Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 6 of 93
Found at i:2726930 original size:3 final size:3
Alignment explanation
Indices: 2726914--2726992 Score: 51
Period size: 3 Copynumber: 26.7 Consensus size: 3
2726904 ATTTGTTCCA
*
2726914 ATT A-T ATT ATTT ATT ATT ATT ATT ATTT ATTT ATT TTT CATT -TT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT A-TT A-TT ATT ATT -ATT ATT ATT
* * *
2726961 ATT ATC ATT ATT -TT TTT A-T ATT TTT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2726993 ATTTAAAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
2 10 0.16
3 39 0.64
4 12 0.20
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:2726939 original size:16 final size:16
Alignment explanation
Indices: 2726914--2726992 Score: 66
Period size: 16 Copynumber: 5.3 Consensus size: 16
2726904 ATTTGTTCCA
2726914 ATTA-TATTATTTATT
1 ATTATTATTATTTATT
2726929 ATTATTATTATTTATTT
1 ATTATTATTATTTA-TT
*
2726946 ATT-TT-TCATTTTATT
1 ATTATTATTA-TTTATT
*
2726961 ATTATCATTATTT-TT
1 ATTATTATTATTTATT
2726976 -TTA-TATT-TTTATT
1 ATTATTATTATTTATT
2726989 -TTAT
1 ATTAT
2726993 ATTTAAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
12 3 0.06
13 8 0.15
14 3 0.06
15 13 0.25
16 19 0.36
17 7 0.13
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTATTATTATTTATT
Found at i:2726964 original size:32 final size:33
Alignment explanation
Indices: 2726923--2726992 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
2726913 AATTATATTA
*
2726923 TTTATTATTATTATTATTTATTTAT-TTTTCAT
1 TTTATTATTATCATTATTTATTTATATTTTCAT
* *
2726955 TTTATTATTATCATTATTTTTTTATATTTTTAT
1 TTTATTATTATCATTATTTATTTATATTTTCAT
2726988 TTTAT
1 TTTAT
2726993 ATTTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 23 0.68
33 11 0.32
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (33 bp):
TTTATTATTATCATTATTTATTTATATTTTCAT
Found at i:2727012 original size:7 final size:7
Alignment explanation
Indices: 2727002--2727027 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2726992 TATTTAAAAA
2727002 ATATAAT
1 ATATAAT
2727009 ATATAAT
1 ATATAAT
2727016 ATATAAT
1 ATATAAT
2727023 ATATA
1 ATATA
2727028 TTTGCATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:2727956 original size:13 final size:13
Alignment explanation
Indices: 2727938--2727967 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2727928 TCCCCTTTTT
2727938 TTATAATTTTTAA
1 TTATAATTTTTAA
*
2727951 TTATAATTTTTTA
1 TTATAATTTTTAA
2727964 TTAT
1 TTAT
2727968 TTTAGTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATAATTTTTAA
Found at i:2727977 original size:23 final size:21
Alignment explanation
Indices: 2727934--2728002 Score: 52
Period size: 23 Copynumber: 3.1 Consensus size: 21
2727924 GCCATCCCCT
*
2727934 TTTTTTATAATTTTTAATTATAA
1 TTTTTTATTA-TTTTAATTAT-A
*
2727957 TTTTTTATTATTTTAGTT-TA
1 TTTTTTATTATTTTAATTATA
*
2727977 TTTTATT-TTATTATATATATATA
1 TTTT-TTATTATTTTA-AT-TATA
2728000 TTT
1 TTT
2728003 ATAGGTGTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 12 0.32
21 4 0.11
22 8 0.21
23 14 0.37
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (21 bp):
TTTTTTATTATTTTAATTATA
Found at i:2741916 original size:12 final size:13
Alignment explanation
Indices: 2741901--2741933 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2741891 CTTTTTTTTT
2741901 TTTTTTTAATA-A
1 TTTTTTTAATATA
2741913 TTTTTTTAATATA
1 TTTTTTTAATATA
*
2741926 CTTTTTTA
1 TTTTTTTA
2741934 TATTTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTTAATATA
Found at i:2745799 original size:22 final size:22
Alignment explanation
Indices: 2745771--2745815 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2745761 TATAGATGGG
2745771 TGGCTGAGATTTTGAAGTTGAC
1 TGGCTGAGATTTTGAAGTTGAC
2745793 TGGCTGAGATTTTGAAGTTGAC
1 TGGCTGAGATTTTGAAGTTGAC
2745815 T
1 T
2745816 ATATATCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (22 bp):
TGGCTGAGATTTTGAAGTTGAC
Found at i:2750383 original size:2 final size:2
Alignment explanation
Indices: 2750376--2750400 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2750366 TATGAAATGT
2750376 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2750401 TAAAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2754819 original size:2 final size:2
Alignment explanation
Indices: 2754802--2754843 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
2754792 TGTCTCTATT
*
2754802 TA TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2754842 TA
1 TA
2754844 CAGAGAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2766624 original size:2 final size:2
Alignment explanation
Indices: 2766619--2766662 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2766609 TCTCTCTCTC
2766619 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2766659 TA TA
1 TA TA
2766663 GGAAAAAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2799432 original size:9 final size:9
Alignment explanation
Indices: 2799426--2799473 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
2799416 TGGGGGAGAG
2799426 GAAGGAGGA
1 GAAGGAGGA
2799435 GAAGGAGGA
1 GAAGGAGGA
*
2799444 TAAGGAGGA
1 GAAGGAGGA
*
2799453 TAAGGAGGA
1 GAAGGAGGA
*
2799462 TAAGGAGG-
1 GAAGGAGGA
2799470 GAAG
1 GAAG
2799474 CGTGCATAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
8 3 0.08
9 34 0.92
ACGTcount: A:0.44, C:0.00, G:0.50, T:0.06
Consensus pattern (9 bp):
GAAGGAGGA
Found at i:2799448 original size:18 final size:18
Alignment explanation
Indices: 2799427--2799473 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2799417 GGGGGAGAGG
2799427 AAGGAGGAGAAGGAGGAT
1 AAGGAGGAGAAGGAGGAT
*
2799445 AAGGAGGATAAGGAGGAT
1 AAGGAGGAGAAGGAGGAT
2799463 AAGGAGG-GAAG
1 AAGGAGGAGAAG
2799474 CGTGCATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.45, C:0.00, G:0.49, T:0.06
Consensus pattern (18 bp):
AAGGAGGAGAAGGAGGAT
Found at i:2817815 original size:41 final size:43
Alignment explanation
Indices: 2817758--2817840 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 43
2817748 ATTGCTGTGT
**
2817758 TTCTGCTCAACTGCTGCT-GGATGTTTT-TAAGAGGCAGGTCA
1 TTCTGCTCAACTGCTGCTAAAATGTTTTATAAGAGGCAGGTCA
2817799 TTCTGCTCAACTGCTGCTAAAATGTTTTATAAGAGGCAGGTC
1 TTCTGCTCAACTGCTGCTAAAATGTTTTATAAGAGGCAGGTC
2817841 CAAGACACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 18 0.47
42 7 0.18
43 13 0.34
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (43 bp):
TTCTGCTCAACTGCTGCTAAAATGTTTTATAAGAGGCAGGTCA
Found at i:2833676 original size:2 final size:2
Alignment explanation
Indices: 2833598--2833661 Score: 53
Period size: 2 Copynumber: 32.0 Consensus size: 2
2833588 AATTTGACTA
*
2833598 AT AT AT AT AT AT CAGT CAA AT AT AT AT AT AT AT AT AT AT -T A-
1 AT AT AT AT AT AT -A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2833639 AT -T TT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
2833662 TGACTAATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
1 3 0.06
2 45 0.87
3 1 0.02
4 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2855968 original size:2 final size:2
Alignment explanation
Indices: 2855956--2855987 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2855946 CATCCCTCCT
*
2855956 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2855988 AATTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:2856703 original size:20 final size:19
Alignment explanation
Indices: 2856662--2856702 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2856652 CACATGTCTC
*
2856662 TTTAATAATTATATTAAAT
1 TTTAAAAATTATATTAAAT
2856681 TTTAAAAATATATATT-AAT
1 TTTAAAAAT-TATATTAAAT
2856700 TTT
1 TTT
2856703 TTAATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAAAAATTATATTAAAT
Found at i:2858616 original size:19 final size:18
Alignment explanation
Indices: 2858588--2858623 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2858578 ATAATTATAA
*
2858588 CAAAATAATAATATCTAT
1 CAAAATAATAAAATCTAT
2858606 CAAATATAATAAAATCTA
1 CAAA-ATAATAAAATCTA
2858624 CAATCATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (18 bp):
CAAAATAATAAAATCTAT
Found at i:2865445 original size:13 final size:13
Alignment explanation
Indices: 2865427--2865485 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 13
2865417 TTTTAAAATA
2865427 ATTTAAAAATAAT
1 ATTTAAAAATAAT
2865440 ATTTAAATAAGATAA-
1 ATTT-AA-AA-ATAAT
*
2865455 A-TTAAAAAAAAT
1 ATTTAAAAATAAT
2865467 ACTTTAAAAATAAT
1 A-TTTAAAAATAAT
2865481 ATTTA
1 ATTTA
2865486 TTTTTTATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
11 3 0.08
12 3 0.08
13 10 0.26
14 15 0.39
15 3 0.08
16 4 0.11
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (13 bp):
ATTTAAAAATAAT
Found at i:2865611 original size:41 final size:41
Alignment explanation
Indices: 2865481--2865621 Score: 103
Period size: 41 Copynumber: 3.5 Consensus size: 41
2865471 TAAAAATAAT
* * * * *
2865481 ATTTATTTTTTATCAATCAAAATTTAATTATTAGTCATCTA
1 ATTTATTTTTAATCAATTAAAATTTAATTATTAATTATTTA
* * * * *
2865522 ATTTGTTTTTAAATAAATCAACATAATTTAA-AAATAA-TATTT-
1 ATTTATTTTT-AATCAAT-TA-A-AATTTAATTATTAATTATTTA
*
2865564 -TATATTTTTAATCAATTAAAATTTAATTATTAATTATTTA
1 ATTTATTTTTAATCAATTAAAATTTAATTATTAATTATTTA
*
2865604 ATTTATTTCTAAT-AATTA
1 ATTTATTTTTAATCAATTA
2865622 TGTTAATTTA
Statistics
Matches: 75, Mismatches: 17, Indels: 17
0.69 0.16 0.16
Matches are distributed among these distances:
37 7 0.09
38 5 0.07
39 6 0.08
40 11 0.15
41 26 0.35
42 5 0.07
43 4 0.05
44 4 0.05
45 7 0.09
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (41 bp):
ATTTATTTTTAATCAATTAAAATTTAATTATTAATTATTTA
Found at i:2889603 original size:108 final size:108
Alignment explanation
Indices: 2889414--2889613 Score: 310
Period size: 108 Copynumber: 1.9 Consensus size: 108
2889404 TAAAATGATT
* ** * * * *
2889414 AAATATGTTGATTTGGTTATAATTTTCACAATTTAGAAATACACATACTTTTAAAATTATTTAAC
1 AAATATATTGATTTAATTACAACTTTCACAATTTACAAATACACATACTTTTAAAATTATTCAAC
*
2889479 TCTTACCCAATTTACCTTTTATTTAAATTTGCTCAAATTAGCA
66 ACTTACCCAATTTACCTTTTATTTAAATTTGCTCAAATTAGCA
* *
2889522 AAATATATTGATTTAATTACAACTTTCACAATTTACAAATACACATTCTTTTACAATTATTCAAC
1 AAATATATTGATTTAATTACAACTTTCACAATTTACAAATACACATACTTTTAAAATTATTCAAC
2889587 ACTTACCCAATTTACCTTTTATTTAAA
66 ACTTACCCAATTTACCTTTTATTTAAA
2889614 CTGACTCAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 82 1.00
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (108 bp):
AAATATATTGATTTAATTACAACTTTCACAATTTACAAATACACATACTTTTAAAATTATTCAAC
ACTTACCCAATTTACCTTTTATTTAAATTTGCTCAAATTAGCA
Found at i:2891291 original size:21 final size:22
Alignment explanation
Indices: 2891262--2891309 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
2891252 AATATTATTG
* * *
2891262 ATAACTAAAT-TATTAATTTAT
1 ATAATTAAATATATAAAGTTAT
2891283 ATAATTAAATATATAAAGTTAT
1 ATAATTAAATATATAAAGTTAT
2891305 -TAATT
1 ATAATT
2891310 TTTTTGACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
ATAATTAAATATATAAAGTTAT
Found at i:2891706 original size:22 final size:23
Alignment explanation
Indices: 2891676--2891725 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
2891666 TTGGTTGATA
2891676 AATATAATT-TTAGTATAAATATT
1 AATATAATTATTAGTA-AAATATT
*
2891699 AATA-AATTATTATTAAAATATT
1 AATATAATTATTAGTAAAATATT
2891721 AATAT
1 AATAT
2891726 GATTTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AATATAATTATTAGTAAAATATT
Found at i:2891838 original size:22 final size:21
Alignment explanation
Indices: 2891813--2891869 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 21
2891803 TTAATAATTG
*
2891813 ATTATTAAAATATCATTAAGTT
1 ATTATTAAAATAT-ATTAACTT
2891835 ATTATTAAAATAGTATTAACTT
1 ATTATTAAAATA-TATTAACTT
2891857 ATTATTAAAATAT
1 ATTATTAAAATAT
2891870 TAATATGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (21 bp):
ATTATTAAAATATATTAACTT
Found at i:2891841 original size:11 final size:11
Alignment explanation
Indices: 2891813--2891871 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
2891803 TTAATAATTG
2891813 ATTATTAAAAT
1 ATTATTAAAAT
* **
2891824 ATCATTAAGTT
1 ATTATTAAAAT
2891835 ATTATTAAAAT
1 ATTATTAAAAT
* **
2891846 AGTATTAACTT
1 ATTATTAAAAT
2891857 ATTATTAAAAT
1 ATTATTAAAAT
2891868 ATTA
1 ATTA
2891872 ATATGAAATT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (11 bp):
ATTATTAAAAT
Found at i:2894988 original size:29 final size:29
Alignment explanation
Indices: 2894926--2894992 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
2894916 ATATCTATGG
* *
2894926 GTAATTTTTCAGTTTTTGGGGTAAAAAAT
1 GTAATTTTTCACTTTATGGGGTAAAAAAT
* *
2894955 ATAATTTTTCACTTTATGGGAGT-AAAAGT
1 GTAATTTTTCACTTTATGGG-GTAAAAAAT
2894984 GTAATTTTT
1 GTAATTTTT
2894993 TAAAATTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 30 0.94
30 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.46
Consensus pattern (29 bp):
GTAATTTTTCACTTTATGGGGTAAAAAAT
Found at i:2896159 original size:13 final size:13
Alignment explanation
Indices: 2896141--2896165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2896131 GAAAAATGAG
2896141 ATTTTATAAAATA
1 ATTTTATAAAATA
2896154 ATTTTATAAAAT
1 ATTTTATAAAAT
2896166 TTTTTAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:2897332 original size:14 final size:15
Alignment explanation
Indices: 2897308--2897356 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
2897298 TTTAAAGATC
2897308 AAAGATTTTGGTTTT
1 AAAGATTTTGGTTTT
2897323 AAAG-TTTTGGATTTT
1 AAAGATTTTGG-TTTT
* *
2897338 AAAGTTTTTAGTTTT
1 AAAGATTTTGGTTTT
2897353 AAAG
1 AAAG
2897357 TTGTTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 6 0.19
15 20 0.65
16 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (15 bp):
AAAGATTTTGGTTTT
Found at i:2901229 original size:13 final size:12
Alignment explanation
Indices: 2901211--2901240 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2901201 ATTGAAAAAA
2901211 TAATTAATTTTAT
1 TAATTAATTTT-T
2901224 TAATTAATTTTT
1 TAATTAATTTTT
2901236 TAATT
1 TAATT
2901241 TTTTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TAATTAATTTTT
Found at i:2901623 original size:21 final size:21
Alignment explanation
Indices: 2901599--2901661 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2901589 AAAAAACTTT
2901599 TTTATTATTAAATATTAATAA
1 TTTATTATTAAATATTAATAA
* *
2901620 TTTATCATTTAAATATTAA-GA
1 TTTATTA-TTAAATATTAATAA
*
2901641 TTTATTATAAAAATATTAATA
1 TTTATTAT-TAAATATTAATA
2901662 TGATTTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 22 0.65
22 11 0.32
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTATTATTAAATATTAATAA
Found at i:2901683 original size:14 final size:14
Alignment explanation
Indices: 2901664--2901709 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
2901654 TATTAATATG
2901664 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
*
2901678 ATTTTTATTTTTTC
1 ATTTTTATTTTTTT
* *
2901692 AGTTTT-TTCTTTT
1 ATTTTTATTTTTTT
2901705 ATTTT
1 ATTTT
2901710 ATTAAAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.80
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:2904154 original size:17 final size:17
Alignment explanation
Indices: 2904132--2904175 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
2904122 CGTGAGTTCT
*
2904132 TTTTTTTTTCT-ATTTC
1 TTTTTTCTTCTCATTTC
2904148 ATTTTTTCTTCTCATTTC
1 -TTTTTTCTTCTCATTTC
2904166 -TTTTTCTTCT
1 TTTTTTCTTCT
2904176 TTTTTCCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 10 0.40
17 10 0.40
18 5 0.20
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTCTTCTCATTTC
Found at i:2904162 original size:13 final size:13
Alignment explanation
Indices: 2904135--2904196 Score: 58
Period size: 13 Copynumber: 4.7 Consensus size: 13
2904125 GAGTTCTTTT
*
2904135 TTTTTTCTATTTCA
1 TTTTTTCT-TCTCA
2904149 TTTTTTCTTCTCA
1 TTTTTTCTTCTCA
2904162 TTTCTTT-TTCTTC-
1 TTT-TTTCTTC-TCA
2904175 TTTTTTCCTTCT-A
1 TTTTTT-CTTCTCA
2904188 TTTTTTCTT
1 TTTTTTCTT
2904197 TTAAAAGAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
12 6 0.14
13 20 0.48
14 16 0.38
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTCTTCTCA
Found at i:2911874 original size:2 final size:2
Alignment explanation
Indices: 2911867--2911922 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2911857 TTTAAATACA
2911867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2911909 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
2911923 TAATAGCATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2923466 original size:2 final size:2
Alignment explanation
Indices: 2923459--2923506 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2923449 TTATCTCAAT
*
2923459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2923500 TA TA TA T
1 TA TA TA T
2923507 GTAAGATGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2931122 original size:34 final size:33
Alignment explanation
Indices: 2931074--2931139 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
2931064 GCCCCCAAAT
*
2931074 CCCCCTAAATTCATCACTACGATGGTCCCAAAAA
1 CCCCCTAAATTCATCACCA-GATGGTCCCAAAAA
* *
2931108 CCCCTTAAATTCATCACCATATGGTCCCAAAA
1 CCCCCTAAATTCATCACCAGATGGTCCCAAAA
2931140 TCCTAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.41
34 17 0.59
ACGTcount: A:0.35, C:0.35, G:0.08, T:0.23
Consensus pattern (33 bp):
CCCCCTAAATTCATCACCAGATGGTCCCAAAAA
Found at i:2933138 original size:25 final size:24
Alignment explanation
Indices: 2933102--2933157 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
2933092 TTTATTTAAT
*
2933102 TTAAAATAAAAATATAAAAATATTA
1 TTAAAATAAAAAAATAAAAA-ATTA
2933127 TTAAACAT-AAAAAATAAAAAATTA
1 TTAAA-ATAAAAAAATAAAAAATTA
*
2933151 TTTAAAT
1 TTAAAAT
2933158 TTTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 8 0.29
25 16 0.57
26 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
TTAAAATAAAAAAATAAAAAATTA
Found at i:2933147 original size:27 final size:25
Alignment explanation
Indices: 2933102--2933152 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
2933092 TTTATTTAAT
*
2933102 TTAAAATAAAAATATAAAAATATTA
1 TTAAAATAAAAATAAAAAAATATTA
*
2933127 TTAAACATAAAAAATAAAAAATTATT
1 TTAAA-AT-AAAAATAAAAAAATATT
2933153 TAAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 2 0.09
27 15 0.68
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
TTAAAATAAAAATAAAAAAATATTA
Found at i:2942063 original size:84 final size:83
Alignment explanation
Indices: 2941903--2942070 Score: 243
Period size: 84 Copynumber: 2.0 Consensus size: 83
2941893 GTTTTACTGA
* * *
2941903 AAAATGAAAAGCAGTTAAGAAAAAAAATGATAAATACATATTTTTTTTATTCAACGAATTAAGTT
1 AAAATGAAAAGCAGTTAAGAAAAAAAATGATAAATACACATTTTTTTTATTCAACAAAGTAAGTT
2941968 TGATTTTTTTTAGAAAAT
66 TGATTTTTTTTAGAAAAT
2941986 AAAATGAAAAGCAGTTAAGAAAAAAAATTAATGATAAA-A-ACA-TTTTTTTATTCAACAAAGTA
1 AAAATGAAAAGCAGTTAAG--AAAAAA--AATGATAAATACACATTTTTTTTATTCAACAAAGTA
*
2942048 AGTTTTATTTTTTTTAGAAAAT
62 AGTTTGATTTTTTTTAGAAAAT
2942070 A
1 A
2942071 GACTTAATTT
Statistics
Matches: 77, Mismatches: 4, Indels: 7
0.88 0.05 0.08
Matches are distributed among these distances:
83 19 0.25
84 40 0.52
85 8 0.10
86 1 0.01
87 9 0.12
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (83 bp):
AAAATGAAAAGCAGTTAAGAAAAAAAATGATAAATACACATTTTTTTTATTCAACAAAGTAAGTT
TGATTTTTTTTAGAAAAT
Found at i:2955185 original size:17 final size:16
Alignment explanation
Indices: 2955145--2955186 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
2955135 TTAATTCATT
2955145 AATAAATAAATTTAAA
1 AATAAATAAATTTAAA
*
2955161 AGTGAAATAAATGTTAAA
1 AAT-AAATAAAT-TTAAA
2955179 AATAAATA
1 AATAAATA
2955187 TGACACTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 13 0.59
18 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (16 bp):
AATAAATAAATTTAAA
Found at i:2984168 original size:3 final size:3
Alignment explanation
Indices: 2984160--2984193 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2984150 AAGTGGCTTG
* *
2984160 TAT TAT TAT TAT TAT TAT TAT TGT TGT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2984194 GCATTTACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2988986 original size:2 final size:2
Alignment explanation
Indices: 2988981--2989129 Score: 190
Period size: 2 Copynumber: 77.5 Consensus size: 2
2988971 ACACACACAC
2988981 AT AT AT -T AT AT AT AT AT AT AT -T AT AT -T AT AT A- 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
*
2989019 AT AT AT AT A- AT AT AT AT AT AT AT AGT A- AT A- AT A- ACT -T TT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT
*
2989058 AT TT AT NAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2989101 AT 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 AT A
2989130 GTAATAACAT
Statistics
Matches: 132, Mismatches: 3, Indels: 24
0.83 0.02 0.15
Matches are distributed among these distances:
1 9 0.07
2 119 0.90
3 4 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2992827 original size:84 final size:85
Alignment explanation
Indices: 2992685--2992848 Score: 258
Period size: 84 Copynumber: 1.9 Consensus size: 85
2992675 TATCCTTTTC
* *
2992685 AAGATTATTATGGTGATCTAATCATAATCATAAAGTGATTTAAGATCATCGTACTTGACAT-AAT
1 AAGATTATTATAGTGATCTAATCATAATCATAAAGTGATTTAAGATCATCATACTTGACATGAAT
2992749 TTACTTAATAATCATGTGAT
66 TTACTTAATAATCATGTGAT
* * * **
2992769 AAGATTGTTATAGTGATCTAATCATAATCATACAGTGATTTAAGATCATCATATTTGACATGGTT
1 AAGATTATTATAGTGATCTAATCATAATCATAAAGTGATTTAAGATCATCATACTTGACATGAAT
2992834 TTACTTAATAATCAT
66 TTACTTAATAATCAT
2992849 TAATCAGTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
84 56 0.78
85 16 0.22
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (85 bp):
AAGATTATTATAGTGATCTAATCATAATCATAAAGTGATTTAAGATCATCATACTTGACATGAAT
TTACTTAATAATCATGTGAT
Found at i:3004859 original size:53 final size:53
Alignment explanation
Indices: 3004779--3004886 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
3004769 AGTTCTTTGC
*
3004779 ATGAACTATCCCAGGGGCAGTCCTGAAACAGAGGTTTTTCTGAAGTGTGTTAT
1 ATGAACTATCCCAGGGGCAGTCCTGAAACAGAGGGTTTTCTGAAGTGTGTTAT
* *
3004832 ATGAACTATCTCAGGGGCAGTCCTGAAAGAGAGGGTTTTCTGAAGTGTGTTAT
1 ATGAACTATCCCAGGGGCAGTCCTGAAACAGAGGGTTTTCTGAAGTGTGTTAT
3004885 AT
1 AT
3004887 TATTTCTGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (53 bp):
ATGAACTATCCCAGGGGCAGTCCTGAAACAGAGGGTTTTCTGAAGTGTGTTAT
Found at i:3016054 original size:12 final size:12
Alignment explanation
Indices: 3016037--3016061 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3016027 GCACCAGAGT
3016037 GCGAAAGTCAAA
1 GCGAAAGTCAAA
3016049 GCGAAAGTCAAA
1 GCGAAAGTCAAA
3016061 G
1 G
3016062 ACGGAAAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.28, T:0.08
Consensus pattern (12 bp):
GCGAAAGTCAAA
Found at i:3026016 original size:7 final size:7
Alignment explanation
Indices: 3026004--3026041 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
3025994 AGGCAATACC
3026004 TTGGCGG
1 TTGGCGG
3026011 TTGGCGG
1 TTGGCGG
3026018 TTGGCGG
1 TTGGCGG
3026025 TTGGCGG
1 TTGGCGG
3026032 TTGGCGG
1 TTGGCGG
3026039 TTG
1 TTG
3026042 CCACGTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.00, C:0.13, G:0.55, T:0.32
Consensus pattern (7 bp):
TTGGCGG
Found at i:3058325 original size:24 final size:25
Alignment explanation
Indices: 3058298--3058350 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
3058288 ACATAAACTG
3058298 ATAAATATTAT-TTTAA-TAATAAAT
1 ATAAATATTATATTTAATTAA-AAAT
*
3058322 ATAAA-ATTTTATTTAATTAAAAAT
1 ATAAATATTATATTTAATTAAAAAT
3058346 A-AAAT
1 ATAAAT
3058351 TAAAAACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
23 7 0.28
24 15 0.60
25 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATAAATATTATATTTAATTAAAAAT
Found at i:3076950 original size:2 final size:2
Alignment explanation
Indices: 3076937--3076984 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
3076927 ATAGACACAA
* *
3076937 AG AG AA AG AG AG AG AG AG AG AG -G AG GG AG -G AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3076976 AG AG AG AG A
1 AG AG AG AG A
3076985 TGACTAAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3094781 original size:42 final size:42
Alignment explanation
Indices: 3094690--3094773 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
3094680 TAGTAATGAT
* *
3094690 TCCTTCGAATTGTAGCCAAGATGTTTGGAAGCTAGATGAATA
1 TCCTTCGAATTGCAGCCAAGACGTTTGGAAGCTAGATGAATA
3094732 TCCTTCGAATTGCAGCCAAGACGTTTGGAAGCTAGATGAATA
1 TCCTTCGAATTGCAGCCAAGACGTTTGGAAGCTAGATGAATA
3094774 CATTTCGACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (42 bp):
TCCTTCGAATTGCAGCCAAGACGTTTGGAAGCTAGATGAATA
Found at i:3121281 original size:10 final size:10
Alignment explanation
Indices: 3121266--3121296 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3121256 ATTCCTATTC
*
3121266 TTGATTTGCA
1 TTGATTTCCA
3121276 TTGATTTCCA
1 TTGATTTCCA
3121286 TTGATTTCCA
1 TTGATTTCCA
3121296 T
1 T
3121297 CGTCCTTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (10 bp):
TTGATTTCCA
Found at i:3123832 original size:66 final size:66
Alignment explanation
Indices: 3123762--3124267 Score: 303
Period size: 66 Copynumber: 7.6 Consensus size: 66
3123752 TGTAAATTTA
* * *
3123762 TTTCCCACACCAGGGCTTGGACCAGAGTCCTTGATGCCTCCAAGGGTTTG-G-TCGTCAGTTAAC
1 TTTCCCACACCAGGGCTCGGACCAGAGTCCTTGATGCCTCCAA-GATTAGAGCT-GTCAGTTAAC
3123825 TTG
64 TTG
* * * * * * *
3123828 TTTCCCACACCAGGACTCGGGCCTGAATCCTTAATGCCTCCGAGATTAGAGCTGTCAGTTAATTT
1 TTTCCCACACCAGGGCTCGGACCAGAGTCCTTGATGCCTCCAAGATTAGAGCTGTCAGTTAACTT
3123893 G
66 G
* * * * * * *
3123894 TTTCCTACACCAGGGCTGGGACCAGAGTCTTTGATTCCACCTAA-ATT-GAAGCTATCAGTGAAC
1 TTTCCCACACCAGGGCTCGGACCAGAGTCCTTGATGCCTCC-AAGATTAG-AGCTGTCAGTTAAC
3123957 -TG
64 TTG
* * * * * * *
3123959 ATTTCCCACACC-GGGACTTGGACCGGAGTCCTTAATGCCTCCTAGAGT-GAAGCTATCGGTTAA
1 -TTTCCCACACCAGGG-CTCGGACCAGAGTCCTTGATGCCTCCAAGATTAG-AGCTGTCAGTTAA
3124022 CTTG
63 CTTG
* * * * * * * * * *
3124026 TTTCCTACCCCAGGTCTCGGCCCGGAGTCCTTTATACCTCCAAGAGTCGAGCTCTC-GATTAACT
1 TTTCCCACACCAGGGCTCGGACCAGAGTCCTTGATGCCTCCAAGATTAGAGCTGTCAG-TTAACT
3124090 TG
65 TG
* ** * * * * * * *
3124092 TGTCCCTGACCAGGACTCGGCCCGGAGTCCTTTATACCTCCAAGAGTCGAGCTGTC-GATTAACT
1 TTTCCCACACCAGGGCTCGGACCAGAGTCCTTGATGCCTCCAAGATTAGAGCTGTCAG-TTAACT
3124156 TG
65 TG
* * * * * ** *
3124158 TGTCCCTCACCAGGACTCGGACCAGAGTCCTTTATACCTCCAAGAGGCA-AGCTGTCGGTTAACT
1 TTTCCCACACCAGGGCTCGGACCAGAGTCCTTGATGCCTCCAAGA-TTAGAGCTGTCAGTTAACT
3124222 TG
65 TG
** * * * *
3124224 TGCCCCTCACCACCAGAGCTTGGACCAGAGTTCTTAATGCCTCC
1 T-TTCC-CA-CACCAGGGCTCGGACCAGAGTCCTTGATGCCTCC
3124268 GAGGGTCTGA
Statistics
Matches: 359, Mismatches: 65, Indels: 29
0.79 0.14 0.06
Matches are distributed among these distances:
65 12 0.03
66 307 0.86
67 11 0.03
68 1 0.00
69 28 0.08
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.27
Consensus pattern (66 bp):
TTTCCCACACCAGGGCTCGGACCAGAGTCCTTGATGCCTCCAAGATTAGAGCTGTCAGTTAACTT
G
Found at i:3124117 original size:132 final size:132
Alignment explanation
Indices: 3123967--3124315 Score: 337
Period size: 132 Copynumber: 2.6 Consensus size: 132
3123957 TGATTTCCCA
* * * * * *
3123967 CACCGGGACTTGGACCGGAGTCCTTAATGCCTCCTAGAGT-GAAGCTATCGGTTAACTTGT-TTC
1 CACCAGGACTCGGACCGGAGTCCTTAATACCTCCAAGAGTCG-AGCTATCGATTAACTTGTGTCC
* * * * * * *
3124030 CTACCCCAGGTCTCGGCCCGGAGTCCTTTATACCTCCAAGAGTCGAGCTCTCGATTAACTTGTGT
65 CT-CACCAGGACTCGGACCAGAGTCCTTTATACCTCCAAGAGGCAAGCTCTCGATTAACTTGTGC
3124095 CCCT
129 CCCT
* * * *
3124099 GACCAGGACTCGGCCCGGAGTCCTTTATACCTCCAAGAGTCGAGCTGTCGATTAACTTGTGTCCC
1 CACCAGGACTCGGACCGGAGTCCTTAATACCTCCAAGAGTCGAGCTATCGATTAACTTGTGTCCC
* *
3124164 TCACCAGGACTCGGACCAGAGTCCTTTATACCTCCAAGAGGCAAGCTGTCGGTTAACTTGTGCCC
66 TCACCAGGACTCGGACCAGAGTCCTTTATACCTCCAAGAGGCAAGCTCTCGATTAACTTGTGCCC
3124229 CT
131 CT
* * * * * * * *
3124231 CACCACCAGAGCTTGGACCAGAGTTCTTAATGCCTCCGAGGGTCTGA-CTATC-AGTGAACTTGT
1 CACCA--GGA-CTCGGACCGGAGTCCTTAATACCTCCAAGAGTC-GAGCTATCGA-TTAACTTGT
* * *
3124294 GTCCCCCGCCAGGACTTGGACC
61 GTCCCTCACCAGGACTCGGACC
3124316 TGACTCTTTG
Statistics
Matches: 176, Mismatches: 34, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
132 110 0.62
133 5 0.03
134 3 0.02
135 56 0.32
136 2 0.01
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.25
Consensus pattern (132 bp):
CACCAGGACTCGGACCGGAGTCCTTAATACCTCCAAGAGTCGAGCTATCGATTAACTTGTGTCCC
TCACCAGGACTCGGACCAGAGTCCTTTATACCTCCAAGAGGCAAGCTCTCGATTAACTTGTGCCC
CT
Found at i:3126300 original size:22 final size:22
Alignment explanation
Indices: 3126261--3126338 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 22
3126251 GGCATTGCTC
* * *
3126261 AAAAATCAGTTACATAATGTCT
1 AAAAATCAGTCACGTAATGACT
*
3126283 AAAAATCAGTCATGTAAT-ACT
1 AAAAATCAGTCACGTAATGACT
* * * *
3126304 TAAAACCAATCACGTAATGCCT
1 AAAAATCAGTCACGTAATGACT
*
3126326 AAAAATTAGTCAC
1 AAAAATCAGTCAC
3126339 ACAGTGATTA
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
21 16 0.38
22 26 0.62
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.27
Consensus pattern (22 bp):
AAAAATCAGTCACGTAATGACT
Found at i:3126381 original size:22 final size:22
Alignment explanation
Indices: 3126356--3126397 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3126346 TTAAGTCACG
3126356 TAATACCTAAAAACCAGTCTCA
1 TAATACCTAAAAACCAGTCTCA
*
3126378 TAATACTTAAAAACCAGTCT
1 TAATACCTAAAAACCAGTCT
3126398 AATTAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (22 bp):
TAATACCTAAAAACCAGTCTCA
Found at i:3163512 original size:32 final size:32
Alignment explanation
Indices: 3163467--3163530 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3163457 TTTATATAAT
* * *
3163467 AATTTATAAAAATTAAGTTTTTATATTTTTTA
1 AATTAATAAAAATTAAATTTTTATATCTTTTA
*
3163499 AATTAATAAAAATTAAATTTTTCTATCTTTTA
1 AATTAATAAAAATTAAATTTTTATATCTTTTA
3163531 TACTACTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (32 bp):
AATTAATAAAAATTAAATTTTTATATCTTTTA
Found at i:3163613 original size:20 final size:18
Alignment explanation
Indices: 3163588--3163627 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 18
3163578 ATGACATGAT
3163588 TTTTTTTATTTATTTTACAA
1 TTTTTTTA-TTATTTTA-AA
3163608 TTTTTTTATTATTTTAAA
1 TTTTTTTATTATTTTAAA
3163626 TT
1 TT
3163628 ATAAAGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTTATTATTTTAAA
Found at i:3163849 original size:22 final size:22
Alignment explanation
Indices: 3163824--3163867 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3163814 ACATTTATTA
3163824 CATCATTAATAAATTATCAAAT
1 CATCATTAATAAATTATCAAAT
* *
3163846 CATCATTATTATATTATCAAAT
1 CATCATTAATAAATTATCAAAT
3163868 TTAATATCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (22 bp):
CATCATTAATAAATTATCAAAT
Found at i:3169186 original size:2 final size:2
Alignment explanation
Indices: 3169179--3169272 Score: 101
Period size: 2 Copynumber: 49.0 Consensus size: 2
3169169 ATGAAGAATT
*
3169179 TA TA TA TA TA TA -A TA TA TA TA -A TA TA TA TA TA TA -A AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3169217 TT TA -A AA CT- TNA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3169259 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
3169273 AAATTAGTGT
Statistics
Matches: 81, Mismatches: 3, Indels: 16
0.81 0.03 0.16
Matches are distributed among these distances:
1 6 0.07
2 74 0.91
3 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3173089 original size:45 final size:45
Alignment explanation
Indices: 3173040--3173179 Score: 169
Period size: 45 Copynumber: 3.1 Consensus size: 45
3173030 ATATGGCATT
*
3173040 TAACAATTTAACTATGGAGTGTCACATGTTTTTGTATAT-AGCGTA
1 TAACAACTTAACTATGGAGTGTCACATGTTTTTGTATATGA-CGTA
* * * *
3173085 TAACAACTTAATTATGG-GATGTCACATATTTTTGTACATGACGTG
1 TAACAACTTAACTATGGAG-TGTCACATGTTTTTGTATATGACGTA
* *
3173130 TAACAACCTAACTAT-GACGTGTCACATGTTTTTGTATATGACGTG
1 TAACAACTTAACTATGGA-GTGTCACATGTTTTTGTATATGACGTA
3173175 TAACA
1 TAACA
3173180 TATTTCTGTA
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
44 2 0.02
45 78 0.95
46 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (45 bp):
TAACAACTTAACTATGGAGTGTCACATGTTTTTGTATATGACGTA
Found at i:3173174 original size:24 final size:24
Alignment explanation
Indices: 3173142--3173203 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
3173132 ACAACCTAAC
* * *
3173142 TATGACGTGTCACATGTTTTTGTA
1 TATGACGTGTAACATATTTCTGTA
3173166 TATGACGTGTAACATATTTCTGTA
1 TATGACGTGTAACATATTTCTGTA
*
3173190 CATGACGTGTAACA
1 TATGACGTGTAACA
3173204 ACCTAATCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (24 bp):
TATGACGTGTAACATATTTCTGTA
Found at i:3173221 original size:69 final size:69
Alignment explanation
Indices: 3173108--3173351 Score: 328
Period size: 69 Copynumber: 3.5 Consensus size: 69
3173098 ATGGGATGTC
** * * * *
3173108 ACATATTTTTGTACATGACGTGTAACAACCTAA-CTATGACGTGTCACATGTTTTTGTATATGAC
1 ACATATTTTTGTACATGACGTGTAACAACCTAATC-ATGGTGTGTCACGTATTTTTATACATGAC
3173172 GTGTA
65 GTGTA
*
3173177 ACATATTTCTGTACATGACGTGTAACAACCTAATCATGGTGTGTCACGTATTTTTATACATGACG
1 ACATATTTTTGTACATGACGTGTAACAACCTAATCATGGTGTGTCACGTATTTTTATACATGACG
3173242 TGTA
66 TGTA
* * * * *
3173246 ACATATTTTTGTACATGATGTGTAACAACATAATCATAGTGTGTTACGTATTTTTATACATTACG
1 ACATATTTTTGTACATGACGTGTAACAACCTAATCATGGTGTGTCACGTATTTTTATACATGACG
3173311 TGTA
66 TGTA
* ** *
3173315 ACATGTTTTTGTACATGATATTTAACAACCTAATCAT
1 ACATATTTTTGTACATGACGTGTAACAACCTAATCAT
3173352 AGCATGTAAT
Statistics
Matches: 157, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
69 156 0.99
70 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (69 bp):
ACATATTTTTGTACATGACGTGTAACAACCTAATCATGGTGTGTCACGTATTTTTATACATGACG
TGTA
Found at i:3173238 original size:24 final size:24
Alignment explanation
Indices: 3173211--3173333 Score: 83
Period size: 24 Copynumber: 5.2 Consensus size: 24
3173201 ACAACCTAAT
* * *
3173211 CATGGTGTGTCACGTATTTTTATA
1 CATGATGTGTAACATATTTTTATA
* *
3173235 CATGACGTGTAACATATTTTTGTA
1 CATGATGTGTAACATATTTTTATA
** *
3173259 CATGATGTGTAACA-A-CATAAT-
1 CATGATGTGTAACATATTTTTATA
* *
3173280 CAT-AGTGTGTTACGTATTTTTATA
1 CATGA-TGTGTAACATATTTTTATA
* * * *
3173304 CATTACGTGTAACATGTTTTTGTA
1 CATGATGTGTAACATATTTTTATA
3173328 CATGAT
1 CATGAT
3173334 ATTTAACAAC
Statistics
Matches: 72, Mismatches: 22, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
20 1 0.01
21 10 0.14
22 3 0.04
23 4 0.06
24 53 0.74
25 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (24 bp):
CATGATGTGTAACATATTTTTATA
Found at i:3173380 original size:21 final size:21
Alignment explanation
Indices: 3173341--3173381 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3173331 GATATTTAAC
* *
3173341 AACCTAATCATAGCATGTAAT
1 AACCTAACCATAACATGTAAT
*
3173362 AACCTAACCATAACTTGTAA
1 AACCTAACCATAACATGTAA
3173382 CATATTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (21 bp):
AACCTAACCATAACATGTAAT
Found at i:3174276 original size:41 final size:41
Alignment explanation
Indices: 3174228--3174311 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
3174218 ACGGCATTAG
3174228 CCTATAAGTCTGATCACTTGTCTCCTTGCTTTCAAACCTCT
1 CCTATAAGTCTGATCACTTGTCTCCTTGCTTTCAAACCTCT
3174269 CCTATAAGTCTGATCACTTGTCTCCTTGCTTTCAAACCTCT
1 CCTATAAGTCTGATCACTTGTCTCCTTGCTTTCAAACCTCT
3174310 CC
1 CC
3174312 GGCTTAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (41 bp):
CCTATAAGTCTGATCACTTGTCTCCTTGCTTTCAAACCTCT
Found at i:3178418 original size:30 final size:30
Alignment explanation
Indices: 3178382--3178441 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3178372 AAGTTTACTT
*
3178382 GAAATTATGTTATTTAATACGAAGTATACG
1 GAAATTACGTTATTTAATACGAAGTATACG
*
3178412 GAAATTACGTTATTTAATATGAAGTATACG
1 GAAATTACGTTATTTAATACGAAGTATACG
3178442 ATTTTCTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (30 bp):
GAAATTACGTTATTTAATACGAAGTATACG
Found at i:3179999 original size:67 final size:67
Alignment explanation
Indices: 3179891--3180017 Score: 245
Period size: 67 Copynumber: 1.9 Consensus size: 67
3179881 AATATAGTTA
3179891 AAAAAAAAAAGAACAATCCAATCTAATTAACTTCAACAAGCTGCTTATTAATTATATGACATGAG
1 AAAAAAAAAAGAACAATCCAATCTAATTAACTTCAACAAGCTGCTTATTAATTATATGACATGAG
3179956 TG
66 TG
*
3179958 AAAAAAACAAGAACAATCCAATCTAATTAACTTCAACAAGCTGCTTATTAATTATATGAC
1 AAAAAAAAAAGAACAATCCAATCTAATTAACTTCAACAAGCTGCTTATTAATTATATGAC
3180018 GTCGTTTACA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.27
Consensus pattern (67 bp):
AAAAAAAAAAGAACAATCCAATCTAATTAACTTCAACAAGCTGCTTATTAATTATATGACATGAG
TG
Found at i:3190070 original size:12 final size:12
Alignment explanation
Indices: 3190047--3190176 Score: 84
Period size: 12 Copynumber: 10.8 Consensus size: 12
3190037 AAGACATGAG
*
3190047 AGGGAGAAGGAA
1 AGGGAAAAGGAA
* *
3190059 CGTGAAAAGGAA
1 AGGGAAAAGGAA
* *
3190071 AGGGAGAAGGAT
1 AGGGAAAAGGAA
* *
3190083 CGTGAAAAGGAA
1 AGGGAAAAGGAA
*
3190095 AGGGAGAAGGAA
1 AGGGAAAAGGAA
*
3190107 CA-TGAAAAGGAA
1 -AGGGAAAAGGAA
*
3190119 AGGGAGAAGGAA
1 AGGGAAAAGGAA
* *
3190131 CA-TGCAAAGGAA
1 -AGGGAAAAGGAA
*
3190143 AGGGAGAAGGAA
1 AGGGAAAAGGAA
* *
3190155 TGCGAAAAGGAA
1 AGGGAAAAGGAA
*
3190167 AGGGAGAAGG
1 AGGGAAAAGG
3190177 TTGAAAGGGA
Statistics
Matches: 84, Mismatches: 30, Indels: 8
0.69 0.25 0.07
Matches are distributed among these distances:
11 2 0.02
12 80 0.95
13 2 0.02
ACGTcount: A:0.49, C:0.05, G:0.42, T:0.05
Consensus pattern (12 bp):
AGGGAAAAGGAA
Found at i:3190075 original size:24 final size:24
Alignment explanation
Indices: 3190047--3190176 Score: 206
Period size: 24 Copynumber: 5.4 Consensus size: 24
3190037 AAGACATGAG
3190047 AGGGAGAAGGAACGTGAAAAGGAA
1 AGGGAGAAGGAACGTGAAAAGGAA
*
3190071 AGGGAGAAGGATCGTGAAAAGGAA
1 AGGGAGAAGGAACGTGAAAAGGAA
*
3190095 AGGGAGAAGGAACATGAAAAGGAA
1 AGGGAGAAGGAACGTGAAAAGGAA
* *
3190119 AGGGAGAAGGAACATGCAAAGGAA
1 AGGGAGAAGGAACGTGAAAAGGAA
* *
3190143 AGGGAGAAGGAATGCGAAAAGGAA
1 AGGGAGAAGGAACGTGAAAAGGAA
3190167 AGGGAGAAGG
1 AGGGAGAAGG
3190177 TTGAAAGGGA
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 98 1.00
ACGTcount: A:0.49, C:0.05, G:0.42, T:0.05
Consensus pattern (24 bp):
AGGGAGAAGGAACGTGAAAAGGAA
Found at i:3193212 original size:2 final size:2
Alignment explanation
Indices: 3193205--3193233 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3193195 CCCTCTTTTC
3193205 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3193234 ACTCAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3200980 original size:16 final size:16
Alignment explanation
Indices: 3200937--3200980 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
3200927 ATAGTTAAAG
*
3200937 TTCAAGTCAATTTGGA
1 TTCAAGTCATTTTGGA
* *
3200953 TTCAAATAATTTTGGA
1 TTCAAGTCATTTTGGA
*
3200969 TTTAAGTCATTT
1 TTCAAGTCATTT
3200981 ACGTTTCGAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (16 bp):
TTCAAGTCATTTTGGA
Found at i:3208136 original size:28 final size:28
Alignment explanation
Indices: 3208103--3208159 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
3208093 ATATATTCAC
3208103 TTGACAATTCTTGATTACATTTTATAAT
1 TTGACAATTCTTGATTACATTTTATAAT
*
3208131 TTGACAATTCTTGATTATATTTTATAAT
1 TTGACAATTCTTGATTACATTTTATAAT
3208159 T
1 T
3208160 AATTTGTGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.53
Consensus pattern (28 bp):
TTGACAATTCTTGATTACATTTTATAAT
Found at i:3215449 original size:22 final size:22
Alignment explanation
Indices: 3215370--3215457 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
3215360 GGTTTTAAGT
* *
3215370 ATTATGAGACTAATTTTTTGAC
1 ATTATGTGACTAATTTTTAGAC
** *
3215392 ATTACATGACTGATTTTTAGAC
1 ATTATGTGACTAATTTTTAGAC
*
3215414 ATTATGTGACTAATTTTTAGGC
1 ATTATGTGACTAATTTTTAGAC
* * *
3215436 ATTGTGTTATTAATTTTT-GAC
1 ATTATGTGACTAATTTTTAGAC
3215457 A
1 A
3215458 ATGCCTAAGT
Statistics
Matches: 53, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
21 3 0.06
22 50 0.94
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (22 bp):
ATTATGTGACTAATTTTTAGAC
Found at i:3221286 original size:28 final size:29
Alignment explanation
Indices: 3221224--3221291 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 29
3221214 ATTAAATTTT
* *
3221224 TAATTAAAAATATTAATATTTTTAATAAA
1 TAATCAAAAATATTAATATTTATAATAAA
* *
3221253 TTATCAAAAA-ATTAATATTTCATATTAAA
1 TAATCAAAAATATTAATATTT-ATAATAAA
*
3221282 -AATCATAAAT
1 TAATCAAAAAT
3221292 TATAATAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATCAAAAATATTAATATTTATAATAAA
Found at i:3224442 original size:2 final size:2
Alignment explanation
Indices: 3224435--3224466 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3224425 TAATACGTTA
3224435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3224467 CAGCATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3235808 original size:30 final size:30
Alignment explanation
Indices: 3235772--3235835 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
3235762 AATTATATTT
*
3235772 TTATATTTTTATTTTAAGTCAAATAAGTTC
1 TTATATTTTTATTTTAAATCAAATAAGTTC
*
3235802 TTATATTTTTATTTTAAATCAAATAATTTC
1 TTATATTTTTATTTTAAATCAAATAAGTTC
3235832 TTAT
1 TTAT
3235836 TAATAATGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (30 bp):
TTATATTTTTATTTTAAATCAAATAAGTTC
Found at i:3235956 original size:33 final size:33
Alignment explanation
Indices: 3235907--3235970 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
3235897 ATATGTTAAA
* *
3235907 ATATCATAATTTATAATAATATGACATATTAGC
1 ATATCATAATTAATAATAATATAACATATTAGC
* *
3235940 ATATTATAATTAATAATGATATAACATATTA
1 ATATCATAATTAATAATAATATAACATATTA
3235971 ATTTGATATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (33 bp):
ATATCATAATTAATAATAATATAACATATTAGC
Found at i:3256302 original size:65 final size:65
Alignment explanation
Indices: 3256198--3256394 Score: 349
Period size: 65 Copynumber: 3.0 Consensus size: 65
3256188 TTAATTTTTT
*
3256198 CTTCAGTTTCTCTATTCTTCCTTTCTTTCTCTTCCTGTTATGCACAATGATGACATTTGAGATGG
1 CTTCAGTTTCTCTATTCTTCCTTTCTTTCTCTTCCTGTTATGCTCAATGATGACATTTGAGATGG
* * *
3256263 CTTCAGTTTCTCTATTCCTCCCTTCTTTCTCTTTCTGTTATGCTCAATGATGACATTTGAGATGG
1 CTTCAGTTTCTCTATTCTTCCTTTCTTTCTCTTCCTGTTATGCTCAATGATGACATTTGAGATGG
*
3256328 CTTCAGTTTCTCTATTCTTCCTTTCTTTCTCTTCCTGTTATGGTCAATGATGACATTTGAGATGG
1 CTTCAGTTTCTCTATTCTTCCTTTCTTTCTCTTCCTGTTATGCTCAATGATGACATTTGAGATGG
3256393 CT
1 CT
3256395 ATTGTGCGTT
Statistics
Matches: 124, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 124 1.00
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.47
Consensus pattern (65 bp):
CTTCAGTTTCTCTATTCTTCCTTTCTTTCTCTTCCTGTTATGCTCAATGATGACATTTGAGATGG
Found at i:3264678 original size:25 final size:24
Alignment explanation
Indices: 3264644--3264690 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
3264634 CAATCTTGTT
3264644 TTCATTTATAGTACTGCA-ACTGATC
1 TTCATTTATA-T-CTGCAGACTGATC
3264669 TTCATTTATATCTGCAGACTGA
1 TTCATTTATATCTGCAGACTGA
3264691 GGATAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 6 0.29
25 10 0.48
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (24 bp):
TTCATTTATATCTGCAGACTGATC
Found at i:3265232 original size:60 final size:60
Alignment explanation
Indices: 3265132--3265313 Score: 346
Period size: 60 Copynumber: 3.0 Consensus size: 60
3265122 TCTGTACATG
* *
3265132 CTACTTGTTCAGTTCAGATGCTGCGGTATTCGGAGGTTTACATTGTGCTTGGGGATATTC
1 CTACTTGTTCAGTTCAGATGCTGCGGTATTCGTAGTTTTACATTGTGCTTGGGGATATTC
3265192 CTACTTGTTCAGTTCAGATGCTGCGGTATTCGTAGTTTTACATTGTGCTTGGGGATATTC
1 CTACTTGTTCAGTTCAGATGCTGCGGTATTCGTAGTTTTACATTGTGCTTGGGGATATTC
3265252 CTACTTGTTCAGTTCAGATGCTGCGGTATTCGTAGTTTTACATTGTGCTTGGGGATATTC
1 CTACTTGTTCAGTTCAGATGCTGCGGTATTCGTAGTTTTACATTGTGCTTGGGGATATTC
3265312 CT
1 CT
3265314 TTCTTTGGTG
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 120 1.00
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (60 bp):
CTACTTGTTCAGTTCAGATGCTGCGGTATTCGTAGTTTTACATTGTGCTTGGGGATATTC
Found at i:3265251 original size:29 final size:29
Alignment explanation
Indices: 3265158--3265311 Score: 104
Period size: 29 Copynumber: 5.2 Consensus size: 29
3265148 GATGCTGCGG
* *
3265158 TATTCGGAGGTTTACATTGTGCTTGGGGA
1 TATTCGTAGTTTTACATTGTGCTTGGGGA
* * *
3265187 TATTCCTACTTGTT-CAGTTCAGATGC-TGCGG-
1 TATTCGTAGTT-TTACA-TT--G-TGCTTGGGGA
3265218 TATTCGTAGTTTTACATTGTGCTTGGGGA
1 TATTCGTAGTTTTACATTGTGCTTGGGGA
* * *
3265247 TATTCCTACTTGTT-CAGTTCAGATGC-TGCGG-
1 TATTCGTAGTT-TTACA-TT--G-TGCTTGGGGA
3265278 TATTCGTAGTTTTACATTGTGCTTGGGGA
1 TATTCGTAGTTTTACATTGTGCTTGGGGA
3265307 TATTC
1 TATTC
3265312 CTTTCTTTGG
Statistics
Matches: 95, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
27 6 0.06
28 10 0.11
29 25 0.26
30 16 0.17
31 22 0.23
32 10 0.11
33 6 0.06
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.42
Consensus pattern (29 bp):
TATTCGTAGTTTTACATTGTGCTTGGGGA
Found at i:3282768 original size:24 final size:24
Alignment explanation
Indices: 3282736--3282790 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
3282726 GCTTGGAGCT
3282736 GGTGCAGGAACCTCAACAGTTGTC
1 GGTGCAGGAACCTCAACAGTTGTC
*
3282760 GGTGCAGGAACCTCAGCAGTTGTC
1 GGTGCAGGAACCTCAACAGTTGTC
3282784 GGTGCAG
1 GGTGCAG
3282791 CAACAGGAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.35, T:0.20
Consensus pattern (24 bp):
GGTGCAGGAACCTCAACAGTTGTC
Found at i:3283013 original size:30 final size:30
Alignment explanation
Indices: 3282970--3283031 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
3282960 AGCCGCAGCC
* *
3282970 GGTGGGGACGAAGTTGGTGGTGAAGAAGTT
1 GGTGGGGAAGAAGTTGGCGGTGAAGAAGTT
*
3283000 GGTGGTGAAGAAGTTGGCGGTGAAGAAGTT
1 GGTGGGGAAGAAGTTGGCGGTGAAGAAGTT
3283030 GG
1 GG
3283032 AGCAGTGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.03, G:0.50, T:0.23
Consensus pattern (30 bp):
GGTGGGGAAGAAGTTGGCGGTGAAGAAGTT
Found at i:3283021 original size:18 final size:15
Alignment explanation
Indices: 3282979--3283031 Score: 97
Period size: 15 Copynumber: 3.5 Consensus size: 15
3282969 CGGTGGGGAC
3282979 GAAGTTGGTGGTGAA
1 GAAGTTGGTGGTGAA
3282994 GAAGTTGGTGGTGAA
1 GAAGTTGGTGGTGAA
*
3283009 GAAGTTGGCGGTGAA
1 GAAGTTGGTGGTGAA
3283024 GAAGTTGG
1 GAAGTTGG
3283032 AGCAGTGGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.26, C:0.02, G:0.47, T:0.25
Consensus pattern (15 bp):
GAAGTTGGTGGTGAA
Found at i:3298524 original size:3 final size:3
Alignment explanation
Indices: 3298518--3298542 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3298508 CCCNCACCCC
3298518 CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT C
3298543 TTGAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:3299534 original size:94 final size:94
Alignment explanation
Indices: 3299394--3299568 Score: 244
Period size: 94 Copynumber: 1.9 Consensus size: 94
3299384 GCCGCTGTAA
* * * * *
3299394 TTTTAATTTTGTTGATTTTGGGACAAAAAGTAACGAAATTATAATATTTCACAG-AATATTTTGT
1 TTTTAATCTAGTTGATTTTGGAACAAAAAATAACGAAATTAGAATATTTCA-AGTAATATTTTGT
*
3299458 TAATGCAATTGGCAAATCTTGCCACTATAC
65 TAATGCAAATGGCAAATCTTGCCACTATAC
* * * *
3299488 TTTTAATCTAGTTGATTTTTGAACAAAAAATAATGAAATTGGAATATTTCATGTAATATTTTGTT
1 TTTTAATCTAGTTGATTTTGGAACAAAAAATAACGAAATTAGAATATTTCAAGTAATATTTTGTT
3299553 AATGCAAATGGCAAAT
66 AATGCAAATGGCAAAT
3299569 TTCCATCAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
93 1 0.01
94 69 0.99
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (94 bp):
TTTTAATCTAGTTGATTTTGGAACAAAAAATAACGAAATTAGAATATTTCAAGTAATATTTTGTT
AATGCAAATGGCAAATCTTGCCACTATAC
Found at i:3300128 original size:16 final size:16
Alignment explanation
Indices: 3300107--3300139 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3300097 GCCTAAACGA
*
3300107 AAAATTAATCATGTGG
1 AAAATTAATCATATGG
3300123 AAAATTAATCATATGG
1 AAAATTAATCATATGG
3300139 A
1 A
3300140 GCATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.30
Consensus pattern (16 bp):
AAAATTAATCATATGG
Found at i:3307054 original size:40 final size:41
Alignment explanation
Indices: 3306978--3307057 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 41
3306968 TTGGCTATTT
* *
3306978 TTCACCTTAATGGGGTTTTCTGACCTTGTCAAGATTGATGG
1 TTCACCTTAATGGGGTTTTCTAACCTCGTCAAGATTGATGG
*
3307019 TTCACCTTAATGGGG-TTTCTAACCTCGTCACGATTGATG
1 TTCACCTTAATGGGGTTTTCTAACCTCGTCAAGATTGATG
3307058 TCTTTCACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 21 0.58
41 15 0.42
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
TTCACCTTAATGGGGTTTTCTAACCTCGTCAAGATTGATGG
Found at i:3307343 original size:28 final size:28
Alignment explanation
Indices: 3307311--3307378 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
3307301 TACTTTAAAA
*
3307311 AAATTAAATAA-AATTTTATTTT-TTATT
1 AAATTAAATAAGAATTATATTTTATT-TT
* *
3307338 ACAATTAATTAAGCATTATATTTTATTTT
1 A-AATTAAATAAGAATTATATTTTATTTT
3307367 AAATTAAATAAG
1 AAATTAAATAAG
3307379 TTTTCATCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.03
28 19 0.56
29 12 0.35
30 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (28 bp):
AAATTAAATAAGAATTATATTTTATTTT
Found at i:3307518 original size:21 final size:21
Alignment explanation
Indices: 3307478--3307518 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3307468 GAGAGTATAT
*
3307478 ATGTCACATAGTTATGTCATC
1 ATGTCACATAGTTATATCATC
3307499 ATGTCACATAAG-TATATCAT
1 ATGTCACAT-AGTTATATCAT
3307519 GTTATCATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCACATAGTTATATCATC
Found at i:3335357 original size:28 final size:27
Alignment explanation
Indices: 3335320--3335407 Score: 115
Period size: 28 Copynumber: 3.1 Consensus size: 27
3335310 GATAACTAAA
*
3335320 TTTTCAATATAATGAGTAATAATTATAT
1 TTTTTAATATAAT-AGTAATAATTATAT
*
3335348 TTTTTAATATGATATGTAATAATTATAT
1 TTTTTAATATAATA-GTAATAATTATAT
3335376 TTTTTAATATAACATA-TAATAATTATAT
1 TTTTTAATAT-A-ATAGTAATAATTATAT
3335404 TTTT
1 TTTT
3335408 AACATGTCGT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
27 1 0.02
28 50 0.93
30 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (27 bp):
TTTTTAATATAATAGTAATAATTATAT
Found at i:3335423 original size:27 final size:27
Alignment explanation
Indices: 3335336--3335462 Score: 96
Period size: 27 Copynumber: 4.6 Consensus size: 27
3335326 ATATAATGAG
* * *
3335336 TAATAATTATATTTTTTAATATGAT-ATG
1 TAATAATTATA-TTTTTAACATG-TCGTA
* ** *
3335364 TAATAATTATATTTTTTAATATAACATA
1 TAATAATTATA-TTTTTAACATGTCGTA
3335392 TAATAATTATATTTTTAACATGTCGTA
1 TAATAATTATATTTTTAACATGTCGTA
* * * * *
3335419 CAATAATTAAATATTCAGCATGAT-GTA
1 TAATAATTATATTTTTAACATG-TCGTA
3335446 TAATAATTATATTTTTA
1 TAATAATTATATTTTTA
3335463 GAACGATTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
27 45 0.56
28 36 0.44
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (27 bp):
TAATAATTATATTTTTAACATGTCGTA
Found at i:3335820 original size:2 final size:2
Alignment explanation
Indices: 3335813--3335851 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3335803 AATATGTCCG
3335813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3335852 GAATAGTAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3338887 original size:20 final size:19
Alignment explanation
Indices: 3338862--3338901 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
3338852 AATTTAAAAC
3338862 AAAATAACATAAATTTAACT
1 AAAATAACATAAA-TTAACT
*
3338882 AAAATAACTTAAATTAACT
1 AAAATAACATAAATTAACT
3338901 A
1 A
3338902 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATAACATAAATTAACT
Found at i:3340809 original size:15 final size:17
Alignment explanation
Indices: 3340771--3340827 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
3340761 GTTATGAATA
* *
3340771 TATATATATATATAATA
1 TATACATATATATAATT
* *
3340788 CAAACATAT-TAT-ATT
1 TATACATATATATAATT
*
3340803 TATACATATATTTAATT
1 TATACATATATATAATT
3340820 TATACATA
1 TATACATA
3340828 AGCATTACTA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 9 0.29
16 5 0.16
17 17 0.55
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
TATACATATATATAATT
Found at i:3342166 original size:21 final size:23
Alignment explanation
Indices: 3342118--3342166 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
3342108 ATAATATTTG
3342118 AAAATA-ATTATAATTGTTATAT
1 AAAATATATTATAATTGTTATAT
*
3342140 -ATATATA-TATAATT-TTATAT
1 AAAATATATTATAATTGTTATAT
3342160 AAAATAT
1 AAAATAT
3342167 GTTTTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 6 0.26
21 16 0.70
22 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATATATTATAATTGTTATAT
Found at i:3381748 original size:22 final size:20
Alignment explanation
Indices: 3381714--3381760 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
3381704 TTTGGGGGCA
3381714 CTTTTTTCCTTGGAGCT-GTT
1 CTTTTTTCCTTGG-GCTAGTT
*
3381734 GCTTTTTTACGTTGGGCTAGTT
1 -CTTTTTT-CCTTGGGCTAGTT
3381756 CTTTT
1 CTTTT
3381761 AGGAGTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.06, C:0.17, G:0.21, T:0.55
Consensus pattern (20 bp):
CTTTTTTCCTTGGGCTAGTT
Found at i:3383039 original size:24 final size:24
Alignment explanation
Indices: 3382977--3383026 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3382967 TCTAAAATGC
*
3382977 AAAAATAAAAA--AAAATAAATTA
1 AAAAATAAAAATTGAAATAAATTA
*
3382999 AAAAATAAAAATTGAAATAAATTT
1 AAAAATAAAAATTGAAATAAATTA
3383023 AAAA
1 AAAA
3383027 GTAATATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
24 13 0.54
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAAATAAAAATTGAAATAAATTA
Found at i:3383041 original size:25 final size:25
Alignment explanation
Indices: 3382977--3383052 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 25
3382967 TCTAAAATGC
*
3382977 AAAAATAAAAA---AAAATAAATTA
1 AAAAATAAAAATTGAAAATAAATTT
3382999 AAAAATAAAAATTG-AAATAAATTT
1 AAAAATAAAAATTGAAAATAAATTT
* * * *
3383023 AAAAGT-AATATATGAAAATACATAT
1 AAAAATAAAAAT-TGAAAATAAATTT
3383048 AAAAA
1 AAAAA
3383053 ATTAATTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 11 0.26
23 4 0.09
24 16 0.37
25 12 0.28
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (25 bp):
AAAAATAAAAATTGAAAATAAATTT
Found at i:3388065 original size:12 final size:12
Alignment explanation
Indices: 3388029--3388071 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
3388019 ATTATTTAAT
*
3388029 ATTATTTTTATT
1 ATTATTTTTATA
*
3388041 TTTATTTTATTATA
1 ATTA-TTT-TTATA
3388055 ATTATTTTTATA
1 ATTATTTTTATA
3388067 ATTAT
1 ATTAT
3388072 AGATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 13 0.50
13 6 0.23
14 7 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTATTTTTATA
Found at i:3388124 original size:20 final size:20
Alignment explanation
Indices: 3388037--3388126 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
3388027 ATATTATTTT
* *
3388037 TATTTTTATTTTATTATAAT
1 TATTTTTATTTAATTATAAA
*
3388057 TATTTTTA--TAATTATAGA
1 TATTTTTATTTAATTATAAA
** *
3388075 T-TTTAAATTTAAATAATAAA
1 TATTTTTATTT-AATTATAAA
*
3388095 -A-TTATATTTAATTATAAA
1 TATTTTTATTTAATTATAAA
3388113 TATTTTTATTTAAT
1 TATTTTTATTTAAT
3388127 CGTGTTAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
17 4 0.07
18 16 0.30
19 9 0.17
20 25 0.46
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
TATTTTTATTTAATTATAAA
Found at i:3388145 original size:18 final size:18
Alignment explanation
Indices: 3388122--3388160 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3388112 ATATTTTTAT
*
3388122 TTAATCGTGTTAAATGTG
1 TTAATCGTGTTAAACGTG
*
3388140 TTAATCGTGTTGAACGTG
1 TTAATCGTGTTAAACGTG
3388158 TTA
1 TTA
3388161 TTAATCGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44
Consensus pattern (18 bp):
TTAATCGTGTTAAACGTG
Found at i:3397043 original size:2 final size:2
Alignment explanation
Indices: 3397002--3397030 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3396992 ATTCTTAAAT
3397002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3397031 GTATCAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3408206 original size:20 final size:20
Alignment explanation
Indices: 3408181--3408222 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3408171 GATCTCCAAA
3408181 TGGATCTCTTTTGAGTGGTT
1 TGGATCTCTTTTGAGTGGTT
3408201 TGGATCTCTTTTGAGTGGTT
1 TGGATCTCTTTTGAGTGGTT
3408221 TG
1 TG
3408223 TAGACACTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.10, G:0.31, T:0.50
Consensus pattern (20 bp):
TGGATCTCTTTTGAGTGGTT
Found at i:3417068 original size:2 final size:2
Alignment explanation
Indices: 3417061--3417089 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3417051 ATGGAGAGGA
3417061 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3417090 ACCAAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3418153 original size:61 final size:61
Alignment explanation
Indices: 3418058--3418180 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
3418048 AAATTAACTA
* *
3418058 AACACCTTTGTAGTACTGTTACATTCTCCATCTTGATGGATTCAATTGTAAGGACATATAT
1 AACACCTTTATAGTACTGTTACATTCTCCATCTTGATGGATTCAATTGGAAGGACATATAT
3418119 AACACCTTTATAGTACTGTTACATTCTCCATCTTGATGGATTCAATTGGAAGGACATATAT
1 AACACCTTTATAGTACTGTTACATTCTCCATCTTGATGGATTCAATTGGAAGGACATATAT
3418180 A
1 A
3418181 TGCATATATG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (61 bp):
AACACCTTTATAGTACTGTTACATTCTCCATCTTGATGGATTCAATTGGAAGGACATATAT
Found at i:3418965 original size:2 final size:2
Alignment explanation
Indices: 3418958--3419046 Score: 83
Period size: 2 Copynumber: 42.5 Consensus size: 2
3418948 TTCCAACCCT
*
3418958 TC TC TC TC TC TC TC TC TNC TAC TAC TA TC TAC -C TAC -C TC TC TC
1 TC TC TC TC TC TC TC TC T-C T-C T-C TC TC T-C TC T-C TC TC TC TC
* *
3419001 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TGA TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC TC
3419044 TC T
1 TC T
3419047 GTCACCAACT
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
1 2 0.03
2 62 0.84
3 10 0.14
ACGTcount: A:0.07, C:0.44, G:0.01, T:0.47
Consensus pattern (2 bp):
TC
Found at i:3423074 original size:32 final size:32
Alignment explanation
Indices: 3423038--3423101 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
3423028 TTATAATGTG
3423038 TAAGAATGATTTAAAACCAAATAAATATCCAT
1 TAAGAATGATTTAAAACCAAATAAATATCCAT
3423070 TAAGAATGATTTAAAACCAAATAAATATCCAT
1 TAAGAATGATTTAAAACCAAATAAATATCCAT
3423102 ATAGACCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (32 bp):
TAAGAATGATTTAAAACCAAATAAATATCCAT
Found at i:3427357 original size:2 final size:2
Alignment explanation
Indices: 3427352--3427376 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3427342 TTTTTATCTC
3427352 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 A
3427377 AATAGTACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3427751 original size:18 final size:17
Alignment explanation
Indices: 3427716--3427755 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
3427706 GCAGATTAAG
*
3427716 ATAAATAATTATAAAAT
1 ATAAATAATAATAAAAT
*
3427733 ATAAGATAATAATATAAT
1 ATAA-ATAATAATAAAAT
3427751 ATAAA
1 ATAAA
3427756 AATTTTATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATAAATAATAATAAAAT
Found at i:3435914 original size:4 final size:4
Alignment explanation
Indices: 3435905--3435931 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3435895 GAACCAAACC
3435905 AAGA AAGA AAGA AAGA AAGA AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAG
3435932 GGCTACCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:3436725 original size:174 final size:173
Alignment explanation
Indices: 3436530--3436846 Score: 490
Period size: 174 Copynumber: 1.8 Consensus size: 173
3436520 TATATATATA
* * **
3436530 TATTTATTTATTTATAAATCTGTATTAATATGAAATTACAAGTTATAAATTTTAAATGATATATT
1 TATTGATTTATTTATAAATCTGTATTAATATAAAATTACAAGTTATAAATTTTAAATGATATAAC
* * *
3436595 TTATATGATAAGATTATAATATATGATAGTCAACATCTTACATATTAATATATTATAATTATTAC
66 TTATATGATAAGATTAAAATATATGATAGTAAACATCCTACATATTAATATATTATAATTATTAC
3436660 ACTTTAGTAATGTATCGTAATATAAAATGTNATTTAATTTAATT
131 ACTTTAGTAATGTATCGTAATATAAAATGT-ATTTAATTTAATT
*
3436704 TATTGATTTATTTATAAATCTGTATTAATATAAAATTACAAGTTATATATTTTAAATGATATAAC
1 TATTGATTTATTTATAAATCTGTATTAATATAAAATTACAAGTTATAAATTTTAAATGATATAAC
* ** ** * *
3436769 TTATATGTTAATTTTAAAATATATGATAGTAAATTTCCTACGTATTAATATGTTATAATTATTAC
66 TTATATGATAAGATTAAAATATATGATAGTAAACATCCTACATATTAATATATTATAATTATTAC
3436834 ACTTTAGTAATGT
131 ACTTTAGTAATGT
3436847 TTTATAACAT
Statistics
Matches: 128, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
174 128 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (173 bp):
TATTGATTTATTTATAAATCTGTATTAATATAAAATTACAAGTTATAAATTTTAAATGATATAAC
TTATATGATAAGATTAAAATATATGATAGTAAACATCCTACATATTAATATATTATAATTATTAC
ACTTTAGTAATGTATCGTAATATAAAATGTATTTAATTTAATT
Found at i:3437175 original size:218 final size:211
Alignment explanation
Indices: 3436917--3437355 Score: 605
Period size: 218 Copynumber: 2.0 Consensus size: 211
3436907 TATATATATA
* * * * * *
3436917 TTATACATAAGCATTATTATAACTTTTAATAAATTTTATTTATATGATTACATTTAATAACTTTA
1 TTATACATAAACATTACTACAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTA
*
3436982 TTAATTATCACT-TTAGTTTTTATAACATATTGTTTATAATTAGTTATTATTTATACAACCTTTG
66 TTAATTATC-CTCTTAATTTTTATAACATATTGTTTATAATTAGTTATTATTTATACAACCTTTG
* *
3437046 ATATAAAACATTATAACATAT-AAGTTGTGTCATTAATTTTATACATACATGATAAAGTAATGTA
130 ATATAAAA-ATTAAAACATATGAA-TTGTGTCATTAATTTTAT--ATACATAATAAAGTAA--TA
3437110 TATTACATATATA-CATATATTTAAT
189 TATT--ATATATACCA-ATATTTAAT
* * * *
3437135 TTATACATAAATATTACTACAACTTATAATAGACTTTATTTATATGATTACACTTAATAATTTTT
1 TTATACATAAACATTACTACAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTA
* *
3437200 TTAGTTATCGTCTTAATTTTTATAACATATTGTTTATAATTAGTTATTATTTATACAACCTTTGA
66 TTAATTATCCTCTTAATTTTTATAACATATTGTTTATAATTAGTTATTATTTATACAACCTTTGA
* *
3437265 TGTAAAAATTAAAACATATGAATTGTGTCATTAATTTTATATATATAATAAAGTAATATATTATA
131 TATAAAAATTAAAACATATGAATTGTGTCATTAATTTTATATACATAATAAAGTAATATATTATA
*
3437330 TATACCAATATTTTAT
196 TATACCAATATTTAAT
3437346 TTATACATAA
1 TTATACATAA
3437356 TTTGTATATA
Statistics
Matches: 200, Mismatches: 18, Indels: 13
0.87 0.08 0.06
Matches are distributed among these distances:
211 25 0.12
212 2 0.01
213 6 0.03
215 14 0.07
217 30 0.15
218 123 0.62
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (211 bp):
TTATACATAAACATTACTACAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTA
TTAATTATCCTCTTAATTTTTATAACATATTGTTTATAATTAGTTATTATTTATACAACCTTTGA
TATAAAAATTAAAACATATGAATTGTGTCATTAATTTTATATACATAATAAAGTAATATATTATA
TATACCAATATTTAAT
Found at i:3451481 original size:15 final size:16
Alignment explanation
Indices: 3451463--3451540 Score: 63
Period size: 15 Copynumber: 4.8 Consensus size: 16
3451453 TTATTTTATT
3451463 TTTTAAAT-ATTAATA
1 TTTTAAATAATTAATA
*
3451478 TTTTATAATTAATTAAAA
1 TTTTA-AA-TAATTAATA
*
3451496 TATT-AATAATTAATA
1 TTTTAAATAATTAATA
*
3451511 ATTTAAA-AATATCAATA
1 TTTTAAATAAT-T-AATA
3451528 TTTTAATATAATT
1 TTTTAA-ATAATT
3451541 TAATTACTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
15 18 0.37
16 7 0.14
17 10 0.20
18 11 0.22
19 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTTAAATAATTAATA
Found at i:3451496 original size:26 final size:24
Alignment explanation
Indices: 3451467--3451532 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 24
3451457 TTTATTTTTT
*
3451467 AAATATTAATATTTTATAATTAATTA
1 AAATATTAATATTTTATAATT--TAA
* *
3451493 AAATATTAATAATTAATAATTTAA
1 AAATATTAATATTTTATAATTTAA
*
3451517 AAATATCAATATTTTA
1 AAATATTAATATTTTA
3451533 ATATAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 15 0.44
26 19 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATATTAATATTTTATAATTTAA
Found at i:3451683 original size:16 final size:15
Alignment explanation
Indices: 3451658--3451691 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3451648 ATTTAATAAA
3451658 TAAAACATTAATAGTT
1 TAAAACATTAATA-TT
*
3451674 TAAAATATTAATATT
1 TAAAACATTAATATT
3451689 TAA
1 TAA
3451692 TATTTTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
TAAAACATTAATATT
Found at i:3451691 original size:23 final size:23
Alignment explanation
Indices: 3451639--3451716 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
3451629 AAAATTAAAT
* *
3451639 ATATTAATAATTTAATAA-ATAAA
1 ATATTAATAGTTTAATAATAT-TA
*
3451662 ACATTAATAGTTTAA-AATATTA
1 ATATTAATAGTTTAATAATATTA
* *
3451684 ATATTTAATATTTTAATCATATTA
1 ATA-TTAATAGTTTAATAATATTA
3451708 ATATTAATA
1 ATATTAATA
3451717 ATGTTTCAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
22 5 0.11
23 32 0.70
24 9 0.20
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (23 bp):
ATATTAATAGTTTAATAATATTA
Found at i:3451731 original size:26 final size:24
Alignment explanation
Indices: 3451678--3451751 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 24
3451668 ATAGTTTAAA
3451678 ATATTAATATTTAAT-ATTTTAATC
1 ATATTAATA-TTAATAATTTTAATC
*
3451702 ATATTAATATTAATAATGTTTCAATT
1 ATATTAATATTAATAAT-TTT-AATC
3451728 ATATATAAAATATTAAT-ATTTTAA
1 ATAT-T--AATATTAATAATTTTAA
3451752 ATTTTACAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
23 5 0.12
24 11 0.26
25 3 0.07
26 9 0.21
27 4 0.09
28 2 0.05
29 9 0.21
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (24 bp):
ATATTAATATTAATAATTTTAATC
Found at i:3451746 original size:15 final size:15
Alignment explanation
Indices: 3451627--3451746 Score: 52
Period size: 15 Copynumber: 7.9 Consensus size: 15
3451617 TTATACTCAT
3451627 TAAAA-ATTAAATATA
1 TAAAATATT-AATATA
*
3451642 TTAATAAT-TTAATAAA
1 -TAA-AATATTAATATA
* *
3451658 TAAAACATTAATAGTT
1 TAAAATATTAATA-TA
*
3451674 TAAAATATTAATATT
1 TAAAATATTAATATA
* *
3451689 TAATATTTTAATCATA
1 TAAAATATTAAT-ATA
* *
3451705 T-TAATATTAATAATG
1 TAAAATATTAAT-ATA
***
3451720 TTTCA-ATT-ATATA
1 TAAAATATTAATATA
3451733 TAAAATATTAATAT
1 TAAAATATTAATAT
3451747 TTTAAATTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
13 4 0.05
14 7 0.09
15 38 0.49
16 25 0.32
17 4 0.05
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (15 bp):
TAAAATATTAATATA
Found at i:3452907 original size:2 final size:2
Alignment explanation
Indices: 3452902--3452946 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
3452892 GTGTACATAC
*
3452902 AT AT AT AT AT AT AT AC 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
3452944 AT A
1 AT A
3452947 ATAAAAAAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3459963 original size:5 final size:5
Alignment explanation
Indices: 3459955--3459990 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
3459945 GATCCCCACA
* *
3459955 CCCCA CCCCA CCCCT CCCCT CCCCT CCCCT CCCCT C
1 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT C
3459991 AAGTTATGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.06, C:0.81, G:0.00, T:0.14
Consensus pattern (5 bp):
CCCCT
Done.