Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 187 of 189
Found at i:55819888 original size:42 final size:42
Alignment explanation
Indices: 55819767--55819992 Score: 281
Period size: 42 Copynumber: 5.3 Consensus size: 42
55819757 TTTCCATGAC
* * *
55819767 CTTTAGCGGCATTTTTGGGGAAAGCGTCGTTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTTT-GGGAAAGCGCCGCTAAAGGTCTTGTT
* ** * *
55819810 CTTTAGCGGCATTTTTGAAAAAAGCGCTGTTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTTTG-GGAAAGCGCCGCTAAAGGTCTTGTT
* * *
55819853 CTTTAGTGACGTTTTTGGAAAAGCGCCGCTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGTT
*
55819895 CTTTAGCGGCGTTTTTGGGAAAGCGCTGCTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGTT
* ** **
55819937 CTTTAGCGGCGTTTTTGGGAAAGCGCCACTAAAGGTCACGAC
1 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGTT
55819979 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
55819993 ATTTTTAAAA
Statistics
Matches: 162, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
42 111 0.69
43 51 0.31
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGTT
Found at i:55821134 original size:24 final size:24
Alignment explanation
Indices: 55821102--55821147 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
55821092 CATTAAAAAC
*
55821102 AACATAACTCTTGACCTTTCATAT
1 AACATAACTCTTGACATTTCATAT
55821126 AACATAACTCTTGACATTTCAT
1 AACATAACTCTTGACATTTCAT
55821148 TTAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (24 bp):
AACATAACTCTTGACATTTCATAT
Found at i:55823479 original size:49 final size:49
Alignment explanation
Indices: 55823418--55823560 Score: 223
Period size: 49 Copynumber: 2.9 Consensus size: 49
55823408 ATGTGAACAT
*
55823418 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
55823468 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * *
55823517 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATC
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATC
55823561 AGAAAACGAA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 83 0.95
50 4 0.05
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:55826754 original size:37 final size:37
Alignment explanation
Indices: 55826707--55826853 Score: 217
Period size: 37 Copynumber: 4.0 Consensus size: 37
55826697 TGATAGCTTC
* **
55826707 GGCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
55826744 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
* *
55826781 GGCTACACTTATGTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
**
55826818 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
55826853 G
1 G
55826854 ATCATACGTA
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 86 0.85
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Found at i:55828467 original size:21 final size:21
Alignment explanation
Indices: 55828436--55828484 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
55828426 ATCATTGATT
*
55828436 TTAATCATATTACTACAA-TA
1 TTAATCTTATTACTACAATTA
*
55828456 TTCAATCTTATTGCTACAATTA
1 TT-AATCTTATTACTACAATTA
55828478 TTAATCT
1 TTAATCT
55828485 CACTGACACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAATCTTATTACTACAATTA
Found at i:55830101 original size:6 final size:6
Alignment explanation
Indices: 55830082--55830125 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
55830072 ATTTTCCAGG
*
55830082 TCATCT TCATTTT TCATTT TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCA-TTT TCATTT TCATTT TCATTT TCATTT TCATTT T
55830126 GGAGAAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (6 bp):
TCATTT
Found at i:55831479 original size:6 final size:6
Alignment explanation
Indices: 55831468--55831496 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
55831458 ACTTGCTTGA
55831468 CCTCTC CCTCTC CCTCTC CCTCTC CCTCT
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCT
55831497 TCTTCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCTCTC
Found at i:55836807 original size:3 final size:3
Alignment explanation
Indices: 55836799--55836823 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55836789 ACAAGAACAA
55836799 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
55836824 GCCAAATTAG
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:55845655 original size:21 final size:21
Alignment explanation
Indices: 55845624--55845672 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
55845614 GTCATTGATT
*
55845624 TTAATCATATTACTACAA-TA
1 TTAATCTTATTACTACAATTA
*
55845644 TTCAATCTTATTGCTACAATTA
1 TT-AATCTTATTACTACAATTA
55845666 TTAATCT
1 TTAATCT
55845673 CACTGACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAATCTTATTACTACAATTA
Found at i:55846438 original size:43 final size:43
Alignment explanation
Indices: 55846391--55846530 Score: 183
Period size: 43 Copynumber: 3.3 Consensus size: 43
55846381 TTGGGGTCTT
* * * *
55846391 TAGCGGCGCTCTTACTACAAACGCTGCAATAGACCCTGAGCTA
1 TAGCGGCGCTTTTACTAAAAACGCCGCAATAGACCCTGATCTA
*
55846434 TAGCGGCGCTTTTTCTAAAAACGCCGCAATAGACACC-GATCTA
1 TAGCGGCGCTTTTACTAAAAACGCCGCAATAGAC-CCTGATCTA
* **
55846477 TAGCGGCGCTTTTACAAAAAACGCCGCCGTAGACCCTGATCTA
1 TAGCGGCGCTTTTACTAAAAACGCCGCAATAGACCCTGATCTA
*
55846520 TAACGGCGCTT
1 TAGCGGCGCTT
55846531 CGGATAAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
42 2 0.02
43 81 0.95
44 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (43 bp):
TAGCGGCGCTTTTACTAAAAACGCCGCAATAGACCCTGATCTA
Found at i:55846977 original size:21 final size:21
Alignment explanation
Indices: 55846944--55847036 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
55846934 TTTGACGTTG
*
55846944 CTCTTCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
* *
55846965 CTCTACTTGCCTCGCTACAGC
1 CTCTACTTCCCTCGCTGCAGC
*
55846986 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
* ** *
55847007 CTGTACTTCTATCGCTGCCGC
1 CTCTACTTCCCTCGCTGCAGC
55847028 CTCTACTTC
1 CTCTACTTC
55847037 TCTTACTGCC
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.09, C:0.44, G:0.15, T:0.32
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:55847127 original size:66 final size:66
Alignment explanation
Indices: 55847027--55847173 Score: 197
Period size: 66 Copynumber: 2.2 Consensus size: 66
55847017 ATCGCTGCCG
* ** * **
55847027 CCTCTACTTCTCTTACTGCCGCATTTGCTCTAAGCTGTTGCTGGAGTTCTTCATA-CTTTCGTTG
1 CCTCAACTTCTCTCGCTGCCGCATCTGCTCTAAGCTACTGCTGGAGTTCTTCATATCTTT-GTTG
55847091 AA
65 AA
* * *
55847093 CCTCAGCTTCTCTCGCTGCTGCATCTGCTCTAAGCTACTGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAACTTCTCTCGCTGCCGCATCTGCTCTAAGCTACTGCTGGAGTTCTTCATATCTTTGTTGA
55847158 A
66 A
55847159 CCTCAACTTCTCTCG
1 CCTCAACTTCTCTCG
55847174 ATGTTGCCTC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
66 66 0.94
67 4 0.06
ACGTcount: A:0.15, C:0.30, G:0.16, T:0.39
Consensus pattern (66 bp):
CCTCAACTTCTCTCGCTGCCGCATCTGCTCTAAGCTACTGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:55848851 original size:21 final size:20
Alignment explanation
Indices: 55848823--55848872 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
55848813 TCATCATTCG
*
55848823 TAATTTAAGTAAGTTATGTA
1 TAATTTAAGTAACTTATGTA
*
55848843 TAATATTAATTAACTTATG--
1 TAAT-TTAAGTAACTTATGTA
55848862 TAATTTAAGTA
1 TAATTTAAGTA
55848873 TAATATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.23
19 4 0.15
20 4 0.15
21 12 0.46
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (20 bp):
TAATTTAAGTAACTTATGTA
Found at i:55848928 original size:34 final size:34
Alignment explanation
Indices: 55848847--55849027 Score: 198
Period size: 34 Copynumber: 5.5 Consensus size: 34
55848837 TATGTATAAT
*
55848847 ATTAATTAACTTATGTAATTTAA-GTATAATATTA
1 ATTAATTAAGTTATGTAA-TTAATGTATAATATTA
*
55848881 A-T--GTAAGTTATGTAATTAATGTATAATATTA
1 ATTAATTAAGTTATGTAATTAATGTATAATATTA
* *
55848912 ATTAATTAAGTCATGTAATTTATGTATAATATTA
1 ATTAATTAAGTTATGTAATTAATGTATAATATTA
** *
55848946 A-T--GCAAGTTCTGTAA-TATATGTATAATATTA
1 ATTAATTAAGTTATGTAATTA-ATGTATAATATTA
*
55848977 ATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATTAATTAAGTTATGTAATTAATGTATAATATTA
* *
55849011 AATAATCAAGTTATGTA
1 ATTAATTAAGTTATGTA
55849028 TAATATTAAT
Statistics
Matches: 122, Mismatches: 16, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
30 5 0.04
31 46 0.38
32 2 0.02
33 2 0.02
34 66 0.54
35 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (34 bp):
ATTAATTAAGTTATGTAATTAATGTATAATATTA
Found at i:55848928 original size:65 final size:65
Alignment explanation
Indices: 55848847--55849011 Score: 269
Period size: 65 Copynumber: 2.5 Consensus size: 65
55848837 TATGTATAAT
* * *
55848847 ATTAATTAACTTATGTAATTTAAGTATAATATTAATGTAAGTTATGTAAT-TAATGTATAATATT
1 ATTAATTAAGTTATGTAATTTATGTATAATATTAATGCAAGTTATGTAATAT-ATGTATAATATT
55848911 A
65 A
* *
55848912 ATTAATTAAGTCATGTAATTTATGTATAATATTAATGCAAGTTCTGTAATATATGTATAATATTA
1 ATTAATTAAGTTATGTAATTTATGTATAATATTAATGCAAGTTATGTAATATATGTATAATATTA
55848977 ATTAATTAAGTTATGTAATTTATGTATAATATTAA
1 ATTAATTAAGTTATGTAATTTATGTATAATATTAA
55849012 ATAATCAAGT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
65 92 0.99
66 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (65 bp):
ATTAATTAAGTTATGTAATTTATGTATAATATTAATGCAAGTTATGTAATATATGTATAATATTA
Found at i:55849016 original size:21 final size:22
Alignment explanation
Indices: 55848992--55849036 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
55848982 TTAAGTTATG
55848992 TAAT-TTATGTATAATATTAAA
1 TAATATTATGTATAATATTAAA
55849013 TAATCAAGTTATGTATAATATTAA
1 TAAT--A-TTATGTATAATATTAA
55849037 TTTTTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
25 16 0.80
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
TAATATTATGTATAATATTAAA
Found at i:55849351 original size:43 final size:43
Alignment explanation
Indices: 55849302--55849677 Score: 449
Period size: 43 Copynumber: 8.8 Consensus size: 43
55849292 ACGTCGCTAA
* * *
55849302 CTTTAGCGGCGCTTTTACC-ACAAATGCCGCTAAAGACCAAGAT
1 CTTTAGCGGCGCTTTT-CCTACAAACGCCGCTAAAGACCATGAC
* * * *
55849345 CTTTAGCGGCGCTTTTCCTACAAATGCCACTAAAGACCAAGAT
1 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACCATGAC
* * * * **
55849388 CTTTAACGACGCTTCTCCTACAAACGCCGCTAAAAATTATGAC
1 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACCATGAC
* * *
55849431 CTTTAACGGCGCTTCTCCTACAATCGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACCATGAC
*
55849474 CTTTAGCGGCGCTTCTCCTACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACCATGAC
*
55849517 CTTTAGCGGCACTTTTCCTACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACCATGAC
*
55849560 CTTTAGCGGC-ATTTTCCTACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACCATGAC
* *
55849602 CTTTAGCGGCACTTTTCCCT-CAAACGCCGCTATAGA--ATAGAC
1 CTTTAGCGGCGCTTTT-CCTACAAACGCCGCTAAAGACCAT-GAC
** * *
55849644 CTTTAGCAACGCTTTTGAC-ACAGACGCCGCTAAA
1 CTTTAGCGGCGCTTTT-CCTACAAACGCCGCTAAA
55849678 AATATCTTTT
Statistics
Matches: 298, Mismatches: 30, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
41 2 0.01
42 72 0.24
43 221 0.74
44 3 0.01
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACCATGAC
Found at i:55854864 original size:20 final size:22
Alignment explanation
Indices: 55854839--55854887 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
55854829 ATAATCTAAA
*
55854839 CCCTAAACT-CTAACC-CGAAT
1 CCCTAAACTCCTAACCACGAAC
*
55854859 CCCT-AACTCCTAACCACTAAC
1 CCCTAAACTCCTAACCACGAAC
55854880 CCCTAAAC
1 CCCTAAAC
55854888 CTTATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 10 0.42
21 7 0.29
22 3 0.12
ACGTcount: A:0.35, C:0.45, G:0.02, T:0.18
Consensus pattern (22 bp):
CCCTAAACTCCTAACCACGAAC
Found at i:55855000 original size:29 final size:29
Alignment explanation
Indices: 55854940--55855000 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
55854930 TAAACCCTAA
*
55854940 CCTGACACTGAATCTATAAACCCCAAATC
1 CCTGACACTGAATCTATAAACCCCAAACC
* * * * *
55854969 CCTGACTCTTAATCTCTAACCCCCTAACC
1 CCTGACACTGAATCTATAAACCCCAAACC
55854998 CCT
1 CCT
55855001 AAATCACAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.41, G:0.05, T:0.25
Consensus pattern (29 bp):
CCTGACACTGAATCTATAAACCCCAAACC
Found at i:55855627 original size:40 final size:40
Alignment explanation
Indices: 55855577--55855713 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
55855567 TGGGCTTAGG
* *
55855577 TTTTTTGCGGCGTTTTTCCATAAAACGCCGCTAATGCTC-A
1 TTTTTAGCGGCGTTTTT-CATAAAGCGCCGCTAATGCTCAA
* * * *
55855617 TTTTTAGCGGCGCTTTACTTAAAGTGCCGCTAATGCTCAA
1 TTTTTAGCGGCGTTTTTCATAAAGCGCCGCTAATGCTCAA
* * * *
55855657 TCTTTAGCGGCGTGTTAT-GTAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGT-TTTTCATAAAGCGCCGCTAATGCTCAA
*
55855697 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
55855714 TTATCCAAAC
Statistics
Matches: 79, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
39 21 0.27
40 56 0.71
41 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCATAAAGCGCCGCTAATGCTCAA
Found at i:55858054 original size:90 final size:89
Alignment explanation
Indices: 55857901--55858228 Score: 377
Period size: 81 Copynumber: 3.8 Consensus size: 89
55857891 CCCAAACCCC
* *
55857901 ACCCCTAAACCCTAAACACTATTTAATATAT-AATTTAAAAAATACTAATTAATCTAAATCCTAA
1 ACCCCTAACCCCTAAACATTATTTAATATATAAATTTAAAAAATACTAATTAATCTAAATCCTAA
55857965 ACCCTAACTCGACCACGAATCACTA
66 ACCCTAACTCGACC-CGAATCACTA
*
55857990 ACCCCCAACCCCTAAACATTATTTAATATATAAATTTAAAAAATACTAATTAATCTAAATCCTAA
1 ACCCCTAACCCCTAAACATTATTTAATATATAAATTTAAAAAATACTAATTAATCTAAATCCTAA
55858055 ACCCTAACTCGACCCCGAAT--C--
66 ACCCTAACTCGA-CCCGAATCACTA
*
55858076 A---CTAACCCCTAAACATTATTTAATATATAAA--TAAAAAACACTAATTAATCTAAATCCTAA
1 ACCCCTAACCCCTAAACATTATTTAATATATAAATTTAAAAAATACTAATTAATCTAAATCCTAA
* *
55858136 ACCCCTAGCT-AACCC---T-A--A
66 A-CCCTAACTCGACCCGAATCACTA
* * * *
55858154 ATCCCTAACCCCTAAACATTATTTAATATTATATAATTTAAAATATATTAATTAGTCTAAA-CAC
1 ACCCCTAACCCCTAAACATTATTTAATA-TATA-AATTTAAAAAATACTAATTAATCTAAATC-C
*
55858218 TAAACTCTAAC
63 TAAACCCTAAC
55858229 CTAACACCGA
Statistics
Matches: 213, Mismatches: 13, Indels: 31
0.83 0.05 0.12
Matches are distributed among these distances:
77 1 0.00
78 1 0.00
80 3 0.01
81 54 0.25
82 11 0.05
83 31 0.15
84 6 0.03
85 24 0.11
86 1 0.00
88 1 0.00
89 28 0.13
90 50 0.23
91 2 0.01
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (89 bp):
ACCCCTAACCCCTAAACATTATTTAATATATAAATTTAAAAAATACTAATTAATCTAAATCCTAA
ACCCTAACTCGACCCGAATCACTA
Found at i:55858909 original size:113 final size:114
Alignment explanation
Indices: 55858710--55859415 Score: 875
Period size: 113 Copynumber: 6.3 Consensus size: 114
55858700 AGATAAAATG
* * * * * *
55858710 TTTTTGCGGCGC-TTTATAAAAAACACCGCTAAAGGCATCAGCATTAGCGGCGCTTATTCA-GAA
1 TTTTTGCGGCGCTTTTA-AAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTT-TACATAAA
*
55858773 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAAGC
64 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
*
55858824 -TTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
* * *
55858888 GCCACTAAAGACCCCAAAAACTTAGAAAACGGTGCCGTTGGGTTTAGGC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * **
55858937 TTTTTGCGGCGCTTTTGAAAAAACGCAGCTAAAGACCTTAGCATTAGCGGCGCTTT--ATAGATG
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATA-AAA
* *
55859000 TGCCGCTAAAGACCCCCAAAAACTCAGAAAATGGTGCCGTTGGGCTTAGGC
65 CGCCGCTAAAGA-CCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
55859051 TTTTTGCGGCGCATTTAAAAAAA-GCCGCTAAAGACCTGAACATTAGCGGCGCTTTACAT-AAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
* * *
55859114 GCCGCGAAAGACCCCGAAAACTCAGAAAACGGTGCCGTTGAGCTTAGGC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
** * *
55859163 --TTT---GCGC-TTTAAAAAAACGCCGCTAAAGATATGAGCATTAGCGACACTTTACATAAAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
* ** *
55859222 GCCACTAAAGACCCC-AAAACTCAGAAAACGGTGCCGTTGGATTTAGAC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * * * *
55859270 TTTTTGCGGTGCTTTTAAAACAACGCCACTAAAGACCTGAGTATTAGCAGCGCTTTTACA-GAAA
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGC-TTTACATAAAA
* * * *
55859334 CGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTTGTCTTTGTC
65 CGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
55859384 TTTCTGCGGCGCTTTTATAAAAACGCCGCTAA
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAA
55859416 TGCTTATTTT
Statistics
Matches: 510, Mismatches: 65, Indels: 34
0.84 0.11 0.06
Matches are distributed among these distances:
106 10 0.02
107 64 0.13
108 17 0.03
109 3 0.01
110 3 0.01
112 44 0.09
113 195 0.38
114 172 0.34
115 2 0.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (114 bp):
TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
Found at i:55859433 original size:39 final size:39
Alignment explanation
Indices: 55859389--55859517 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 39
55859379 TTGTCTTTCT
55859389 GCGGCGCTTTTATAAAAACGCCGCTAATGCTT-ATTTTTA
1 GCGGCG-TTTTATAAAAACGCCGCTAATGCTTGATTTTTA
* ** ** *
55859428 GCGGCGTTTGT-TACAAATCGCCGCTAATAATTGACCTTCA
1 GCGGCGTTT-TATA-AAAACGCCGCTAATGCTTGATTTTTA
* *
55859468 GCGGCGTTTTTATAGAAATGCCGCTACA-GCTTGATTTTTA
1 GCGGCG-TTTTATAAAAACGCCGCTA-ATGCTTGATTTTTA
*
55859508 GTGGCGTTTT
1 GCGGCGTTTT
55859518 CTGTCTAAAC
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
38 5 0.07
39 26 0.38
40 32 0.46
41 6 0.09
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (39 bp):
GCGGCGTTTTATAAAAACGCCGCTAATGCTTGATTTTTA
Found at i:55860122 original size:6 final size:6
Alignment explanation
Indices: 55860103--55860140 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
55860093 ATTTTTCAGG
*
55860103 TCATCT TCATTTT TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCA-TTT TCATTT TCATTT TCATTT TCATTT T
55860141 GGAGAAAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (6 bp):
TCATTT
Found at i:55860185 original size:63 final size:62
Alignment explanation
Indices: 55860108--55860235 Score: 202
Period size: 63 Copynumber: 2.0 Consensus size: 62
55860098 TCAGGTCATC
*
55860108 TTCATTTTTCATTTTCATTTTCATTTTCATTTTGGAGAAAACCACATTAATTTCCAAATGAT
1 TTCATTTTTCATTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGAT
* * * *
55860170 TTCATTTTTTCATTTTCATTTTCATTTTCATTTTGGAGAAAACTATAATCATTTTCAAATGAT
1 TTCA-TTTTTCATTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGAT
55860233 TTC
1 TTC
55860236 CCATTTCTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
62 4 0.07
63 56 0.93
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (62 bp):
TTCATTTTTCATTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGAT
Found at i:55860187 original size:6 final size:6
Alignment explanation
Indices: 55860176--55860203 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55860166 TGATTTCATT
55860176 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
55860204 GGAGAAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCA
Found at i:55860241 original size:57 final size:58
Alignment explanation
Indices: 55860117--55860252 Score: 148
Period size: 63 Copynumber: 2.2 Consensus size: 58
55860107 CTTCATTTTT
* *
55860117 CATTTTCATTTTCATTTTCATTTTGGAGAAAACCACATTAATTTCCAAATGATTTCATTTTTT
1 CATTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGATTTC-----TC
* * * *
55860180 CATTTTCATTTTCATTTTCATTTTGGAGAAAACTATAATCATTTTCAAATGATTTC-C
1 CATTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGATTTCTC
55860237 CATTTCTCCATTTTCA
1 CATTT-T-CATTTTCA
55860253 CCATTTCTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
57 5 0.08
58 1 0.02
59 8 0.12
63 51 0.78
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.49
Consensus pattern (58 bp):
CATTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGATTTCTC
Found at i:55868484 original size:18 final size:19
Alignment explanation
Indices: 55868463--55868501 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55868453 TTTGATTTAA
55868463 TTTTATAAT-ACTAATATT
1 TTTTATAATAACTAATATT
* *
55868481 TTTTATAGTAATTAATATT
1 TTTTATAATAACTAATATT
55868500 TT
1 TT
55868502 AAAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTATAATAACTAATATT
Found at i:55876200 original size:10 final size:10
Alignment explanation
Indices: 55876185--55876209 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55876175 ACTAACTATA
55876185 TGATCGAATC
1 TGATCGAATC
55876195 TGATCGAATC
1 TGATCGAATC
55876205 TGATC
1 TGATC
55876210 AGCAACTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (10 bp):
TGATCGAATC
Found at i:55878698 original size:75 final size:75
Alignment explanation
Indices: 55878629--55878792 Score: 188
Period size: 75 Copynumber: 2.2 Consensus size: 75
55878619 CAGATAACTT
* * * *
55878629 GCCACAAAGGCTTTCCAGATTATAACT-CACATAGGCTTTTTACATAACTTGTCACAATAACTTT
1 GCCACAAAGGCTTTCCAGATAAT-ACTCCACATAGGCTTTTCAAATAACTTGACACAATAACTTT
55878693 CCAGATAATAC
65 CCAGATAATAC
* * * * *
55878704 GCCATAATGGTTTTTCAGATAATACTCCACATAGGCTTTTCAAATAACTTGACACAA-AGGCTTT
1 GCCACAAAGGCTTTCCAGATAATACTCCACATAGGCTTTTCAAATAACTTGACACAATA-ACTTT
* *
55878768 CTAGACAATAC
65 CCAGATAATAC
*
55878779 GCCACATAGGCTTT
1 GCCACAAAGGCTTT
55878793 GTTTGGTTTA
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
74 4 0.06
75 68 0.94
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (75 bp):
GCCACAAAGGCTTTCCAGATAATACTCCACATAGGCTTTTCAAATAACTTGACACAATAACTTTC
CAGATAATAC
Found at i:55878743 original size:25 final size:25
Alignment explanation
Indices: 55878689--55878792 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 25
55878679 GTCACAATAA
* *
55878689 CTTTCCAGATAATACGCCATA-ATGG
1 CTTTTCAGATAATACGCCACATA-GG
* *
55878714 TTTTTCAGATAATACTCCACATAGG
1 CTTTTCAGATAATACGCCACATAGG
* * * *
55878739 CTTTTCAAATAACT-TGACACAAAGG
1 CTTTTCAGATAA-TACGCCACATAGG
*
55878764 C-TTTCTAGACAATACGCCACATAGG
1 CTTTTC-AGATAATACGCCACATAGG
55878789 CTTT
1 CTTT
55878793 GTTTGGTTTA
Statistics
Matches: 59, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
24 5 0.08
25 50 0.85
26 4 0.07
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (25 bp):
CTTTTCAGATAATACGCCACATAGG
Found at i:55882672 original size:14 final size:14
Alignment explanation
Indices: 55882650--55882682 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
55882640 GTGATTGATA
*
55882650 TTTCCTTTAATTTT
1 TTTCTTTTAATTTT
55882664 TTTCTTTTAATTTT
1 TTTCTTTTAATTTT
55882678 TTTCT
1 TTTCT
55882683 CTATGTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTTTAATTTT
Found at i:55883703 original size:15 final size:14
Alignment explanation
Indices: 55883683--55883715 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
55883673 ATTTTGTATG
55883683 TTATTTTAAATTTAT
1 TTATTTTAAATTT-T
55883698 TTATTTTAAATTTT
1 TTATTTTAAATTTT
55883712 TTAT
1 TTAT
55883716 ATGTTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTTTAAATTTT
Found at i:55883771 original size:26 final size:25
Alignment explanation
Indices: 55883742--55883819 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 25
55883732 GTGATGGAGG
55883742 TTATTTATTTTAAATTGCTGTGTATA
1 TTATTTATTTTAAATTG-TGTGTATA
* * * *
55883768 TTATTCATTTTAATTTGTTTTGCATA
1 TTATTTATTTTAAATTG-TGTGTATA
*
55883794 TTATTTACTTTAAAATTGTGT-TATA
1 TTATTTA-TTTTAAATTGTGTGTATA
55883819 T
1 T
55883820 ATTATGTCGT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
25 4 0.10
26 29 0.71
27 8 0.20
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.59
Consensus pattern (25 bp):
TTATTTATTTTAAATTGTGTGTATA
Found at i:55886574 original size:20 final size:20
Alignment explanation
Indices: 55886533--55886575 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
55886523 TTGTTTGGAA
**
55886533 CTTTTTCCAGGATTCTTGAT
1 CTTTTTCCAGGATTCTCCAT
*
55886553 CTTTTTCTAGGATTCTCCAT
1 CTTTTTCCAGGATTCTCCAT
55886573 CTT
1 CTT
55886576 AAAATATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.12, T:0.51
Consensus pattern (20 bp):
CTTTTTCCAGGATTCTCCAT
Found at i:55897564 original size:47 final size:47
Alignment explanation
Indices: 55897421--55897655 Score: 197
Period size: 44 Copynumber: 5.1 Consensus size: 47
55897411 TCATATAAGA
*
55897421 ATATTTATTATTAAGAATTTTATG-AATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
* **
55897467 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATT
* * * *
55897511 AAATTTATTATCAAGAATTTTATGAAATTACATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
* ** *
55897558 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAA-A
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATT-AT-TAAATT
* * * *
55897602 AAATTTATTATCAAGAATTTGATGAAATTATATATTATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
55897649 ATATTTA
1 ATATTTA
55897656 ATAATAATTA
Statistics
Matches: 144, Mismatches: 28, Indels: 33
0.70 0.14 0.16
Matches are distributed among these distances:
43 6 0.04
44 47 0.33
45 17 0.12
46 27 0.19
47 41 0.28
48 6 0.04
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
Found at i:55897575 original size:91 final size:91
Alignment explanation
Indices: 55897406--55897690 Score: 473
Period size: 91 Copynumber: 3.1 Consensus size: 91
55897396 ATGATTTTAG
* *
55897406 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATG-AATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
55897470 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
55897496 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTACATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
55897561 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* * *
55897587 TAAATTCATATAAAAAAATTTATTATCAAGAATTTGATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
* * *
55897652 TTTAATAATAATTATATTAAATAATA
66 TTTAATATTAATTATTTTAAATTATA
*
55897678 CAAATTCATATAA
1 TAAATTCATATAA
55897691 TTAAATTATA
Statistics
Matches: 183, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
90 37 0.20
91 146 0.80
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:55897683 original size:19 final size:17
Alignment explanation
Indices: 55897643--55897711 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
55897633 ATATTATTAT
*
55897643 TAAATTATATTTAATAA
1 TAAATTATATTAAATAA
55897660 T-AATTATATTAAATAA
1 TAAATTATATTAAATAA
55897676 TACAAATTCATA-T-AAT--
1 T--AAATT-ATATTAAATAA
*
55897692 TAAATTATATTTAATAA
1 TAAATTATATTAAATAA
55897709 TAA
1 TAA
55897712 TAATTTTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
13 3 0.07
14 6 0.14
15 3 0.07
16 16 0.37
17 4 0.09
18 3 0.07
19 5 0.12
20 3 0.07
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTATATTAAATAA
Found at i:55897729 original size:91 final size:91
Alignment explanation
Indices: 55897406--55897729 Score: 318
Period size: 91 Copynumber: 3.6 Consensus size: 91
55897396 ATGATTTTAG
* *
55897406 TAAATTCATATAAGAATATT-TA-TTAT--TAAGAATTTTATG-AATTATATATCATTATTAAAT
1 TAAATTCATATAA-AA-ATTATATTTATAATAATAA-TTTATGAAATTAT-TATTATTATTAAAT
55897466 TATATTTAATATTAATTATTTTAAATTATA
62 TATATTTAATATTAATTATTTTAAATTATA
* * *
55897496 TAAATTCATATAAGAAAATT-TA-TTATCAAGAAT--TTTATGAAATTACATATCATTATTAAAT
1 TAAATTCATAT-A-AAAATTATATTTAT-AATAATAATTTATGAAATTA-TTATTATTATTAAAT
55897557 TATATTTAATATTAATTATTTTAAATTATA
62 TATATTTAATATTAATTATTTTAAATTATA
* *
55897587 TAAATTCATATAAAAA--A-ATTTATTATCAAGAATTTGATGAAATTATATATTATTATTAAATT
1 TAAATTCATATAAAAATTATATTTATAAT-AATAATTT-ATGAAATTAT-TATTATTATTAAATT
* * *
55897649 ATATTTAATAATAATTATATTAAATAATA
63 ATATTTAATATTAATTATTTTAAATTATA
*
55897678 CAAATTCATATAATTAAATTATATTTAATAATAATAATTT-T-AAATT-TTATTA
1 TAAATTCATATAA--AAATTATATTT-ATAATAATAATTTATGAAATTATTATTA
55897730 AATCATATAT
Statistics
Matches: 200, Mismatches: 14, Indels: 39
0.79 0.06 0.15
Matches are distributed among these distances:
87 2 0.01
88 6 0.03
89 4 0.02
90 30 0.15
91 129 0.64
92 2 0.01
93 10 0.05
94 1 0.00
95 1 0.00
96 11 0.05
97 4 0.02
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAAAATTATATTTATAATAATAATTTATGAAATTATTATTATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:55897736 original size:49 final size:52
Alignment explanation
Indices: 55897637--55897782 Score: 167
Period size: 49 Copynumber: 2.8 Consensus size: 52
55897627 AATTATATAT
* * *
55897637 TATT-ATTAAATTATATTTAATAATAATTATATTAAATAATA-CAAATTC-A
1 TATTAATTAAATTATATTTAATAATAATTATTTTAAATTATATTAAATTCAA
* *
55897686 TA-TAATTAAATTATATTTAATAATAATAATTTTAAATTTTATTAAA-TCATA
1 TATTAATTAAATTATATTTAATAATAATTATTTTAAATTATATTAAATTCA-A
* *
55897737 TATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATT
1 TA--TTAATTAAATTATATTTAATAATAATTATTTTAAATTATATT
55897783 TTATACTATC
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
48 1 0.01
49 37 0.46
50 3 0.04
51 3 0.04
54 37 0.46
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (52 bp):
TATTAATTAAATTATATTTAATAATAATTATTTTAAATTATATTAAATTCAA
Found at i:55897777 original size:54 final size:55
Alignment explanation
Indices: 55897688--55898027 Score: 199
Period size: 54 Copynumber: 5.8 Consensus size: 55
55897678 CAAATTCATA
* * *
55897688 TAATTAAATTATATTTAATAATAATAAT-TTTAAATTTTATTAAATCATATATTT
1 TAATTAAAATATATTTAATAATAATTATATTAAAATTTTATTAAATCATATATTT
* *
55897742 TAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATACTATCATATATTAT
1 TAATTAAAATATATTTAATAATAATTATATTAAAATT-T-TATTA-A--ATCATATATT-T
* * * *
55897802 GATTTTAGGAAAT-TCATATAAGAAT-ATTGATTATTAAGAATTTTATTAAATCATATATTT
1 TA-ATTA--AAATAT-ATTTAATAATAATT-A-TATTAA-AATTTTATTAAATCATATATTT
* * *
55897862 TAATTAAAATATATTGAATAATAATTATCTTAAATTATATTT-TATAGTATCATATATTAT
1 TAATTAAAATATATTTAATAATAATTATATTAAA--AT-TTTAT-TA-AATCATATATT-T
* * * * * *
55897922 GATTTGAGTAAAT-TCATATAACAAT-ATTGATTATTAAGATTTTTATTAAATTATATATTT
1 TAATT-A--AAATAT-ATTTAATAATAATT-A-TATTAA-AATTTTATTAAATCATATATTT
* * * *
55897982 TAATTAAAATATATTTAATAACAATTATGTTAAAATATGATTAAAT
1 TAATTAAAATATATTTAATAATAATTATATTAAAATTTTATTAAAT
55898028 TATTTATTAC
Statistics
Matches: 219, Mismatches: 35, Indels: 63
0.69 0.11 0.20
Matches are distributed among these distances:
54 33 0.15
55 12 0.05
56 14 0.06
57 28 0.13
58 13 0.06
59 24 0.11
60 12 0.05
61 23 0.11
62 13 0.06
63 28 0.13
64 10 0.05
65 5 0.02
66 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (55 bp):
TAATTAAAATATATTTAATAATAATTATATTAAAATTTTATTAAATCATATATTT
Found at i:55897852 original size:120 final size:120
Alignment explanation
Indices: 55897720--55898015 Score: 495
Period size: 120 Copynumber: 2.5 Consensus size: 120
55897710 AATAATTTTA
55897720 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTT-AAATTATATTT
* *
55897784 TATACTATCATATATTATGATTTTAGGAAATTCATATAAGAATATTGATTATTAAG
65 TATACTATCATATATTATGATTTGAGGAAATTCATATAACAATATTGATTATTAAG
*
55897840 AATTTTATTAAATCATATATTTTAATTAAAATATATTGAATAATAATTATCTTAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAATTATATTTT
* *
55897905 ATAGTATCATATATTATGATTTGAGTAAATTCATATAACAATATTGATTATTAAG
66 ATACTATCATATATTATGATTTGAGGAAATTCATATAACAATATTGATTATTAAG
* * * *
55897960 ATTTTTATTAAATTATATATTTTAATTAAAATATATTTAATAACAATTATGTTAAA
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAA
55898016 ATATGATTAA
Statistics
Matches: 165, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
120 163 0.99
121 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAATTATATTTT
ATACTATCATATATTATGATTTGAGGAAATTCATATAACAATATTGATTATTAAG
Found at i:55897855 original size:61 final size:60
Alignment explanation
Indices: 55897790--55897980 Score: 162
Period size: 61 Copynumber: 3.2 Consensus size: 60
55897780 ATTTTATACT
55897790 ATCATATATTATGATTTTAGGAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTTA-GAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
* * * * * *
55897851 ATCATATATT-TTA-ATTA-AAA-T-ATAT-TGAATAATAATTATCTTAAATTATATTTTA-TAG
1 ATCATATATTATGATTTTAGAAATTCATATAAGAATATTGATTA--TT-AA-GA-ATTTTATTA-
*
55897909 T
60 A
* * *
55897910 ATCATATATTATGATTTGAGTAAATTCATATAACAATATTGATTATTAAGATTTTTATTAA
1 ATCATATATTATGATTTTAG-AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
*
55897971 ATTATATATT
1 ATCATATATT
55897981 TTAATTAAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 28
0.68 0.12 0.19
Matches are distributed among these distances:
54 10 0.10
55 4 0.04
56 3 0.03
57 5 0.05
58 3 0.03
59 19 0.19
60 4 0.04
61 26 0.27
62 3 0.03
63 5 0.05
64 3 0.03
65 4 0.04
66 9 0.09
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (60 bp):
ATCATATATTATGATTTTAGAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
Found at i:55897977 original size:59 final size:59
Alignment explanation
Indices: 55897794--55897977 Score: 133
Period size: 59 Copynumber: 3.1 Consensus size: 59
55897784 TATACTATCA
* * * *
55897794 TATATTATGATTTTAGGAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAACAATATTGATTATTAAGATTTTTATTAAAT
* * * * * * * * * * * *
55897853 CATATATTTTAATTAAAATATATTGA-ATAATAATTATCTTA-AATT-ATATTTTATAGTATCA-
1 --TATATTATGATTTAAGTAAATTCATATAACAA-TAT-TGATTATTAAGATTTT-TATTA-AAT
*
55897914 TATATTATGATTTGAGTAAATTCATATAACAATATTGATTATTAAGATTTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAACAATATTGATTATTAAGATTTTTATTAAAT
55897973 TATAT
1 TATAT
55897978 ATTTTAATTA
Statistics
Matches: 87, Mismatches: 28, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
58 3 0.03
59 32 0.37
60 23 0.26
61 26 0.30
62 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (59 bp):
TATATTATGATTTAAGTAAATTCATATAACAATATTGATTATTAAGATTTTTATTAAAT
Found at i:55897987 original size:18 final size:18
Alignment explanation
Indices: 55897960--55897995 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55897950 GATTATTAAG
* *
55897960 ATTTTTATTAAATTATAT
1 ATTTTAATTAAAATATAT
55897978 ATTTTAATTAAAATATAT
1 ATTTTAATTAAAATATAT
55897996 TTAATAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTAATTAAAATATAT
Found at i:55901204 original size:12 final size:12
Alignment explanation
Indices: 55901175--55901224 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
55901165 AACTAATTAA
**
55901175 GTTATTATTGCT
1 GTTATTATTATT
*
55901187 GATATTATTATT
1 GTTATTATTATT
*
55901199 GTTATTATTATG
1 GTTATTATTATT
*
55901211 GGTATTATTATT
1 GTTATTATTATT
55901223 GT
1 GT
55901225 GTTGGTTTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.24, C:0.02, G:0.16, T:0.58
Consensus pattern (12 bp):
GTTATTATTATT
Found at i:55906454 original size:16 final size:17
Alignment explanation
Indices: 55906433--55906470 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
55906423 TTTTATATGG
*
55906433 ATTTTACT-TTTATTTT
1 ATTTTACTATGTATTTT
55906449 ATTTTACTAATGTATTTT
1 ATTTTACT-ATGTATTTT
55906467 ATTT
1 ATTT
55906471 AAATAAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTACTATGTATTTT
Found at i:55923555 original size:4 final size:4
Alignment explanation
Indices: 55923546--55923573 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
55923536 TGTTGAAAAT
55923546 GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA
55923574 AGAGCTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:55926245 original size:16 final size:15
Alignment explanation
Indices: 55926217--55926251 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
55926207 AAACCATGAA
*
55926217 AAAAGAAAGGAAAAC
1 AAAAGAAAAGAAAAC
55926232 AAAAGAAAAAGAAAAC
1 AAAAG-AAAAGAAAAC
55926248 AAAA
1 AAAA
55926252 AAATCACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAC
Found at i:55926856 original size:17 final size:17
Alignment explanation
Indices: 55926834--55926869 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
55926824 TAAATGAATA
55926834 TTCAA-TAAATTAATAAT
1 TTCAATTAAA-TAATAAT
55926851 TTCAATTAAATAATAAT
1 TTCAATTAAATAATAAT
55926868 TT
1 TT
55926870 TTCGGTCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TTCAATTAAATAATAAT
Found at i:55928867 original size:27 final size:27
Alignment explanation
Indices: 55928820--55928883 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
55928810 AAATGTTCTC
**
55928820 TAAATTAAT-AAATATTAATTTATTGA
1 TAAATTAATAAAATATTAATTTATCAA
*
55928846 TAAATTAATAAAATATTCATTTATCAA
1 TAAATTAATAAAATATTAATTTATCAA
*
55928873 TAAACTAATAA
1 TAAATTAATAA
55928884 CCTCGATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (27 bp):
TAAATTAATAAAATATTAATTTATCAA
Found at i:55929801 original size:31 final size:29
Alignment explanation
Indices: 55929737--55929805 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
55929727 ACGAAAACGT
** *
55929737 AAGTGACTAAAATGTAACATTTCAAACAT
1 AAGTGACTAAAATGTAACATGACAAACAA
*
55929766 AAGTGACTAAAATGTAACCTGAGACAAACAA
1 AAGTGACTAAAATGTAACAT--GACAAACAA
55929797 AAGTGACTA
1 AAGTGACTA
55929806 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATGACAAACAA
Found at i:55930478 original size:14 final size:14
Alignment explanation
Indices: 55930443--55930484 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
55930433 GGCCCACCAT
55930443 AAACCAAA-AAATA
1 AAACCAAATAAATA
*
55930456 ATA--AAATAAATA
1 AAACCAAATAAATA
55930468 AAACCAAATAAATA
1 AAACCAAATAAATA
55930482 AAA
1 AAA
55930485 GTTCAAGTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 3 0.12
12 7 0.29
13 2 0.08
14 12 0.50
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (14 bp):
AAACCAAATAAATA
Found at i:55936735 original size:106 final size:106
Alignment explanation
Indices: 55936592--55936816 Score: 362
Period size: 106 Copynumber: 2.1 Consensus size: 106
55936582 ACCTCTTTTT
** * * *
55936592 AGGATTAAGTAG-GTTGCCAATGGTGATATTGTGCTTAAGGTGTCTATGCTCGGTTTTAATTTGA
1 AGGATTAAGTAGAGTTGAAAATAGTGATATTGTCCTTAAGGTGTCTATGCTCGGTTTTAACTTGA
* *
55936656 TTTTTATCTCCCTACTTTGAGGAGAGCTCACGAAATTTGAC
66 ATTTTATCTCCCTACTTCGAGGAGAGCTCACGAAATTTGAC
*
55936697 AGGATTAAGTAGAGTTGAAAATAGTGATATTGTCCTTAAGGTGTCTATGCTTGGTTTTAACTTGA
1 AGGATTAAGTAGAGTTGAAAATAGTGATATTGTCCTTAAGGTGTCTATGCTCGGTTTTAACTTGA
55936762 ATTTTATCTCCCTACTTCGAGGAGAGCTCACGAAATTTGAC
66 ATTTTATCTCCCTACTTCGAGGAGAGCTCACGAAATTTGAC
*
55936803 GGGATTAAGTAGAG
1 AGGATTAAGTAGAG
55936817 ATAAATTGAT
Statistics
Matches: 110, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
105 12 0.11
106 98 0.89
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (106 bp):
AGGATTAAGTAGAGTTGAAAATAGTGATATTGTCCTTAAGGTGTCTATGCTCGGTTTTAACTTGA
ATTTTATCTCCCTACTTCGAGGAGAGCTCACGAAATTTGAC
Found at i:55940797 original size:9 final size:9
Alignment explanation
Indices: 55940779--55940809 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55940769 TTTGGTTAAA
*
55940779 AATTAACCG
1 AATTACCCG
55940788 AATTACCCG
1 AATTACCCG
55940797 AATTACCCG
1 AATTACCCG
55940806 AATT
1 AATT
55940810 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTACCCG
Found at i:55940839 original size:17 final size:17
Alignment explanation
Indices: 55940817--55940879 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
55940807 ATTGAATCAC
55940817 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
55940834 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
55940854 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
55940871 TACATAATT
1 TACATAATT
55940880 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:55940854 original size:37 final size:37
Alignment explanation
Indices: 55940808--55940882 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
55940798 ATTACCCGAA
*
55940808 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
55940845 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
55940882 T
1 T
55940883 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:55941088 original size:44 final size:45
Alignment explanation
Indices: 55941020--55941118 Score: 173
Period size: 45 Copynumber: 2.2 Consensus size: 45
55941010 AGAGTTAGAC
*
55941020 TTTAGTTTTATTTTTATTGAGTT-GGTAATTGGGTAGACTTTAGT
1 TTTAGTTTTAGTTTTATTGAGTTGGGTAATTGGGTAGACTTTAGT
*
55941064 TTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGTAGACTTTAGT
1 TTTAGTTTTAGTTTTATTGAGTTGGGTAATTGGGTAGACTTTAGT
55941109 TTTAGTTTTA
1 TTTAGTTTTA
55941119 TTGGGTTGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
44 21 0.40
45 31 0.60
ACGTcount: A:0.19, C:0.02, G:0.24, T:0.55
Consensus pattern (45 bp):
TTTAGTTTTAGTTTTATTGAGTTGGGTAATTGGGTAGACTTTAGT
Found at i:55941109 original size:39 final size:39
Alignment explanation
Indices: 55941015--55941135 Score: 154
Period size: 39 Copynumber: 3.0 Consensus size: 39
55941005 ACTTAAGAGT
* *
55941015 TAGACTTTAGTTTTATTTTTATTGAGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
55941053 TAGACTTTAGTTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGAC------TTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
55941098 TAGACTTTAGTTTTAGTTTTATTGGGTTGAGTAATTGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGG
55941136 ATTGGGTTGG
Statistics
Matches: 73, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
38 5 0.07
39 32 0.44
44 21 0.29
45 15 0.21
ACGTcount: A:0.20, C:0.02, G:0.26, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:55941150 original size:17 final size:16
Alignment explanation
Indices: 55941118--55941168 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 16
55941108 TTTTAGTTTT
55941118 ATTGGGTTGAGTAATTGG
1 ATTGGGTTG-GTAATT-G
55941136 ATTGGGTTGGTAATTG
1 ATTGGGTTGGTAATTG
55941152 AGTTGGGTTGGATAATT
1 A-TTGGGTTGG-TAATT
55941169 TTATTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.06
17 15 0.48
18 14 0.45
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (16 bp):
ATTGGGTTGGTAATTG
Found at i:55942098 original size:23 final size:23
Alignment explanation
Indices: 55942064--55942107 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
55942054 TTCTACCCAT
55942064 AATTATCATCTCAACA-CAAAGG
1 AATTATCATCTCAACATCAAAGG
* *
55942086 AATTGATCTTCTCTACATCAAA
1 AATT-ATCATCTCAACATCAAA
55942108 CCAAATCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (23 bp):
AATTATCATCTCAACATCAAAGG
Found at i:55944453 original size:6 final size:6
Alignment explanation
Indices: 55944442--55944483 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
55944432 CAAGAGCAGT
* *
55944442 ACCAGC ACCAGC ACCAAC ACCAAC ACCAAC ACCAAC ACCAAC
1 ACCAAC ACCAAC ACCAAC ACCAAC ACCAAC ACCAAC ACCAAC
55944484 CCCCTCCCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.45, C:0.50, G:0.05, T:0.00
Consensus pattern (6 bp):
ACCAAC
Found at i:55947026 original size:17 final size:16
Alignment explanation
Indices: 55946993--55947028 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
55946983 CCCACTCATA
55946993 TTATTTTTTTAAATAT
1 TTATTTTTTTAAATAT
*
55947009 TTATTTTATTTTAATAT
1 TTATTTT-TTTAAATAT
55947026 TTA
1 TTA
55947029 ATAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTTTTTAAATAT
Found at i:55950209 original size:3 final size:3
Alignment explanation
Indices: 55950201--55950229 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55950191 ATGGGAAGCT
55950201 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55950230 TTGGAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:55956431 original size:4 final size:4
Alignment explanation
Indices: 55956422--55956462 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
55956412 TACCTCTTTT
55956422 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA T
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA T
55956463 CAGTATTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (4 bp):
TTCA
Found at i:55963765 original size:44 final size:45
Alignment explanation
Indices: 55963435--55963926 Score: 295
Period size: 44 Copynumber: 10.9 Consensus size: 45
55963425 TAGAGAATTT
* * * * *
55963435 TATA-TCCTTGAAGTTACAGTGGA-TCATATTAAAGCTACAAATCT
1 TATACTCCCTGAAGTTGCAGTGGAGT-AGATTGAAGCTACAAATCC
* * * *
55963479 TAT-CTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTACAAATCT
1 TATACTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCC
* * * *
55963523 TAT-CTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCT
1 TATACTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCC
* * *
55963567 TAT-CTCCCTAAAGTTGCTA-TGGAGCAGATTGAAACTACAAATCC
1 TATACTCCCTGAAGTTGC-AGTGGAGTAGATTGAAGCTACAAATCC
* * * * *
55963611 TGTAC-CCCTAAAGTTGCAGTTG-GTCGAATTGAAGCCAGAACAACAAAT-C
1 TATACTCCCTGAAGTTGCAGTGGAGTAG-ATTG-A---AG--CTACAAATCC
* * * * *
55963660 T-TACCTCCCTAAACTTGCAATGGAGTAGATTGAAGCTACGAATCT
1 TATA-CTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCC
*
55963705 TA-ACTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCC
1 TATACTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCC
* * * * *
55963749 TATAC-CCCTCAAGTTGTAGTGG-GTTGGATTGAATCTACCATAGAGAACC
1 TATACTCCCTGAAGTTGCAGTGGAG-TAGATTGAAGCTA-C--A-A-ATCC
* *
55963798 T-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACGAAT-C
1 TATA-CTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCC
* * * *
55963842 TCAGT--TCCTTAAAGTTGCAGTGGAGTAGATTGAAACTACAATTCGC
1 T-A-TACTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATC-C
* *
55963888 -ATAC-CCCTGAAGTTGTAGTGG-GTTAGAATGAAGCTACAA
1 TATACTCCCTGAAGTTGCAGTGGAG-TAGATTGAAGCTACAA
55963927 CGAAAAATCT
Statistics
Matches: 360, Mismatches: 53, Indels: 70
0.75 0.11 0.14
Matches are distributed among these distances:
43 6 0.02
44 269 0.75
45 9 0.03
46 4 0.01
47 2 0.01
48 6 0.02
49 10 0.03
50 50 0.14
51 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (45 bp):
TATACTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCC
Found at i:55963868 original size:182 final size:180
Alignment explanation
Indices: 55963377--55963926 Score: 464
Period size: 182 Copynumber: 3.0 Consensus size: 180
55963367 CAGTGAAATC
* * * * ** *
55963377 ACAAATCCTACACCCCTGAAGTTGCAGTGGGTCGGGTTGAAGTC-ACCATAGAGAATTTTATATC
1 ACAAATCCTATACCCCTAAAGTTGTAGTGGGTCGGATTGAA-TCTACCATAGAGAACCTTATCTC
* * * * * *
55963441 CTTGAAGTTACAGTGGATCATATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAATGGAGCAG
65 CCTGAAGTTGCAGTGGATCAGATTGAAGCTACAAATCTTAT-TCCCTAAAGTTGCAATGGAGTAG
* * * * *
55963506 ATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
129 ATTGAAGCTAC-AATCTTAACTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCT
* * * * *
55963559 ATAAATCTTAT-CTCCCTAAAGTTGCTA-TGGAG-CAGATTGAAACTA-C--A-A-ATCCTGTA-
1 ACAAATCCTATAC-CCCTAAAGTTG-TAGTGG-GTCGGATTGAATCTACCATAGAGAACCT-TAT
* * * *
55963615 C-CCCTAAAGTTGCAGTTGG-TC-GAATTGAAGCCAGAACAACAAATCTTACCTCCCTAAACTTG
62 CTCCCTGAAGTTGCAG-TGGATCAG-ATTG-A---AG--CTACAAATCTTA-TTCCCTAAAGTTG
55963677 CAATGGAGTAGATTGAAGCTACGAATCTTAACTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCT
118 CAATGGAGTAGATTGAAGCTAC-AATCTTAACTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCT
* *
55963741 ACAAATCCTATACCCCTCAAGTTGTAGTGGGTTGGATTGAATCTACCATAGAGAACCTTATCTCC
1 ACAAATCCTATACCCCTAAAGTTGTAGTGGGTCGGATTGAATCTACCATAGAGAACCTTATCTCC
* * * * *
55963806 CTGAAGTTGCAGTGGAGCAGATTGAAGCTACGAATCTCAGTTCCTTAAAGTTGCAGTGGAGTAGA
66 CTGAAGTTGCAGTGGATCAGATTGAAGCTACAAATCTTA-TTCCCTAAAGTTGCAATGGAGTAGA
* ** *
55963871 TTGAAACTACAATTCGCATAC-CCCTGAAGTTGTAGTGG-GTTAGAATGAAGCT
130 TTGAAGCTACAA-TCTTA-ACTCCCTGAAGTTGTAGTGGAG-TAGATTGAAGCT
55963923 ACAA
1 ACAA
55963927 CGAAAAATCT
Statistics
Matches: 290, Mismatches: 49, Indels: 58
0.73 0.12 0.15
Matches are distributed among these distances:
176 16 0.06
177 6 0.02
178 3 0.01
179 1 0.00
180 2 0.01
181 9 0.03
182 213 0.73
183 6 0.02
184 2 0.01
185 1 0.00
186 3 0.01
187 9 0.03
188 18 0.06
189 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (180 bp):
ACAAATCCTATACCCCTAAAGTTGTAGTGGGTCGGATTGAATCTACCATAGAGAACCTTATCTCC
CTGAAGTTGCAGTGGATCAGATTGAAGCTACAAATCTTATTCCCTAAAGTTGCAATGGAGTAGAT
TGAAGCTACAATCTTAACTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCT
Found at i:55963873 original size:94 final size:94
Alignment explanation
Indices: 55963703--55963880 Score: 218
Period size: 94 Copynumber: 1.9 Consensus size: 94
55963693 AGCTACGAAT
* * * *
55963703 CTTAACTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCCTATACCCCTCAAGTTGTAG
1 CTTAACTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCCTATACCCCTAAAGTTGCAG
* *
55963768 TGGGTTGGATTGAATCTACCATAGAGAAC
66 TGGGTTAGATTGAAACTACCATAGAGAAC
* * * *
55963797 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACGAAT-CTCAGT-TCCTTAAAGTTGC
1 CTTAACTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCCT-A-TACCCCTAAAGTTGC
55963860 AGTGGAG-TAGATTGAAACTAC
64 AGTGG-GTTAGATTGAAACTAC
55963881 AATTCGCATA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
93 2 0.03
94 67 0.94
95 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (94 bp):
CTTAACTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCCTATACCCCTAAAGTTGCAG
TGGGTTAGATTGAAACTACCATAGAGAAC
Found at i:55963970 original size:138 final size:138
Alignment explanation
Indices: 55963517--55963971 Score: 456
Period size: 138 Copynumber: 3.3 Consensus size: 138
55963507 TTAAAGCTAC
* * * ** * *
55963517 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAAATCTTATCTCCCTAAAGTT
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGTAGATTGAAGCTACGAATCTCAACTCCCTAAAGTT
* * * * *
55963582 GCTA-TGGAGCAGATTGAAACTACAAATCCTGTACCCCTAAAGTTGCAGTTGG-TCGAATTGAAG
66 GC-AGTGGAGTAGATTGAAACTACAAATCCTATACCCCTAAAGTTGTAGTGGGTTAGAA-TGAAG
* *
55963645 CCAGAAC-AA
129 CTACAACGAA
* * * * *
55963654 CAAATCTTACCTCCCTAAACTTGCAATGGAGTAGATTGAAGCTACGAATCTTAACTCCCTGAAGT
1 -AAATCTTATCTCCCTGAAGTTGCAATGGAGTAGATTGAAGCTACGAATCTCAACTCCCTAAAGT
* * * * * *
55963719 TGTAGTGGAGTAGATTGAAGCTACAAATCCTATACCCCTCAAGTTGTAGTGGGTTGGATTGAATC
65 TGCAGTGGAGTAGATTGAAACTACAAATCCTATACCCCTAAAGTTGTAGTGGGTTAGAATGAAGC
55963784 TACCATA-G-A
130 TA-CA-ACGAA
* * * * ** *
55963793 GAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACGAATCTCAGTTCCTTAAAGTT
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGTAGATTGAAGCTACGAATCTCAACTCCCTAAAGTT
* *
55963858 GCAGTGGAGTAGATTGAAACTACAATTCGC-ATACCCCTGAAGTTGTAGTGGGTTAGAATGAAGC
66 GCAGTGGAGTAGATTGAAACTACAAATC-CTATACCCCTAAAGTTGTAGTGGGTTAGAATGAAGC
55963922 TACAACGAA
130 TACAACGAA
** * *
55963931 AAATCTTATCTCTTTGAAGTTGGAAAGGAGTAGGA-TGAAGC
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGTA-GATTGAAGC
55963972 CGTGATACCA
Statistics
Matches: 259, Mismatches: 49, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
136 1 0.00
137 4 0.02
138 245 0.95
139 8 0.03
140 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (138 bp):
AAATCTTATCTCCCTGAAGTTGCAATGGAGTAGATTGAAGCTACGAATCTCAACTCCCTAAAGTT
GCAGTGGAGTAGATTGAAACTACAAATCCTATACCCCTAAAGTTGTAGTGGGTTAGAATGAAGCT
ACAACGAA
Found at i:55970051 original size:41 final size:41
Alignment explanation
Indices: 55969994--55970143 Score: 237
Period size: 41 Copynumber: 3.7 Consensus size: 41
55969984 TTTAACATAT
* * *
55969994 TCACCGGCATTTAGCCTGCTAAGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* * *
55970035 TCACCGACACTTAGCCTGCTAGGTTTATAATCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
55970076 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
55970117 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
55970144 AAGTCTGAAA
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:55970151 original size:82 final size:80
Alignment explanation
Indices: 55969992--55970180 Score: 247
Period size: 82 Copynumber: 2.3 Consensus size: 80
55969982 AATTTAACAT
* *
55969992 ATTCACCGGCATTTAGCCTGCTAAGCTTATAGCCTGATTCAGATCACCGACACTTAGCCTGCTAG
1 ATTCACCGGCA-TTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAG
** * *
55970057 GTTTATAATCTGATTCAG
65 ACTTATAATCTGA--AAA
*
55970075 A-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAG
1 ATTCACCGGCA-TTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAG
55970139 ACTTA-AAGTCTGAAAA
65 ACTTATAA-TCTGAAAA
55970155 ATTCACCGGCATTAAGCCTGCTAGGC
1 ATTCACCGGCATT-AGCCTGCTAGGC
55970181 GCTTAGCCTA
Statistics
Matches: 95, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
80 4 0.04
81 23 0.24
82 67 0.71
83 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (80 bp):
ATTCACCGGCATTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAGA
CTTATAATCTGAAAA
Found at i:55970689 original size:12 final size:12
Alignment explanation
Indices: 55970661--55970693 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
55970651 AGCTCATCAA
55970661 ATATACA-ATAG
1 ATATACATATAG
*
55970672 ATATACATATAT
1 ATATACATATAG
55970684 ATATACATAT
1 ATATACATAT
55970694 TCGAACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
ATATACATATAG
Found at i:55970763 original size:114 final size:114
Alignment explanation
Indices: 55970487--55970913 Score: 754
Period size: 112 Copynumber: 3.8 Consensus size: 114
55970477 ACACAAGTGC
*
55970487 ATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAACTCATCAAATA
1 ATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATA
55970552 TACAATAGATATAC--ATATATATACATATTCGAACTTCATTTATGTGT
66 TACAATAGATATACATATATATATACATATTCGAACTTCATTTATGTGT
55970599 ATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATA
1 ATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATA
55970664 TACAATAGATATACATATATATATACATATTCGAACTTCATTTATGTGT
66 TACAATAGATATACATATATATATACATATTCGAACTTCATTTATGTGT
*
55970713 ATATAAATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATA
1 ATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATA
* *
55970778 TACAATAGATATACATATACATATACATATTCGAACTTCATTTA--TGC
66 TACAATAGATATACATATATATATACATATTCGAACTTCATTTATGTGT
* * *
55970825 ATATATATATCATTCATACTTAACTAATTTCAATTCGTATACTTTTAATTATAGCTCATCAAATG
1 ATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATA
*
55970890 TACAATAGTTATACATATATATAT
66 TACAATAGATATACATATATATAT
55970914 GCTGATTTAA
Statistics
Matches: 303, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
112 163 0.54
114 140 0.46
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.41
Consensus pattern (114 bp):
ATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATA
TACAATAGATATACATATATATATACATATTCGAACTTCATTTATGTGT
Found at i:55970797 original size:6 final size:6
Alignment explanation
Indices: 55970775--55970807 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
55970765 AGCTCATCAA
*
55970775 ATATAC A-ATAG ATATAC ATATAC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATAT
55970808 TCGAACTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:55970858 original size:226 final size:225
Alignment explanation
Indices: 55970487--55970913 Score: 757
Period size: 226 Copynumber: 1.9 Consensus size: 225
55970477 ACACAAGTGC
*
55970487 ATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAACTCATCAAATA
1 ATATAAATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAACTCATCAAATA
*
55970552 TACAATAGATATACATATATATACATATTCGAACTTCATTTATGTGTATATATATAACATTCATA
66 TACAATAGATATACATATATATACATATTCGAACTTCATTTA-GTGCATATATATAACATTCATA
55970617 CTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAGATATACATAT
130 CTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAGATATACATAT
55970682 ATATATACATATTCGAACTTCATTTATGTGT
195 ATATATACATATTCGAACTTCATTTATGTGT
*
55970713 ATATAAATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATA
1 ATATAAATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAACTCATCAAATA
*
55970778 TACAATAGATATACATATACATATACATATTCGAACTTCATTTA-TGCATATATATATCATTCAT
66 TACAATAGATATACATAT--ATATACATATTCGAACTTCATTTAGTGCATATATATAACATTCAT
* * *
55970842 ACTTAACTAATTTCAATTCGTATACTTTTAATTATAGCTCATCAAATGTACAATAGTTATACATA
129 ACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAGATATACATA
55970907 TATATAT
194 TATATAT
55970914 GCTGATTTAA
Statistics
Matches: 192, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
226 168 0.88
228 24 0.12
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.41
Consensus pattern (225 bp):
ATATAAATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAACTCATCAAATA
TACAATAGATATACATATATATACATATTCGAACTTCATTTAGTGCATATATATAACATTCATAC
TTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAGATATACATATA
TATATACATATTCGAACTTCATTTATGTGT
Found at i:55971900 original size:13 final size:13
Alignment explanation
Indices: 55971882--55971906 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55971872 CAATCAAATG
55971882 CACACAAAATAAA
1 CACACAAAATAAA
55971895 CACACAAAATAA
1 CACACAAAATAA
55971907 TATTAAATTA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:55973957 original size:3 final size:3
Alignment explanation
Indices: 55973949--55973981 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
55973939 AAATTCAAAC
55973949 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55973982 TAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55974754 original size:16 final size:17
Alignment explanation
Indices: 55974733--55974766 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
55974723 ACGAAATAAC
*
55974733 TTAAAATCTT-AAAATT
1 TTAAAATATTGAAAATT
55974749 TTAAAATATTGAAAATT
1 TTAAAATATTGAAAATT
55974766 T
1 T
55974767 ATGAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTAAAATATTGAAAATT
Found at i:55975512 original size:7 final size:7
Alignment explanation
Indices: 55975500--55975525 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55975490 ATTAGTTTTG
55975500 TTTATAA
1 TTTATAA
55975507 TTTATAA
1 TTTATAA
55975514 TTTATAA
1 TTTATAA
55975521 TTTAT
1 TTTAT
55975526 TTTTGATAAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTATAA
Found at i:55983139 original size:22 final size:22
Alignment explanation
Indices: 55983114--55983155 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55983104 GAGGAATAAA
*
55983114 AATTGAGTGAGAA-TTAAAAGGG
1 AATTGAGAGA-AATTTAAAAGGG
55983136 AATTGAGAGAAATTTAAAAG
1 AATTGAGAGAAATTTAAAAG
55983156 AGCTTTGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (22 bp):
AATTGAGAGAAATTTAAAAGGG
Found at i:55983363 original size:52 final size:52
Alignment explanation
Indices: 55983299--55983402 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
55983289 GGAGCCGTTG
* *
55983299 GGATTTTTACCATTGGGGTGTGGGGTAGTCATTATGGAAAACGCTTCCAGCT
1 GGATTTTCACCATTGGGGTGTGGGGTAGCCATTATGGAAAACGCTTCCAGCT
*
55983351 GGATTTTCACCATTGGGGTGTGGGGTAGCCATTATGGAAAATGCTTCCAGCT
1 GGATTTTCACCATTGGGGTGTGGGGTAGCCATTATGGAAAACGCTTCCAGCT
55983403 AGATGCGTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (52 bp):
GGATTTTCACCATTGGGGTGTGGGGTAGCCATTATGGAAAACGCTTCCAGCT
Found at i:55983477 original size:28 final size:29
Alignment explanation
Indices: 55983421--55983478 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
55983411 TTTTATTTTT
*
55983421 TCGACCTAATTCAGTAAATTTTGAAAAAA
1 TCGACCTAATCCAGTAAATTTTGAAAAAA
* *
55983450 TCGACCTAATCCAGTAATTTTTCAAAAAA
1 TCGACCTAATCCAGTAAATTTTGAAAAAA
55983479 AAACAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (29 bp):
TCGACCTAATCCAGTAAATTTTGAAAAAA
Found at i:55993768 original size:3 final size:3
Alignment explanation
Indices: 55993760--55993852 Score: 168
Period size: 3 Copynumber: 31.0 Consensus size: 3
55993750 ATCTAGGAGC
*
55993760 CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
55993808 CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
55993853 TAACAAATGA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:55996005 original size:113 final size:114
Alignment explanation
Indices: 55995854--55996504 Score: 725
Period size: 114 Copynumber: 5.7 Consensus size: 114
55995844 TGATTTCCAT
* *
55995854 AAAGCGCCGC-AAAATACCTAAGCCCAACGACGTCGTTTT-TCGAGCTTTCGGGGATTTAGCGGC
1 AAAGCGCCACAAAAAAACCTAAGCCCAACGACGTCGTTTTCT-GAGCTTTCGGGGATTTAGCGGC
* * *
55995917 GTTTTTAAGAAAGCGCCGCTAATGCTCAAGGCTTTCGCGGCGTTTTCGAG
65 GTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
* * *
55995967 AAAGCGCCACAAAAAAACCAAAGCCC-AGGACGTCGTTTTCTGAGCTTTCGGGGATTTAGTGGCG
1 AAAGCGCCACAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
* *
55996031 TTTTTAAGTAAA-CGCTGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
66 TTTTTAAG-AAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
* * * * *
55996080 AAAGCACCGA-AAAAATAA-CTAAGCCCAACGATGCCGTTTTCTGAGCTTTCGAGGATTTAGTGG
1 AAAGCGCC-ACAAAAA-AACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTCGGGGATTTAGCGG
*
55996143 CGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
64 CGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
* * * *
55996194 AAAGTGCCACAAAAAAACCAAAGCCCAACGACG-CTGTTTTTTGAGCTTTCGGGGATTTAGTGGC
1 AAAGCGCCACAAAAAAACCTAAGCCCAACGACGTC-GTTTTCTGAGCTTTCGGGGATTTAGCGGC
* * * *
55996258 GTTTTTAAGTAAGCGCCACTAATG-TACAGTGCTTTAGTGGCGTTTTTGA-
65 GTTTTTAAGAAAGCGCCGCTAATGCT-CAGGGCTTTAGCGGCGTTTTTGAG
* ** * * *
55996307 AGAAGCGTCACAACAAAAA-CTAAGCCCAACGACACCATTTTCTGA-CAATTCGTGGGCTTTAGC
1 A-AAGCGCCACAA-AAAAACCTAAGCCCAACGACGTCGTTTTCTGAGC-TTTCG-GGGATTTAGC
* * * *
55996370 GGCG-TTTTAAGAATGCGCTGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGTTG
62 GGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG-AG
** * * * ** *
55996423 -AAGCGCTGCAAAAAAACCTAAGCCCAACGGCGTCGTTTTCTAAACTTTTAGGGCTTTAGCGGCG
1 AAAGCGCCACAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
*
55996487 TTTTTAAAAAAGCGCCGC
66 TTTTTAAGAAAGCGCCGC
55996505 AAAAACTTTT
Statistics
Matches: 457, Mismatches: 59, Indels: 43
0.82 0.11 0.08
Matches are distributed among these distances:
113 130 0.28
114 307 0.67
115 20 0.04
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (114 bp):
AAAGCGCCACAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
Found at i:55996861 original size:14 final size:15
Alignment explanation
Indices: 55996833--55996865 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
55996823 AACGTTTATA
55996833 GATTATGGAATTAGG
1 GATTATGGAATTAGG
55996848 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
55996862 GATT
1 GATT
55996866 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:55996902 original size:14 final size:15
Alignment explanation
Indices: 55996870--55996919 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
55996860 GGGATTCTGG
55996870 TTTAAGGGTT-GTA-A
1 TTTAAGGGTTAG-AGA
55996884 TTTAAGGGTTAGAGA
1 TTTAAGGGTTAGAGA
* *
55996899 -TTAAGAGTTAGGGA
1 TTTAAGGGTTAGAGA
55996913 TTTAAGG
1 TTTAAGG
55996920 TTTTATGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 23 0.77
15 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (15 bp):
TTTAAGGGTTAGAGA
Found at i:55997024 original size:80 final size:82
Alignment explanation
Indices: 55996939--55997095 Score: 221
Period size: 80 Copynumber: 1.9 Consensus size: 82
55996929 TTTGGTGTTA
* * * *
55996939 GGTTAGGATTTAGGGTTTAGATTAATTAGTGTGTTTTAATTT-T-TATGAAATAAGGTTTAAGGG
1 GGTTAGGATTTAAGGTTTAGATTAATTAATAT-TTTTAATTTGTATATGAAATAAGATTTAAGGG
55997002 TTAG-GGTTAGGGATTTG
65 TTAGTGGTTAGGGATTTG
* * *
55997019 GGTTAGGATTTAAGGTTTTGATTAATTAATATTTTTAATTTGTATATTAAATAAGATTTAGGGGT
1 GGTTAGGATTTAAGGTTTAGATTAATTAATATTTTTAATTTGTATATGAAATAAGATTTAAGGGT
55997084 TAGTGGTTAGGG
66 TAGTGGTTAGGG
55997096 GTTAGTGGTT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
79 9 0.13
80 29 0.43
81 21 0.31
82 8 0.12
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (82 bp):
GGTTAGGATTTAAGGTTTAGATTAATTAATATTTTTAATTTGTATATGAAATAAGATTTAAGGGT
TAGTGGTTAGGGATTTG
Found at i:55997100 original size:21 final size:21
Alignment explanation
Indices: 55997076--55997121 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
55997066 TAAATAAGAT
*
55997076 TTAG-GGGTTAGTGGTTAGGGG
1 TTAGTGGGTTAG-GGTTAAGGG
*
55997097 TTAGTGGTTTAGGGTTAAGGG
1 TTAGTGGGTTAGGGTTAAGGG
55997118 TTAG
1 TTAG
55997122 AAGTTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (21 bp):
TTAGTGGGTTAGGGTTAAGGG
Found at i:55997113 original size:14 final size:15
Alignment explanation
Indices: 55997075--55997110 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
55997065 TTAAATAAGA
55997075 TTTAGGGGTTAGTGG
1 TTTAGGGGTTAGTGG
55997090 -TTAGGGGTTAGTGG
1 TTTAGGGGTTAGTGG
55997104 TTTAGGG
1 TTTAGGG
55997111 TTAAGGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.14, C:0.00, G:0.47, T:0.39
Consensus pattern (15 bp):
TTTAGGGGTTAGTGG
Found at i:55997542 original size:21 final size:21
Alignment explanation
Indices: 55997499--55997566 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
55997489 GGTTTTGACT
* * **
55997499 TTTAGGGTTTGGGATTTGGGG
1 TTTAGAGTTTGGGGTTTATGG
55997520 TTTAGAGTTTGGGGTTTATGG
1 TTTAGAGTTTGGGGTTTATGG
*
55997541 TTT-G-GTTTTGTGGTTTATGG
1 TTTAGAG-TTTGGGGTTTATGG
55997561 TTTAGA
1 TTTAGA
55997567 ATTTATGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 17 0.44
21 21 0.54
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (21 bp):
TTTAGAGTTTGGGGTTTATGG
Found at i:55998594 original size:147 final size:147
Alignment explanation
Indices: 55998415--55998739 Score: 345
Period size: 147 Copynumber: 2.2 Consensus size: 147
55998405 TACGTTGCTA
* * * ** * * *
55998415 TTAGTGGTGCTTTCCATCAAAA-GCCACAAAATTGTAATAA-TGTTTATTGAAATGTTGTCGTTT
1 TTAGTGGCGCTTTAC-TCAAAACGCCGCAAAATTGTAATAACT-TTTATAAAAATGCTGCCATTT
** * *
55998478 TGTCTATGGTATTAGTGGCGTTTTTAT-GAAAACGCCACAAGCTTGAGTTAACTGTTGGGGAAAC
64 TGTAAATGGTATTAGTGGCGTTTTT-TCGAAAACGCCACAAGCTTGAGGTAACTGTTGAGGAAAC
*
55998542 GACTTCG-TTTGAGCTTATAG
128 GACTGCGTTTTGA-CTTATAG
**
55998562 TTAGTGGCGCTTTACTCAAAACGCCGCAAAATTGTTCTAACTTTTATAAAAATGCTGCCATTTTG
1 TTAGTGGCGCTTTACTCAAAACGCCGCAAAATTGTAATAACTTTTATAAAAATGCTGCCATTTTG
* ** * * * *
55998627 TAAATGTTATTAGTGGCGTTTTTTCGAAAACGCCACGGGTTTGAGGTAAGTGTTGATGAAGCGAC
66 TAAATGGTATTAGTGGCGTTTTTTCGAAAACGCCACAAGCTTGAGGTAACTGTTGAGGAAACGAC
*
55998692 TGCGTTTTGATTTATAG
131 TGCGTTTTGACTTATAG
* *
55998709 TTAGTGGCGCTTCAGTTC-AAACGCCGCAAAA
1 TTAGTGGCGCTTTA-CTCAAAACGCCGCAAAA
55998740 ATGTTTTAAC
Statistics
Matches: 148, Mismatches: 25, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
146 7 0.05
147 133 0.90
148 8 0.05
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (147 bp):
TTAGTGGCGCTTTACTCAAAACGCCGCAAAATTGTAATAACTTTTATAAAAATGCTGCCATTTTG
TAAATGGTATTAGTGGCGTTTTTTCGAAAACGCCACAAGCTTGAGGTAACTGTTGAGGAAACGAC
TGCGTTTTGACTTATAG
Found at i:55998755 original size:147 final size:147
Alignment explanation
Indices: 55998487--55998755 Score: 355
Period size: 147 Copynumber: 1.8 Consensus size: 147
55998477 TTGTCTATGG
* * *
55998487 TATTAGTGGCGTTTTTATGAAAACGCCACAAGCTTGAGTTAACTGTTGGGGAAACGACTTCGTTT
1 TATTAGTGGCGTTTTTATGAAAACGCCACAAGCTTGAGGTAACTGTTGAGGAAACGACTGCGTTT
* * *
55998552 GAGCTTATAGTTAGTGGCGCTTTACTCAAAACGCCGCAAAATTGTTCTAACTTTTATAAAAATGC
66 GAGCTTATAGTTAGTGGCGCTTCACTCAAAACGCCGCAAAAATGTTCTAACATTTATAAAAATGC
55998617 TGCCATTTTGTAAATGT
131 TGCCATTTTGTAAATGT
** * * * *
55998634 TATTAGTGGCGTTTTT-TCGAAAACGCCACGGGTTTGAGGTAAGTGTTGATGAAGCGACTGCGTT
1 TATTAGTGGCGTTTTTAT-GAAAACGCCACAAGCTTGAGGTAACTGTTGAGGAAACGACTGCG-T
* * *
55998698 TTGA-TTTATAGTTAGTGGCGCTTCAGTTC-AAACGCCGCAAAAATGTTTTAACATTTAT
64 TTGAGCTTATAGTTAGTGGCGCTTCA-CTCAAAACGCCGCAAAAATGTTCTAACATTTAT
55998756 TGATACGAGG
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
146 1 0.01
147 96 0.92
148 7 0.07
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (147 bp):
TATTAGTGGCGTTTTTATGAAAACGCCACAAGCTTGAGGTAACTGTTGAGGAAACGACTGCGTTT
GAGCTTATAGTTAGTGGCGCTTCACTCAAAACGCCGCAAAAATGTTCTAACATTTATAAAAATGC
TGCCATTTTGTAAATGT
Found at i:56000232 original size:15 final size:15
Alignment explanation
Indices: 56000212--56000243 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
56000202 AGGGTTGAAG
56000212 TATTTGGTACTAATT
1 TATTTGGTACTAATT
56000227 TATTTGGTACTAATT
1 TATTTGGTACTAATT
56000242 TA
1 TA
56000244 CTGTTATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.53
Consensus pattern (15 bp):
TATTTGGTACTAATT
Found at i:56001044 original size:20 final size:19
Alignment explanation
Indices: 56000999--56001054 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 19
56000989 AAATAACTTA
*
56000999 TTAATATATATTTTAA-AG
1 TTAATATATATTTTAATAT
56001017 TTAATATATATTTTCAATAT
1 TTAATATATATTTT-AATAT
*
56001037 TTATTATAT-TTTTAATAT
1 TTAATATATATTTTAATAT
56001055 ATTTTTACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 19 0.56
19 6 0.18
20 9 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTAATATATATTTTAATAT
Found at i:56001221 original size:13 final size:13
Alignment explanation
Indices: 56001205--56001369 Score: 136
Period size: 13 Copynumber: 12.5 Consensus size: 13
56001195 TTACTAAAAT
*
56001205 TTACTTTAATATA
1 TTACTTAAATATA
*
56001218 TTACTTGAATATA
1 TTACTTAAATATA
*
56001231 TTACTTAAATAAA
1 TTACTTAAATATA
*
56001244 TTACTTAAATACA
1 TTACTTAAATATA
*
56001257 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
56001271 TTGGTTAAATTTA
1 TTACTTAAATATA
*
56001284 TTACTTAAATATG
1 TTACTTAAATATA
*
56001297 TTACTTAAATACA
1 TTACTTAAATATA
*
56001310 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
56001324 TTGTTTAAATTTA
1 TTACTTAAATATA
*
56001337 TTACTTAAATATG
1 TTACTTAAATATA
*
56001350 TTACTTAAATACA
1 TTACTTAAATATA
56001363 TTACTTA
1 TTACTTA
56001370 CTAAAATTTA
Statistics
Matches: 118, Mismatches: 28, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
12 6 0.05
13 96 0.81
14 10 0.08
15 6 0.05
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:56001286 original size:53 final size:53
Alignment explanation
Indices: 56001229--56001378 Score: 273
Period size: 53 Copynumber: 2.8 Consensus size: 53
56001219 TACTTGAATA
**
56001229 TATTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
*
56001282 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGTTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
56001335 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
56001379 AAGTATATAT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 94 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (53 bp):
TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
Found at i:56001562 original size:29 final size:32
Alignment explanation
Indices: 56001513--56001688 Score: 84
Period size: 33 Copynumber: 5.5 Consensus size: 32
56001503 TACGTACAAG
*
56001513 AACTTACATAACTTATTCAT-A-TT-TATATA
1 AACTTACATAACTTATACATAACTTATATATA
*
56001542 AACTTACATAAC-TATCACATAAACTTATATGTA
1 AACTTACATAACTTAT-ACAT-AACTTATATATA
* * *
56001575 AACTTACATAA-TACATAACTTATAATTTTTTTTATATA
1 AACTTACATAACT-TAT-AC--ATAA---CTTATATATA
* * *
56001613 AACTTACATAAC----ACATTACTTACATATT
1 AACTTACATAACTTATACATAACTTATATATA
* *
56001641 AACTTACATAAGTTATCTACA-AGCTTATATATA
1 AACTTACATAACTTA--TACATAACTTATATATA
*
56001674 AACTTGCATAACTTA
1 AACTTACATAACTTA
56001689 CGTAATAACA
Statistics
Matches: 109, Mismatches: 19, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
28 20 0.18
29 15 0.14
31 4 0.04
32 2 0.02
33 39 0.36
34 7 0.06
35 2 0.02
36 2 0.02
38 18 0.17
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (32 bp):
AACTTACATAACTTATACATAACTTATATATA
Found at i:56001735 original size:9 final size:9
Alignment explanation
Indices: 56001703--56002039 Score: 280
Period size: 9 Copynumber: 38.8 Consensus size: 9
56001693 ATAACATAAC
56001703 AACTTACAT
1 AACTTACAT
56001712 AA--TACAT
1 AACTTACAT
* *
56001719 AGCATACAT
1 AACTTACAT
56001728 AACTTACAT
1 AACTTACAT
*
56001737 AA--TACAA
1 AACTTACAT
56001744 AACTTACAT
1 AACTTACAT
*
56001753 AACTTAAAT
1 AACTTACAT
* *
56001762 ATCTTACAC
1 AACTTACAT
56001771 AACTTACAT
1 AACTTACAT
*
56001780 AACCTACAT
1 AACTTACAT
56001789 AA--TACATTT
1 AACTTACA--T
56001798 AACTTACAT
1 AACTTACAT
56001807 AACTTACAT
1 AACTTACAT
*
56001816 AA--TACAA
1 AACTTACAT
56001823 AACTTACAT
1 AACTTACAT
*
56001832 AACTTAAAT
1 AACTTACAT
* *
56001841 ATCTTACAC
1 AACTTACAT
56001850 AACTTACAT
1 AACTTACAT
*
56001859 AACCTACAT
1 AACTTACAT
56001868 AA--TACATTT
1 AACTTACA--T
56001877 AACTTACAT
1 AACTTACAT
56001886 AACTTACAT
1 AACTTACAT
56001895 AACTTACAT
1 AACTTACAT
*
56001904 AATACATA-AT
1 -A-ACTTACAT
56001914 AACTTAC--
1 AACTTACAT
56001921 AACTTACAT
1 AACTTACAT
*
56001930 AACATACAT
1 AACTTACAT
* **
56001939 TACTTTGAT
1 AACTTACAT
56001948 AACTTACAT
1 AACTTACAT
56001957 AACTTACAT
1 AACTTACAT
*
56001966 AA--TACAC
1 AACTTACAT
56001973 AACTTACAT
1 AACTTACAT
* *
56001982 AGCTTACTT
1 AACTTACAT
56001991 AA--TACAT
1 AACTTACAT
56001998 AACTTACAT
1 AACTTACAT
56002007 AACTT--AT
1 AACTTACAT
*
56002014 ACACGTACAT
1 A-ACTTACAT
56002024 AACTTACAT
1 AACTTACAT
*
56002033 AATTTAC
1 AACTTAC
56002040 TTAATACATA
Statistics
Matches: 262, Mismatches: 40, Indels: 52
0.74 0.11 0.15
Matches are distributed among these distances:
7 48 0.18
8 7 0.03
9 189 0.72
10 6 0.02
11 12 0.05
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:56001806 original size:79 final size:79
Alignment explanation
Indices: 56001707--56001987 Score: 365
Period size: 79 Copynumber: 3.7 Consensus size: 79
56001697 CATAACAACT
* *
56001707 TACATAATACA--TAGCATACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACA
1 TACATAATACATTTAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACA
56001770 CAACTTACATAACC
66 CAACTTACATAACC
56001784 TACATAATACATTTAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACA
1 TACATAATACATTTAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACA
56001849 CAACTTACATAACC
66 CAACTTACATAACC
*
56001863 TACATAATACATTTAACTTACATAACTTACATAACTTACATAA--TACATAA--T--A-A-CTT-
1 TACATAATACATTTAACTTACATAACTTACATAA--TACAAAACTTACATAACTTAAATATCTTA
*
56001919 -ACAACTTACATAACA
64 CACAACTTACATAACC
* * *
56001934 TACAT--TACTTTGATAACTTACATAACTTACATAATACACAACTTACATAGCTTA
1 TACATAATACATT--TAACTTACATAACTTACATAATACAAAACTTACATAACTTA
56001988 CTTAATACAT
Statistics
Matches: 186, Mismatches: 7, Indels: 25
0.85 0.03 0.11
Matches are distributed among these distances:
69 11 0.06
71 46 0.25
73 4 0.02
74 1 0.01
75 1 0.01
77 12 0.06
79 105 0.56
81 6 0.03
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (79 bp):
TACATAATACATTTAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACA
CAACTTACATAACC
Found at i:56001981 original size:71 final size:68
Alignment explanation
Indices: 56001848--56002035 Score: 181
Period size: 71 Copynumber: 2.7 Consensus size: 68
56001838 AATATCTTAC
* *
56001848 ACAACTTACATAACCTACATAATACATT-TAACTTACATAACTTACATAACTTACATAATACATA
1 ACAACTTACATAACATACAT--TAC-TTATAACTTACATAACTTACATAA--TACACAATACATA
56001912 -ATAACTT
61 GATAACTT
56001919 ACAACTTACATAACATACATTACTTTGATAACTTACATAACTTACATAATACACAACTTACATAG
1 ACAACTTACATAACATACATTAC-TT-ATAACTTACATAACTTACATAATACACAA--TACATAG
* *
56001984 CTTACTT
62 ATAACTT
* * *
56001991 --AA--TACATAACTTACATAACTTATACACGTACATAACTTACATAAT
1 ACAACTTACATAACATACATTACTTATA-ACTTACATAACTTACATAAT
56002036 TTACTTAATA
Statistics
Matches: 103, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
66 3 0.03
67 21 0.20
68 15 0.15
69 11 0.11
70 2 0.02
71 46 0.45
72 5 0.05
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (68 bp):
ACAACTTACATAACATACATTACTTATAACTTACATAACTTACATAATACACAATACATAGATAA
CTT
Found at i:56001987 original size:25 final size:25
Alignment explanation
Indices: 56001876--56002047 Score: 123
Period size: 25 Copynumber: 6.6 Consensus size: 25
56001866 ATAATACATT
*
56001876 TAACTTACATAACTTACATAACTTACA
1 TAACTTACATAA--TACACAACTTACA
56001903 TAA--TACATAATAACTTACAACTTACA
1 TAACTTACATAAT-AC--ACAACTTACA
* * ** *
56001929 TAACATACATTACTTTGATAACTTACA
1 TAACTTACA-TA-ATACACAACTTACA
56001956 TAACTTACATAATACACAACTTACA
1 TAACTTACATAATACACAACTTACA
* * *
56001981 TAGCTTACTTAATACATAACTTACA
1 TAACTTACATAATACACAACTTACA
* * * *
56002006 TAACTTATACACGTACATAACTTACA
1 TAACTTACATA-ATACACAACTTACA
* *
56002032 TAATTTACTTAATACA
1 TAACTTACATAATACA
56002048 TAAATATATA
Statistics
Matches: 114, Mismatches: 23, Indels: 18
0.74 0.15 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.02
25 50 0.44
26 34 0.30
27 20 0.18
28 4 0.04
29 2 0.02
30 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (25 bp):
TAACTTACATAATACACAACTTACA
Found at i:56004076 original size:21 final size:21
Alignment explanation
Indices: 56004050--56004122 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
56004040 TACAACTTAG
*
56004050 AGCAGAGGC-GACAGCGAGGGA
1 AGCAGAGGCTG-CAGCGAGAGA
56004071 AGCAGAGGCTGCAGCGAGAGA
1 AGCAGAGGCTGCAGCGAGAGA
*
56004092 AGCAGAGGCTGCAGTGAGAGA
1 AGCAGAGGCTGCAGCGAGAGA
*
56004113 AACAGAGGCT
1 AGCAGAGGCT
56004123 CAAAAGAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
21 47 0.98
22 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.42, T:0.05
Consensus pattern (21 bp):
AGCAGAGGCTGCAGCGAGAGA
Found at i:56004736 original size:22 final size:21
Alignment explanation
Indices: 56004691--56004736 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
56004681 TTTTGTGGCG
**
56004691 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAAC
56004712 CTAAAAAAGCGCCGCTAAAAAC
1 CTAAAAAA-CGCCGCTAAAAAC
56004734 CTA
1 CTA
56004737 TTTTTGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.46, C:0.28, G:0.15, T:0.11
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAAC
Found at i:56005867 original size:20 final size:22
Alignment explanation
Indices: 56005824--56005869 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
56005814 AAGAGTAGAT
56005824 ATTATCTTATATTAGTTATAAA
1 ATTATCTTATATTAGTTATAAA
* *
56005846 ATTATTTTA-ATTA-TTATTAA
1 ATTATCTTATATTAGTTATAAA
56005866 ATTA
1 ATTA
56005870 CATTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 4 0.18
22 8 0.36
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTATCTTATATTAGTTATAAA
Found at i:56011583 original size:51 final size:51
Alignment explanation
Indices: 56011510--56011645 Score: 157
Period size: 51 Copynumber: 2.7 Consensus size: 51
56011500 TGGAAACATG
*
56011510 ATCTTAAAAGAT-TTGATATTATAATCTTAGAGATCTTAGATATGATATGGA
1 ATCTTAAAAGATATT-ATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* * ** * * *
56011561 ATCTTATAAGATATTATTTTATAAGATTACATATCTTAGATAAGATATGTA
1 ATCTTAAAAGATATTATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* * *
56011612 ATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 ATCTTAAAAGATATTATATTATAATCTTAGAGAT
56011646 TTGATGGTAG
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
51 66 0.97
52 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (51 bp):
ATCTTAAAAGATATTATATTATAATCTTAGAGATCTTAGATAAGATATGGA
Found at i:56013496 original size:96 final size:96
Alignment explanation
Indices: 56013332--56013619 Score: 450
Period size: 96 Copynumber: 3.0 Consensus size: 96
56013322 TCCGAGGAAG
* * * * * * * * *
56013332 TCTGTTATCGATGGGAATGATCGAGCAAATACGGAGCCCAAGAAGCTTGGTTTGAGCAAGGGAAA
1 TCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGGTAA
56013397 AGCCGAAGCCAAGAGGGCAAAGAGGAGCAAA
66 AGCCGAAGCCAAGAGGGCAAAGAGGAGCAAA
56013428 TCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGGTAA
1 TCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGGTAA
*
56013493 AGCCGAAGCCAAGAGGGCAAAGAGGAGCAAG
66 AGCCGAAGCCAAGAGGGCAAAGAGGAGCAAA
* *
56013524 TCTGTCATCAAAGGAAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGGTAA
1 TCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGGTAA
**
56013589 AGCCGAAGCCAAGAGGGTTAAGAGGAGCAAA
66 AGCCGAAGCCAAGAGGGCAAAGAGGAGCAAA
56013620 AAGAAGCGAG
Statistics
Matches: 177, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 177 1.00
ACGTcount: A:0.36, C:0.18, G:0.33, T:0.12
Consensus pattern (96 bp):
TCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGGTAA
AGCCGAAGCCAAGAGGGCAAAGAGGAGCAAA
Found at i:56014587 original size:51 final size:51
Alignment explanation
Indices: 56014523--56014658 Score: 173
Period size: 51 Copynumber: 2.7 Consensus size: 51
56014513 TGGAAACATG
*
56014523 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGGA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* * * ** * * *
56014574 ATCTTATAAGATATTATTTTATAAGATTACATATCTTAGATAAGATATGTA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* *
56014625 ATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 ATCTTAAAAGATATGATATTATAATCTTAGAGAT
56014659 TTGATGGTAG
Statistics
Matches: 68, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40
Consensus pattern (51 bp):
ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
Found at i:56027758 original size:64 final size:64
Alignment explanation
Indices: 56027657--56027776 Score: 231
Period size: 64 Copynumber: 1.9 Consensus size: 64
56027647 GGACTACCTG
*
56027657 AGGAGCTGAAAGATTTTAGGCGGTTGTTAGATCAATGCTCAGAAGCCAATGTTAGTACTGCCTA
1 AGGAGCTAAAAGATTTTAGGCGGTTGTTAGATCAATGCTCAGAAGCCAATGTTAGTACTGCCTA
56027721 AGGAGCTAAAAGATTTTAGGCGGTTGTTAGATCAATGCTCAGAAGCCAATGTTAGT
1 AGGAGCTAAAAGATTTTAGGCGGTTGTTAGATCAATGCTCAGAAGCCAATGTTAGT
56027777 TACTTAATCT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (64 bp):
AGGAGCTAAAAGATTTTAGGCGGTTGTTAGATCAATGCTCAGAAGCCAATGTTAGTACTGCCTA
Found at i:56028866 original size:24 final size:24
Alignment explanation
Indices: 56028834--56028886 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
56028824 TTAGCAAACC
* * *
56028834 TGCACCTCTGGACGTACCTCTGGT
1 TGCACCTCTAGACGTACATCTAGT
*
56028858 TGCACCTCTAGATGTACATCTAGT
1 TGCACCTCTAGACGTACATCTAGT
56028882 TGCAC
1 TGCAC
56028887 ATTCTATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (24 bp):
TGCACCTCTAGACGTACATCTAGT
Found at i:56030586 original size:18 final size:18
Alignment explanation
Indices: 56030563--56030599 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
56030553 CGAAGAAACA
56030563 TCATCATCCTCATCGTCC
1 TCATCATCCTCATCGTCC
*
56030581 TCATCATCGTCATCGTCC
1 TCATCATCCTCATCGTCC
56030599 T
1 T
56030600 TTTTGCAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.41, G:0.08, T:0.35
Consensus pattern (18 bp):
TCATCATCCTCATCGTCC
Found at i:56036675 original size:15 final size:15
Alignment explanation
Indices: 56036657--56036688 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
56036647 CATTTTACTA
*
56036657 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
56036672 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
56036687 TT
1 TT
56036689 TGCATGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:56048719 original size:36 final size:36
Alignment explanation
Indices: 56048672--56048744 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
56048662 CATATGCTAA
* *
56048672 TTATGATCAATGGCCCACTTATCCTTTAAGTTTTTT
1 TTATGATCAATGGCCCACTGATCCTCTAAGTTTTTT
*
56048708 TTATGATCAATGGCCTACTGATCCTCTAAGTTTTTT
1 TTATGATCAATGGCCCACTGATCCTCTAAGTTTTTT
56048744 T
1 T
56048745 GTATTTAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (36 bp):
TTATGATCAATGGCCCACTGATCCTCTAAGTTTTTT
Found at i:56051926 original size:23 final size:21
Alignment explanation
Indices: 56051870--56051946 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
56051860 TACGACACAT
* * *
56051870 AAGTACCTGAAACGACACACG
1 AAGTGCCTGATACAACACACG
56051891 AAGTGCCTGATACAACACACG
1 AAGTGCCTGATACAACACACG
* * * **
56051912 AGGTGCTTGACATACGACACATA
1 AAGTGCCTG--ATACAACACACG
56051935 AAGTGCCTGATA
1 AAGTGCCTGATA
56051947 TACGACACAT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 28 0.64
23 16 0.36
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (21 bp):
AAGTGCCTGATACAACACACG
Found at i:56051949 original size:23 final size:22
Alignment explanation
Indices: 56051859--56051965 Score: 94
Period size: 23 Copynumber: 4.9 Consensus size: 22
56051849 CCTGATCAGT
*
56051859 ATACGACACAT-AAGTACCTGA
1 ATACGACACATAAAGTGCCTGA
**
56051880 A-ACGACACACGAAGTGCCTG-
1 ATACGACACATAAAGTGCCTGA
* ** * *
56051900 ATACAACACACGAGGTGCTTGA
1 ATACGACACATAAAGTGCCTGA
56051922 CATACGACACATAAAGTGCCTGA
1 -ATACGACACATAAAGTGCCTGA
*
56051945 TATACGACACATATAGTGCCT
1 -ATACGACACATAAAGTGCCT
56051966 AATCGGCAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
20 9 0.13
21 25 0.36
23 36 0.51
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGA
Found at i:56054718 original size:36 final size:36
Alignment explanation
Indices: 56054637--56054707 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
56054627 TTATATAAAT
* * *
56054637 ACATATACTTTCATAAACTTCCATTCACTTGAATTA
1 ACATATACATCCATAAACTTCCATTCAATTGAATTA
**
56054673 ACATATACATCCATAAACTTTTATTCAATTGAATT
1 ACATATACATCCATAAACTTCCATTCAATTGAATT
56054708 GACAATTACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (36 bp):
ACATATACATCCATAAACTTCCATTCAATTGAATTA
Found at i:56065624 original size:41 final size:42
Alignment explanation
Indices: 56065508--56065624 Score: 143
Period size: 41 Copynumber: 2.8 Consensus size: 42
56065498 TTGTATAAAA
* *
56065508 CACCGGCATAAAGCCTGCTAGGCACAAAGCCTG-ATACATTT
1 CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAATACATTT
* *
56065549 CATCGGCA-CAAAGCCTGCTAGGCATAAAGTCTGAATTA-A-TT
1 CACCGGCATC-AAGCCTGCTAGGCATAAAGCCTGAA-TACATTT
*
56065590 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAA
1 CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAA
56065625 AATCTCAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
41 60 0.92
42 3 0.05
43 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (42 bp):
CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAATACATTT
Found at i:56065831 original size:64 final size:64
Alignment explanation
Indices: 56065710--56065831 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 64
56065700 TCGAACCATA
* * *
56065710 CACATATGTATGTAAAATTCATAAATTAAATTCAGCTCAAGAACTTTATAACCTATATTTGAAT
1 CACATATGTATATAAAATTCATAAATTAAATTCAGCTCAAGAACTTTAAAACATATATTTGAAT
* * * *
56065774 CACATATGTATATAAAATTCGTACATTAATTTCAGCTCAAGAACTTTAAAATATATAT
1 CACATATGTATATAAAATTCATAAATTAAATTCAGCTCAAGAACTTTAAAACATATAT
56065832 ATATTCGAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (64 bp):
CACATATGTATATAAAATTCATAAATTAAATTCAGCTCAAGAACTTTAAAACATATATTTGAAT
Found at i:56065981 original size:60 final size:60
Alignment explanation
Indices: 56065860--56065986 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
56065850 TATATATATA
* * * **
56065860 TATATATATATATTTCATAATATTAAGTTCAACTCAAAGAACTTGTATCATACATTCAAC
1 TATATATATATAATTCATAATATTAAATTCAACTCAAAGAAATTAAATCATACATTCAAC
* *
56065920 TATATATATATAATTCATAACT-TTAAATTCAACTC-ATGAAATTAAATCTTACATTCGAAC
1 TATATATATATAATTCATAA-TATTAAATTCAACTCAAAGAAATTAAATCATACATTC-AAC
*
56065980 TACATAT
1 TATATAT
56065987 CCATGTAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
59 16 0.28
60 40 0.70
61 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.39
Consensus pattern (60 bp):
TATATATATATAATTCATAATATTAAATTCAACTCAAAGAAATTAAATCATACATTCAAC
Found at i:56068472 original size:78 final size:78
Alignment explanation
Indices: 56068240--56068465 Score: 380
Period size: 78 Copynumber: 2.9 Consensus size: 78
56068230 TATGACTTTT
56068240 ACCTTGGACTTTTCTAGTAAATTTTTACGCAAATTCAACCAATTTGATGCTCTTTATGAATGCAA
1 ACCTTGGACTTTTCTAGTAAATTTTTACGCAAATTCAACCAATTTGATGCTCTTTATGAATGCAA
*
56068305 TGCTTACATGATC
66 TGCTTACAGGATC
* * *
56068318 ACCTTGGACTTTTCTAGTAAATTTTCACACAAATTCAACCAATTTGATGCTCTTTATAAATGCAA
1 ACCTTGGACTTTTCTAGTAAATTTTTACGCAAATTCAACCAATTTGATGCTCTTTATGAATGCAA
*
56068383 TTCTTACAGGATC
66 TGCTTACAGGATC
* * *
56068396 ACCTTGGACTTTTCTAGTAAATTTTTACGCATATTCATCCAAATTGATGCTCTTTATGAATGCAA
1 ACCTTGGACTTTTCTAGTAAATTTTTACGCAAATTCAACCAATTTGATGCTCTTTATGAATGCAA
56068461 TGCTT
66 TGCTT
56068466 GTAGGATGAA
Statistics
Matches: 136, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 136 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (78 bp):
ACCTTGGACTTTTCTAGTAAATTTTTACGCAAATTCAACCAATTTGATGCTCTTTATGAATGCAA
TGCTTACAGGATC
Found at i:56079095 original size:3 final size:3
Alignment explanation
Indices: 56079087--56079129 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
56079077 CTCAAGCTGT
56079087 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
56079130 ATTTTGGTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.