Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 24 of 335
Found at i:8987375 original size:42 final size:40
Alignment explanation
Indices: 8987258--8987385 Score: 112
Period size: 42 Copynumber: 3.0 Consensus size: 40
8987248 ATCTCAATGC
* * **
8987258 AGTGCATCATCAGATAACTGAAGGAAAGATATTGGCACACA
1 AGTGCATCATCAAATAACTGAA-GAAATATATTGGCACGTA
* * * *
8987299 TAGTGCATCATCGATTAAACCGAAGCAATCATATTGGCACGTA
1 -AGTGCATCATCAAAT-AACTGAAGAAAT-ATATTGGCACGTA
*
8987342 AGTGCATCATCAAATGCACTGAAGAAAATATATTGGCACTGTA
1 AGTGCATCATCAAAT-AACTGAAG-AAATATATTGGCAC-GTA
8987385 A
1 A
8987386 CACCCCCTAT
Statistics
Matches: 68, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
42 44 0.65
43 24 0.35
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (40 bp):
AGTGCATCATCAAATAACTGAAGAAATATATTGGCACGTA
Found at i:8987906 original size:16 final size:17
Alignment explanation
Indices: 8987875--8987907 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8987865 TTCATAAGTA
*
8987875 TATATCCATCATTTCAT
1 TATATCAATCATTTCAT
8987892 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
8987908 GCTCCATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:8988253 original size:46 final size:46
Alignment explanation
Indices: 8988188--8988541 Score: 516
Period size: 46 Copynumber: 7.7 Consensus size: 46
8988178 TTATCTTTGA
* * * * *
8988188 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* *** *
8988234 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT-AT
*
8988281 ACA-G-TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 -CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
8988326 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
8988372 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTGATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
8988418 CCTATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
8988464 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
8988510 CATGTTGCCATGGTATCTTTCAACTATGGTCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCT
8988542 AAATCCCCTG
Statistics
Matches: 280, Mismatches: 23, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
44 1 0.00
45 6 0.02
46 269 0.96
47 2 0.01
48 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:8993234 original size:22 final size:22
Alignment explanation
Indices: 8993206--8993273 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
8993196 TATGCACTAT
*
8993206 TAAACAGAGAGCACTAAAGTGC
1 TAAACAGAGAGCACTAATGTGC
*
8993228 TATACAGAGAGCA-TGAATGTGC
1 TAAACAGAGAGCACT-AATGTGC
*
8993250 TAAACAAAGAGCACTAATGTGC
1 TAAACAGAGAGCACTAATGTGC
8993272 TA
1 TA
8993274 GTAATCGGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (22 bp):
TAAACAGAGAGCACTAATGTGC
Found at i:8993453 original size:2 final size:2
Alignment explanation
Indices: 8993446--8993488 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
8993436 ACATTTGCAC
8993446 AT AT AT AT -T CAT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8993487 AT
1 AT
8993489 TCCAATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 35 0.92
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8995549 original size:35 final size:35
Alignment explanation
Indices: 8995510--8995912 Score: 445
Period size: 35 Copynumber: 11.6 Consensus size: 35
8995500 CATGGTAAAG
*
8995510 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
*
8995545 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *
8995580 TGTGAAATGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *
8995615 TGTAAAACGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * * *
8995650 TGTGAAACATAGGTATGGTATTAACCATACTGAGC
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
8995685 TGTGAAATGTAGGTATGGTAT-TTCCATACTGAGC
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *
8995719 TGTGAAACGTAGGTATGGTAT-TTCCATACTGAGC
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *
8995753 TGTGAAACGTAGATATGG-AGTCATCCATACTGAGC
1 TGTGAAACGTAGGTATGGTA-TCATCCATACTGAGT
* * * *
8995788 TATGATACGTAGGTATGGCATCGTCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* ** * ** *
8995823 TATGAAATATAGGTATGGTTTTTTCCATACCGAG-
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
** * * ** *
8995857 CATGAAAAGTAGGTATGGTGTTTTCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
*
8995892 TGTGAAACATAGGTATGGTAT
1 TGTGAAACGTAGGTATGGTAT
8995913 TTCAATGAGG
Statistics
Matches: 324, Mismatches: 40, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
33 1 0.00
34 92 0.28
35 230 0.71
36 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
Found at i:8995801 original size:173 final size:173
Alignment explanation
Indices: 8995510--8995915 Score: 528
Period size: 173 Copynumber: 2.3 Consensus size: 173
8995500 CATGGTAAAG
* *
8995510 TGTGAAATGTAGGTATGGTATCATCCATACTGAGTTGTGAAACGTAGGTATGGTATCATCCATAC
1 TGTGAAATGTAGGTATGGTAT-TTCCATACTGAGTTGTGAAACGTAGGTATGGTAT-TTCCATAC
* * * * * *
8995575 CGAGTTGTGAAATGTAGGTATGGTATCATCCATACCGAGTTGTAAAACGTAGGTATGGTATCATC
64 CGAGCTGTGAAACGTAGATATGGTATCATCCATACCGAGCTATAAAACGTAGGTATGGCATCATC
* *
8995640 CATACCGAGTTGTGAAACATAGGTATGGTATTAACCATACTGAGC
129 CATACCGAGTTATGAAACATAGGTATGGTATTAACCATACCGAGC
* *
8995685 TGTGAAATGTAGGTATGGTATTTCCATACTGAGCTGTGAAACGTAGGTATGGTATTTCCATACTG
1 TGTGAAATGTAGGTATGGTATTTCCATACTGAGTTGTGAAACGTAGGTATGGTATTTCCATACCG
* * * *
8995750 AGCTGTGAAACGTAGATATGG-AGTCATCCATACTGAGCTATGATACGTAGGTATGGCATCGTCC
66 AGCTGTGAAACGTAGATATGGTA-TCATCCATACCGAGCTATAAAACGTAGGTATGGCATCATCC
* * * **
8995814 ATACTGAGTTATGAAATATAGGTATGGTTTTTTCCATACCGAGC
130 ATACCGAGTTATGAAACATAGGTATGGTATTAACCATACCGAGC
* * * * *
8995858 -ATGAAAAGTAGGTATGGTGTTTTCCATACCGAGTTGTGAAACATAGGTATGGTATTTC
1 TGTGAAATGTAGGTATGGT-ATTTCCATACTGAGTTGTGAAACGTAGGTATGGTATTTC
8995916 AATGAGGAAA
Statistics
Matches: 202, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
172 17 0.08
173 132 0.65
174 32 0.16
175 21 0.10
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (173 bp):
TGTGAAATGTAGGTATGGTATTTCCATACTGAGTTGTGAAACGTAGGTATGGTATTTCCATACCG
AGCTGTGAAACGTAGATATGGTATCATCCATACCGAGCTATAAAACGTAGGTATGGCATCATCCA
TACCGAGTTATGAAACATAGGTATGGTATTAACCATACCGAGC
Found at i:8997483 original size:5 final size:5
Alignment explanation
Indices: 8997475--8997527 Score: 99
Period size: 5 Copynumber: 10.8 Consensus size: 5
8997465 TTTTTTGTTT
8997475 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
8997524 TATA
1 TATA
8997528 CTTAACTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.09
5 43 0.91
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:9008080 original size:26 final size:25
Alignment explanation
Indices: 9008043--9008110 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 25
9008033 TGTTTTGTAG
*
9008043 AAAATTTTAAATATTTTTAATAATGT
1 AAAATTTAAAATATTTTTAATAAT-T
*
9008069 AAAATTTAAAATATATATT-ATAATT
1 AAAATTTAAAATAT-TTTTAATAATT
*
9008094 -AAA-TAAAAATATTTTTA
1 AAAATTTAAAATATTTTTA
9008111 TTGTAGAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
22 3 0.08
23 8 0.22
24 3 0.08
25 1 0.03
26 18 0.50
27 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (25 bp):
AAAATTTAAAATATTTTTAATAATT
Found at i:9008583 original size:8 final size:8
Alignment explanation
Indices: 9008572--9008621 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
9008562 TTAATTAATT
9008572 TTTTAAAA
1 TTTTAAAA
9008580 TTTTAAAA
1 TTTTAAAA
* *
9008588 TATAAAAA
1 TTTTAAAA
*
9008596 TATTAAAA
1 TTTTAAAA
9008604 TTATTAAAA
1 TT-TTAAAA
9008613 TTATTAAAA
1 TT-TTAAAA
9008622 ACTATTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
8 22 0.59
9 15 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTTTAAAA
Found at i:9008627 original size:10 final size:9
Alignment explanation
Indices: 9008574--9008621 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
9008564 AATTAATTTT
9008574 TTAAAATT-
1 TTAAAATTA
9008582 TTAAAA-TA
1 TTAAAATTA
*
9008590 -TAAAAATA
1 TTAAAATTA
9008598 TTAAAATTA
1 TTAAAATTA
9008607 TTAAAATTA
1 TTAAAATTA
9008616 TTAAAA
1 TTAAAA
9008622 ACTATTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
7 6 0.17
8 8 0.22
9 22 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TTAAAATTA
Found at i:9018234 original size:15 final size:16
Alignment explanation
Indices: 9018214--9018247 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
9018204 TTGGCTTTTC
9018214 TATCTGAGTTTT-ATA
1 TATCTGAGTTTTAATA
9018229 TATCTGAGTTTTAATA
1 TATCTGAGTTTTAATA
9018245 TAT
1 TAT
9018248 TTGATCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (16 bp):
TATCTGAGTTTTAATA
Found at i:9021722 original size:21 final size:22
Alignment explanation
Indices: 9021693--9021735 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9021683 ATTTTTAATG
9021693 TTTTCT-AAATCAAATTATTTTA
1 TTTTCTAAAATCAAA-TATTTTA
*
9021715 TTTT-TAAAATTAAATATTTTA
1 TTTTCTAAAATCAAATATTTTA
9021736 GTCGTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTCTAAAATCAAATATTTTA
Found at i:9027740 original size:21 final size:21
Alignment explanation
Indices: 9027714--9027756 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
9027704 AGAATTAAAG
9027714 CAGAACCACGTCACAGAATAT
1 CAGAACCACGTCACAGAATAT
9027735 CAGAACCACGTCACAGAATAT
1 CAGAACCACGTCACAGAATAT
9027756 C
1 C
9027757 TGTGCACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.30, G:0.14, T:0.14
Consensus pattern (21 bp):
CAGAACCACGTCACAGAATAT
Found at i:9047596 original size:43 final size:43
Alignment explanation
Indices: 9047535--9047630 Score: 183
Period size: 43 Copynumber: 2.2 Consensus size: 43
9047525 TATTACACAG
9047535 TAGATTTTTGCTTTTCTAGAGGGGGCTGGGGAGGAGGGGGTGA
1 TAGATTTTTGCTTTTCTAGAGGGGGCTGGGGAGGAGGGGGTGA
9047578 TAGATTTTTGCTTTTCTAGAGGGGGCTGGGGAGGAGGGGGTGA
1 TAGATTTTTGCTTTTCTAGAGGGGGCTGGGGAGGAGGGGGTGA
9047621 TAGTATTTTT
1 TAG-ATTTTT
9047631 ATTATTGAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 46 0.88
44 6 0.12
ACGTcount: A:0.17, C:0.06, G:0.43, T:0.34
Consensus pattern (43 bp):
TAGATTTTTGCTTTTCTAGAGGGGGCTGGGGAGGAGGGGGTGA
Found at i:9048417 original size:12 final size:12
Alignment explanation
Indices: 9048400--9048425 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9048390 TGTAACTCCC
9048400 GCTACTGCTGCT
1 GCTACTGCTGCT
9048412 GCTACTGCTGCT
1 GCTACTGCTGCT
9048424 GC
1 GC
9048426 CGCTGCTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.35, G:0.27, T:0.31
Consensus pattern (12 bp):
GCTACTGCTGCT
Found at i:9051563 original size:40 final size:37
Alignment explanation
Indices: 9051497--9051631 Score: 143
Period size: 35 Copynumber: 3.7 Consensus size: 37
9051487 CATGGAAAAG
9051497 TGTGAAATGTAGGTATGGTA--TCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
* *
9051532 TGTGAAATGTAGATATGGTATTATCAAATCCATACTTAGT
1 TGTGAAATGTAGGTATGGTATT-TC--ATCCATACTGAGT
** * * *
9051572 TAAGAAACGTAGGTATGGCATTTC--CCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
*
9051607 TGTAAAATGTAGGTATGGTATTTCA
1 TGTGAAATGTAGGTATGGTATTTCA
9051632 ATGAGGAAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
35 47 0.59
38 2 0.03
39 2 0.03
40 29 0.36
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
Found at i:9054119 original size:26 final size:26
Alignment explanation
Indices: 9054090--9054148 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
9054080 ATATATAATA
* * * *
9054090 ATATATTATTTAATATTTAAGTAAAT
1 ATATATAATATAATAATAAAGTAAAT
9054116 ATATATAATATAATAATAAAGTAAAT
1 ATATATAATATAATAATAAAGTAAAT
9054142 ATA-ATAA
1 ATATATAA
9054149 ACAGGACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
ATATATAATATAATAATAAAGTAAAT
Found at i:9054185 original size:4 final size:4
Alignment explanation
Indices: 9054176--9054232 Score: 51
Period size: 4 Copynumber: 13.0 Consensus size: 4
9054166 ATGAATAAAC
* *
9054176 AAAG AAAG AAACA AAACG AACAG AAAGG AAAG AAAG AAAAG AAAA AAAG
1 AAAG AAAG AAA-G AAA-G AA-AG AAA-G AAAG AAAG -AAAG AAAG AAAG
9054225 AAAG AAAG
1 AAAG AAAG
9054233 GAGAAAGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 27 0.60
5 17 0.38
6 1 0.02
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:9054237 original size:28 final size:32
Alignment explanation
Indices: 9054176--9054240 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
9054166 ATGAATAAAC
9054176 AAAG-AAAGAAACAAAACGAACAGAAAGGAAAG
1 AAAGAAAAGAAACAAAACGAACAGAAAGG-AAG
9054208 AAAGAAAAGAAA-AAAA-GAA-AGAAAGG-AG
1 AAAGAAAAGAAACAAAACGAACAGAAAGGAAG
9054236 AAAGA
1 AAAGA
9054241 TAATATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
28 7 0.22
30 7 0.22
31 3 0.09
32 8 0.25
33 7 0.22
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (32 bp):
AAAGAAAAGAAACAAAACGAACAGAAAGGAAG
Found at i:9055183 original size:40 final size:37
Alignment explanation
Indices: 9055108--9055190 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 37
9055098 GTCGATGATG
* **
9055108 CACTGGGTGTCAATTTACTTCAGTTTAACGGATGAGA
1 CACTGGGTGTCAATTTACTTCAGATTAACCAATGAGA
* *
9055145 CACTGGGTGTCAATTTACTACTTCAGATTATCCAATGAGG
1 CACTGGGTGTCAA-TT--TACTTCAGATTAACCAATGAGA
9055185 CACTGG
1 CACTGG
9055191 TGCCAAACTG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 13 0.34
38 2 0.05
40 23 0.61
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (37 bp):
CACTGGGTGTCAATTTACTTCAGATTAACCAATGAGA
Found at i:9055989 original size:26 final size:24
Alignment explanation
Indices: 9055950--9056009 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
9055940 TTATTTCATT
* * *
9055950 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
9055974 TAAATTAAATATATTTAAAAACATAA
1 -AAA-TAAATATATTTAAAAACATAA
9056000 AAATAAATAT
1 AAATAAATAT
9056010 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.23
25 6 0.19
26 18 0.58
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:9056021 original size:22 final size:22
Alignment explanation
Indices: 9055980--9056038 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
9055970 ATAATAAATT
* *
9055980 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
9056000 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
9056022 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
9056039 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:9056115 original size:15 final size:16
Alignment explanation
Indices: 9056085--9056117 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
9056075 AAATAGTTAT
9056085 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
9056102 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
9056117 A
1 A
9056118 AAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:9060558 original size:25 final size:25
Alignment explanation
Indices: 9060515--9060563 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
9060505 TTATTGTTGT
* *
9060515 TGTAATAATTTAAAAGATTTAATGA
1 TGTAATAAGTTAAAAGATTGAATGA
**
9060540 TGTAATAAGTTAATGGATTGAATG
1 TGTAATAAGTTAAAAGATTGAATG
9060564 GTACAAGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (25 bp):
TGTAATAAGTTAAAAGATTGAATGA
Found at i:9061410 original size:42 final size:43
Alignment explanation
Indices: 9061329--9061410 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
9061319 AATACATACG
***
9061329 GTGGAGAGTTTCCTACATCAAAGGGTCATATATGTATAACCTT
1 GTGGAGAGTTTCCTACATCAAAGGGTCATATACCAATAACCTT
* * *
9061372 GTGGAGAGTTTCTTACATC-AAGGGTCATTTCCCAATAAC
1 GTGGAGAGTTTCCTACATCAAAGGGTCATATACCAATAAC
9061411 ATAAGCAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 15 0.45
43 18 0.55
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (43 bp):
GTGGAGAGTTTCCTACATCAAAGGGTCATATACCAATAACCTT
Found at i:9071620 original size:22 final size:23
Alignment explanation
Indices: 9071580--9071622 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
9071570 TTACCAAACC
9071580 AATAATTTAAATGAAAATTTTCA
1 AATAATTTAAATGAAAATTTTCA
*
9071603 AATAATTT-AATGATAATTTT
1 AATAATTTAAATGAAAATTTT
9071623 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
AATAATTTAAATGAAAATTTTCA
Found at i:9073774 original size:17 final size:17
Alignment explanation
Indices: 9073747--9073780 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
9073737 AAGGGCGTTA
9073747 ACGTTCAGGTCA-TTTT
1 ACGTTCAGGTCAGTTTT
9073763 ACGTTGCAGGTCAGTTTT
1 ACGTT-CAGGTCAGTTTT
9073781 TCCCCATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (17 bp):
ACGTTCAGGTCAGTTTT
Found at i:9077562 original size:40 final size:39
Alignment explanation
Indices: 9077507--9077585 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 39
9077497 TTTGAAAAGA
9077507 AGTTTGAGGTTGGTTATTGTTCTTAGTTCGATATTATATG
1 AGTTTGAGGTTGGTTATTGTTCTTAG-TCGATATTATATG
9077547 AGTTTGAGGTTGGTTATTGTTCTTAGTCGATATTATATG
1 AGTTTGAGGTTGGTTATTGTTCTTAGTCGATATTATATG
9077586 CATTTTACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 13 0.33
40 26 0.67
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.49
Consensus pattern (39 bp):
AGTTTGAGGTTGGTTATTGTTCTTAGTCGATATTATATG
Found at i:9085879 original size:27 final size:27
Alignment explanation
Indices: 9085826--9085880 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
9085816 TTTGGATAAT
**
9085826 AATATATATCTTATCTTTTCTGATTAA
1 AATATATATCTTATCTTTTAAGATTAA
*
9085853 AATATATAT-TATATCTTTTAAGTTTAA
1 AATATATATCT-TATCTTTTAAGATTAA
9085880 A
1 A
9085881 CATGAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (27 bp):
AATATATATCTTATCTTTTAAGATTAA
Found at i:9086809 original size:15 final size:15
Alignment explanation
Indices: 9086791--9086824 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
9086781 AATTGGAAGA
*
9086791 GTTGATGTTGTTGTT
1 GTTGATGTTGATGTT
9086806 GTTGATGTTGATGTT
1 GTTGATGTTGATGTT
9086821 GTTG
1 GTTG
9086825 CACTCCTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.00, G:0.35, T:0.56
Consensus pattern (15 bp):
GTTGATGTTGATGTT
Found at i:9087200 original size:2 final size:2
Alignment explanation
Indices: 9087193--9087219 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9087183 TCATTTTAAA
9087193 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9087220 CATTTGTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9090629 original size:23 final size:22
Alignment explanation
Indices: 9090597--9090641 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
9090587 TAATTTATAT
9090597 ATAATATAT-ATTTTCTTTGGTC
1 ATAATATATAATTTT-TTTGGTC
9090619 ATAATCATATAATTTTTTTGGTC
1 ATAAT-ATATAATTTTTTTGGTC
9090642 GAAATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 11 0.52
24 5 0.24
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (22 bp):
ATAATATATAATTTTTTTGGTC
Found at i:9096596 original size:33 final size:33
Alignment explanation
Indices: 9096558--9096643 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
9096548 AATATATATT
* *
9096558 TTTTAAATATGTATAATTGAATTAAAATCAAAA
1 TTTTAAATATATATAATTGAATCAAAATCAAAA
* * *
9096591 TTTTAAATATATATACTTGAATCACAATTAAAA
1 TTTTAAATATATATAATTGAATCAAAATCAAAA
*
9096624 TTTCATATATATATATAATT
1 TTT--TAAATATATATAATT
9096644 ACCCTAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 31 0.70
35 13 0.30
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (33 bp):
TTTTAAATATATATAATTGAATCAAAATCAAAA
Found at i:9097032 original size:16 final size:16
Alignment explanation
Indices: 9097004--9097055 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
9096994 GTTTGTTTCA
9097004 CTGTAA-TGAAATAGAG
1 CTGTAATTG-AATAGAG
*
9097020 CTGTAATTGAATAAAG
1 CTGTAATTGAATAGAG
* *
9097036 TTGTAATTGAATAGAA
1 CTGTAATTGAATAGAG
9097052 CTGT
1 CTGT
9097056 TTGGTTGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 28 0.93
17 2 0.07
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (16 bp):
CTGTAATTGAATAGAG
Found at i:9103424 original size:1 final size:1
Alignment explanation
Indices: 9103418--9103442 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
9103408 GCTGATCAAG
9103418 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
9103443 ACTAATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9108381 original size:15 final size:15
Alignment explanation
Indices: 9108361--9108390 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9108351 CAATGTGTAT
9108361 TTTTTAAAATATTTA
1 TTTTTAAAATATTTA
*
9108376 TTTTTAAAATTTTTA
1 TTTTTAAAATATTTA
9108391 CTATACTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTAAAATATTTA
Found at i:9115871 original size:20 final size:20
Alignment explanation
Indices: 9115833--9115871 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9115823 CCTCAAAACG
*
9115833 ATATTAGTTACTTTATAATA
1 ATATTAGATACTTTATAATA
9115853 ATATTAGAT-CTTTAGTAAT
1 ATATTAGATACTTTA-TAAT
9115872 TTCACAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (20 bp):
ATATTAGATACTTTATAATA
Found at i:9116114 original size:15 final size:16
Alignment explanation
Indices: 9116091--9116123 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9116081 TGATTGAATT
*
9116091 AATT-TTTTTTTAAAA
1 AATTATTTTATTAAAA
9116106 AATTATTTTATTAAAA
1 AATTATTTTATTAAAA
9116122 AA
1 AA
9116124 ATTAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTATTTTATTAAAA
Found at i:9124354 original size:62 final size:62
Alignment explanation
Indices: 9124257--9124380 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
9124247 TGGAAGGCAT
9124257 CAGCTAAGCAAAAAATGAAGATTGTGCATTGTTCATGGAACATGGAGGGAAATGAAACTATA
1 CAGCTAAGCAAAAAATGAAGATTGTGCATTGTTCATGGAACATGGAGGGAAATGAAACTATA
9124319 CAGCTAAGCAAAAAATGAAGATTGTGCATTGTTCATGGAACATGGAGGGAAATGAAACTATA
1 CAGCTAAGCAAAAAATGAAGATTGTGCATTGTTCATGGAACATGGAGGGAAATGAAACTATA
9124381 GGAAATTTGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.23
Consensus pattern (62 bp):
CAGCTAAGCAAAAAATGAAGATTGTGCATTGTTCATGGAACATGGAGGGAAATGAAACTATA
Found at i:9128123 original size:6 final size:6
Alignment explanation
Indices: 9128112--9128152 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
9128102 ATAATTTAAT
9128112 AAATAA AAATAA AAATATA AAACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATA-A AAA-TAA AAATAA AAATAA AAA
9128153 CATATAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 23 0.70
7 8 0.24
8 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:9128131 original size:26 final size:26
Alignment explanation
Indices: 9128089--9128168 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
9128079 CAACCTAATC
* *
9128089 ATAAAAATTACAA-ATAATTTAATAA
1 ATAAAAATAAAAATATAATTTAATAA
**
9128114 ATAAAAATAAAAATATAAAACTAA-AA
1 ATAAAAATAAAAATAT-AATTTAATAA
*
9128140 ATAAAAATAAAAACATATAATTTTATAA
1 ATAAAAAT-AAAA-ATATAATTTAATAA
9128168 A
1 A
9128169 AATAATTCGG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
25 11 0.26
26 12 0.28
27 13 0.30
28 7 0.16
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (26 bp):
ATAAAAATAAAAATATAATTTAATAA
Found at i:9128140 original size:20 final size:19
Alignment explanation
Indices: 9128115--9128153 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
9128105 ATTTAATAAA
9128115 TAAAAATAAAAATATAAAAC
1 TAAAAATAAAAATA-AAAAC
9128135 TAAAAATAAAAATAAAAAC
1 TAAAAATAAAAATAAAAAC
9128154 ATATAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (19 bp):
TAAAAATAAAAATAAAAAC
Found at i:9128185 original size:9 final size:9
Alignment explanation
Indices: 9128171--9128292 Score: 156
Period size: 9 Copynumber: 13.6 Consensus size: 9
9128161 TTTATAAAAA
9128171 TAATTCGGT
1 TAATTCGGT
9128180 TAATTCGGT
1 TAATTCGGT
* *
9128189 TAATTTGGG
1 TAATTCGGT
*
9128198 TAATTCGGG
1 TAATTCGGT
*
9128207 TAATTCGAT
1 TAATTCGGT
*
9128216 TAATTCGAT
1 TAATTCGGT
9128225 TAATTCAGG-
1 TAATTC-GGT
9128234 TAATTCGGT
1 TAATTCGGT
*
9128243 TAATTCGGG
1 TAATTCGGT
9128252 TAATTCGGT
1 TAATTCGGT
*
9128261 TAATTCGAT
1 TAATTCGGT
9128270 TAATTCGGT
1 TAATTCGGT
*
9128279 TAATTCAGT
1 TAATTCGGT
9128288 TAATT
1 TAATT
9128293 TTATACTTGT
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
8 2 0.02
9 97 0.97
10 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
TAATTCGGT
Found at i:9128605 original size:24 final size:24
Alignment explanation
Indices: 9128574--9128621 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
9128564 TTTTTCTATT
9128574 TTTCTTTTTGCAATTATATGATGA
1 TTTCTTTTTGCAATTATATGATGA
9128598 TTTCTTTTTGCAATTATATGATGA
1 TTTCTTTTTGCAATTATATGATGA
9128622 GATATACTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.54
Consensus pattern (24 bp):
TTTCTTTTTGCAATTATATGATGA
Found at i:9128773 original size:31 final size:31
Alignment explanation
Indices: 9128738--9128805 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
9128728 TTGCCTAAAC
*
9128738 CCGACCCAGATAAAAATGCTAAAATTTGAGT
1 CCGACCCAGATAAAAATGCTAAAATTCGAGT
**
9128769 CCGACCTGGATAAAAATGCTAAAATTCGAGT
1 CCGACCCAGATAAAAATGCTAAAATTCGAGT
9128800 CCGACC
1 CCGACC
9128806 TGACCTGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (31 bp):
CCGACCCAGATAAAAATGCTAAAATTCGAGT
Found at i:9128806 original size:31 final size:31
Alignment explanation
Indices: 9128746--9128807 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
9128736 ACCCGACCCA
*
9128746 GATAAAAATGCTAAAATTTGAGTCCGACCTG
1 GATAAAAATGCTAAAATTCGAGTCCGACCTG
9128777 GATAAAAATGCTAAAATTCGAGTCCGACCTG
1 GATAAAAATGCTAAAATTCGAGTCCGACCTG
9128808 ACCTGCCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (31 bp):
GATAAAAATGCTAAAATTCGAGTCCGACCTG
Found at i:9149295 original size:3 final size:3
Alignment explanation
Indices: 9149272--9149437 Score: 128
Period size: 3 Copynumber: 55.3 Consensus size: 3
9149262 GGGGAGAGTG
* * * *
9149272 TTA TTT TTA ATA TTG TTA TTA TTA TATA TTA TTA CTTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA -TTA TTA TTA TTA
* * *
9149319 TTA -TA TTA -TA TTTA TT- TTA TTA CTG TTA CTA TTA TT- TATA TATA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA
* ** * *
9149363 TTTA TTA TTA TTA TTA TTA TTA TTA GTA ACA -TA TTG TTA TTT TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9149408 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9149438 CATGGTACTA
Statistics
Matches: 130, Mismatches: 22, Indels: 22
0.75 0.13 0.13
Matches are distributed among these distances:
2 10 0.08
3 105 0.81
4 14 0.11
5 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:9149318 original size:26 final size:24
Alignment explanation
Indices: 9149289--9149437 Score: 108
Period size: 23 Copynumber: 6.0 Consensus size: 24
9149279 TAATATTGTT
9149289 ATTATTATATATTATTACTTATTATA
1 ATTATTAT-TATTATTA-TTATTATA
*
9149315 ATTATTA-TATTA-TATTTATT-TT
1 ATTATTATTATTATTA-TTATTATA
* * *
9149337 ATTACTGTTACTATTATTTATATATA
1 ATTATTATTATTATTA-TTAT-TATA
9149363 TTTATTATTATTATTATTATTATTAGTA
1 ---ATTATTATTATTATTATTATTA-TA
* * * *
9149391 ACATATTGTTATTTTTATTATT-TT
1 A-TTATTATTATTATTATTATTATA
9149415 ATTATTATTATTATTATTATTAT
1 ATTATTATTATTATTATTATTAT
9149438 CATGGTACTA
Statistics
Matches: 97, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
22 6 0.06
23 28 0.29
24 15 0.15
25 2 0.02
26 25 0.26
27 2 0.02
28 6 0.06
29 13 0.13
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTATTATTATTATTATTATTATA
Found at i:9149325 original size:14 final size:14
Alignment explanation
Indices: 9149291--9149340 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
9149281 ATATTGTTAT
9149291 TATTATATATTATTA
1 TATTATA-ATTATTA
9149306 CTTATTATAATTATTA
1 --TATTATAATTATTA
* *
9149322 TATTATATTTATTT
1 TATTATAATTATTA
9149336 TATTA
1 TATTA
9149341 CTGTTACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 17 0.55
16 7 0.23
17 7 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATAATTATTA
Found at i:9156030 original size:17 final size:16
Alignment explanation
Indices: 9156008--9156061 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
9155998 ACATTCTCTT
9156008 TTTCTTTTATTTTCATA
1 TTTCTTTTATTTTC-TA
*
9156025 TTTCTTTT-GTTT-T-
1 TTTCTTTTATTTTCTA
9156038 TTT-TTTTATTTTCTTA
1 TTTCTTTTATTTTC-TA
9156054 TTTCTTTT
1 TTTCTTTT
9156062 TTTACTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 4 0.13
13 6 0.20
14 1 0.03
15 1 0.03
16 6 0.20
17 12 0.40
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTCTTTTATTTTCTA
Found at i:9156047 original size:29 final size:28
Alignment explanation
Indices: 9156006--9156077 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 28
9155996 ACACATTCTC
*
9156006 TTTTTCTTTTATTTTCATATTTCTTTTGT
1 TTTTTTTTTTATTTTCATATTTCTTTT-T
*
9156035 TTTTTTTTTTATTTTCTTATTTCTTTTT
1 TTTTTTTTTTATTTTCATATTTCTTTTT
**
9156063 TTACTTTTTTATTTT
1 TTTTTTTTTTATTTT
9156078 GTTCCTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 14 0.36
29 25 0.64
ACGTcount: A:0.10, C:0.08, G:0.01, T:0.81
Consensus pattern (28 bp):
TTTTTTTTTTATTTTCATATTTCTTTTT
Found at i:9156063 original size:20 final size:20
Alignment explanation
Indices: 9156038--9156076 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
9156028 CTTTTGTTTT
9156038 TTTTTTTA-TTTTCTTATTTC
1 TTTTTTTACTTTT-TTATTTC
9156058 TTTTTTTACTTTTTTATTT
1 TTTTTTTACTTTTTTATTT
9156077 TGTTCCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTACTTTTTTATTTC
Found at i:9156116 original size:16 final size:17
Alignment explanation
Indices: 9156095--9156126 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9156085 AATAAATTGT
9156095 CTTTTT-ATTTTTTTCC
1 CTTTTTGATTTTTTTCC
9156111 CTTTTTGATTTTTTTC
1 CTTTTTGATTTTTTTC
9156127 TTATTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (17 bp):
CTTTTTGATTTTTTTCC
Found at i:9156267 original size:34 final size:33
Alignment explanation
Indices: 9156206--9156284 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 33
9156196 AATGTTTTAT
* *
9156206 AATATTTTTTAAATTTTAATTATTATTTTTAAA
1 AATATTTTTTTAACTTTAATTATTATTTTTAAA
*
9156239 AATATTTTTTTAACTTTAGA-TATATATTTTTGAA
1 AATATTTTTTTAACTTTA-ATTAT-TATTTTTAAA
* *
9156273 ATTAATTTTTTA
1 AATATTTTTTTA
9156285 TATATTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 19 0.49
34 20 0.51
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (33 bp):
AATATTTTTTTAACTTTAATTATTATTTTTAAA
Found at i:9156298 original size:24 final size:24
Alignment explanation
Indices: 9156259--9156306 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
9156249 TAACTTTAGA
**
9156259 TATATATTTTTGAAAT-TAATTTTT
1 TATATATTTTAAAAATGT-ATTTTT
9156283 TATATATTTTAAAAATGTATTTTT
1 TATATATTTTAAAAATGTATTTTT
9156307 CAAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TATATATTTTAAAAATGTATTTTT
Found at i:9156327 original size:23 final size:24
Alignment explanation
Indices: 9156300--9156350 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
9156290 TTTAAAAATG
*
9156300 TATTTTTCAA-ATTAATTTTTGAAA
1 TATTTTTAAATATTAATTTTT-AAA
9156324 -A-TTTTAAATATTAATTTTTAAA
1 TATTTTTAAATATTAATTTTTAAA
9156346 TATTT
1 TATTT
9156351 ATCATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
22 9 0.39
23 12 0.52
24 2 0.09
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTTTAAATATTAATTTTTAAA
Found at i:9156341 original size:36 final size:36
Alignment explanation
Indices: 9156263--9156346 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 36
9156253 TTTAGATATA
* *
9156263 TATTTTTGAAATTAATTTTTTATATATTTTAAAAATG
1 TATTTTT-AAATTAATTTTTGATAAATTTTAAAAATG
*
9156300 TATTTTTCAAATTAATTTTTGA-AAATTTTAAATAT-
1 TATTTTT-AAATTAATTTTTGATAAATTTTAAAAATG
9156335 TAATTTTTAAAT
1 T-ATTTTTAAAT
9156347 ATTTATCATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 5 0.12
36 17 0.40
37 20 0.48
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (36 bp):
TATTTTTAAATTAATTTTTGATAAATTTTAAAAATG
Found at i:9156357 original size:23 final size:23
Alignment explanation
Indices: 9156303--9156358 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
9156293 AAAAATGTAT
*
9156303 TTTTCAAATTAATTTTTGAAA-A
1 TTTTCATATTAATTTTTGAAATA
*
9156325 TTTTAAATATTAATTTTT-AAATA
1 TTTT-CATATTAATTTTTGAAATA
9156348 TTTATCATATT
1 TTT-TCATATT
9156359 TTTAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.25
23 20 0.71
24 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTCATATTAATTTTTGAAATA
Found at i:9156581 original size:18 final size:19
Alignment explanation
Indices: 9156537--9156575 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
9156527 ATTTTATTTG
9156537 AAGTAAATTTTAAAAACATA
1 AAGTAAATTTT-AAAACATA
9156557 AAGTAAATTTT-AAACATA
1 AAGTAAATTTTAAAACATA
9156575 A
1 A
9156576 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
AAGTAAATTTTAAAACATA
Found at i:9156693 original size:36 final size:36
Alignment explanation
Indices: 9156647--9156755 Score: 127
Period size: 36 Copynumber: 3.1 Consensus size: 36
9156637 TAATAATTTC
* *
9156647 AAAATTAATTTGAAAAATATATATTTAAATTTATAA
1 AAAAATAATTTCAAAAATATATATTTAAATTTATAA
* * *
9156683 AAAAATAATTTCACAAATATATATCTAAA-GT-T-A
1 AAAAATAATTTCAAAAATATATATTTAAATTTATAA
*
9156716 AAAAATAATTTTAAAAATA-ATAATTTAAATTTATAA
1 AAAAATAATTTCAAAAATATAT-ATTTAAATTTATAA
9156752 AAAA
1 AAAA
9156756 TTGTAAAACA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
32 2 0.03
33 24 0.40
34 2 0.03
35 2 0.03
36 30 0.50
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (36 bp):
AAAAATAATTTCAAAAATATATATTTAAATTTATAA
Found at i:9156842 original size:18 final size:18
Alignment explanation
Indices: 9156792--9156844 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
9156782 CAAATTTTTA
* *
9156792 AAATTAATAATATAAATT
1 AAATAAATAATATAAAAT
* *
9156810 AAATAAACAAAATAAAAT
1 AAATAAATAATATAAAAT
9156828 AAGA-AAATAATATAAAA
1 AA-ATAAATAATATAAAA
9156845 CTTAAAAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
AAATAAATAATATAAAAT
Found at i:9156863 original size:36 final size:37
Alignment explanation
Indices: 9156797--9156908 Score: 107
Period size: 37 Copynumber: 3.2 Consensus size: 37
9156787 TTTTAAAATT
9156797 AATAATATAAATTAAATAAACAAAATAAAA-TAAGAA
1 AATAATATAAATTAAATAAACAAAATAAAATTAAGAA
*
9156833 AATAATATAAAACTTAAA-AAAGAAAA-AAAATTAAGAA
1 AATAATAT-AAA-TTAAATAAACAAAATAAAATTAAGAA
* *
9156870 AA-AGACA-AAATTAAATAAA-AAAGTAAAA--AA-AA
1 AATA-ATATAAATTAAATAAACAAAATAAAATTAAGAA
9156902 AATAATA
1 AATAATA
9156909 AGGGTTGCAG
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
32 6 0.09
33 3 0.05
34 8 0.12
35 10 0.15
36 13 0.20
37 20 0.31
38 5 0.08
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (37 bp):
AATAATATAAATTAAATAAACAAAATAAAATTAAGAA
Found at i:9157086 original size:14 final size:14
Alignment explanation
Indices: 9157067--9157093 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9157057 AAAAATATGG
9157067 TTAATATTTAAAAA
1 TTAATATTTAAAAA
9157081 TTAATATTTAAAA
1 TTAATATTTAAAA
9157094 TTTTCAAAAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATATTTAAAAA
Found at i:9157108 original size:37 final size:37
Alignment explanation
Indices: 9157072--9157147 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 37
9157062 TATGGTTAAT
* *
9157072 ATTT-AAAAATTA-ATATTTAAAAT-TTTCAAAAATTA
1 ATTTGAAAAA-TACATATTTAAAATATATAAAAAATTA
*
9157107 ATTTGAAAAATACATTTTTAAAATATATAAAAAATTA
1 ATTTGAAAAATACATATTTAAAATATATAAAAAATTA
9157144 ATTT
1 ATTT
9157148 CACATATCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 6 0.17
36 15 0.43
37 14 0.40
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (37 bp):
ATTTGAAAAATACATATTTAAAATATATAAAAAATTA
Found at i:9157218 original size:23 final size:22
Alignment explanation
Indices: 9157165--9157258 Score: 61
Period size: 22 Copynumber: 4.2 Consensus size: 22
9157155 CTAAAGTTAA
9157165 AAAATATTTTTAAAAATAATAAT
1 AAAA-ATTTTTAAAAATAATAAT
* *
9157188 TAAAATTTTTAAAAA-ATATTAT
1 AAAAATTTTTAAAAATA-ATAAT
*
9157210 AAAACA-TTTTAAATATACAT--T
1 AAAA-ATTTTTAAAAATA-ATAAT
* **
9157231 ACAAATTTTTTAAAGTTAATAAT
1 A-AAAATTTTTAAAAATAATAAT
9157254 AAAAA
1 AAAAA
9157259 ATAAAACAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
21 5 0.09
22 41 0.75
23 9 0.16
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (22 bp):
AAAAATTTTTAAAAATAATAAT
Found at i:9157363 original size:17 final size:17
Alignment explanation
Indices: 9157341--9157403 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
9157331 ATAAAAAAGT
9157341 AAAATAAAAGAAATATG
1 AAAATAAAAGAAATATG
*
9157358 AAAATAAAAGGAAA-A-A
1 AAAATAAAA-GAAATATG
*
9157374 AAAACAAAAGAAATATG
1 AAAATAAAAGAAATATG
9157391 AAAATAAAAGAAA
1 AAAATAAAAGAAA
9157404 AAGAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 4 0.10
16 9 0.23
17 22 0.56
18 4 0.10
ACGTcount: A:0.76, C:0.02, G:0.11, T:0.11
Consensus pattern (17 bp):
AAAATAAAAGAAATATG
Found at i:9157387 original size:33 final size:32
Alignment explanation
Indices: 9157341--9157405 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 32
9157331 ATAAAAAAGT
*
9157341 AAAATAAAAGAAATATGAAAATAAAAGGAAAAA
1 AAAACAAAAGAAATATGAAAATAAAA-GAAAAA
9157374 AAAACAAAAGAAATATGAAAATAAAAGAAAAA
1 AAAACAAAAGAAATATGAAAATAAAAGAAAAA
9157406 GAGAATGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.11
Consensus pattern (32 bp):
AAAACAAAAGAAATATGAAAATAAAAGAAAAA
Found at i:9159239 original size:16 final size:16
Alignment explanation
Indices: 9159195--9159244 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
9159185 TGACCCTTGG
9159195 TAAAATTTT-AATTT-
1 TAAAATTTTAAATTTA
**
9159209 TAATTTTTTATAATTTA
1 TAAAATTTTA-AATTTA
*
9159226 TAAAATTTTAAATTAA
1 TAAAATTTTAAATTTA
9159242 TAA
1 TAA
9159245 TAATAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 7 0.25
16 13 0.46
17 8 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAAAATTTTAAATTTA
Found at i:9159297 original size:26 final size:26
Alignment explanation
Indices: 9159259--9159308 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
9159249 AAATTTATAT
*
9159259 TTTAATCTCTTAAAAATAATAAAAAA
1 TTTAATATCTTAAAAATAATAAAAAA
* * *
9159285 TTTAATATTTTAAAATTTATAAAA
1 TTTAATATCTTAAAAATAATAAAA
9159309 TTATATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
TTTAATATCTTAAAAATAATAAAAAA
Found at i:9159309 original size:34 final size:33
Alignment explanation
Indices: 9159215--9159309 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 33
9159205 ATTTTAATTT
* *
9159215 TTTATAATTTATAAAATTTTAAATTAATAATAATAAA
1 TTTAT-ATTT-TAAAATCTTAAA--AATAATAAAAAA
**
9159252 TTTATATTTTAATCTCTTAAAAATAATAAAAAA
1 TTTATATTTTAAAATCTTAAAAATAATAAAAAA
9159285 TTTAATATTTTAAAAT-TTATAAAAT
1 TTT-ATATTTTAAAATCTTA-AAAAT
9159310 TATATTTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
33 17 0.34
34 15 0.30
35 9 0.18
36 4 0.08
37 5 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (33 bp):
TTTATATTTTAAAATCTTAAAAATAATAAAAAA
Found at i:9159435 original size:12 final size:12
Alignment explanation
Indices: 9159418--9159446 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
9159408 AGCGAACGGT
9159418 AAGCATTGACAA
1 AAGCATTGACAA
9159430 AAGCA-TGACAA
1 AAGCATTGACAA
9159441 AAGCAT
1 AAGCAT
9159447 CAAAACTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.52, C:0.17, G:0.17, T:0.14
Consensus pattern (12 bp):
AAGCATTGACAA
Found at i:9170292 original size:23 final size:24
Alignment explanation
Indices: 9170266--9170310 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9170256 AACTTTCTTT
*
9170266 ATATATT-TTTTAGAATTTTTAAA
1 ATATATTAATTTAGAATTTTTAAA
*
9170289 ATATATTAATTTGGAATTTTTA
1 ATATATTAATTTAGAATTTTTA
9170311 TACATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (24 bp):
ATATATTAATTTAGAATTTTTAAA
Found at i:9176366 original size:14 final size:15
Alignment explanation
Indices: 9176347--9176376 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9176337 ATACAATATA
9176347 TTAAAA-ATGATGTT
1 TTAAAATATGATGTT
9176361 TTAAAATATGATGTT
1 TTAAAATATGATGTT
9176376 T
1 T
9176377 CGTATGATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
TTAAAATATGATGTT
Found at i:9178545 original size:15 final size:14
Alignment explanation
Indices: 9178493--9178559 Score: 89
Period size: 14 Copynumber: 4.7 Consensus size: 14
9178483 GTTTGCAGGT
* *
9178493 AAAATGTTTTCCGG
1 AAAATGATTTCTGG
*
9178507 AAAATGATTTCTGA
1 AAAATGATTTCTGG
*
9178521 AAAATAATTTCTTGG
1 AAAATGATTTC-TGG
9178536 AAAATGATTTCTGG
1 AAAATGATTTCTGG
9178550 AAAATGATTT
1 AAAATGATTT
9178560 ACTTTTCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 34 0.74
15 12 0.26
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:9178715 original size:2 final size:2
Alignment explanation
Indices: 9178708--9178737 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9178698 GTTTACTTTT
9178708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9178738 ATAAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9179614 original size:27 final size:27
Alignment explanation
Indices: 9179576--9179628 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
9179566 AGGGGAGTCG
9179576 CGCCTCTGCAGCAGGAGCGACTGGTCA
1 CGCCTCTGCAGCAGGAGCGACTGGTCA
9179603 CGCCTCTGCAGCAGGAGCGACTGGTC
1 CGCCTCTGCAGCAGGAGCGACTGGTC
9179629 GAGGCTCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.17, C:0.34, G:0.34, T:0.15
Consensus pattern (27 bp):
CGCCTCTGCAGCAGGAGCGACTGGTCA
Found at i:9179738 original size:22 final size:21
Alignment explanation
Indices: 9179689--9179747 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 21
9179679 ATTTAAAAAT
9179689 TATTAAAATATAATAAAATAATAA
1 TATTAAAA-A-AAT-AAATAATAA
* * *
9179713 TATTTTAAAAAATAAATTATAT
1 TA-TTAAAAAAATAAATAATAA
9179735 TATTAAAAAAATA
1 TATTAAAAAAATA
9179748 GGTCGCCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 10 0.33
22 9 0.30
23 3 0.10
24 3 0.10
25 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TATTAAAAAAATAAATAATAA
Found at i:9179742 original size:19 final size:18
Alignment explanation
Indices: 9179703--9179744 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
9179693 AAAATATAAT
9179703 AAAATAATAATATTTTAA
1 AAAATAATAATATTTTAA
*
9179721 AAAATAAATTATATTATTAA
1 AAAAT-AATAATATT-TTAA
9179741 AAAA
1 AAAA
9179745 ATAGGTCGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATAATAATATTTTAA
Found at i:9187953 original size:11 final size:11
Alignment explanation
Indices: 9187939--9187972 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
9187929 AAACCTTAAT
9187939 TTTTCCTTTTC
1 TTTTCCTTTTC
9187950 TTTTCCTTTTC
1 TTTTCCTTTTC
*
9187961 TTCTTTCTTTTC
1 TT-TTCCTTTTC
9187973 CCCCATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCCTTTTC
Found at i:9188500 original size:5 final size:5
Alignment explanation
Indices: 9188492--9188535 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
9188482 TATTTATTTC
* * *
9188492 ATAAT ATAAT ATAAT ATAAT ATAAT -TATT ATAAT TTAAC ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
9188536 TAAATTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 3 0.09
5 29 0.91
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
ATAAT
Found at i:9188525 original size:19 final size:19
Alignment explanation
Indices: 9188491--9188537 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
9188481 TTATTTATTT
*
9188491 CATAATATAATATAATATAA
1 CATAAT-TATTATAATATAA
* *
9188511 TATAATTATTATAATTTAA
1 CATAATTATTATAATATAA
9188530 CATAATTA
1 CATAATTA
9188538 AATTTATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
CATAATTATTATAATATAA
Found at i:9189730 original size:40 final size:40
Alignment explanation
Indices: 9189686--9189765 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
9189676 CTGTCACATC
9189686 AACATTCCATTCATTGACCAAAGCATTTCAACAGTGAAGT
1 AACATTCCATTCATTGACCAAAGCATTTCAACAGTGAAGT
*
9189726 AACATTCCATTCATTGACTAAAGCATTTCAACAGTGAAGT
1 AACATTCCATTCATTGACCAAAGCATTTCAACAGTGAAGT
9189766 GATTTATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (40 bp):
AACATTCCATTCATTGACCAAAGCATTTCAACAGTGAAGT
Found at i:9198657 original size:22 final size:20
Alignment explanation
Indices: 9198631--9198675 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
9198621 TTTTAAATTT
*
9198631 TATTTAAAATAAAAAATTACAA
1 TATTT-AAA-AAAAAATTAAAA
*
9198653 TATTTACAAAAAAATTAAAA
1 TATTTAAAAAAAAATTAAAA
9198673 TAT
1 TAT
9198676 AAATAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 2 0.10
22 5 0.24
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
TATTTAAAAAAAAATTAAAA
Found at i:9199704 original size:3 final size:3
Alignment explanation
Indices: 9199696--9199754 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
9199686 AAGAAATGTT
9199696 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9199744 TTA TTA TTA TT
1 TTA TTA TTA TT
9199755 TATGAATATG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9201873 original size:18 final size:16
Alignment explanation
Indices: 9201836--9201886 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
9201826 TAATTTTAAA
9201836 AAATTAATATAAAAAC
1 AAATTAATATAAAAAC
*
9201852 AAATTAATTTAACAATAC
1 AAATTAATATAA-AA-AC
*
9201870 AAA-TAAAATAAATAAC
1 AAATTAATATAAA-AAC
9201886 A
1 A
9201887 TGTAAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 15 0.52
17 9 0.31
18 5 0.17
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATTAATATAAAAAC
Found at i:9202007 original size:15 final size:16
Alignment explanation
Indices: 9201970--9202007 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
9201960 GTATTATTGT
*
9201970 AATATTAAATATTTTA
1 AATATAAAATATTTTA
*
9201986 AAAATAAAATA-TTTA
1 AATATAAAATATTTTA
9202001 AATATAA
1 AATATAA
9202008 CAGATGATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATAAAATATTTTA
Found at i:9204741 original size:36 final size:36
Alignment explanation
Indices: 9204699--9204790 Score: 175
Period size: 36 Copynumber: 2.6 Consensus size: 36
9204689 TTTATAGCCT
9204699 CCCAAAACGACGTCGTTTTAAGGGCTGCCTTTTAAA
1 CCCAAAACGACGTCGTTTTAAGGGCTGCCTTTTAAA
*
9204735 CCCAAAACGACGTCGTTTTAGGGGCTGCCTTTTAAA
1 CCCAAAACGACGTCGTTTTAAGGGCTGCCTTTTAAA
9204771 CCCAAAACGACGTCGTTTTA
1 CCCAAAACGACGTCGTTTTA
9204791 CTTGACCCTG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (36 bp):
CCCAAAACGACGTCGTTTTAAGGGCTGCCTTTTAAA
Found at i:9205202 original size:21 final size:22
Alignment explanation
Indices: 9205170--9205222 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
9205160 ATTAATGCTA
*
9205170 GTATATGTTTT-AT-TATATAT
1 GTATATATTTTAATATATATAT
9205190 GTATATATCTTTAATATATATAT
1 GTATATAT-TTTAATATATATAT
9205213 GTATATATTT
1 GTATATATTT
9205223 ATGTAGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 7 0.24
21 3 0.10
22 4 0.14
23 15 0.52
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (22 bp):
GTATATATTTTAATATATATAT
Found at i:9205270 original size:36 final size:34
Alignment explanation
Indices: 9205229--9205311 Score: 82
Period size: 36 Copynumber: 2.4 Consensus size: 34
9205219 ATTTATGTAG
9205229 TATTATTAATAGTCGTTTTTAT-T-TCTAATATGTATA
1 TATTATTAATA-T--TTTTTATATAT-TAATATGTATA
*
9205265 TATTATGTATATATTTTTTATATATTATTATGTATA
1 TATTAT-TA-ATATTTTTTATATATTAATATGTATA
9205301 TATT-TTAATAT
1 TATTATTAATAT
9205312 CATTAGTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
33 4 0.10
34 2 0.05
35 8 0.19
36 21 0.50
37 4 0.10
38 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (34 bp):
TATTATTAATATTTTTTATATATTAATATGTATA
Found at i:9205289 original size:22 final size:22
Alignment explanation
Indices: 9205261--9205351 Score: 87
Period size: 24 Copynumber: 3.9 Consensus size: 22
9205251 TTCTAATATG
9205261 TATATATTATGTATATATTTTT
1 TATATATTATGTATATATTTTT
9205283 TATATATTAT-TATGTATATATTTT
1 TATATATTATGTA--TATAT-TTTT
*
9205307 AATATCATTA-GTTATATATTTTT
1 TATAT-ATTATG-TATATATTTTT
*
9205330 ATACTATTTTATGTATATATTT
1 -TA-TATATTATGTATATATTT
9205352 CTAATACTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
21 2 0.04
22 10 0.18
23 9 0.16
24 26 0.46
25 8 0.14
26 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TATATATTATGTATATATTTTT
Found at i:9205304 original size:11 final size:11
Alignment explanation
Indices: 9205257--9205292 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
9205247 TTATTTCTAA
9205257 TATGTATATAT
1 TATGTATATAT
9205268 TATGTATATAT
1 TATGTATATAT
* *
9205279 TTTTTATATAT
1 TATGTATATAT
9205290 TAT
1 TAT
9205293 TATGTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (11 bp):
TATGTATATAT
Found at i:9205316 original size:25 final size:25
Alignment explanation
Indices: 9205181--9205398 Score: 104
Period size: 25 Copynumber: 8.6 Consensus size: 25
9205171 TATATGTTTT
9205181 ATTATATATGTATATATCTTTAATAT-
1 ATTAT-TATGTATATAT-TTTAATATC
* *
9205207 A-TA-TATGTATATATTTATGTAGTATT
1 ATTATTATGTATATA-TT-T-TAATATC
* * * *
9205233 ATTAATAGTCGTTTTTATTTCTAATATGT
1 ATTATTA-T-GTATATATTT-TAATAT-C
*
9205262 ATATATTATGTATATATTTTTTATAT-
1 AT-TATTATGTATATA-TTTTAATATC
9205288 ATTATTATGTATATATTTTAATATC
1 ATTATTATGTATATATTTTAATATC
9205313 ATTAGTTA--TATAT-TTTT-ATA-C
1 ATTA-TTATGTATATATTTTAATATC
9205334 TATT-TTATGTATATATTTCTAATA-C
1 -ATTATTATGTATATATTT-TAATATC
* *
9205359 --TATATATTGTATAT-TTCTAATACC
1 ATTAT-TA-TGTATATATTTTAATATC
*
9205383 ATTATTATTTATATAT
1 ATTATTATGTATATAT
9205399 ATATACATAC
Statistics
Matches: 154, Mismatches: 12, Indels: 53
0.70 0.05 0.24
Matches are distributed among these distances:
20 3 0.02
21 1 0.01
22 12 0.08
23 24 0.16
24 27 0.18
25 38 0.25
26 10 0.06
27 2 0.01
28 18 0.12
29 10 0.06
30 9 0.06
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.56
Consensus pattern (25 bp):
ATTATTATGTATATATTTTAATATC
Found at i:9205322 original size:36 final size:36
Alignment explanation
Indices: 9205257--9205350 Score: 97
Period size: 36 Copynumber: 2.6 Consensus size: 36
9205247 TTATTTCTAA
**
9205257 TATGTATATATTATGTATATATTTTTTATATATTAT
1 TATGTATATATTATGTATATATTAGTTATATATTAT
9205293 TATGTATATATT-T-TAATATCATTAGTTATATATT-T
1 TATGTATATATTATGT-ATAT-ATTAGTTATATATTAT
* *
9205328 T-TATACTATTTTATGTATATATT
1 TATGTA-TATATTATGTATATATT
9205351 TCTAATACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
34 4 0.08
35 15 0.31
36 29 0.59
37 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (36 bp):
TATGTATATATTATGTATATATTAGTTATATATTAT
Found at i:9205339 original size:11 final size:10
Alignment explanation
Indices: 9205261--9205339 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 10
9205251 TTCTAATATG
*
9205261 TATATATTATG
1 TATATATT-TT
9205272 TATATATTTTT
1 TATATA-TTTT
9205283 TATATATTATTAT
1 TATATA-T-TT-T
9205296 GTATATATTTT
1 -TATATATTTT
* *
9205307 AATATCATTAGT
1 TATAT-ATT-TT
9205319 TATATATTTT
1 TATATATTTT
9205329 TATACTATTTT
1 TATA-TATTTT
9205340 ATGTATATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
10 9 0.16
11 28 0.50
12 11 0.20
13 2 0.04
14 6 0.11
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (10 bp):
TATATATTTT
Found at i:9205372 original size:47 final size:47
Alignment explanation
Indices: 9205272--9205398 Score: 145
Period size: 47 Copynumber: 2.7 Consensus size: 47
9205262 ATATATTATG
9205272 TATATATTTTTTATA-TATTATTATGTATATATTTTAATATCATTAGT
1 TATATA-TTTTTATACTATTATTATGTATATATTTTAATATCATTAGT
9205319 TATATATTTTTATACTATT-TTATGTATATATTTCTAATA-CTATATA-T
1 TATATATTTTTATACTATTATTATGTATATATTT-TAATATC-AT-TAGT
* * * *
9205366 TGTATATTTCTAATACCATTATTATTTATATAT
1 TATATATTT-TTATACTATTATTATGTATATAT
9205399 ATATACATAC
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
46 23 0.33
47 26 0.37
48 10 0.14
49 11 0.16
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (47 bp):
TATATATTTTTATACTATTATTATGTATATATTTTAATATCATTAGT
Found at i:9205404 original size:71 final size:71
Alignment explanation
Indices: 9205267--9205401 Score: 161
Period size: 71 Copynumber: 1.9 Consensus size: 71
9205257 TATGTATATA
* * * * * *
9205267 TTATGTATATATTTTTTATATATTATTATGTATATATTTTAATATCATTAGTTATATATTTTTAT
1 TTATGTATATATTTCTAATATATTATTATGTATATATTCTAATACCATTAGTTATATATATATAT
9205332 ACTATT
66 ACTATT
*
9205338 TTATGTATATATTTCTAATACTA-TA-TATTGTATAT-TTCTAATACCATTA-TTATTTATATAT
1 TTATGTATATATTTCTAATA-TATTATTA-TGTATATATTCTAATACCATTAGTTATATATATAT
9205399 ATA
64 ATA
9205402 TACATACGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
69 12 0.22
70 14 0.25
71 27 0.49
72 2 0.04
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (71 bp):
TTATGTATATATTTCTAATATATTATTATGTATATATTCTAATACCATTAGTTATATATATATAT
ACTATT
Found at i:9205528 original size:55 final size:54
Alignment explanation
Indices: 9205469--9205591 Score: 135
Period size: 55 Copynumber: 2.2 Consensus size: 54
9205459 CTAATATATA
* **
9205469 TATATATCATGTATATATGATTTTTTTATATGTA-TTATGTATATATCTTTAAT-AC
1 TATATAT-ATGTATATAT-ATATTTGCATAT-TACTTATGTATATATCTTTAATAAC
* *
9205524 TATATTATATATATATATATATTTGCATATTATCTTATGTATATATTTTTAATAAC
1 TATA-TATATGTATATATATATTTGCATATTA-CTTATGTATATATCTTTAATAAC
9205580 TATAT-TATGTAT
1 TATATATATGTAT
9205592 GTATTTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
53 2 0.03
54 15 0.26
55 32 0.55
56 9 0.16
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (54 bp):
TATATATATGTATATATATATTTGCATATTACTTATGTATATATCTTTAATAAC
Found at i:9205593 original size:30 final size:28
Alignment explanation
Indices: 9205495--9205660 Score: 113
Period size: 26 Copynumber: 6.1 Consensus size: 28
9205485 ATGATTTTTT
*
9205495 TATATGTATTATGTATATATCTTTAATAC
1 TATAT-TATTATGTATATATTTTTAATAC
* **
9205524 TATATTATATATATATATATATTTGCATA-
1 TATATTAT-TATGTATATAT-TTTTAATAC
*
9205553 T-TA-TCTTATGTATATATTTTTAATA-
1 TATATTATTATGTATATATTTTTAATAC
* *
9205578 -ACTA-TATTATGTATGTATTTTTAACAC
1 TA-TATTATTATGTATATATTTTTAATAC
*
9205605 --TA-TATTATGTATATACTTTTT-ATTC
1 TATATTATTATGTATATA-TTTTTAATAC
*
9205630 T-TATTATTACGTATATA-TTTTAATAC
1 TATATTATTATGTATATATTTTTAATAC
9205656 ATATA
1 -TATA
9205661 CGTATATATT
Statistics
Matches: 110, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
25 26 0.24
26 41 0.37
27 15 0.14
28 7 0.06
29 16 0.15
30 5 0.05
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.54
Consensus pattern (28 bp):
TATATTATTATGTATATATTTTTAATAC
Found at i:9205651 original size:51 final size:50
Alignment explanation
Indices: 9205558--9205688 Score: 126
Period size: 51 Copynumber: 2.6 Consensus size: 50
9205548 GCATATTATC
* * *
9205558 TTATGTATATATTTTTAATAAC-TA-TATTATGTATGTATTTTTAACACTATA
1 TTATGTATATATTTTT-AT-TCTTATTATTACGTATATATTTTTAACAC-ATA
*
9205609 TTATGTATATACTTTTTATTCTTATTATTACGTATATA-TTTTAATACATA
1 TTATGTATATA-TTTTTATTCTTATTATTACGTATATATTTTTAACACATA
* *
9205659 -TACGTATATATTTATGTATTGTTATTATTA
1 TTATGTATATATTT-T-TATTCTTATTATTA
9205689 GTTATTTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
48 3 0.04
49 10 0.14
50 17 0.25
51 23 0.33
52 16 0.23
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (50 bp):
TTATGTATATATTTTTATTCTTATTATTACGTATATATTTTTAACACATA
Found at i:9213992 original size:20 final size:20
Alignment explanation
Indices: 9213967--9214010 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
9213957 TTCATAGGAA
9213967 AAAAATCGATACCTTAATTC
1 AAAAATCGATACCTTAATTC
9213987 AAAAATCGATACCTTAATTC
1 AAAAATCGATACCTTAATTC
9214007 AAAA
1 AAAA
9214011 TTTGACTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAAATCGATACCTTAATTC
Found at i:9217192 original size:15 final size:16
Alignment explanation
Indices: 9217174--9217207 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
9217164 TTATATAATC
9217174 AAATCATATT-ATATT
1 AAATCATATTAATATT
*
9217189 AAATTATATTAATATT
1 AAATCATATTAATATT
9217205 AAA
1 AAA
9217208 AAATAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATCATATTAATATT
Found at i:9218883 original size:24 final size:24
Alignment explanation
Indices: 9218856--9218905 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
9218846 TCATCCTAAA
9218856 AACAGTTTACAACTAAACAAAACG
1 AACAGTTTACAACTAAACAAAACG
9218880 AACAGTTTACAACTAAACAAAACG
1 AACAGTTTACAACTAAACAAAACG
9218904 AA
1 AA
9218906 AAGCTCTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (24 bp):
AACAGTTTACAACTAAACAAAACG
Found at i:9224530 original size:19 final size:18
Alignment explanation
Indices: 9224482--9224521 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
9224472 GTAAATTTTA
9224482 TTAT-ATAATTTAATAAT
1 TTATAATAATTTAATAAT
9224499 TTATAATAATTTAATAAAT
1 TTATAATAATTTAAT-AAT
9224518 TTAT
1 TTAT
9224522 TTTTATTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATAATAATTTAATAAT
Found at i:9225107 original size:19 final size:20
Alignment explanation
Indices: 9225075--9225136 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
9225065 TAATTTATCC
9225075 TAATTTTAAAAAATATATAAA
1 TAATTTT-AAAAATATATAAA
9225096 T-ATTTTAAAAATATA-ATAA
1 TAATTTTAAAAATATATA-AA
*
9225115 TAAATTT-AAAATATAT-AA
1 TAATTTTAAAAATATATAAA
9225133 TAAT
1 TAAT
9225137 AATATTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 6 0.17
19 20 0.56
20 9 0.25
21 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATTTTAAAAATATATAAA
Found at i:9225114 original size:20 final size:21
Alignment explanation
Indices: 9225075--9225145 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
9225065 TAATTTATCC
9225075 TAATTTTAAAAA-ATATATAAA
1 TAATTTTAAAAATATA-ATAAA
9225096 T-ATTTTAAAAATATAAT-AA
1 TAATTTTAAAAATATAATAAA
*
9225115 TAAATTTAAAATATATAAT-AA
1 TAATTTTAAAA-ATATAATAAA
*
9225136 TAATATTAAA
1 TAATTTTAAA
9225146 TAAAATAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.07
20 20 0.45
21 21 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTTTAAAAATATAATAAA
Found at i:9225121 original size:21 final size:21
Alignment explanation
Indices: 9225076--9225138 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 21
9225066 AATTTATCCT
9225076 AATTTTAAAAA-ATATATAA-A
1 AATTTTAAAAATATA-ATAATA
*
9225096 TATTTTAAAAATATAATAATA
1 AATTTTAAAAATATAATAATA
9225117 AA-TTTAAAATATATAATAATA
1 AATTTTAAAA-ATATAATAATA
9225138 A
1 A
9225139 TATTAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTTAAAAATATAATAATA
Found at i:9225152 original size:18 final size:19
Alignment explanation
Indices: 9225103--9225153 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
9225093 AAATATTTTA
*
9225103 AAAATATAATAATAAATTT
1 AAAATAAAATAATAAATTT
9225122 AAAATATATAATAAT-AATATT
1 AAAATA-A-AATAATAAAT-TT
9225143 -AAATAAAATAA
1 AAAATAAAATAA
9225154 AATCCCTCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 7 0.25
20 8 0.29
21 8 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATAAAATAATAAATTT
Found at i:9225751 original size:20 final size:19
Alignment explanation
Indices: 9225706--9225764 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
9225696 ATTTAATATT
**
9225706 AATATTATTATACAATTTAA
1 AATATTATTATA-TTTTTAA
*
9225726 ATTATTATTATATTTTTAAA
1 AATATTATTATATTTTT-AA
9225746 AATATTTATATATATTTTT
1 AATA-TTAT-TATATTTTT
9225765 TGAATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.09
20 16 0.50
21 4 0.12
22 9 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTATTATATTTTTAA
Found at i:9226961 original size:20 final size:20
Alignment explanation
Indices: 9226924--9226966 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
9226914 TTGATAAAAA
* *
9226924 AATATTTTAAATAGTTAAGT
1 AATATTTTAAAGAGTTAAAT
9226944 AATATTTTATAAGA-TTAAAT
1 AATATTTTA-AAGAGTTAAAT
9226964 AAT
1 AAT
9226967 CAGAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
AATATTTTAAAGAGTTAAAT
Found at i:9227235 original size:27 final size:28
Alignment explanation
Indices: 9227179--9227229 Score: 81
Period size: 25 Copynumber: 1.9 Consensus size: 28
9227169 ATTTAATCTA
9227179 ATTTTAACAATTATAATATATATTTGTT
1 ATTTTAACAATTATAATATATATTTGTT
9227207 ATTTT-ACAATTA-AAT-TATATTTG
1 ATTTTAACAATTATAATATATATTTG
9227230 AATTATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.35
26 3 0.13
27 7 0.30
28 5 0.22
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (28 bp):
ATTTTAACAATTATAATATATATTTGTT
Found at i:9229331 original size:2 final size:2
Alignment explanation
Indices: 9229324--9229358 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
9229314 TCATTGCAGG
* *
9229324 TC TC TC TC TC TC TC TC TC TC TC TC AC TC AC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9229359 TAAGATATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.06, C:0.49, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:9232534 original size:22 final size:22
Alignment explanation
Indices: 9232509--9232551 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
9232499 AATGGGCTGT
9232509 CCTAAGTTCATTATTGGCAAAG
1 CCTAAGTTCATTATTGGCAAAG
9232531 CCTAAGTTCATTATTGGCAAA
1 CCTAAGTTCATTATTGGCAAA
9232552 TGCTTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (22 bp):
CCTAAGTTCATTATTGGCAAAG
Found at i:9232813 original size:4 final size:4
Alignment explanation
Indices: 9232804--9232828 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9232794 CCTGTCAATC
9232804 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
9232829 GTATATAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:9239340 original size:24 final size:22
Alignment explanation
Indices: 9239292--9239347 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
9239282 AATCATTAAT
*
9239292 TTAAAAAA-TTGTTAGAAATTT
1 TTAAAAAATTTGTTAGAAATTA
*
9239313 TTAAAAAATTTGTATTGAAAATTA
1 TTAAAAAATTTGT-TAG-AAATTA
*
9239337 TTAATAAATTT
1 TTAAAAAATTT
9239348 AGGAAGAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.28
22 4 0.14
23 2 0.07
24 15 0.52
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (22 bp):
TTAAAAAATTTGTTAGAAATTA
Found at i:9255036 original size:21 final size:23
Alignment explanation
Indices: 9254996--9255045 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
9254986 TAAAATGAAA
*
9254996 TTTTTTAAATATGAATACTT-GT
1 TTTTTTAAATATGAATACTTAAT
9255018 TTTTTTAAA-A-GAATGACTTAAT
1 TTTTTTAAATATGAAT-ACTTAAT
9255040 TTTTTT
1 TTTTTT
9255046 TTTGAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.16
21 5 0.20
22 16 0.64
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTTTTAAATATGAATACTTAAT
Found at i:9261049 original size:31 final size:32
Alignment explanation
Indices: 9260992--9261051 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
9260982 ACATTTTTCC
*
9260992 TTTAATTAATTTAGAAATTTCTATTAATTAAA
1 TTTAATTAATTTAAAAATTTCTATTAATTAAA
*
9261024 TTTATTTAA-TTAAAAATTT-TAATTAATT
1 TTTAATTAATTTAAAAATTTCT-ATTAATT
9261052 TATCTAGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.04
31 16 0.64
32 8 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (32 bp):
TTTAATTAATTTAAAAATTTCTATTAATTAAA
Found at i:9269805 original size:104 final size:105
Alignment explanation
Indices: 9269611--9269805 Score: 241
Period size: 104 Copynumber: 1.9 Consensus size: 105
9269601 GGTCGCCGTC
* * * *
9269611 AGTGAAATATAGGGATCAAAATTGAAATATAATCATAAAAAATTAGAGGTATTAGAATTAAAATT
1 AGTGAAATATAAGGATCAAAACTGAAATATAACCATAAAAAATTAGAGGTATTAAAATTAAAATT
* * * ** * *
9269676 TAGCTATTATCTTCTTTATGTAAAAAAAAAAAGAAATTTG
66 TAACCATTATCTTATCAAAGAAAAAAAAAAAAGAAATTTG
* * *
9269716 AGTGAAATATAAGGATC-AAACTGAAATTTAACCATAAAAAAATTATAGG-ATTAAAATTGAAAT
1 AGTGAAATATAAGGATCAAAACTGAAATATAACCAT-AAAAAATTAGAGGTATTAAAATTAAAAT
9269779 TTAACCATTATCTTATCAAAGAAAAAA
65 TTAACCATTATCTTATCAAAGAAAAAA
9269806 GAAACATTGG
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
104 47 0.63
105 28 0.37
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (105 bp):
AGTGAAATATAAGGATCAAAACTGAAATATAACCATAAAAAATTAGAGGTATTAAAATTAAAATT
TAACCATTATCTTATCAAAGAAAAAAAAAAAAGAAATTTG
Found at i:9269992 original size:25 final size:25
Alignment explanation
Indices: 9269964--9270013 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
9269954 CTTTGACTGT
* *
9269964 GCTTTTAAATGTCGCAAAAAACGCC
1 GCTTTTAAACGCCGCAAAAAACGCC
*
9269989 GCTTTTAAGCGCCGCAAAAAACGCC
1 GCTTTTAAACGCCGCAAAAAACGCC
9270014 ACTATAGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (25 bp):
GCTTTTAAACGCCGCAAAAAACGCC
Found at i:9274288 original size:9 final size:8
Alignment explanation
Indices: 9274263--9274309 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
9274253 ATATTAAATA
9274263 TTAAGTTT
1 TTAAGTTT
9274271 TTAAGTTT
1 TTAAGTTT
9274279 TTAAGTTT
1 TTAAGTTT
*
9274287 TTTA-TTT
1 TTAAGTTT
*
9274294 TTTA-TTT
1 TTAAGTTT
*
9274301 TTAAATTT
1 TTAAGTTT
9274309 T
1 T
9274310 AATTTTTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 13 0.36
8 23 0.64
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.70
Consensus pattern (8 bp):
TTAAGTTT
Done.