTAAATTAAGAATTAAATTAGG
29539573 A
1 A
29539574 TTTTCCTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAAGAATTAAATTAGG
Found at i:29543876 original size:25 final size:25
Alignment explanation
Indices: 29543842--29543892 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29543832 TTCCTAATAA
* **
29543842 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGAAATTAGATTAGG
29543867 ACTTTAAATTAGAAATTAGATTAGG
1 ACTTTAAATTAGAAATTAGATTAGG
29543892 A
1 A
29543893 TTTTCCTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGAAATTAGATTAGG
Found at i:29547710 original size:18 final size:18
Alignment explanation
Indices: 29547687--29547750 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
29547677 ACTCATTTCC
29547687 TTAAAAAAATAAAAGAAA
1 TTAAAAAAATAAAAGAAA
*
29547705 TTAAAAATATAAAATG-AA
1 TTAAAAAAATAAAA-GAAA
**
29547723 TGGAAAAAATAAAA-AAA
1 TTAAAAAAATAAAAGAAA
29547740 CTTAAAAAAAT
1 -TTAAAAAAAT
29547751 TAGTTAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.05
18 34 0.92
19 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (18 bp):
TTAAAAAAATAAAAGAAA
Found at i:29549034 original size:3 final size:3
Alignment explanation
Indices: 29549026--29549247 Score: 74
Period size: 3 Copynumber: 77.0 Consensus size: 3
29549016 TTTAATATAC
* * * *
29549026 TAT TAT TAT T-T TAC TAT TAT TAT TAT T-T T-T TTT TAT TTT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * *
29549071 TTT TTT TAT TTT TTT TAT TTT TTT TAT T-T TTT TAT TCT TAT TCT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
29549118 TAT TA- TCT TAT T-T T-T TAT TAT TAT CT-T TTT TA- AAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
* * * * *
29549159 TAC TGT TAT T-T TTT TAT T-T AACA TAT TAT TAT TAT TAT TACT T-T
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TAT
* * * * *
29549203 TTT GTGT TAT TAT TAT TAT TAC TAT T-G TAT TAT TAC TAT TAT TAT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29549248 ATTTTCATCT
Statistics
Matches: 164, Mismatches: 40, Indels: 30
0.70 0.17 0.13
Matches are distributed among these distances:
2 21 0.13
3 137 0.84
4 6 0.04
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:29549042 original size:14 final size:14
Alignment explanation
Indices: 29549023--29549049 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29549013 TAATTTAATA
29549023 TACTATTATTATTT
1 TACTATTATTATTT
29549037 TACTATTATTATT
1 TACTATTATTATT
29549050 ATTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TACTATTATTATTT
Found at i:29549057 original size:1 final size:1
Alignment explanation
Indices: 29549051--29549103 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
29549041 ATTATTATTA
* * * * *
29549051 TTTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29549104 ATTCTTATTC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:29549064 original size:9 final size:9
Alignment explanation
Indices: 29549052--29549139 Score: 106
Period size: 9 Copynumber: 9.2 Consensus size: 9
29549042 TTATTATTAT
29549052 TTTTTTTTA
1 TTTTTTTTA
29549061 TTTTTTTTA
1 TTTTTTTTA
29549070 TTTTTTTTA
1 TTTTTTTTA
29549079 TTTTTTTTA
1 TTTTTTTTA
29549088 TTTTTTTTA
1 TTTTTTTTA
29549097 -TTTTTTTA
1 TTTTTTTTA
29549105 TTCTTATTCTTA
1 TT-TT-TT-TTA
*
29549117 TTATTATCTTA
1 TT-TT-TTTTA
29549128 TTTTTTATTA
1 TTTTTT-TTA
29549138 TT
1 TT
29549140 ATCTTTTTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
8 8 0.11
9 38 0.54
10 9 0.13
11 7 0.10
12 9 0.13
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:29549250 original size:14 final size:15
Alignment explanation
Indices: 29549210--29549247 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
29549200 TTTTTTGTGT
29549210 TATTATTATTATTAC
1 TATTATTATTATTAC
*
29549225 TATT-GTATTATTAC
1 TATTATTATTATTAC
29549239 TATTATTAT
1 TATTATTAT
29549248 ATTTTCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:29549316 original size:25 final size:25
Alignment explanation
Indices: 29549284--29549362 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
29549274 TATTTATCTA
*
29549284 ATTT-TATTTATTTATTTATTATAT
1 ATTTATATTTATTTATATATTATAT
*
29549308 ATTTATATTTCTGTTA-ATATTATAT
1 ATTTATATTTAT-TTATATATTATAT
* * *
29549333 -TTTATATATTATATCTCTA-TATAT
1 ATTTATAT-TTATTTATATATTATAT
29549357 ATTTAT
1 ATTTAT
29549363 GTATTAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
24 17 0.39
25 24 0.55
26 3 0.07
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (25 bp):
ATTTATATTTATTTATATATTATAT
Found at i:29549357 original size:17 final size:16
Alignment explanation
Indices: 29549303--29549359 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
29549293 ATTTATTTAT
29549303 TATATAT-TTATATTTC
1 TATATATATTATA-TTC
*
29549319 TGT-TAATATTATATT-
1 TATAT-ATATTATATTC
29549334 T-TATATATTATATCTC
1 TATATATATTATAT-TC
29549350 TATATATATT
1 TATATATATT
29549360 TATGTATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
14 10 0.29
15 4 0.12
16 7 0.21
17 13 0.38
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (16 bp):
TATATATATTATATTC
Found at i:29549611 original size:18 final size:17
Alignment explanation
Indices: 29549588--29549626 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
29549578 CATATAATAC
*
29549588 TTATTTATATTATTATTT
1 TTATTTATATT-TTATGT
*
29549606 TTATTTTTATTTTATGT
1 TTATTTATATTTTATGT
29549623 TTAT
1 TTAT
29549627 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTATTTATATTTTATGT
Found at i:29549696 original size:3 final size:3
Alignment explanation
Indices: 29549682--29549802 Score: 86
Period size: 3 Copynumber: 40.3 Consensus size: 3
29549672 TACTTATTTG
* * * * **
29549682 TAT TAT TTT TAT TAT CAA TAT T-T TATT TAT TAT CAT TAT TAT TCC
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * * *
29549727 TAT TAT TAT TAC TAT TAT T-T TTT TAC TAT TAT TATT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* *
29549772 TAT TGT TAC TAT TAT T-T TATT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
29549803 GTAATGACCC
Statistics
Matches: 89, Mismatches: 23, Indels: 12
0.72 0.19 0.10
Matches are distributed among these distances:
2 6 0.07
3 74 0.83
4 9 0.10
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29549737 original size:42 final size:42
Alignment explanation
Indices: 29549700--29549798 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
29549690 TTATTATCAA
*
29549700 TATTTTATTTATTATCATTA-TTATTCCTATTATTATTACTAT
1 TATTTTATTTATTATCATTATTTATT-ATATTATTATTACTAT
* * *
29549742 TATTTT-TTTACTATTATTATTTATTATCATTATTGTTACTAT
1 TATTTTATTTATTATCATTATTTATTAT-ATTATTATTACTAT
29549784 TATTTTATTTATTAT
1 TATTTTATTTATTAT
29549799 TATTGTAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
41 12 0.24
42 30 0.61
43 7 0.14
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (42 bp):
TATTTTATTTATTATCATTATTTATTATATTATTATTACTAT
Found at i:29549767 original size:54 final size:56
Alignment explanation
Indices: 29549682--29549802 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 56
29549672 TACTTATTTG
*
29549682 TATTATTTTTATTATCAATATTTTATTTATTATCATTATTATTCCTATTATTATTAC
1 TATTATTTTTATTATC-ATATTTTATTTATTATCATTATTATTACTATTATTATTAC
*
29549739 TATTATTTTT-TTA-C-TATTATTATTTATTATCATTATTGTTACTATTATT-TTA-
1 TATTATTTTTATTATCATATT-TTATTTATTATCATTATTATTACTATTATTATTAC
*
29549791 T-TTATTATTATT
1 TATTATTTTTATT
29549803 GTAATGACCC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
51 7 0.12
52 3 0.05
53 7 0.12
54 28 0.47
55 1 0.02
56 3 0.05
57 10 0.17
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (56 bp):
TATTATTTTTATTATCATATTTTATTTATTATCATTATTATTACTATTATTATTAC
Found at i:29550113 original size:16 final size:16
Alignment explanation
Indices: 29550094--29550144 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
29550084 TACTTTATTA
29550094 AATTATTATATTATAT
1 AATTATTATATTATAT
* *
29550110 AATTATTATTTTATTT
1 AATTATTATATTATAT
*
29550126 AA--ATTATAATATA-
1 AATTATTATATTATAT
29550139 AATTAT
1 AATTAT
29550145 AGATAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 2 0.07
14 8 0.29
15 2 0.07
16 16 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTATTATATTATAT
Found at i:29551514 original size:46 final size:46
Alignment explanation
Indices: 29551363--29551676 Score: 403
Period size: 46 Copynumber: 6.8 Consensus size: 46
29551353 TGATGTCATA
* * ** ** * * *
29551363 GTATCTTTCAACTATGGTTTTACTTGTTTTTTGTCATGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* * *** *
29551409 GTATCTTTCAACCATAGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGTTGCCATG
*
29551456 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
29551502 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
29551548 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
29551594 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
29551640 GTATCTTTCAACCATGGTCTTACACATTCCATATCAG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
29551677 AGACCACACT
Statistics
Matches: 244, Mismatches: 23, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
46 204 0.84
47 40 0.16
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
Found at i:29554642 original size:51 final size:51
Alignment explanation
Indices: 29554523--29554642 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
29554513 ACTAAGTTAA
* * * *
29554523 CCGGATGAAATATGAAGCTCTTGTTGGAACTAGAGCAATAAAGTAATATAT
1 CCGGATGAAATATGAAGTTCTTGTTGGAACCAGAACAACAAAGTAATATAT
29554574 CCGGATGAAATATGAAGTTCTTGTT-GAAGCCAGAACAACAAAGTAATA-ATT
1 CCGGATGAAATATGAAGTTCTTGTTGGAA-CCAGAACAACAAAGTAATATA-T
*
29554625 CCGGATGAAGTATGAAGT
1 CCGGATGAAATATGAAGT
29554643 AAGTTTGAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 4 0.06
51 58 0.94
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (51 bp):
CCGGATGAAATATGAAGTTCTTGTTGGAACCAGAACAACAAAGTAATATAT
Found at i:29561268 original size:16 final size:17
Alignment explanation
Indices: 29561243--29561292 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
29561233 TTTTCTTACT
29561243 TTAT-TAAATTATTATA
1 TTATATAAATTATTATA
*
29561259 TTATAT-AATTATTATT
1 TTATATAAATTATTATA
* *
29561275 TTATTTAAATTATAATA
1 TTATATAAATTATTATA
29561292 T
1 T
29561293 GAATTATAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATAAATTATTATA
Found at i:29562305 original size:51 final size:51
Alignment explanation
Indices: 29562186--29562305 Score: 170
Period size: 51 Copynumber: 2.4 Consensus size: 51
29562176 ACTAAGTTAA
* * * *
29562186 CCGGATGAAATATGAAGCTCTTGTTGAAACTAGAGCAATAAAGTAATATAT
1 CCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAACAAAGTAATATAT
*
29562237 CCGGATGAAATATGAAGTTCTTGTTGAAGCCAGAACAACAAAGTAATA-ATT
1 CCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAACAAAGTAATATA-T
*
29562288 CCGGATGAAGTATGAAGT
1 CCGGATGAAATATGAAGT
29562306 AAGTTTGGGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 1 0.02
51 61 0.98
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (51 bp):
CCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAACAAAGTAATATAT
Found at i:29563993 original size:10 final size:10
Alignment explanation
Indices: 29563960--29564018 Score: 66
Period size: 10 Copynumber: 5.7 Consensus size: 10
29563950 TTTTGTTTAG
29563960 TATTTTTATT
1 TATTTTTATT
29563970 T-TCTTTTACTTT
1 TAT-TTTTA--TT
29563982 TATTTTTATT
1 TATTTTTATT
*
29563992 TATATTTATT
1 TATTTTTATT
*
29564002 TATATTTATT
1 TATTTTTATT
29564012 TATTTTT
1 TATTTTT
29564019 TTATTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 1 0.02
10 33 0.77
12 8 0.19
13 1 0.02
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.76
Consensus pattern (10 bp):
TATTTTTATT
Found at i:29563993 original size:16 final size:15
Alignment explanation
Indices: 29563963--29564028 Score: 68
Period size: 16 Copynumber: 4.5 Consensus size: 15
29563953 TGTTTAGTAT
29563963 TTTTATTTTCT-TTTA
1 TTTTATTTT-TATTTA
29563978 CTTTTATTTTTATTTA
1 -TTTTATTTTTATTTA
*
29563994 TATTTATTTATATTTA
1 T-TTTATTTTTATTTA
29564010 -TTTA-TTTT-TTTA
1 TTTTATTTTTATTTA
29564022 TTTTATT
1 TTTTATT
29564029 AATTAGCTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
14 5 0.11
15 2 0.05
16 26 0.59
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTATTTA
Found at i:29566451 original size:20 final size:20
Alignment explanation
Indices: 29566426--29566519 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
29566416 ACAATTTTAA
*
29566426 AATCAAGTCAAAATGATTTT
1 AATCAAGTCAAAATAATTTT
*
29566446 AATCAAGTCAAAATAATTTC
1 AATCAAGTCAAAATAATTTT
* * *
29566466 AACCAAGTTAAAATCATTTT
1 AATCAAGTCAAAATAATTTT
29566486 AA-CACA-TCAAAATAATTTT
1 AATCA-AGTCAAAATAATTTT
*
29566505 CAAACAAGTCAAAAT
1 -AATCAAGTCAAAAT
29566520 TGCTCCAGGC
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
19 13 0.21
20 40 0.65
21 9 0.15
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (20 bp):
AATCAAGTCAAAATAATTTT
Found at i:29566479 original size:40 final size:40
Alignment explanation
Indices: 29566418--29566519 Score: 127
Period size: 40 Copynumber: 2.5 Consensus size: 40
29566408 ATTTTGAAAC
* *
29566418 AATTTTAAAATCAAGTCAAAATGATTTTAATCA-AGTCAAAAT
1 AATTTTCAAA-CAAGTCAAAATCATTTTAA-CACA-TCAAAAT
* *
29566460 AA-TTTCAACCAAGTTAAAATCATTTTAACACATCAAAAT
1 AATTTTCAAACAAGTCAAAATCATTTTAACACATCAAAAT
29566499 AATTTTCAAACAAGTCAAAAT
1 AATTTTCAAACAAGTCAAAAT
29566520 TGCTCCAGGC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
39 11 0.21
40 34 0.65
41 5 0.10
42 2 0.04
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (40 bp):
AATTTTCAAACAAGTCAAAATCATTTTAACACATCAAAAT
Found at i:29567779 original size:28 final size:26
Alignment explanation
Indices: 29567736--29567805 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 26
29567726 AGATGAACTG
* *
29567736 CACAATTAATACCATGGAGATAGTAA
1 CACAATTAATAACATGAAGATAGTAA
* *
29567762 CACGATTAAAATAACATGAAGGTAGTAA
1 CACAATT--AATAACATGAAGATAGTAA
29567790 CACAATTAATAACATG
1 CACAATTAATAACATG
29567806 TACTGAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 15 0.41
28 22 0.59
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (26 bp):
CACAATTAATAACATGAAGATAGTAA
Found at i:29569443 original size:47 final size:47
Alignment explanation
Indices: 29569380--29569773 Score: 608
Period size: 47 Copynumber: 8.4 Consensus size: 47
29569370 CCCTTCGGGA
* * * *
29569380 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
29569427 CTTATCACATATATACACCTTCACATCCATCACATCGACCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29569474 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
29569521 CTTATCACATATACACACTTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29569568 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29569615 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29569662 CATATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29569709 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29569756 CTTATCACATATACACAC
1 CTTATCACATATATACAC
29569774 CTTGTACACC
Statistics
Matches: 324, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 324 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29569718 original size:22 final size:22
Alignment explanation
Indices: 29569690--29569765 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
29569680 TTTCACATTC
29569690 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
*** *** *
29569712 ATCACATATACACACTTTCACATT
1 ATCACATCGGC-CA-TTAGGCCTT
29569736 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
29569759 ATCACAT
1 ATCACAT
29569766 ATACACACCT
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 15 0.41
23 7 0.19
24 7 0.19
25 8 0.22
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.29
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:29573225 original size:29 final size:25
Alignment explanation
Indices: 29573169--29573216 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
29573159 TCAAGCAAAT
29573169 AACCCATTTCGGTATTTTTTTTTAA
1 AACCCATTTCGGTATTTTTTTTTAA
* *
29573194 AACCTATTTCGGTATTTATTTTT
1 AACCCATTTCGGTATTTTTTTTT
29573217 GTAGTAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (25 bp):
AACCCATTTCGGTATTTTTTTTTAA
Found at i:29580805 original size:35 final size:35
Alignment explanation
Indices: 29580758--29580829 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
29580748 GAAATCAGAG
*
29580758 AAAAAAATAGTTCAAATTTTGACTTACAAATTCGT
1 AAAAAAACAGTTCAAATTTTGACTTACAAATTCGT
* *
29580793 AAAAAAACAGTTCAAATTTTGACTTACCAATTTGT
1 AAAAAAACAGTTCAAATTTTGACTTACAAATTCGT
29580828 AA
1 AA
29580830 TGTCTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.33
Consensus pattern (35 bp):
AAAAAAACAGTTCAAATTTTGACTTACAAATTCGT
Found at i:29583697 original size:18 final size:17
Alignment explanation
Indices: 29583646--29583744 Score: 65
Period size: 17 Copynumber: 5.7 Consensus size: 17
29583636 GCAAGACTAT
* *
29583646 GAGCTCACCAAAAGTTC
1 GAGCTCACCAAAACTGC
*
29583663 GAGCTCTA-CAAAGCTGC
1 GAGCTC-ACCAAAACTGC
29583680 GAGCTCACCCAAAACTGC
1 GAGCTCA-CCAAAACTGC
* **
29583698 AAGCTCACTCATGACTGC
1 GAGCTCAC-CAAAACTGC
* * * *
29583716 GAGTTCTCCAATAGTGC
1 GAGCTCACCAAAACTGC
*
29583733 GAGCTCATCAAA
1 GAGCTCACCAAA
29583745 GCTACGAAGT
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
16 1 0.02
17 33 0.54
18 27 0.44
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.19
Consensus pattern (17 bp):
GAGCTCACCAAAACTGC
Found at i:29586399 original size:13 final size:14
Alignment explanation
Indices: 29586375--29586404 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
29586365 TAGATTCGAA
29586375 AAAATAAAATAAAG
1 AAAATAAAATAAAG
29586389 AAAAT-AAATAAAG
1 AAAATAAAATAAAG
29586402 AAA
1 AAA
29586405 GAAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAATAAAATAAAG
Found at i:29586861 original size:26 final size:26
Alignment explanation
Indices: 29586838--29586889 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
29586828 GGTTGTTTGG
*
29586838 GTTT-GTTTGGGGTTTAGTTGGTTTA
1 GTTTGGTTTGGGGTGTAGTTGGTTTA
*
29586863 GTTTGGTTTTGGGTGTAGTTGGGTTTA
1 GTTTGGTTTGGGGTGTAGTT-GGTTTA
29586890 TTTTATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 13 0.57
27 6 0.26
ACGTcount: A:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (26 bp):
GTTTGGTTTGGGGTGTAGTTGGTTTA
Found at i:29586898 original size:26 final size:26
Alignment explanation
Indices: 29586838--29586898 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
29586828 GGTTGTTTGG
* *
29586838 GTTTG-TTTGGGGTTTAGTTGGTTTA
1 GTTTGATTTTGGGTGTAGTTGGTTTA
*
29586863 GTTTGGTTTTGGGTGTAGTTGGGTTTA
1 GTTTGATTTTGGGTGTAGTT-GGTTTA
*
29586890 -TTTTATTTT
1 GTTTGATTTT
29586899 ATTGGGCCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 19 0.63
27 6 0.20
ACGTcount: A:0.08, C:0.00, G:0.33, T:0.59
Consensus pattern (26 bp):
GTTTGATTTTGGGTGTAGTTGGTTTA
Found at i:29588006 original size:26 final size:25
Alignment explanation
Indices: 29587970--29588063 Score: 134
Period size: 26 Copynumber: 3.6 Consensus size: 25
29587960 TGGTACAAAT
29587970 TGATAATAGGTTAGGTAAATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTC-A
*
29587996 TGATAATAGGTTAGGTAAATCTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
*
29588022 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
*
29588048 TGATAATGGGTTAGGT
1 TGATAATAGGTTAGGT
29588064 TTTCATGATA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
26 60 0.95
27 3 0.05
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:29588067 original size:21 final size:23
Alignment explanation
Indices: 29588020--29588074 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 23
29588010 GTAAATCTTC
29588020 CATGATAATGGGTTAGGTAAATGTTT
1 CATGATAATGGGTTAGG---ATGTTT
29588046 CATGATAATGGGTTAGG-T-TTT
1 CATGATAATGGGTTAGGATGTTT
29588067 CATGATAA
1 CATGATAA
29588075 GAATTTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.38
22 1 0.03
26 17 0.59
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.38
Consensus pattern (23 bp):
CATGATAATGGGTTAGGATGTTT
Found at i:29589557 original size:28 final size:26
Alignment explanation
Indices: 29589515--29589585 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
29589505 GAAAGTAGCT
* *
29589515 AAATTACTATAATACCCCTATGTATGAA
1 AAATTACTGTTATACCCCTA-G-ATGAA
* *
29589543 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGAA
*
29589569 AAATTACCGTTATACCC
1 AAATTACTGTTATACCC
29589586 GTAGGGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 19 0.50
27 1 0.03
28 18 0.47
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGAA
Found at i:29589734 original size:27 final size:27
Alignment explanation
Indices: 29589693--29589805 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
29589683 GAGGAAGCGT
*
29589693 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
29589720 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
29589747 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
29589775 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
29589801 TCTGG
1 TCTGG
29589806 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:29589798 original size:54 final size:54
Alignment explanation
Indices: 29589691--29589805 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
29589681 TGGAGGAAGC
*
29589691 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
29589745 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
29589799 GTTCTGG
1 GTTCTGG
29589806 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:29589891 original size:19 final size:22
Alignment explanation
Indices: 29589867--29589906 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
29589857 CTCCCCACAC
29589867 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
29589886 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
29589907 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:29591703 original size:14 final size:14
Alignment explanation
Indices: 29591684--29591738 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
29591674 TGGTACATTA
29591684 ATTTTAGATCTTT-T
1 ATTTTAGAT-TTTAT
29591698 ATTTTAGATTTTAT
1 ATTTTAGATTTTAT
29591712 ATTTTAGAGTTTTGTAT
1 ATTTTAGA--TTT-TAT
*
29591729 ACTTTAGATT
1 ATTTTAGATT
29591739 CAAATTAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
13 3 0.08
14 18 0.50
15 2 0.06
16 3 0.08
17 10 0.28
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.60
Consensus pattern (14 bp):
ATTTTAGATTTTAT
Found at i:29592835 original size:50 final size:49
Alignment explanation
Indices: 29592781--29592883 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 49
29592771 AAATCTATCT
29592781 TAGAAGATCATTCTCAAACCAAGCCCATTAATGAACTTGGTTATTTTTTA
1 TAGAAGATCATTCTCAAACCAAGCCCATTAATGAACTT-GTTATTTTTTA
29592831 TAGAAGATCATTCTCAAACCAAGCCCATTAATGAACTTGTTATTTTTTA
1 TAGAAGATCATTCTCAAACCAAGCCCATTAATGAACTTGTTATTTTTTA
29592880 TAGA
1 TAGA
29592884 GTAATAATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 15 0.28
50 38 0.72
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (49 bp):
TAGAAGATCATTCTCAAACCAAGCCCATTAATGAACTTGTTATTTTTTA
Found at i:29599807 original size:46 final size:48
Alignment explanation
Indices: 29599721--29599887 Score: 188
Period size: 46 Copynumber: 3.6 Consensus size: 48
29599711 GATAGGGTGT
*
29599721 CGATGCCATGTCCCAGACATGGTCTTACACTGAC--ACATCTCGCA-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCG-AGGC
29599767 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGC
* * * * * *
29599813 CTATG-CATGTCCCAAACAT-GTCTTACACTAGCTCT-CGTCTCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TACATCTCGAGGC
*
29599859 CAATGCCATGTCCCAGACATGGTCTTACA
1 CGATGCCATGTCCCAGACATGGTCTTACA
29599888 GTAGCTCACA
Statistics
Matches: 106, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
44 12 0.11
45 15 0.14
46 57 0.54
47 14 0.13
48 8 0.08
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGC
Found at i:29601879 original size:75 final size:76
Alignment explanation
Indices: 29601757--29601929 Score: 208
Period size: 75 Copynumber: 2.3 Consensus size: 76
29601747 CACAACCGTT
* * * *
29601757 GGTTGACCCGACTAGCACTGGGTTCAATTTACCGTTGGTATATCCAACTAGAGCTAGGCTCACAA
1 GGTTAACCTGACTAGCACTGGGTGCAATATACCGTTGGTATATCCAACTAGAGCTAGGCTCAC-A
29601822 TT-ATTA-TCGTC
65 TTCATTACT-GTC
** * *
29601833 GGTTAACCTGACTAGCACTGGGTGCAA-ATATTGTTGGTTTATCCAACTAGAGCTGGGCTCACAT
1 GGTTAACCTGACTAGCACTGGGTGCAATATACCGTTGGTATATCCAACTAGAGCTAGGCTCACAT
29601897 TCATTACTGTC
66 TCATTACTGTC
* * *
29601908 GGTTAATCTCACTAACACTGGG
1 GGTTAACCTGACTAGCACTGGG
29601930 CGCAGCCTCT
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
74 3 0.04
75 56 0.67
76 25 0.30
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (76 bp):
GGTTAACCTGACTAGCACTGGGTGCAATATACCGTTGGTATATCCAACTAGAGCTAGGCTCACAT
TCATTACTGTC
Found at i:29603889 original size:21 final size:22
Alignment explanation
Indices: 29603865--29603908 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29603855 ATTTAACATC
* *
29603865 AATTTAATCCATTTCATA-CTT
1 AATTCAATCCAATTCATATCTT
29603886 AATTCAATCCAATTCATATCTT
1 AATTCAATCCAATTCATATCTT
29603908 A
1 A
29603909 GGCAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTCAATCCAATTCATATCTT
Found at i:29611242 original size:22 final size:21
Alignment explanation
Indices: 29611205--29611249 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
29611195 AACCCAGAAT
* *
29611205 AATAATAATAATAATCATAGA
1 AATAATAAAAATAATCAGAGA
29611226 AATAAGTAAAAATAATCAGAGA
1 AATAA-TAAAAATAATCAGAGA
29611248 AA
1 AA
29611250 AAAAAAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (21 bp):
AATAATAAAAATAATCAGAGA
Found at i:29623536 original size:44 final size:42
Alignment explanation
Indices: 29623469--29623551 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 42
29623459 GATATAAGTT
* *
29623469 TTAAATTTTTAGTTTAATAGATTTCTAGATCTTTTAGCTGAA
1 TTAAATTTTAAGTTTAATAGATTTCTAAATCTTTTAGCTGAA
* *
29623511 TTAAGTTTTAAGTTTAAATTAGATTTTTAAATCTTTTAGCT
1 TTAAATTTTAAGTTT-AA-TAGATTTCTAAATCTTTTAGCT
29623552 CAAGTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 13 0.37
43 2 0.06
44 20 0.57
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (42 bp):
TTAAATTTTAAGTTTAATAGATTTCTAAATCTTTTAGCTGAA
Found at i:29623557 original size:33 final size:34
Alignment explanation
Indices: 29623520--29623588 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
29623510 ATTAAGTTTT
29623520 AAGTTTAAATT-AGATTTTTAAATC-TTTTAGCTC
1 AAGTTTAAATTAAGA-TTTTAAATCTTTTTAGCTC
*
29623553 AAGTTTAAATTAAGATTTTACATCTTTTTAGCTC
1 AAGTTTAAATTAAGATTTTAAATCTTTTTAGCTC
29623587 AA
1 AA
29623589 TTAAGTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 19 0.58
34 14 0.42
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (34 bp):
AAGTTTAAATTAAGATTTTAAATCTTTTTAGCTC
Found at i:29626558 original size:18 final size:17
Alignment explanation
Indices: 29626535--29626581 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
29626525 ATTGTAAGGG
*
29626535 TTAATTTTTTAATATTAT
1 TTAATTTTTTAAT-TTAA
29626553 TTAATTTTTATAATTTAA
1 TTAATTTTT-TAATTTAA
29626571 TTAATATTTTT
1 TTAAT-TTTTT
29626582 TATGATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTTTTAATTTAA
Found at i:29628652 original size:59 final size:57
Alignment explanation
Indices: 29628512--29628699 Score: 229
Period size: 59 Copynumber: 3.2 Consensus size: 57
29628502 ATTGATTTAT
* *
29628512 TTTTGAATATTTTTGTACAAATTGTTTTTATATTGTTCCATTTAATAAAAT---AGTTC
1 TTTTGAATATTTTTGTAC-AATTATTTTTATATTCTT-CATTTAATAAAATAGAAGTTC
*
29628568 TTTTGAATATTTTTGTACAAGTTATTTTAATATTACTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAA-TTATTTTTATATT-CTTCATTTAATAAAATAGAAGTTC
** * *
29628627 TTTTGAATATTTTCATACATATTATTTTTATATTGTTTCATTTAATAAAATAGAAATTC
1 TTTTGAATATTTTTGTACA-ATTATTTTTATATT-CTTCATTTAATAAAATAGAAGTTC
*
29628686 TTTGGAATATTTTT
1 TTTTGAATATTTTT
29628700 TAACAAATAT
Statistics
Matches: 115, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
55 2 0.02
56 42 0.37
57 2 0.02
59 68 0.59
60 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (57 bp):
TTTTGAATATTTTTGTACAATTATTTTTATATTCTTCATTTAATAAAATAGAAGTTC
Found at i:29629010 original size:67 final size:64
Alignment explanation
Indices: 29628883--29629010 Score: 186
Period size: 67 Copynumber: 2.0 Consensus size: 64
29628873 ATTAAACTGT
29628883 AAAACCTTAAACAATTAAAAACTAATACCCTATTTTGTTTTTTTCTAAACCCTAATCAAACCCA
1 AAAACCTTAAACAATTAAAAACTAATACCCTATTTTGTTTTTTTCTAAACCCTAATCAAACCCA
* * *
29628947 AAAATCTTAAACAATTAAAAACTTGATACCCTAATTTAAT-TTTTTTTCTAAATCCTAATCAAAC
1 AAAACCTTAAACAATTAAAAAC-TAATACCCT-ATTT--TGTTTTTTTCTAAACCCTAATCAAAC
29629011 ATCAAAGCCC
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
64 21 0.37
65 8 0.14
66 4 0.07
67 23 0.40
68 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (64 bp):
AAAACCTTAAACAATTAAAAACTAATACCCTATTTTGTTTTTTTCTAAACCCTAATCAAACCCA
Found at i:29630651 original size:27 final size:27
Alignment explanation
Indices: 29630613--29630673 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
29630603 GAAGGCATCT
* *
29630613 CATAGGCGGCACCGATTGTTGGACTGC
1 CATAGGCGGCACCAATGGTTGGACTGC
*
29630640 CATAGGCGGCACCAATGGTTGGGCTGC
1 CATAGGCGGCACCAATGGTTGGACTGC
*
29630667 CAGAGGC
1 CATAGGC
29630674 AACACCCTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.20, C:0.26, G:0.36, T:0.18
Consensus pattern (27 bp):
CATAGGCGGCACCAATGGTTGGACTGC
Found at i:29630812 original size:3 final size:3
Alignment explanation
Indices: 29630799--29630872 Score: 114
Period size: 3 Copynumber: 25.0 Consensus size: 3
29630789 AAGGGAAAGG
* * *
29630799 AGA AG- AGA AGA AGA AGA AGA ATA AGA ATA AGA ATA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
29630846 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
29630873 GAAAGAGGAG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:29631690 original size:25 final size:25
Alignment explanation
Indices: 29631662--29631737 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 25
29631652 ATTATGTACT
29631662 AAAATAATATAAAAAATAAAATACG
1 AAAATAATATAAAAAATAAAATACG
*
29631687 AAAATAGTATATTTTAAAAAATAAAATCCG
1 AAAATA--ATA---TAAAAAATAAAATACG
* *
29631717 AAAATAAAATAAATAATAAAA
1 AAAATAATATAAAAAATAAAA
29631738 ACAAAGGGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
25 17 0.40
27 3 0.07
28 2 0.05
30 21 0.49
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (25 bp):
AAAATAATATAAAAAATAAAATACG
Found at i:29631762 original size:154 final size:152
Alignment explanation
Indices: 29631510--29632170 Score: 948
Period size: 154 Copynumber: 4.4 Consensus size: 152
29631500 GGCGGTTTTT
* **
29631510 TACTAAAATAATAT-AAAAATAAAATACAAAAATAGTTTATTTTAAAAAATAAAATATGAAAAT-
1 TACTAAAATAATATAAAAAATAAAAT--AAAAATAGTATATTTTAAAAAATAAAATCCGAAAATA
* * *
29631573 --A-AAA-AATAAAAACAAATGGCCAAAACCAGAGTTTTTTACTAAATTAATATAAAAAATACTA
64 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACACTA
*
29631634 AAATAATACATTTAAAATATTATG
129 AAATAATACATTTAAAACATTATG
29631658 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATA
1 TACTAAAATAATATAAAAAATAAAATA--AAAATAGTATATTTTAAAAAATAAAATCCGAAAATA
* *
29631723 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTAC-AAATTTATATAAAAAATACTA
64 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACACTA
*
29631787 AAATAATACATTTGAAACCATTATG
129 AAATAATACATTT-AAAACATTATG
** * *
29631812 TACTAAAATAATAT-AAAAATAAAATAAAAATAACATATTTTAAAAATTAAAATCTGAAAATAAA
1 TACTAAAATAATATAAAAAATAAAATAAAAATAGTATATTTTAAAAAATAAAATCCGAAAATAAA
29631876 ATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTTACTAAATTAATATAAAAAAACACTA
66 ATAAATAATAAAAACAAAGGGCCAAAATCAGAG-TTTTTTACTAAATTAATAT-AAAAAACACTA
** *
29631941 AAATAATACATTCGAACCATTATG
129 AAATAATACATTTAAAACATTATG
* *
29631965 TACTAAAATAATATAAAAAATAAAATATGAAGATAGTATATTTTAAAAAAATAAAATCCAAAAAT
1 TACTAAAATAATATAAAAAATAAAATA--AAAATAGTATATTTT-AAAAAATAAAATCCGAAAAT
*
29632030 AAAATAAATAATAAAAACAAAGGGCCAAAATCAGAATTTTTTACTAAATTAATAT-AAAAACACT
63 AAAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACACT
*
29632094 AAAATAATACATTTGAAA-ATTATG
128 AAAATAATACATTTAAAACATTATG
* *
29632118 TATTAAAATAATATAAAAAATAATATAAAAA-AGTATATTTTAAAAAATAAAAT
1 TACTAAAATAATATAAAAAATAAAATAAAAATAGTATATTTTAAAAAATAAAAT
29632171 AAATACCAAA
Statistics
Matches: 469, Mismatches: 28, Indels: 31
0.89 0.05 0.06
Matches are distributed among these distances:
147 1 0.00
148 14 0.03
149 55 0.12
150 10 0.02
151 70 0.15
152 9 0.02
153 112 0.24
154 115 0.25
156 31 0.07
157 52 0.11
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.28
Consensus pattern (152 bp):
TACTAAAATAATATAAAAAATAAAATAAAAATAGTATATTTTAAAAAATAAAATCCGAAAATAAA
ATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACACTAAA
ATAATACATTTAAAACATTATG
Found at i:29632139 original size:12 final size:12
Alignment explanation
Indices: 29632122--29632173 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
29632112 ATTATGTATT
29632122 AAAATAATATAA
1 AAAATAATATAA
29632134 AAAATAATATAA
1 AAAATAATATAA
*
29632146 AAAAGTATATTTTAA
1 AAAA-TA-A-TATAA
*
29632161 AAAATAAAATAA
1 AAAATAATATAA
29632173 A
1 A
29632174 TACCAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 20 0.59
13 3 0.09
14 3 0.09
15 8 0.24
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:29642352 original size:45 final size:45
Alignment explanation
Indices: 29642231--29642352 Score: 149
Period size: 45 Copynumber: 2.7 Consensus size: 45
29642221 CTAGGAATTA
* *
29642231 AGAAATTCGAGCTCGTTGAG-TGGTCCGAGTTCGTGATATATGTG
1 AGAAATCCGAACTCGTTGAGTTGGTCCGAGTTCGTGATATATGTG
* ** *
29642275 AGAAATCTGAACTTATTGAGTTGGTCCAAGTTCGTGATATATGTG
1 AGAAATCCGAACTCGTTGAGTTGGTCCGAGTTCGTGATATATGTG
* *
29642320 A-AGCATCCGAACTCGTTGAGTTGGTCTGAGTTC
1 AGA-AATCCGAACTCGTTGAGTTGGTCCGAGTTC
29642353 ATTATGGATG
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 16 0.25
45 48 0.75
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (45 bp):
AGAAATCCGAACTCGTTGAGTTGGTCCGAGTTCGTGATATATGTG
Found at i:29652893 original size:32 final size:32
Alignment explanation
Indices: 29652848--29653082 Score: 163
Period size: 32 Copynumber: 7.3 Consensus size: 32
29652838 GCAGAGTGAG
*
29652848 GAGCTAG-AGAGTGGCGAGTTAGCGAGGAGGC
1 GAGCTAGCAGAGTGGCGAGCTAGCGAGGAGGC
* ** *
29652879 GAGCTAGCAGAGTGGCAAGCTAGAAAGTG-GTC
1 GAGCTAGCAGAGTGGCGAGCTAGCGAG-GAGGC
* * * ** ***
29652911 -AGCTAACAGGGTGGCGAGCTAGTAGACAATTAT
1 GAGCTAGCAGAGTGGCGAGCTAG-CGAGGA-GGC
* *
29652944 GAGCTAGCAGAGTGGTGAGCTAGC-AGACAGTGAC
1 GAGCTAGCAGAGTGGCGAGCTAGCGAG-GAG-G-C
* * * *
29652978 GAGCTAGTAGAGTGGTGAGCTAGCGATGAGGT
1 GAGCTAGCAGAGTGGCGAGCTAGCGAGGAGGC
* * *
29653010 GAGCTAGTAGAGTGGCAAGCTAGCGAGGAGGT
1 GAGCTAGCAGAGTGGCGAGCTAGCGAGGAGGC
** *
29653042 GAGCTAGCAGAGTGGTAAGCTAGTGAGGAGGC
1 GAGCTAGCAGAGTGGCGAGCTAGCGAGGAGGC
29653074 GAGCTAGCA
1 GAGCTAGCA
29653083 ATGAGGTGAG
Statistics
Matches: 160, Mismatches: 34, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
31 26 0.16
32 86 0.54
33 3 0.02
34 44 0.28
35 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.40, T:0.17
Consensus pattern (32 bp):
GAGCTAGCAGAGTGGCGAGCTAGCGAGGAGGC
Found at i:29652964 original size:34 final size:34
Alignment explanation
Indices: 29652911--29653001 Score: 110
Period size: 34 Copynumber: 2.7 Consensus size: 34
29652901 GAAAGTGGTC
* * * * * *
29652911 AGCTAACAGGGTGGCGAGCTAGTAGACAATTATG
1 AGCTAGCAGAGTGGTGAGCTAGCAGACAATGACG
*
29652945 AGCTAGCAGAGTGGTGAGCTAGCAGACAGTGACG
1 AGCTAGCAGAGTGGTGAGCTAGCAGACAATGACG
*
29652979 AGCTAGTAGAGTGGTGAGCTAGC
1 AGCTAGCAGAGTGGTGAGCTAGC
29653002 GATGAGGTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.30, C:0.15, G:0.36, T:0.19
Consensus pattern (34 bp):
AGCTAGCAGAGTGGTGAGCTAGCAGACAATGACG
Found at i:29652981 original size:18 final size:18
Alignment explanation
Indices: 29652925--29652984 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
29652915 AACAGGGTGG
* * *
29652925 CGAGCTAGTAGACAATTA
1 CGAGCTAGCAGACAGTGA
* *
29652943 TGAGCTAGCAG--AGTGG
1 CGAGCTAGCAGACAGTGA
*
29652959 TGAGCTAGCAGACAGTGA
1 CGAGCTAGCAGACAGTGA
29652977 CGAGCTAG
1 CGAGCTAG
29652985 TAGAGTGGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 13 0.39
18 20 0.61
ACGTcount: A:0.32, C:0.17, G:0.33, T:0.18
Consensus pattern (18 bp):
CGAGCTAGCAGACAGTGA
Found at i:29653062 original size:16 final size:16
Alignment explanation
Indices: 29652835--29653064 Score: 130
Period size: 16 Copynumber: 14.2 Consensus size: 16
29652825 CGTCACTCTA
29652835 CTAGCAGAGTGAG-GAG
1 CTAGCAGAGTG-GTGAG
*
29652851 CTAG-AGAGTGGCGAG
1 CTAGCAGAGTGGTGAG
* * *
29652866 TTAGC-GAGGAGGCGAG
1 CTAGCAGA-GTGGTGAG
**
29652882 CTAGCAGAGTGGCAAG
1 CTAGCAGAGTGGTGAG
* *
29652898 CTAG-AAAGTGGTCAG
1 CTAGCAGAGTGGTGAG
* * *
29652913 CTAACAGGGTGGCGAG
1 CTAGCAGAGTGGTGAG
* * **
29652929 CTAGTAGACAATTATGAG
1 CTAGCAG--AGTGGTGAG
29652947 CTAGCAGAGTGGTGAG
1 CTAGCAGAGTGGTGAG
**
29652963 CTAGCAGACAGTGACGAG
1 CTAGCAG--AGTGGTGAG
*
29652981 CTAGTAGAGTGGTGAG
1 CTAGCAGAGTGGTGAG
*
29652997 CTAGC-GATGAGGTGAG
1 CTAGCAGA-GTGGTGAG
* **
29653013 CTAGTAGAGTGGCAAG
1 CTAGCAGAGTGGTGAG
*
29653029 CTAGC-GAGGAGGTGAG
1 CTAGCAGA-GTGGTGAG
*
29653045 CTAGCAGAGTGGTAAG
1 CTAGCAGAGTGGTGAG
29653061 CTAG
1 CTAG
29653065 TGAGGAGGCG
Statistics
Matches: 160, Mismatches: 41, Indels: 26
0.70 0.18 0.11
Matches are distributed among these distances:
14 1 0.01
15 29 0.18
16 101 0.63
17 6 0.04
18 23 0.14
ACGTcount: A:0.29, C:0.14, G:0.40, T:0.17
Consensus pattern (16 bp):
CTAGCAGAGTGGTGAG
Found at i:29653063 original size:48 final size:48
Alignment explanation
Indices: 29652943--29653098 Score: 156
Period size: 48 Copynumber: 3.2 Consensus size: 48
29652933 TAGACAATTA
* * * *
29652943 TGAGCTAGCAGAGTGGTGAGCTAGCAGACAGTGACGAGCTAG-TAGAGTGG
1 TGAGCTAGCAGAGTGGTGAGCTAGTAG--AGTGGCGAGCTAGCAAG-GAGG
* * *
29652993 TGAGCTAGC-GATGAGGTGAGCTAGTAGAGTGGCAAGCTAGCGAGGAGG
1 TGAGCTAGCAGA-GTGGTGAGCTAGTAGAGTGGCGAGCTAGCAAGGAGG
* * *
29653041 TGAGCTAGCAGAGTGGTAAGCTAGT-GAGGAGGCGAGCTAGCAATGAGG
1 TGAGCTAGCAGAGTGGTGAGCTAGTAGA-GTGGCGAGCTAGCAAGGAGG
29653089 TGAGCTAGCA
1 TGAGCTAGCA
29653099 AAGCGTCGCA
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
47 2 0.02
48 60 0.67
49 6 0.07
50 22 0.24
ACGTcount: A:0.28, C:0.13, G:0.41, T:0.17
Consensus pattern (48 bp):
TGAGCTAGCAGAGTGGTGAGCTAGTAGAGTGGCGAGCTAGCAAGGAGG
Found at i:29653088 original size:16 final size:16
Alignment explanation
Indices: 29653069--29653099 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29653059 AGCTAGTGAG
29653069 GAGGCGAGCTAGCAAT
1 GAGGCGAGCTAGCAAT
*
29653085 GAGGTGAGCTAGCAA
1 GAGGCGAGCTAGCAA
29653100 AGCGTCGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.39, T:0.13
Consensus pattern (16 bp):
GAGGCGAGCTAGCAAT
Found at i:29654521 original size:16 final size:16
Alignment explanation
Indices: 29654476--29654531 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
29654466 AAAGGTTAAG
*
29654476 AAAA-AAATATTTAGAA
1 AAAATAAATATTT-GTA
*
29654492 AAATATAAAAATTTGTA
1 AAA-ATAAATATTTGTA
29654509 AAAATAAATATTT-TA
1 AAAATAAATATTTGTA
29654524 AATAATAA
1 AA-AATAA
29654532 TTAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.12
16 17 0.50
17 6 0.18
18 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (16 bp):
AAAATAAATATTTGTA
Found at i:29654550 original size:20 final size:20
Alignment explanation
Indices: 29654513--29654550 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29654503 TTTGTAAAAA
*
29654513 TAAATATTTTAAATAATAAT
1 TAAATATTTTAAAGAATAAT
*
29654533 TAAATATTTTTAAGAATA
1 TAAATATTTTAAAGAATA
29654551 TTTTAAAATT
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:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TAAATATTTTAAAGAATAAT
Found at i:29654625 original size:51 final size:51
Alignment explanation
Indices: 29654521--29654630 Score: 118
Period size: 51 Copynumber: 2.1 Consensus size: 51
29654511 AATAAATATT
* * *
29654521 TTAAATAATAATTAAATATTTTTAAGAATATTTTAAAATTGTAAAAAAGTTA
1 TTAAA-AATAATAAAATATTTTTAAGAATATTTTAAAACTGCAAAAAAGTTA
* *
29654573 TTGAAAATAATAAAATATTTTTTAA-AAT-TTATTAAAAACTGCAAATAA-TTA
1 TTAAAAATAATAAAATA-TTTTTAAGAATATT-TT-AAAACTGCAAAAAAGTTA
29654624 TTAAAAA
1 TTAAAAA
29654631 ATTGTAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.04
51 25 0.51
52 22 0.45
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.40
Consensus pattern (51 bp):
TTAAAAATAATAAAATATTTTTAAGAATATTTTAAAACTGCAAAAAAGTTA
Found at i:29654626 original size:20 final size:21
Alignment explanation
Indices: 29654601--29654644 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29654591 TTTTTAAAAT
29654601 TTATT-AAAAACTGCAAATAA
1 TTATTAAAAAACTGCAAATAA
* *
29654621 TTATTAAAAAATTGTAAATAA
1 TTATTAAAAAACTGCAAATAA
29654642 TTA
1 TTA
29654645 ACTAATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (21 bp):
TTATTAAAAAACTGCAAATAA
Found at i:29654898 original size:20 final size:19
Alignment explanation
Indices: 29654873--29654985 Score: 102
Period size: 19 Copynumber: 5.8 Consensus size: 19
29654863 TTTAAATAAT
29654873 TTTTTAATAATTATTTACAA
1 TTTTTAATAATT-TTTACAA
*
29654893 TTTTTAATAA-TTTTCCAAA
1 TTTTTAATAATTTTTAC-AA
* **
29654912 ATTTTAATAATTTTCCCAA
1 TTTTTAATAATTTTTACAA
*
29654931 ATTTTAATAATTTTTACAAA
1 TTTTTAATAATTTTTAC-AA
* * **
29654951 TTTTAAAAAATTTTTTGTAA
1 TTTTTAATAA-TTTTTACAA
29654971 TTTTTAATAATTTTT
1 TTTTTAATAATTTTT
29654986 TAATATTTTA
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.05
19 34 0.44
20 34 0.44
21 5 0.06
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (19 bp):
TTTTTAATAATTTTTACAA
Found at i:29654918 original size:19 final size:19
Alignment explanation
Indices: 29654894--29655022 Score: 98
Period size: 19 Copynumber: 6.6 Consensus size: 19
29654884 TATTTACAAT
29654894 TTTTAATAATTTTCCAAAA
1 TTTTAATAATTTTCCAAAA
*
29654913 TTTTAATAATTTTCCCAAA
1 TTTTAATAATTTTCCAAAA
*
29654932 TTTTAATAATTTT-TACAAA
1 TTTTAATAATTTTCCA-AAA
* *** *
29654951 TTTTAAAAAATTTTTTGTAAT
1 TTTT-AATAA-TTTTCCAAAA
** *
29654972 TTTTAATAATTTTTTAATA
1 TTTTAATAATTTTCCAAAA
* *
29654991 TTTTAAGTTATTTTCAAAAA
1 TTTTAA-TAATTTTCCAAAA
29655011 TATTTAATAATT
1 T-TTTAATAATT
29655023 ATTTGAAATA
Statistics
Matches: 87, Mismatches: 17, Indels: 11
0.76 0.15 0.10
Matches are distributed among these distances:
19 50 0.57
20 22 0.25
21 15 0.17
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTAATAATTTTCCAAAA
Found at i:29654986 original size:20 final size:20
Alignment explanation
Indices: 29654873--29654986 Score: 108
Period size: 20 Copynumber: 5.8 Consensus size: 20
29654863 TTTAAATAAT
*
29654873 TTTTTAATAATTATTT-ACAA
1 TTTTTAATAATTTTTTCA-AA
*
29654893 TTTTTAATAA-TTTTCCAAA
1 TTTTTAATAATTTTTTCAAA
* **
29654912 ATTTTAATAATTTTCCCAAA
1 TTTTTAATAATTTTTTCAAA
*
29654932 -TTTTAATAATTTTTACAAA
1 TTTTTAATAATTTTTTCAAA
* * **
29654951 TTTTAAAAAATTTTTTGTAA
1 TTTTTAATAATTTTTTCAAA
29654971 TTTTTAATAATTTTTT
1 TTTTTAATAATTTTTT
29654987 AATATTTTAA
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 31 0.40
20 47 0.60
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (20 bp):
TTTTTAATAATTTTTTCAAA
Found at i:29659393 original size:16 final size:16
Alignment explanation
Indices: 29659369--29659399 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29659359 TTGGAGAATG
*
29659369 GAATGGAGTTGTAATA
1 GAATAGAGTTGTAATA
29659385 GAATAGAGTTGTAAT
1 GAATAGAGTTGTAAT
29659400 CAGTAATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (16 bp):
GAATAGAGTTGTAATA
Found at i:29659492 original size:51 final size:51
Alignment explanation
Indices: 29659385--29659481 Score: 128
Period size: 49 Copynumber: 1.9 Consensus size: 51
29659375 AGTTGTAATA
*
29659385 GAATAGAGTTGTAATCAGTAATTCAGTCGTTTGGTTGAAAGGAATGGAATG
1 GAATAGAGTTGTAATCAGTAATTCAGTCGTTTGGTTGAAAGGAATAGAATG
* **
29659436 GAATAGAGTTGTAAT-AGT-ATTCTTGT-GTTTGGTTGATTGGAATAGA
1 GAATAGAGTTGTAATCAGTAATTC-AGTCGTTTGGTTGAAAGGAATAGA
29659482 CATTGTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 21 0.51
50 5 0.12
51 15 0.37
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (51 bp):
GAATAGAGTTGTAATCAGTAATTCAGTCGTTTGGTTGAAAGGAATAGAATG
Found at i:29659643 original size:62 final size:58
Alignment explanation
Indices: 29659577--29659736 Score: 175
Period size: 57 Copynumber: 2.7 Consensus size: 58
29659567 TTTTAATAAG
* * *
29659577 ATTATTATTAAATATAATTTAATAATAAATAATAATAAATAATTTAATCATATTTTAACAT
1 ATTATTATTAAATATAATTTAATAA-AAATAATAAT-AATAATTTAATAACATTCTAA-AT
* *
29659638 AATTATTATTAAATACAATTTAAT-AAAATAAT-AT-ATAATTTAATAACATTCTCAAT
1 -ATTATTATTAAATATAATTTAATAAAAATAATAATAATAATTTAATAACATTCTAAAT
*
29659694 ATTATTATTAAAATATGAA-TTAATAAAAATCATAATATATAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAATA-ATAAT
29659737 ATTATAAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
55 9 0.11
56 12 0.14
57 25 0.29
58 2 0.02
59 2 0.02
60 12 0.14
61 1 0.01
62 22 0.26
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAATAATAATTTAATAACATTCTAAAT
Found at i:29659733 original size:24 final size:23
Alignment explanation
Indices: 29659706--29659755 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
29659696 TATTATTAAA
*
29659706 ATATGAAT-TAATAAAAATCATAAT
1 ATAT-AATATAATAAAAATAAT-AT
*
29659730 ATATAATATTATAAAAATAATAT
1 ATATAATATAATAAAAATAATAT
29659753 ATA
1 ATA
29659756 ACTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATAATATAATAAAAATAATAT
Found at i:29660792 original size:43 final size:43
Alignment explanation
Indices: 29660742--29660877 Score: 209
Period size: 43 Copynumber: 3.2 Consensus size: 43
29660732 GAAAAAAACT
* *
29660742 CCGCTAAAAGTCAAGACTTTTAGTGGCGTTTGTGGGAAAAGCG
1 CCGCTAAAAGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCG
* * *
29660785 CCACTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGTAAAAGCG
1 CCGCTAAAAGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCG
* *
29660828 CCGCTAAAAATCACGGCTTTTAGCGGCGTTTGTGGGAAAAGCG
1 CCGCTAAAAGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCG
29660871 CCGCTAA
1 CCGCTAA
29660878 TTTTGGCAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (43 bp):
CCGCTAAAAGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCG
Found at i:29661007 original size:32 final size:31
Alignment explanation
Indices: 29660930--29661009 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
29660920 CTTCCTGCAT
* * * *
29660930 TAAAATCCAACCAAATATAACAAATATAGTA
1 TAAAATACAACCAAAAACAACAAATATAGCA
* *
29660961 TAAAATACAGCCAAAAACAACAAATTTAGCA
1 TAAAATACAACCAAAAACAACAAATATAGCA
29660992 TAAAAATACAACCAAAAA
1 T-AAAATACAACCAAAAA
29661010 ATTAATTCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 26 0.63
32 15 0.37
ACGTcount: A:0.61, C:0.17, G:0.04, T:0.17
Consensus pattern (31 bp):
TAAAATACAACCAAAAACAACAAATATAGCA
Done.