Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 102 of 230
Found at i:29063761 original size:16 final size:13
Alignment explanation
Indices: 29063728--29063753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29063718 TTTGTGTTCA
29063728 ATTTTTAAATAAT
1 ATTTTTAAATAAT
29063741 ATTTTTAAATAAT
1 ATTTTTAAATAAT
29063754 TTTATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTTAAATAAT
Found at i:29076785 original size:44 final size:44
Alignment explanation
Indices: 29076735--29077046 Score: 144
Period size: 43 Copynumber: 7.2 Consensus size: 44
29076725 GACAAAAGAT
29076735 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
* * * ** ** * * * * *
29076779 CTTGCC-TCTTTCGGTTGTGATAG-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTAC-ATTGACAGCGAAGCAGATCGAAGACACAA-AC
29076823 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
* * * ** ** * * * * *
29076867 CTTGCC-TCTTTCGGTTGTGATAG-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTAC-ATTGACAGCGAAGCAGATCGAAGACACAA-AC
*
29076911 CTTGCCTTCCTACATTAACAGCGAAGCAGATCGAA-A-ACAAAGC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAA-C
* * * ** *
29076954 CTTG-CATCC-ATCGATTG-CAGTGGAGCTAG-TTAAAGA-AGCAGAC
1 CTTGCCTTCCTA-C-ATTGACAGCGAAGC-AGATCGAAGACA-CAAAC
* * * *
29076997 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACA-AAGC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
29077040 CTTGCCT
1 CTTGCCT
29077047 CCATCGGTTG
Statistics
Matches: 185, Mismatches: 64, Indels: 39
0.64 0.22 0.14
Matches are distributed among these distances:
41 1 0.01
42 16 0.09
43 69 0.37
44 68 0.37
45 31 0.17
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (44 bp):
CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
Found at i:29076870 original size:88 final size:88
Alignment explanation
Indices: 29076721--29077056 Score: 457
Period size: 88 Copynumber: 3.9 Consensus size: 88
29076711 GACAGATCAA
*
29076721 TGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
**
29076786 CTTTCGGTTGTGATAGAGCTGGT
66 CCATCGGTTGTGATAGAGCTGGT
*
29076809 TGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
**
29076874 CTTTCGGTTGTGATAGAGCTGGT
66 CCATCGGTTGTGATAGAGCTGGT
*
29076897 TGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCA
1 TGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAA-CCTTGCC
* * * *
29076960 TCCATCGATTG-CAGTGGAGCTAGT
65 TCCATCGGTTGTGA-TAGAGCTGGT
* ** * * * *
29076984 TAAAGA-AGCAGACCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACA-AAGCCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
29077047 CCATCGGTTG
66 CCATCGGTTG
29077057 CATTGGAGCA
Statistics
Matches: 227, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
86 59 0.26
87 31 0.14
88 137 0.60
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (88 bp):
TGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
CCATCGGTTGTGATAGAGCTGGT
Found at i:29077111 original size:86 final size:86
Alignment explanation
Indices: 29076923--29077119 Score: 213
Period size: 86 Copynumber: 2.3 Consensus size: 86
29076913 TGCCTTCCTA
*
29076923 CATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCCATCGATTGCAGTGGAGCTAGTTAA
1 CATTAACAACGAAGCAGATC-AAAGACAAAGCCTTGCATCCATCGATTGCAGTGGAGCTAGTTAA
* *
29076987 AGAAGCAGACCTTGCCTTCCTG
65 AGAAGCAGACCTTACCTCCCTG
* * * * *
29077009 CATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCATTGGAGC-AGATTGA
1 CATTAACAACGAAGCAGATCAAAGACAAAGCCTTGCATCCATCGATTGCAGTGGAGCTAG-TTAA
* * *
29077073 AGCCAG-AGATCTTATCTCCCTG
65 AG-AAGCAGACCTTACCTCCCTG
* *
29077095 AGATT-ACAACGGAGCAGATCAAAGA
1 -CATTAACAACGAAGCAGATCAAAGA
29077120 TAGTAATCCT
Statistics
Matches: 95, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
85 5 0.05
86 85 0.89
87 5 0.05
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (86 bp):
CATTAACAACGAAGCAGATCAAAGACAAAGCCTTGCATCCATCGATTGCAGTGGAGCTAGTTAAA
GAAGCAGACCTTACCTCCCTG
Found at i:29080977 original size:3 final size:3
Alignment explanation
Indices: 29080971--29081008 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
29080961 CTCCTCCTCC
*
29080971 TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TC- TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
29081009 CCTAGTTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:29084683 original size:66 final size:66
Alignment explanation
Indices: 29084575--29084704 Score: 190
Period size: 66 Copynumber: 2.0 Consensus size: 66
29084565 TGAAGCACTA
*
29084575 TTGGCTACTTTCTATAATGTTTTCACTAAACTGCATGAGATTCCGTCACCTTAATCGCAGGATCT
1 TTGGCTACTTTCTATAATGTTTTCACTAAACTGCATGAGATTCCGTCACCTCAATCGCAGGATCT
29084640 C
66 C
* * * * *
29084641 TTGGCTACTTTCTATGATGTTTTTATTAAACTGCAT-AGGATTCCGTCGCCTCAATCGTAGGATC
1 TTGGCTACTTTCTATAATGTTTTCACTAAACTGCATGA-GATTCCGTCACCTCAATCGCAGGATC
29084705 ATGCCATTCC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 1 0.02
66 56 0.98
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (66 bp):
TTGGCTACTTTCTATAATGTTTTCACTAAACTGCATGAGATTCCGTCACCTCAATCGCAGGATCT
C
Found at i:29094344 original size:30 final size:30
Alignment explanation
Indices: 29094308--29094428 Score: 95
Period size: 30 Copynumber: 4.1 Consensus size: 30
29094298 ACTAGGTGCA
*
29094308 GGTGATTTTAGTTTCCAGGTACTATGTACC
1 GGTGATTATAGTTTCCAGGTACTATGTACC
* * ** *
29094338 GGTGATTAAAGTTTCCAAGTTTTATGTACT
1 GGTGATTATAGTTTCCAGGTACTATGTACC
* * ** * * * *
29094368 GGTG-TAATAGTTTTCAGGCCCTCTATGCT
1 GGTGATTATAGTTTCCAGGTACTATGTACC
29094397 GGTGA-TATAGTTT-CAGGTACTATGTACC
1 GGTGATTATAGTTTCCAGGTACTATGTACC
29094425 GGTG
1 GGTG
29094429 GTGGATACCA
Statistics
Matches: 67, Mismatches: 23, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
28 13 0.19
29 26 0.39
30 28 0.42
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (30 bp):
GGTGATTATAGTTTCCAGGTACTATGTACC
Found at i:29100193 original size:75 final size:75
Alignment explanation
Indices: 29100057--29100208 Score: 223
Period size: 75 Copynumber: 2.0 Consensus size: 75
29100047 GGGCGACCCA
* * * *
29100057 TGCAACCTTAGCTATCAAATAGTGGAAATGGGCCCACAAGCCCAAGACATTTGCCCGTGTGGGCC
1 TGCAACCTTAGCCATCAAATAGTGAAAATGGGCCCACAAGCCCAAGAAATTTGCCCATGTGGGCC
29100122 TACACGCCCG
66 TACACGCCCG
* * * *
29100132 TGCAACCTTAGCCATCAAATAGTGAAAATGGGCCCATAAGCCCATGAAATTTTCCCATGTGGGCT
1 TGCAACCTTAGCCATCAAATAGTGAAAATGGGCCCACAAGCCCAAGAAATTTGCCCATGTGGGCC
*
29100197 TCCACGCCCG
66 TACACGCCCG
29100207 TG
1 TG
29100209 TAGCCCACAC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 68 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (75 bp):
TGCAACCTTAGCCATCAAATAGTGAAAATGGGCCCACAAGCCCAAGAAATTTGCCCATGTGGGCC
TACACGCCCG
Found at i:29102160 original size:24 final size:24
Alignment explanation
Indices: 29102133--29102189 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
29102123 CTATTTAAAA
*
29102133 ACTGAAAATGCTATAGATAGTAA-T
1 ACTGAAAATACTATAGATAG-AAGT
* *
29102157 ACTGAGACTACTATAGATAGAATGT
1 ACTGAAAATACTATAGATAGAA-GT
29102182 ACTGAAAA
1 ACTGAAAA
29102190 CACTCAGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 17 0.65
25 7 0.27
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.26
Consensus pattern (24 bp):
ACTGAAAATACTATAGATAGAAGT
Found at i:29102239 original size:10 final size:10
Alignment explanation
Indices: 29102219--29102247 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
29102209 TTATATTGTA
29102219 GTAAA-ACTG
1 GTAAACACTG
29102228 GTAAACACTG
1 GTAAACACTG
29102238 GTAAACACTG
1 GTAAACACTG
29102248 TGTTATACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (10 bp):
GTAAACACTG
Found at i:29104873 original size:19 final size:20
Alignment explanation
Indices: 29104834--29104875 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
29104824 CCCTCCCTTG
*
29104834 TAAATAATATACATTATTATA
1 TAAATAATATA-ATTACTATA
29104855 TAAATAATAT-ATTACTATA
1 TAAATAATATAATTACTATA
29104874 TA
1 TA
29104876 TAAATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
21 10 0.50
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAATATAATTACTATA
Found at i:29104875 original size:21 final size:20
Alignment explanation
Indices: 29104834--29104880 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
29104824 CCCTCCCTTG
29104834 TAAATAATATACATTATTATA
1 TAAATAATATA-ATTATTATA
29104855 TAAATAATAT-ATTACTATATA
1 TAAATAATATAATTA-T-TATA
29104876 TAAAT
1 TAAAT
29104881 TGTAACGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 1 0.04
21 19 0.79
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAATATAATTATTATA
Found at i:29111607 original size:37 final size:37
Alignment explanation
Indices: 29111557--29111635 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
29111547 TTATTACGAA
* * *
29111557 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
29111594 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
29111631 GTCTT
1 GTCTT
29111636 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:29111832 original size:47 final size:47
Alignment explanation
Indices: 29111754--29112070 Score: 510
Period size: 47 Copynumber: 6.7 Consensus size: 47
29111744 CCCTTCGGGA
* * * * * *
29111754 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29111801 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29111848 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29111895 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29111942 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29111989 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
29112036 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
29112071 AGAATCCTAA
Statistics
Matches: 254, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
46 1 0.00
47 253 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29113901 original size:13 final size:13
Alignment explanation
Indices: 29113883--29113907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29113873 TACTAAATTT
29113883 TCATGGATTCAAA
1 TCATGGATTCAAA
29113896 TCATGGATTCAA
1 TCATGGATTCAA
29113908 TATACCATTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:29118675 original size:7 final size:7
Alignment explanation
Indices: 29118663--29118729 Score: 52
Period size: 7 Copynumber: 9.4 Consensus size: 7
29118653 AAGAACCTAG
29118663 TAATATA
1 TAATATA
29118670 TAATATA
1 TAATATA
29118677 T-ATGATA
1 TAAT-ATA
29118684 -AATAGTA
1 TAATA-TA
29118691 TAATATA
1 TAATATA
29118698 TAA-ATAA
1 TAATAT-A
29118705 TAA-ATA
1 TAATATA
29118711 TATATATTA
1 TA-ATA-TA
*
29118720 TTATATA
1 TAATATA
29118727 TAA
1 TAA
29118730 ATAACTTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
6 8 0.16
7 31 0.62
8 8 0.16
9 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (7 bp):
TAATATA
Found at i:29118700 original size:16 final size:15
Alignment explanation
Indices: 29118663--29118732 Score: 60
Period size: 16 Copynumber: 4.9 Consensus size: 15
29118653 AAGAACCTAG
29118663 TAATATAT-AATATA
1 TAATATATAAATATA
*
29118677 T-AT-GATAAATAGTA
1 TAATATATAAATA-TA
29118691 TAATATATAAATA-A
1 TAATATATAAATATA
*
29118705 TAA-ATATATATATTA
1 TAATATATAAATA-TA
*
29118720 TTATATATAAATA
1 TAATATATAAATA
29118733 ACTTTAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
12 2 0.05
13 14 0.32
14 8 0.18
15 5 0.11
16 15 0.34
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TAATATATAAATATA
Found at i:29118717 original size:19 final size:18
Alignment explanation
Indices: 29118664--29118716 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
29118654 AGAACCTAGT
29118664 AATATATAATATATATGATA
1 AATA-ATAATATATAT-ATA
*
29118684 AATAGT-ATA-ATATATA
1 AATAATAATATATATATA
29118700 AATAATAA-ATATATATA
1 AATAATAATATATATATA
29118717 TTATTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 9 0.31
17 12 0.41
18 3 0.10
19 1 0.03
20 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
AATAATAATATATATATA
Found at i:29118976 original size:2 final size:2
Alignment explanation
Indices: 29118964--29119024 Score: 53
Period size: 2 Copynumber: 32.5 Consensus size: 2
29118954 AAACCTTGTA
*
29118964 AT AT AT A- AT AT AT AT GAT AT AT AT -T AT A- AT AT AT AT A- AA
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
29119003 AT GAT A- AT AT -T AT AT AT AT AT A
1 AT -AT AT AT AT AT AT AT AT AT AT A
29119025 ACTTTAACTA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
1 6 0.12
2 40 0.80
3 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29118978 original size:9 final size:9
Alignment explanation
Indices: 29118964--29119025 Score: 60
Period size: 9 Copynumber: 6.9 Consensus size: 9
29118954 AAACCTTGTA
29118964 ATATATAAT
1 ATATATAAT
29118973 ATATATGATAT
1 ATATAT-A-AT
29118984 ATATTATAAT
1 ATA-TATAAT
29118994 ATATATAA-
1 ATATATAAT
29119002 A-ATGATAAT
1 ATAT-ATAAT
29119011 AT-TAT-AT
1 ATATATAAT
29119018 ATATATAA
1 ATATATAA
29119026 CTTTAACTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
7 6 0.13
8 10 0.22
9 14 0.31
10 6 0.13
11 6 0.13
12 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
ATATATAAT
Found at i:29119172 original size:13 final size:13
Alignment explanation
Indices: 29119154--29119194 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
29119144 TATATATTAT
29119154 TATATATAAATAC
1 TATATATAAATAC
29119167 TATATAT---TAC
1 TATATATAAATAC
29119177 TATATATAAATAC
1 TATATATAAATAC
29119190 TATAT
1 TATAT
29119195 GTTACTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.40
13 15 0.60
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATATAAATAC
Found at i:29119174 original size:23 final size:23
Alignment explanation
Indices: 29119144--29119211 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
29119134 TCATATATTA
*
29119144 TATATATTATTATATATAAATAC
1 TATATATTACTATATATAAATAC
29119167 TATATATTACTATATATAAATAC
1 TATATATTACTATATATAAATAC
* *
29119190 TATATGTTACTGTATATAAATA
1 TATATATTACTATATATAAATA
29119212 ATAAATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (23 bp):
TATATATTACTATATATAAATAC
Found at i:29119200 original size:10 final size:10
Alignment explanation
Indices: 29119136--29119206 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
29119126 TTTCTCTTTC
29119136 ATATATTA-T
1 ATATATTACT
*
29119145 ATATATTATT
1 ATATATTACT
29119155 ATATATAAATACT
1 ATATAT---TACT
29119168 ATATATTACT
1 ATATATTACT
29119178 ATATATAAATACT
1 ATATAT---TACT
*
29119191 ATATGTTACT
1 ATATATTACT
*
29119201 GTATAT
1 ATATAT
29119207 AAATAATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
9 8 0.16
10 25 0.49
13 18 0.35
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (10 bp):
ATATATTACT
Found at i:29119205 original size:21 final size:22
Alignment explanation
Indices: 29119144--29119229 Score: 84
Period size: 23 Copynumber: 3.8 Consensus size: 22
29119134 TCATATATTA
*
29119144 TATATATTATTATATATAAATAC
1 TATATATTA-CATATATAAATAC
29119167 TATATATTACTATATATAAATAC
1 TATATATTAC-ATATATAAATAC
* * *
29119190 TATATGTTACTGTATATAAATAA
1 TATATATTAC-ATATATAAATAC
* *
29119213 TAAATAATACATA-ATAA
1 TATATATTACATATATAA
29119230 TATATTATGT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
21 4 0.07
22 2 0.04
23 48 0.89
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
TATATATTACATATATAAATAC
Found at i:29121598 original size:11 final size:11
Alignment explanation
Indices: 29121584--29121633 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
29121574 ATATCTAAAC
29121584 AATAATAATAA
1 AATAATAATAA
*
29121595 AATAATAGTAA
1 AATAATAATAA
* *
29121606 TATAATTATAA
1 AATAATAATAA
**
29121617 AATAATAGCAA
1 AATAATAATAA
29121628 AATAAT
1 AATAAT
29121634 GAGAAAACAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (11 bp):
AATAATAATAA
Found at i:29121640 original size:22 final size:22
Alignment explanation
Indices: 29121584--29121633 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
29121574 ATATCTAAAC
*
29121584 AATAATAATAAAATAATAGTAA
1 AATAATAATAAAATAATAGCAA
* *
29121606 TATAATTATAAAATAATAGCAA
1 AATAATAATAAAATAATAGCAA
29121628 AATAAT
1 AATAAT
29121634 GAGAAAACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AATAATAATAAAATAATAGCAA
Found at i:29122034 original size:11 final size:11
Alignment explanation
Indices: 29122018--29122043 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29122008 ATTTTTTTAA
29122018 TTTTAAAATAC
1 TTTTAAAATAC
29122029 TTTTAAAATAC
1 TTTTAAAATAC
29122040 TTTT
1 TTTT
29122044 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:29122059 original size:41 final size:38
Alignment explanation
Indices: 29122008--29122137 Score: 118
Period size: 40 Copynumber: 3.3 Consensus size: 38
29121998 AAATATTTTT
*
29122008 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAA
1 ATTTTTTTAATTTT-AAATACTTTTAAAAT--TTTTTTAAA
**
29122049 ATTTTTTTAATTTTAAATTTTTTTAAAATTTTTTTAAA
1 ATTTTTTTAATTTTAAATACTTTTAAAATTTTTTTAAA
** * *
29122087 ATACATTTTTTAATTTT-TTTAATTTTAAAATATTTTTAAA
1 AT---TTTTTTAATTTTAAATACTTTTAAAATTTTTTTAAA
*
29122127 ATACTTTTTAA
1 AT-TTTTTTAA
29122138 AATTTTTATT
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
38 18 0.23
40 33 0.43
41 26 0.34
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (38 bp):
ATTTTTTTAATTTTAAATACTTTTAAAATTTTTTTAAA
Found at i:29122064 original size:16 final size:16
Alignment explanation
Indices: 29122043--29122074 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29122033 AAAATACTTT
29122043 TTTTAAATTTTTTTAA
1 TTTTAAATTTTTTTAA
29122059 TTTTAAATTTTTTTAA
1 TTTTAAATTTTTTTAA
29122075 AATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTAAATTTTTTTAA
Found at i:29122084 original size:51 final size:51
Alignment explanation
Indices: 29122018--29122156 Score: 192
Period size: 51 Copynumber: 2.7 Consensus size: 51
29122008 ATTTTTTTAA
* *
29122018 TTTTAAAATACTTTTAAAATACTTTTTTTAAATTTTTTTAATTTT-AAATTT
1 TTTTAAAATATTTTTAAAATACTTTTTTT-AATTTTTTTAATTTTAAAATAT
* *
29122069 TTTTAAAATTTTTTTAAAATACATTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATAT
*
29122120 TTTTAAAATACTTTTTAAAAT-TTTTATTTTAATTTTT
1 TTTTAAAATA-TTTTTAAAATACTTT-TTTTAATTTTT
29122157 AAAATAAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
50 15 0.19
51 42 0.54
52 21 0.27
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (51 bp):
TTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATAT
Found at i:29122113 original size:40 final size:37
Alignment explanation
Indices: 29122069--29122151 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 37
29122059 TTTTAAATTT
* **
29122069 TTTTAAAATTTTTTTAAAATACATTTTTTAATTTTTTTAA
1 TTTTAAAATATTTTTAAAATAC--TTTTTAAAATTTTT-A
29122109 TTTTAAAATATTTTTAAAATACTTTTTAAAATTTTTA
1 TTTTAAAATATTTTTAAAATACTTTTTAAAATTTTTA
29122146 TTTTAA
1 TTTTAA
29122152 TTTTTAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 7 0.17
38 12 0.30
40 21 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (37 bp):
TTTTAAAATATTTTTAAAATACTTTTTAAAATTTTTA
Found at i:29122136 original size:12 final size:11
Alignment explanation
Indices: 29122109--29122144 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
29122099 ATTTTTTTAA
29122109 TTTTAAAATAT
1 TTTTAAAATAT
29122120 TTTTAAAATACT
1 TTTTAAAATA-T
29122132 TTTTAAAAT-T
1 TTTTAAAATAT
29122142 TTT
1 TTT
29122145 ATTTTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:29122155 original size:21 final size:21
Alignment explanation
Indices: 29122103--29122161 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
29122093 TTTTTAATTT
*
29122103 TTTTAATTTTAAAATATTTTTA
1 TTTTAATTTTTAAA-ATTTTTA
*** *
29122125 AAATACTTTTTAAAATTTTTA
1 TTTTAATTTTTAAAATTTTTA
29122146 TTTTAATTTTTAAAAT
1 TTTTAATTTTTAAAAT
29122162 AAATTTTTGG
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTAATTTTTAAAATTTTTA
Found at i:29127966 original size:125 final size:124
Alignment explanation
Indices: 29127736--29128159 Score: 564
Period size: 125 Copynumber: 3.4 Consensus size: 124
29127726 ACGTGGACGT
* * * * *
29127736 GAAGAATTTGTGAAATCGCGCCCTCCTGGACGCACTTTTGTTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
* *
29127801 TTCCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA-CTAGAATGCTCTATGA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC-AG-ATGCTATATGA
* * *
29127861 GAAGAATTTGTTAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATTA
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
* * * *
29127925 TTTCGAGTTAACGTTTCTGAGCAAATAGTATAAAAAGCGCTTCAAGCAGGATGCTATTTGA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTCTAGCA-GATGCTATATGA
* * * * *
29127986 GAAGAATTTCTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCTTGGAAGAAATAA
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
* * * * * *
29128051 TTTTGAGTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTATCAAGATACTTTATTA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC-AGATGCTATATGA
29128111 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
29128160 CATGTTTGGG
Statistics
Matches: 258, Mismatches: 36, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
124 37 0.14
125 182 0.71
126 39 0.15
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (124 bp):
GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGATGCTATATGA
Found at i:29131270 original size:18 final size:19
Alignment explanation
Indices: 29131235--29131271 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29131225 ATTATTAAGA
29131235 ATTTTATTATAAATTATAT
1 ATTTTATTATAAATTATAT
29131254 ATTTTAATTA-AAA-TATAT
1 ATTTT-ATTATAAATTATAT
29131272 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTATTATAAATTATAT
Found at i:29131501 original size:44 final size:45
Alignment explanation
Indices: 29131436--29131526 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
29131426 ACCTCTATTC
* * *
29131436 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
29131480 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
29131525 CA
1 CA
29131527 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:29131528 original size:16 final size:16
Alignment explanation
Indices: 29131507--29131575 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
29131497 GATTAGCTAT
29131507 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
29131523 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
29131540 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
29131556 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
29131572 TACA
1 TACA
29131576 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:29131549 original size:33 final size:32
Alignment explanation
Indices: 29131507--29131575 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
29131497 GATTAGCTAT
29131507 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
29131540 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
29131572 TACA
1 TACA
29131576 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:29139884 original size:17 final size:18
Alignment explanation
Indices: 29139859--29139901 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
29139849 TATAAGAATA
*
29139859 ATTATATTAAGA-ATTTT
1 ATTAAATTAAGATATTTT
29139876 ATTAAATT-AGATATTTT
1 ATTAAATTAAGATATTTT
29139893 ATTAAATTA
1 ATTAAATTA
29139902 TATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTAAATTAAGATATTTT
Found at i:29140153 original size:45 final size:44
Alignment explanation
Indices: 29140064--29140156 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
29140054 ATTACAACAT
* *
29140064 CATTCCATTCAACCAAACACAAGAATACTATTGCAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
*
29140108 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGCTCTATTC
29140153 CATT
1 CATT
29140157 ACACATCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 21 0.48
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:29140159 original size:16 final size:17
Alignment explanation
Indices: 29140138--29140177 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
29140128 TTGAATTACT
29140138 ATTACAGC-TCTATTCC
1 ATTACAGCATCTATTCC
29140154 ATTACA-CATCTATTCC
1 ATTACAGCATCTATTCC
29140170 ATTACAGC
1 ATTACAGC
29140178 GAACCAAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (17 bp):
ATTACAGCATCTATTCC
Found at i:29140361 original size:4 final size:4
Alignment explanation
Indices: 29140352--29140379 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
29140342 AAGTGATGAG
29140352 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
29140380 TACTCTCGAA
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:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:29140909 original size:25 final size:25
Alignment explanation
Indices: 29140880--29140936 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
29140870 TTAAAGTTAT
29140880 TTAAAATTTAAAAA-AAAATTAAAAA
1 TTAAAATTTAAAAAGAAAA-TAAAAA
* *
29140905 TTAAAAATTAAAAAGTAAATAAAAA
1 TTAAAATTTAAAAAGAAAATAAAAA
*
29140930 TAAAAAT
1 TTAAAAT
29140937 ATTCTTTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 24 0.89
26 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (25 bp):
TTAAAATTTAAAAAGAAAATAAAAA
Found at i:29140912 original size:14 final size:14
Alignment explanation
Indices: 29140893--29140923 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29140883 AAATTTAAAA
*
29140893 AAAAATTAAAAATT
1 AAAAATTAAAAAGT
29140907 AAAAATTAAAAAGT
1 AAAAATTAAAAAGT
29140921 AAA
1 AAA
29140924 TAAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAAATTAAAAAGT
Found at i:29141859 original size:9 final size:9
Alignment explanation
Indices: 29141839--29141874 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
29141829 ACCGAAGAAA
*
29141839 CATCATCCT
1 CATCGTCCT
*
29141848 CATCGTCTT
1 CATCGTCCT
29141857 CATCGTCCT
1 CATCGTCCT
29141866 CATCGTCCT
1 CATCGTCCT
29141875 TTTTGCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.14, C:0.42, G:0.08, T:0.36
Consensus pattern (9 bp):
CATCGTCCT
Found at i:29146345 original size:22 final size:22
Alignment explanation
Indices: 29146320--29146369 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
29146310 GTGGAGCCGT
29146320 GGAGGACCGGAGGTGGATCGGC
1 GGAGGACCGGAGGTGGATCGGC
**
29146342 GGAGGATTGGAGGTGGATCGGC
1 GGAGGACCGGAGGTGGATCGGC
29146364 GGAGGA
1 GGAGGA
29146370 TTGGTGTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.12, G:0.56, T:0.12
Consensus pattern (22 bp):
GGAGGACCGGAGGTGGATCGGC
Found at i:29146370 original size:22 final size:22
Alignment explanation
Indices: 29146328--29146373 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
29146318 GTGGAGGACC
29146328 GGAGGTGGATCGGCGGAGGATT
1 GGAGGTGGATCGGCGGAGGATT
29146350 GGAGGTGGATCGGCGGAGGATT
1 GGAGGTGGATCGGCGGAGGATT
29146372 GG
1 GG
29146374 TGTCGGAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.09, G:0.57, T:0.17
Consensus pattern (22 bp):
GGAGGTGGATCGGCGGAGGATT
Found at i:29161281 original size:15 final size:15
Alignment explanation
Indices: 29161261--29161291 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29161251 AAGCCAAGAC
29161261 TTGGGCAAATTTTGG
1 TTGGGCAAATTTTGG
29161276 TTGGGCAAATTTTGG
1 TTGGGCAAATTTTGG
29161291 T
1 T
29161292 ATTTTTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.32, T:0.42
Consensus pattern (15 bp):
TTGGGCAAATTTTGG
Found at i:29164367 original size:16 final size:15
Alignment explanation
Indices: 29164347--29164394 Score: 64
Period size: 14 Copynumber: 3.2 Consensus size: 15
29164337 AGTAAAAAAT
29164347 AATATAAATTTTAT-
1 AATATAAATTTTATA
29164361 AATATATAATCTTTATA
1 AATATA-AAT-TTTATA
29164378 AATA-AAATTTTATA
1 AATATAAATTTTATA
29164392 AAT
1 AAT
29164395 GGTTGAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 15 0.48
15 6 0.19
16 6 0.19
17 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATAAATTTTATA
Found at i:29164393 original size:14 final size:14
Alignment explanation
Indices: 29164347--29164394 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
29164337 AGTAAAAAAT
29164347 AATATAAATTTTATA
1 AATA-AAATTTTATA
*
29164362 ATATATAATCTTTATA
1 A-ATAAAAT-TTTATA
29164378 AATAAAATTTTATA
1 AATAAAATTTTATA
29164392 AAT
1 AAT
29164395 GGTTGAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 9 0.31
15 10 0.34
16 10 0.34
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
AATAAAATTTTATA
Found at i:29164486 original size:21 final size:22
Alignment explanation
Indices: 29164444--29164501 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
29164434 TTTTATAGAT
* *
29164444 AAATTTTGATAAAGAAATTATA
1 AAATTTTTATAAATAAATTATA
*
29164466 AAATTTTTATTAATAAA-TATA
1 AAATTTTTATAAATAAATTATA
**
29164487 TTATTTTTATAAATA
1 AAATTTTTATAAATA
29164502 TAACATGAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
AAATTTTTATAAATAAATTATA
Found at i:29173213 original size:39 final size:40
Alignment explanation
Indices: 29173118--29173379 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
29173108 TTGAATGATG
*
29173118 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
29173156 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
29173197 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
29173236 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
29173275 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
29173314 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
29173353 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
29173380 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:29181486 original size:39 final size:40
Alignment explanation
Indices: 29181391--29181652 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
29181381 TTGAATGATG
*
29181391 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
29181429 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
29181470 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
29181509 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
29181548 TCCGAGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
29181587 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
29181626 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
29181653 AACGAGGAGC
Statistics
Matches: 201, Mismatches: 13, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
39 130 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:29187407 original size:22 final size:21
Alignment explanation
Indices: 29187366--29187407 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29187356 AAAGTTAACC
29187366 TAAAAAAATACAATTAATTAG
1 TAAAAAAATACAATTAATTAG
29187387 TAAAATAAATA-AATTACATTA
1 TAAAA-AAATACAATTA-ATTA
29187408 CAACAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (21 bp):
TAAAAAAATACAATTAATTAG
Found at i:29189957 original size:15 final size:16
Alignment explanation
Indices: 29189937--29189970 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
29189927 ATCCTACTCC
29189937 TAAAATGAT-AAAAAT
1 TAAAATGATCAAAAAT
*
29189952 TAAAATGATCCAAAAT
1 TAAAATGATCAAAAAT
29189968 TAA
1 TAA
29189971 TCACAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
TAAAATGATCAAAAAT
Found at i:29192066 original size:50 final size:51
Alignment explanation
Indices: 29191991--29192117 Score: 168
Period size: 50 Copynumber: 2.5 Consensus size: 51
29191981 GATGGTCAAG
* * *
29191991 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAT-G-ATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGCGTACC-GAATAGCATAGATCACA
* * * *
29192041 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAATAGCATAGATCACA
29192092 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
29192118 TGTGAACCGG
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
49 3 0.04
50 33 0.49
51 32 0.47
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAATAGCATAGATCACA
Found at i:29192127 original size:51 final size:50
Alignment explanation
Indices: 29191991--29192127 Score: 177
Period size: 51 Copynumber: 2.7 Consensus size: 50
29191981 GATGGTCAAG
* * * *
29191991 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGATCACA
* * *
29192041 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGG-ATAGCTTCGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAT-G-ATAGATCACA
*
29192092 TGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
29192128 TATCATCAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
49 2 0.03
50 34 0.45
51 40 0.53
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGATCACA
Found at i:29216114 original size:15 final size:16
Alignment explanation
Indices: 29216094--29216127 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
29216084 ATCCTACTCC
29216094 TAAAATGAT-AAAAAT
1 TAAAATGATCAAAAAT
*
29216109 TAAAATGATCCAAAAT
1 TAAAATGATCAAAAAT
29216125 TAA
1 TAA
29216128 TCACAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
TAAAATGATCAAAAAT
Found at i:29218236 original size:50 final size:51
Alignment explanation
Indices: 29218161--29218287 Score: 168
Period size: 50 Copynumber: 2.5 Consensus size: 51
29218151 GATGGTCAAG
* * *
29218161 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAT-G-ATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGCGTACC-GAATAGCATAGATCACA
* * * *
29218211 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAATAGCATAGATCACA
29218262 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
29218288 TGTGAACCGG
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
49 3 0.04
50 33 0.49
51 32 0.47
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAATAGCATAGATCACA
Found at i:29218297 original size:51 final size:50
Alignment explanation
Indices: 29218161--29218297 Score: 177
Period size: 51 Copynumber: 2.7 Consensus size: 50
29218151 GATGGTCAAG
* * * *
29218161 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGATCACA
* * *
29218211 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGG-ATAGCTTCGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAT-G-ATAGATCACA
*
29218262 TGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
29218298 TATCATCAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
49 2 0.03
50 34 0.45
51 40 0.53
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGATCACA
Found at i:29229074 original size:27 final size:27
Alignment explanation
Indices: 29229043--29229095 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
29229033 AAACCCTAAA
*
29229043 TGTCTGCCGATTGGCACATTTGCTTTC
1 TGTCTGCCGACTGGCACATTTGCTTTC
* *
29229070 TGTCTGCCGCCTGGCACATTTTCTTT
1 TGTCTGCCGACTGGCACATTTGCTTT
29229096 GGTTTTCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.09, C:0.28, G:0.21, T:0.42
Consensus pattern (27 bp):
TGTCTGCCGACTGGCACATTTGCTTTC
Found at i:29235200 original size:11 final size:11
Alignment explanation
Indices: 29235184--29235216 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
29235174 TATTTAAAAA
29235184 TATTTATAATT
1 TATTTATAATT
29235195 TATTTATAATT
1 TATTTATAATT
29235206 TATTTATAATT
1 TATTTATAATT
29235217 ATTATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTATAATT
Found at i:29235347 original size:18 final size:18
Alignment explanation
Indices: 29235321--29235373 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
29235311 AATAGTGAAC
29235321 ATTATAATTATAATTTAA
1 ATTATAATTATAATTTAA
* * *
29235339 ATTACAATTATTAGTTAA
1 ATTATAATTATAATTTAA
*
29235357 A-AATAATTATAATTTAA
1 ATTATAATTATAATTTAA
29235374 TTTTAACATT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTATAATTATAATTTAA
Found at i:29235395 original size:36 final size:35
Alignment explanation
Indices: 29235324--29235399 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
29235314 AGTGAACATT
*
29235324 ATAATTATAATTTAAATTACAATTATTAGTTAAAA
1 ATAATTATAATTTAAATTACAATTATTAGTAAAAA
*
29235359 ATAATTATAATTTAATTTTA-ACATTATTA-TAAAAA
1 ATAATTATAATTTAA-ATTACA-ATTATTAGTAAAAA
29235394 A-AATTA
1 ATAATTA
29235400 CTTTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
34 5 0.14
35 22 0.59
36 10 0.27
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (35 bp):
ATAATTATAATTTAAATTACAATTATTAGTAAAAA
Found at i:29235427 original size:21 final size:20
Alignment explanation
Indices: 29235382--29235434 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
29235372 AATTTTAACA
29235382 TTATTATAAAAAAAATTACTTT
1 TTATT-TAAAAAAAATTA-TTT
29235404 TTATTTAAAAAACAATT-TTGT
1 TTATTTAAAAAA-AATTATT-T
*
29235425 TTATGTAAAA
1 TTATTTAAAA
29235435 TAGAGTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 17 0.61
22 9 0.32
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (20 bp):
TTATTTAAAAAAAATTATTT
Found at i:29238613 original size:25 final size:25
Alignment explanation
Indices: 29238501--29238648 Score: 142
Period size: 25 Copynumber: 6.0 Consensus size: 25
29238491 GTACATGTAT
*
29238501 GCTCATACAAGCTGTA-AACGGTAA
1 GCTCATACAAGCTGAATAACGGTAA
*** *
29238525 GCTTC-TTTGAGCTAAATAACGGTAA
1 GC-TCATACAAGCTGAATAACGGTAA
* *
29238550 GCTCCTCCAAGCTGAATAACGGTAA
1 GCTCATACAAGCTGAATAACGGTAA
*
29238575 GCTCATACAAGCTGAATAATGGTAA
1 GCTCATACAAGCTGAATAACGGTAA
* **
29238600 GCTCATACAAGCTGAGTATTGGTAA
1 GCTCATACAAGCTGAATAACGGTAA
*
29238625 GCTCATA-AGAGCTGAA-ATCGGTAA
1 GCTCATACA-AGCTGAATAACGGTAA
29238649 CCCTAATGAT
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
24 18 0.17
25 86 0.83
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (25 bp):
GCTCATACAAGCTGAATAACGGTAA
Found at i:29238819 original size:14 final size:14
Alignment explanation
Indices: 29238786--29238819 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
29238776 TTCAATCAAA
*
29238786 GAATATAATTACAC
1 GAATTTAATTACAC
29238800 -AATTTAATTACAC
1 GAATTTAATTACAC
29238813 GAATTTA
1 GAATTTA
29238820 CCTCGAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (14 bp):
GAATTTAATTACAC
Found at i:29245752 original size:25 final size:25
Alignment explanation
Indices: 29245718--29245788 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
29245708 ACGAACTGTA
*
29245718 AACGGTAAGCTCCT-CAGAGCTGAAT
1 AACGGTAAGCTCATAC-GAGCTGAAT
*
29245743 AACGGTAAGCTCATACGAGCTGAGT
1 AACGGTAAGCTCATACGAGCTGAAT
* *
29245768 ATCGGTAAGCTCATAGGAGCT
1 AACGGTAAGCTCATACGAGCT
29245789 TAAATCGGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 40 0.98
26 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (25 bp):
AACGGTAAGCTCATACGAGCTGAAT
Found at i:29248623 original size:27 final size:26
Alignment explanation
Indices: 29248556--29248653 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 26
29248546 TTGCTTTTCT
*
29248556 AAAAAT-TTTAAAAAATTAAAATTAA
1 AAAAATATTTAAAAAATTAAAAATAA
*
29248581 AAAAATATTTTTAAAAATTAAAAATAA
1 AAAAATA-TTTAAAAAATTAAAAATAA
*
29248608 TTAAAATGA-TTAAAAAAGTATAAAAATATA
1 -AAAAAT-ATTTAAAAAA-T-TAAAAATA-A
*
29248638 AAAAA-ATATAAAAAAT
1 AAAAATATTTAAAAAAT
29248654 ATTCTTAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
25 6 0.10
27 26 0.44
28 13 0.22
29 13 0.22
30 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (26 bp):
AAAAATATTTAAAAAATTAAAAATAA
Found at i:29248652 original size:10 final size:9
Alignment explanation
Indices: 29248593--29248652 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
29248583 AAATATTTTT
29248593 AAAAATTAA
1 AAAAATTAA
29248602 AAATAATTAA
1 AAA-AATTAA
**
29248612 AATGATT-A
1 AAAAATTAA
* *
29248620 AAAAAGTAT
1 AAAAATTAA
29248629 AAAAATATAA
1 AAAAAT-TAA
29248639 AAAAATATAA
1 AAAAAT-TAA
29248649 AAAA
1 AAAA
29248653 TATTCTTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
8 5 0.12
9 11 0.28
10 24 0.60
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (9 bp):
AAAAATTAA
Found at i:29248655 original size:19 final size:18
Alignment explanation
Indices: 29248573--29248653 Score: 67
Period size: 18 Copynumber: 4.3 Consensus size: 18
29248563 TTAAAAAATT
*
29248573 AAAATTAAAAAAATATTTTTA
1 AAAATTAAAAAAATA---TAA
29248594 AAAATTAAAAATAAT-TAA
1 AAAATTAAAAA-AATATAA
* *
29248612 AATGATTAAAAAAGTAT-A
1 AA-AATTAAAAAAATATAA
29248630 AAAATATAAAAAAATATAA
1 AAAAT-TAAAAAAATATAA
29248649 AAAAT
1 AAAAT
29248654 ATTCTTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
17 2 0.04
18 19 0.38
19 15 0.30
21 11 0.22
22 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAATTAAAAAAATATAA
Found at i:29248916 original size:59 final size:59
Alignment explanation
Indices: 29248844--29248961 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
29248834 TTTTGTAAAG
*
29248844 TTAGAAAGTCAAAAATCATTTTATTTTACTTTAATTCTTAATTTATTTGCCTCTAATAA
1 TTAGAAAGTCAAAAATCATTTTATTTTACTTTAATTCTTAATTGATTTGCCTCTAATAA
*
29248903 TTAGAAGGTCAAAAATCATTTTATTTTACTTTAATTCTTAATTGATTTGCCTCTAATAA
1 TTAGAAAGTCAAAAATCATTTTATTTTACTTTAATTCTTAATTGATTTGCCTCTAATAA
29248962 ATTAAATACA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (59 bp):
TTAGAAAGTCAAAAATCATTTTATTTTACTTTAATTCTTAATTGATTTGCCTCTAATAA
Found at i:29263093 original size:20 final size:20
Alignment explanation
Indices: 29263068--29263106 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29263058 TGAGTTATTT
29263068 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAA-CAGAGTAAGTAAAC
29263088 AAGTAACAGAGTAAGTAAA
1 AAGTAACAGAGTAAGTAAA
29263107 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (20 bp):
AAGTAACAGAGTAAGTAAAC
Found at i:29268355 original size:45 final size:44
Alignment explanation
Indices: 29268262--29268439 Score: 180
Period size: 45 Copynumber: 4.0 Consensus size: 44
29268252 ACAGATTCAT
* * * * * *
29268262 GGTGG-ATCAGCACATAGC-ACCACCCTTATAGTTAATGATACTC
1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAATG-TACCC
* * * * *
29268305 AGTGGAATCAACACATAGCAACCACCTTCATAATCAATAGTACCC
1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAAT-GTACCC
* * *
29268350 GGTGGAATTAGCACACAACAACCACCTTTATAATTAATGATACCT
1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAATG-TACCC
29268395 GGTGGAATCAGCACACAACAACCACCTTTATAATCAATGGTACCC
1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAAT-GTACCC
29268440 TGTACACGTA
Statistics
Matches: 112, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
43 4 0.04
44 13 0.12
45 93 0.83
46 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (44 bp):
GGTGGAATCAGCACACAACAACCACCTTTATAATCAATGTACCC
Found at i:29274913 original size:50 final size:50
Alignment explanation
Indices: 29274853--29274984 Score: 140
Period size: 50 Copynumber: 2.6 Consensus size: 50
29274843 TATTGACGTT
* * * *
29274853 ATGAGAGGTCCCATGTAAGACCATGTCTTGGACAAGGCGTTGACACCCAG
1 ATGAAAGGTCCCATGTAAGACCATGTCTGGGACAAGGCATGGACACCCAG
** * * * *
29274903 ATGAAAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAAAGGTCCCATGTAAGACCATGTCTGGGACAAGGCATGGACACCCAG
* *
29274953 ATGAGAA-CTCCCATGTAAGACCATATCTGGGA
1 ATGA-AAGGTCCCATGTAAGACCATGTCTGGGA
29274985 TATGGCATTG
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
50 65 0.97
51 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (50 bp):
ATGAAAGGTCCCATGTAAGACCATGTCTGGGACAAGGCATGGACACCCAG
Found at i:29275026 original size:49 final size:49
Alignment explanation
Indices: 29274917--29275095 Score: 227
Period size: 49 Copynumber: 3.6 Consensus size: 49
29274907 AAGGTCCCCC
* * * * *
29274917 GTAAGACCATGTCTGGGACATGGCATGGGCACCG-ATATGAGAAC-TCCCAT
1 GTAAGACCATATCTGGGATATGGCATTGGCA--GTACAGGA-AACATCCCAT
29274967 GTAAGACCATATCTGGGATATGGCATTGGCAGTACAGGAAACATCCCAT
1 GTAAGACCATATCTGGGATATGGCATTGGCAGTACAGGAAACATCCCAT
* *
29275016 GTAAGACCATATCTAGGATATGGCATTGACAGTACAGGAAACATCCCAT
1 GTAAGACCATATCTGGGATATGGCATTGGCAGTACAGGAAACATCCCAT
* * *
29275065 GTAAGACCATATCTGAGAAATGGCTTTGGCA
1 GTAAGACCATATCTGGGATATGGCATTGGCA
29275096 TGTTATTTTC
Statistics
Matches: 115, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
48 4 0.03
49 83 0.72
50 28 0.24
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (49 bp):
GTAAGACCATATCTGGGATATGGCATTGGCAGTACAGGAAACATCCCAT
Found at i:29275323 original size:20 final size:20
Alignment explanation
Indices: 29275298--29275336 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29275288 TGAGTTATTT
29275298 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
29275318 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
29275337 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:29278828 original size:14 final size:14
Alignment explanation
Indices: 29278811--29278840 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29278801 CATTTAGTAT
*
29278811 GTATGATCATTTTA
1 GTATAATCATTTTA
29278825 GTATAATCATTTTA
1 GTATAATCATTTTA
29278839 GT
1 GT
29278841 TTAGTTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (14 bp):
GTATAATCATTTTA
Found at i:29281712 original size:51 final size:50
Alignment explanation
Indices: 29281652--29281975 Score: 272
Period size: 51 Copynumber: 6.4 Consensus size: 50
29281642 GATGAACACG
** * *
29281652 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGATCACA
1 TGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGATAAAT-ATGGTCACA
* * * * * *
29281703 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCAAGAAGCTTTGGTCACA
1 TGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGATAA-ATATGGTCACA
* ** * * * *
29281754 TGTGTAATACTGTGTGAAGGCTACTTTGCGAATCGATAAATGATGGTCATA
1 TGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGATAAAT-ATGGTCACA
* * * * * *
29281805 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
1 TGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGATAA-ATATGGTCACA
* ** * *
29281856 TGTGTAGTATTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 TGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGATAAAT-ATGGTCACA
* * * *
29281907 TGTGTAGTGCTAAGTGAAGGCTACTATGTGTACCGA-AAAGTTTTGGTCACG
1 TGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGATAAA--TATGGTCACA
* *
29281958 TATGTAGTACTATGTGAA
1 TGTGTAGTACTAAGTGAA
29281976 CCGTAAAACT
Statistics
Matches: 208, Mismatches: 59, Indels: 12
0.75 0.21 0.04
Matches are distributed among these distances:
50 5 0.02
51 200 0.96
52 3 0.01
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGATAAATATGGTCACA
Found at i:29281828 original size:102 final size:102
Alignment explanation
Indices: 29281648--29281975 Score: 496
Period size: 102 Copynumber: 3.2 Consensus size: 102
29281638 TATCGATGAA
* * *
29281648 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGATCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
29281713 TAAGTGAAGGCTACAATGTGTACCAAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCAAGAAGCTTTGGT
* * ** * *
29281750 CACATGTGTAATACTGTGTGAAGGCTACTTTGCGAATCGATAAATGATGGTCATATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
29281815 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCAAGAAGCTTTGGT
* *
29281852 CACGTGTGTAGTATTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTGC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* *
29281917 TAAGTGAAGGCTACTATGTGTACCGAA-AAGTTTTGGT
66 TAAGTGAAGGCTACAATGTGTACC-AAGAAGCTTTGGT
* *
29281954 CACGTATGTAGTACTATGTGAA
1 CACGTGTGTAGTACTGTGTGAA
29281976 CCGTAAAACT
Statistics
Matches: 201, Mismatches: 24, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
102 200 1.00
103 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCAAGAAGCTTTGGT
Found at i:29282019 original size:50 final size:49
Alignment explanation
Indices: 29281965--29282072 Score: 171
Period size: 50 Copynumber: 2.2 Consensus size: 49
29281955 ACGTATGTAG
* * *
29281965 TACTATGTGAACCGTAAAACTTGATCACGTGTGTAGTACTATGTGAAGGC
1 TACTACGTGAACCGTAAAACTTGATCACGTGTGTAATA-AATGTGAAGGC
*
29282015 TACTACGTGAACCGTAAAACTTGATCACGTGTGTAATAAATGTGAAGGT
1 TACTACGTGAACCGTAAAACTTGATCACGTGTGTAATAAATGTGAAGGC
29282064 TACTACGTG
1 TACTACGTG
29282073 TATCGAATGA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
49 18 0.33
50 36 0.67
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (49 bp):
TACTACGTGAACCGTAAAACTTGATCACGTGTGTAATAAATGTGAAGGC
Found at i:29285939 original size:290 final size:290
Alignment explanation
Indices: 29285419--29285998 Score: 1133
Period size: 290 Copynumber: 2.0 Consensus size: 290
29285409 CAAGAATTTT
29285419 ATCAAAACTGAATGAATTTGAGTTAAAAAGGACATGAAAAAGTGTGTATATTTTCGTGTTTCCAC
1 ATCAAAACTGAATGAATTTGAGTTAAAAAGGACATGAAAAAGTGTGTATATTTTCGTGTTTCCAC
29285484 ACTCCTAAAAAGGGCAAGGAATGCCGTGATGAGGGCACTTTCGTAATAACTCCTTGAACTACTCC
66 ACTCCTAAAAAGGGCAAGGAATGCCGTGATGAGGGCACTTTCGTAATAACTCCTTGAACTACTCC
29285549 CATGCCTCATATAAAGAGTCTTCATCAAGATGCTAAACTGAAGTGATTTCATTTCAGATCTTGGC
131 CATGCCTCATATAAAGAGTCTTCATCAAGATGCTAAACTGAAGTGATTTCATTTCAGATCTTGGC
*
29285614 TGTTAAAGATGGAGGGAAATATTTCATTAAGAAACGTTCAACCAACTCTTGCCATATAGTCGTGG
196 TGTTAAAGATGGAGGGAAATATTTCATTAAGAAACGTTCAACCAACTCTTGCCATATAGTCATGG
29285679 AACCAAATGGTAAGGAGTTCAACCACACTC
261 AACCAAATGGTAAGGAGTTCAACCACACTC
29285709 ATCAAAACTGAATGAATTTGAGTTAAAAAGGACATGAAAAAGTGTGTATATTTTCGTGTTTCCAC
1 ATCAAAACTGAATGAATTTGAGTTAAAAAGGACATGAAAAAGTGTGTATATTTTCGTGTTTCCAC
*
29285774 ACTCCTAAAAAGGTCAAGGAATGCCGTGATGAGGGCACTTTCGTAATAACTCCTTGAACTACTCC
66 ACTCCTAAAAAGGGCAAGGAATGCCGTGATGAGGGCACTTTCGTAATAACTCCTTGAACTACTCC
29285839 CATGCCTCATATAAAGAGTCTTCATCAAGATGCTAAACTGAAGTGATTTCATTTCAGATCTTGGC
131 CATGCCTCATATAAAGAGTCTTCATCAAGATGCTAAACTGAAGTGATTTCATTTCAGATCTTGGC
29285904 TGTTAAAGATGGAGGGAAATATTTCATTAAGAAACGTTCAACCAACTCTTGCCATATAGTCATGG
196 TGTTAAAGATGGAGGGAAATATTTCATTAAGAAACGTTCAACCAACTCTTGCCATATAGTCATGG
*
29285969 AACCGAATGGTAAGGAGTTCAACCACACTC
261 AACCAAATGGTAAGGAGTTCAACCACACTC
29285999 GTGCTCTATC
Statistics
Matches: 287, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
290 287 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (290 bp):
ATCAAAACTGAATGAATTTGAGTTAAAAAGGACATGAAAAAGTGTGTATATTTTCGTGTTTCCAC
ACTCCTAAAAAGGGCAAGGAATGCCGTGATGAGGGCACTTTCGTAATAACTCCTTGAACTACTCC
CATGCCTCATATAAAGAGTCTTCATCAAGATGCTAAACTGAAGTGATTTCATTTCAGATCTTGGC
TGTTAAAGATGGAGGGAAATATTTCATTAAGAAACGTTCAACCAACTCTTGCCATATAGTCATGG
AACCAAATGGTAAGGAGTTCAACCACACTC
Found at i:29299230 original size:11 final size:10
Alignment explanation
Indices: 29299194--29299236 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
29299184 TAACATGCTG
*
29299194 AATTTTATTT
1 AATTTTATTA
29299204 AATTTTATAATA
1 AATTTTAT--TA
29299216 AATTTTGATTA
1 AATTTT-ATTA
29299227 AATTTTATTA
1 AATTTTATTA
29299237 TTTTCGGCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 12 0.41
11 8 0.28
12 7 0.24
13 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
AATTTTATTA
Found at i:29302830 original size:3 final size:3
Alignment explanation
Indices: 29302822--29302859 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
29302812 ATAATCCTTG
*
29302822 TTA TTA TTA TTA TTA TT- TATA TTA TTT TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT
29302860 GTTAATGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 29 0.94
4 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:29302906 original size:18 final size:18
Alignment explanation
Indices: 29302883--29302923 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29302873 CTGTTATAAT
*
29302883 TATTAGTATTATAA-TTTG
1 TATTAGT-TTATAAGTTTA
29302901 TATTAGTTTATAAGTTTA
1 TATTAGTTTATAAGTTTA
29302919 TATTA
1 TATTA
29302924 TTATCATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (18 bp):
TATTAGTTTATAAGTTTA
Found at i:29324812 original size:30 final size:31
Alignment explanation
Indices: 29324757--29324823 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
29324747 ACCCTTAAAA
* * **
29324757 TATTTACACTATTAGTCCTTCAAATTTTTTG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
29324788 TATTTACACT-TTAATCCCTCAAATTTTGAG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
29324818 TATTTA
1 TATTTA
29324824 ATCTTGGGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.49
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAATTTTGAG
Found at i:29341375 original size:20 final size:19
Alignment explanation
Indices: 29341347--29341397 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
29341337 TATCAATTCA
29341347 AATATTAAAAAAATTAAAT
1 AATATTAAAAAAATTAAAT
* *
29341366 AATAATTAAAAAATTTATAT
1 AAT-ATTAAAAAAATTAAAT
*
29341386 CATATTAAAAAA
1 AATATTAAAAAA
29341398 TCGATATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AATATTAAAAAAATTAAAT
Found at i:29341376 original size:19 final size:18
Alignment explanation
Indices: 29341347--29341398 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
29341337 TATCAATTCA
29341347 AATATTAAAAAAATTAAAT
1 AATATT-AAAAAATTAAAT
*
29341366 AATAATTAAAAAATTTATAT
1 AAT-ATTAAAAAA-TTAAAT
*
29341386 CATATTAAAAAAT
1 AATATTAAAAAAT
29341399 CGATATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 1 0.03
19 18 0.62
20 10 0.34
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATTAAAAAATTAAAT
Found at i:29341894 original size:21 final size:22
Alignment explanation
Indices: 29341858--29341907 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
29341848 ACAAATCCTA
29341858 TCTCAAATTCCTTTCAAAATCC
1 TCTCAAATTCCTTTCAAAATCC
* *
29341880 TCTCAATTTCC-TTCAAAATTC
1 TCTCAAATTCCTTTCAAAATCC
29341901 TCTCAAA
1 TCTCAAA
29341908 CTCTCAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.32, C:0.30, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCAAATTCCTTTCAAAATCC
Found at i:29341917 original size:29 final size:30
Alignment explanation
Indices: 29341879--29341937 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
29341869 TTTCAAAATC
*
29341879 CTCTCAATTTCCTT-CAAAATTCTCTCAAA
1 CTCTCAATTTCCTTCCAAAATCCTCTCAAA
29341908 CTCTCAATTTCCTTCCAAAATCCTCTCAAA
1 CTCTCAATTTCCTTCCAAAATCCTCTCAAA
29341938 TTTCTTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.36
Consensus pattern (30 bp):
CTCTCAATTTCCTTCCAAAATCCTCTCAAA
Found at i:29341920 original size:51 final size:52
Alignment explanation
Indices: 29341858--29341959 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 52
29341848 ACAAATCCTA
* *
29341858 TCTCAAATTCCTTTCAAAATCCTCTC-AATTTCCTT-CAAAATTCTCTCAAAC
1 TCTCAAATTCCTTCCAAAATCCTCTCAAATTT-CTTCCAAAAATCTCTCAAAC
*
29341909 TCTCAATTTCCTTCCAAAATCCTCTCAAATTTCTTCCAAAAATCTCTCAAA
1 TCTCAAATTCCTTCCAAAATCCTCTCAAATTTCTTCCAAAAATCTCTCAAA
29341960 TCCATATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
51 27 0.59
52 19 0.41
ACGTcount: A:0.32, C:0.31, G:0.00, T:0.36
Consensus pattern (52 bp):
TCTCAAATTCCTTCCAAAATCCTCTCAAATTTCTTCCAAAAATCTCTCAAAC
Found at i:29341937 original size:11 final size:11
Alignment explanation
Indices: 29341858--29341937 Score: 53
Period size: 11 Copynumber: 7.6 Consensus size: 11
29341848 ACAAATCCTA
*
29341858 TCTCAAATTCC
1 TCTCAAAATCC
*
29341869 TTTCAAAATCC
1 TCTCAAAATCC
**
29341880 TCTCAATTTCC
1 TCTCAAAATCC
*
29341891 T-TCAAAATTC
1 TCTCAAAATCC
29341901 TCTC-AAA--C
1 TCTCAAAATCC
**
29341909 TCTCAATTTCC
1 TCTCAAAATCC
29341920 T-TCCAAAATCC
1 TCT-CAAAATCC
29341931 TCTCAAA
1 TCTCAAA
29341938 TTTCTTCCAA
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
8 5 0.10
9 1 0.02
10 11 0.22
11 33 0.65
12 1 0.02
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (11 bp):
TCTCAAAATCC
Found at i:29341959 original size:22 final size:23
Alignment explanation
Indices: 29341908--29341960 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
29341898 TTCTCTCAAA
29341908 CTCTC-AATTTCCTTCCAAAATC
1 CTCTCAAATTTCCTTCCAAAATC
29341930 CTCTCAAATTT-CTTCCAAAAAT-
1 CTCTCAAATTTCCTTCC-AAAATC
29341952 CTCTCAAAT
1 CTCTCAAAT
29341961 CCATATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 19 0.66
23 10 0.34
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (23 bp):
CTCTCAAATTTCCTTCCAAAATC
Found at i:29342030 original size:34 final size:31
Alignment explanation
Indices: 29341991--29342061 Score: 115
Period size: 34 Copynumber: 2.2 Consensus size: 31
29341981 CCCTCAATTT
29341991 TATTTTTTAAAAATAATTTTATATATTTTTTTTA
1 TATTTTTTAAAAATAATTTTA-A-A-TTTTTTTA
29342025 TATTTTTTAAAAATAATTTTAAATTTTTTTA
1 TATTTTTTAAAAATAATTTTAAATTTTTTTA
29342056 TATTTT
1 TATTTT
29342062 CATCAATAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
31 14 0.38
32 1 0.03
33 1 0.03
34 21 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TATTTTTTAAAAATAATTTTAAATTTTTTTA
Found at i:29344411 original size:29 final size:29
Alignment explanation
Indices: 29344367--29345230 Score: 1348
Period size: 29 Copynumber: 29.9 Consensus size: 29
29344357 ATAAAAAAAT
* *
29344367 CCTAATTTATTTTAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
29344397 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29344426 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
29344455 CCTAATTTAATTAAAAGCCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
29344484 CTTAATTTAATTAAAAACCCTAACCCTGA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
**
29344513 CCTAATTTTTTTAAAAACCCTAAACCCT-A
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
29344542 CCTAATTT-ATT--AAACCCTAA-CCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29344567 -CTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29344595 CCTAATTTAATT-AAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29344623 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
29344652 CCTAATTT-ATTTAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29344680 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29344709 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* * * *
29344738 CCTAATTTATTTTAAAACCCTAAACTTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* * *
29344767 CTTAATTTATTTTAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29344796 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
29344826 CCTAATTTAATCAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
29344855 CCTAATTTAATTAAAAACCCTAACACTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29344884 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* * *
29344913 CCTAATTTATTTTAGAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
29344943 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29344972 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29345001 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
** * *
29345031 CCTAATTTAATTAAAAACTTTAACTCTAC
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29345060 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
29345089 CCTAATTTAATTAAAAACTCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
29345118 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* * * *
29345147 CCTAATGTATTTTAAAACCCTAAACTCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
29345177 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
29345206 CCTAATTTAATTAAAAACCCTAACC
1 CCTAATTTAATTAAAAACCCTAACC
29345231 ATTAACAAAA
Statistics
Matches: 769, Mismatches: 52, Indels: 27
0.91 0.06 0.03
Matches are distributed among these distances:
24 10 0.01
25 6 0.01
26 7 0.01
27 9 0.01
28 62 0.08
29 544 0.71
30 131 0.17
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:29344504 original size:117 final size:116
Alignment explanation
Indices: 29344367--29345230 Score: 1348
Period size: 117 Copynumber: 7.5 Consensus size: 116
29344357 ATAAAAAAAT
* *
29344367 CCTAATTTATTTTAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAT
1 CCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAT
*
29344432 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAGCCCTAACCCTAA
65 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
* * **
29344484 CTTAATTTAATTAAAAACCCTAACCCTGACCTAATTTTTTTAAAAACCCTAAACCCT-ACCTAAT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAACCTAAT
29344548 TT-ATT--AAACCCTAA-CCTAA-CTAATTTAATTAAAAACCCTAACCCTAA
65 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
29344595 CCTAATTTAATT-AAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
*
29344659 T-ATTTAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
66 TAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
* * * * *
29344709 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTATTTTAAAACCCTAAACTTAACTTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
* *
29344774 TATTTTAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
66 TAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAA
* *
29344826 CCTAATTTAATCAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACACTAACCTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
* * *
29344891 TAATTAAAAACCCTAACCCTAACCTAATTTATTTTAGAACCCTAAACCCTAA
66 TAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAA
29344943 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
** * *
29345008 TAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACTTTAACTCTAC
66 TAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
* *
29345060 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACTCTAACCCTAACTTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
* * * *
29345125 TAATTAAAAACCCTAACCCTAACCTAATGTATTTTAAAACCCTAAACTCTAA
66 TAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAA
29345177 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC
29345231 ATTAACAAAA
Statistics
Matches: 689, Mismatches: 47, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
109 6 0.01
110 46 0.07
111 38 0.06
112 14 0.02
113 14 0.02
114 40 0.06
115 51 0.07
116 99 0.14
117 357 0.52
118 24 0.03
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (116 bp):
CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
TAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:29348528 original size:124 final size:124
Alignment explanation
Indices: 29348308--29348582 Score: 471
Period size: 124 Copynumber: 2.2 Consensus size: 124
29348298 ACGAGGGCGT
* * *
29348308 GATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCGAA
1 GATTTTATACTATTTGCTCAGAAACGTAAAAAAAAATCATTTCTTACATGACCAACTGTAACGAA
*
29348373 ATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGC
66 ATCGCGTCCACGAGGGCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGC
*
29348432 GATTTTATACTATTTTCTCAGAAACGTAAAAAAAAATCATTTCTTACATGACCAACTGTAACGAA
1 GATTTTATACTATTTGCTCAGAAACGTAAAAAAAAATCATTTCTTACATGACCAACTGTAACGAA
* *
29348497 ATCGTGTCCACGAGGGCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGGAGC
66 ATCGCGTCCACGAGGGCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGC
29348556 GATTTTATACTATTTGAC-CAGAAACGT
1 GATTTTATACTATTTG-CTCAGAAACGT
29348583 CAACTCAAAA
Statistics
Matches: 142, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
124 141 0.99
125 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (124 bp):
GATTTTATACTATTTGCTCAGAAACGTAAAAAAAAATCATTTCTTACATGACCAACTGTAACGAA
ATCGCGTCCACGAGGGCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGC
Found at i:29350806 original size:27 final size:26
Alignment explanation
Indices: 29350766--29350816 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
29350756 TCATATTGGT
*
29350766 AAATAGAATGTGTAAGAAAATGTGATG
1 AAATAGAATATGTAAGAAAA-GTGATG
* *
29350793 AAATAGTATATGTATGAAAAGTGA
1 AAATAGAATATGTAAGAAAAGTGA
29350817 AAGAGAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (26 bp):
AAATAGAATATGTAAGAAAAGTGATG
Found at i:29357259 original size:14 final size:14
Alignment explanation
Indices: 29357240--29357278 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
29357230 TACCACAGGC
29357240 GGATTGGTATTTGT
1 GGATTGGTATTTGT
29357254 GGATTGGTATTTGT
1 GGATTGGTATTTGT
29357268 GGATTGGTATT
1 GGATTGGTATT
29357279 CATTGTTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (14 bp):
GGATTGGTATTTGT
Found at i:29359861 original size:11 final size:11
Alignment explanation
Indices: 29359832--29359871 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
29359822 TTGTTTTTAG
29359832 TTTAGTTTATA
1 TTTAGTTTATA
*
29359843 TTCAGTTTATA
1 TTTAGTTTATA
*
29359854 TTTTGTTT-TA
1 TTTAGTTTATA
29359864 TTTAGTTT
1 TTTAGTTT
29359872 GCTTGAGGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.20, C:0.03, G:0.10, T:0.68
Consensus pattern (11 bp):
TTTAGTTTATA
Found at i:29363690 original size:27 final size:28
Alignment explanation
Indices: 29363633--29363686 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
29363623 TGACATCTAT
*
29363633 GAATAGCCTTTG-TGACGGACTCTGAAA
1 GAATAGCCTTTGTTGACGAACTCTGAAA
*
29363660 GAATAGCCTTTGTTG-TGAACT-TGAAA
1 GAATAGCCTTTGTTGACGAACTCTGAAA
29363686 G
1 G
29363687 GAATTCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 16 0.67
28 2 0.08
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (28 bp):
GAATAGCCTTTGTTGACGAACTCTGAAA
Found at i:29369009 original size:178 final size:178
Alignment explanation
Indices: 29368703--29369057 Score: 559
Period size: 178 Copynumber: 2.0 Consensus size: 178
29368693 CATTCCCAAC
*
29368703 ATCATTTCTTGATTCACCACACATTTTCAGCTATAAAATAGAAACATTTTATAATCAACATCAAA
1 ATCATTTCTTGATTCACCACACATTTTCAACTATAAAATAGAAACATTTTATAATCAACATCAAA
* * * * * *
29368768 ATCCTGACTCAACTCGAATTAACTTGGCATGTACCTTTAGACTTAATTCTGAACTTGATTTTAGT
66 ATCCAGACTCAACTCGAATCAACTTGGCATATACCTCTAGACTCAATTCTGAACTTCATTTTAGT
* * *
29368833 CTAAGAATCGGCTAAACCAATAGCTCTGACACCATTAACTGTAACACT
131 CCAAGAATCAGCTAAACCAATAGCTCTGACACCATTAAATGTAACACT
* * *
29368881 ATCATTTCTTGATTCACCATACATTTTCAACTATACAATAGAAACATTTTATAATCAACATCCAA
1 ATCATTTCTTGATTCACCACACATTTTCAACTATAAAATAGAAACATTTTATAATCAACATCAAA
*
29368946 ATCCCAG-CTTAACTCGAATCAACTTGGCATATACCTCTAGACTCAATTCTGAACTTCATTTTAG
66 AT-CCAGACTCAACTCGAATCAACTTGGCATATACCTCTAGACTCAATTCTGAACTTCATTTTAG
*
29369010 TCCAAGAATTAGCTAAACCAATAGCTCTGACACCATTAAATGTAACAC
130 TCCAAGAATCAGCTAAACCAATAGCTCTGACACCATTAAATGTAACAC
29369058 CACATACCCG
Statistics
Matches: 161, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
178 158 0.98
179 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (178 bp):
ATCATTTCTTGATTCACCACACATTTTCAACTATAAAATAGAAACATTTTATAATCAACATCAAA
ATCCAGACTCAACTCGAATCAACTTGGCATATACCTCTAGACTCAATTCTGAACTTCATTTTAGT
CCAAGAATCAGCTAAACCAATAGCTCTGACACCATTAAATGTAACACT
Found at i:29369628 original size:21 final size:20
Alignment explanation
Indices: 29369587--29369631 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
29369577 CCTTACCAAT
* *
29369587 CATAACTTAAACAACTAATG
1 CATAACTTAAAAAAATAATG
*
29369607 CATAACATTAAAAAAATTATG
1 CATAAC-TTAAAAAAATAATG
29369628 CATA
1 CATA
29369632 CATACCTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (20 bp):
CATAACTTAAAAAAATAATG
Found at i:29375994 original size:39 final size:39
Alignment explanation
Indices: 29375912--29376171 Score: 311
Period size: 39 Copynumber: 6.6 Consensus size: 39
29375902 TTGAATGATG
*
29375912 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
29375950 ATCCGGACTAAGATCCG-AGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
29375990 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
29376029 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
29376068 T-CGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
*
29376106 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
29376145 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
29376172 AACGAGGAGC
Statistics
Matches: 198, Mismatches: 14, Indels: 17
0.86 0.06 0.07
Matches are distributed among these distances:
38 43 0.22
39 97 0.49
40 57 0.29
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:29384034 original size:39 final size:40
Alignment explanation
Indices: 29383929--29384190 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
29383919 TTGAATGATG
*
29383929 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
29383967 ATCCGGACTAAGAT-CCGAGGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
29384008 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
29384047 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
29384086 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
29384125 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
29384164 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
29384191 AACGATGAGC
Statistics
Matches: 201, Mismatches: 13, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
39 130 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:29386590 original size:20 final size:20
Alignment explanation
Indices: 29386565--29386604 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29386555 GTTTGAAACA
*
29386565 AAATCACTGACAACAATCTT
1 AAATCACTAACAACAATCTT
29386585 AAATCACTAACAACAATCTT
1 AAATCACTAACAACAATCTT
29386605 TCTCATGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (20 bp):
AAATCACTAACAACAATCTT
Found at i:29391302 original size:15 final size:15
Alignment explanation
Indices: 29391282--29391311 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29391272 CTGATACACT
29391282 TTTGGCGAACTCCCC
1 TTTGGCGAACTCCCC
29391297 TTTGGCGAACTCCCC
1 TTTGGCGAACTCCCC
29391312 AGTTCGCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.40, G:0.20, T:0.27
Consensus pattern (15 bp):
TTTGGCGAACTCCCC
Found at i:29397613 original size:23 final size:20
Alignment explanation
Indices: 29397587--29397635 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
29397577 ATTACAATTG
29397587 TAATTATAAGTAATACATTCAAA
1 TAATTATAAGTAA-A-A-TCAAA
*
29397610 TAATTATAATTAAAATCAAA
1 TAATTATAAGTAAAATCAAA
29397630 TAATTA
1 TAATTA
29397636 CAAAGCACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 1 0.04
23 12 0.48
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (20 bp):
TAATTATAAGTAAAATCAAA
Found at i:29398011 original size:20 final size:21
Alignment explanation
Indices: 29397976--29398019 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
29397966 TTAAACACAT
29397976 AATTTAATCTATTTTTAAATA
1 AATTTAATCTATTTTTAAATA
*
29397997 AATTTAATTTA-TTTTAAATA
1 AATTTAATCTATTTTTAAATA
29398017 AAT
1 AAT
29398020 AAGTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTAATCTATTTTTAAATA
Found at i:29398759 original size:22 final size:22
Alignment explanation
Indices: 29398711--29398761 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
29398701 GTATCTAACG
29398711 AAAATT-AAATAAATAAAAATA
1 AAAATTAAAATAAATAAAAATA
* *
29398732 ATAATTAAAATAAA-AATAATTA
1 AAAATTAAAATAAATAA-AAATA
29398754 AAAATTAA
1 AAAATTAA
29398762 CACACTATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATTAAAATAAATAAAAATA
Found at i:29404029 original size:21 final size:21
Alignment explanation
Indices: 29404005--29404066 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
29403995 AATTCTATTT
29404005 TTTGTTTGAATTGCATGGTGC
1 TTTGTTTGAATTGCATGGTGC
* *
29404026 TTTG-AT-AATT-CTAT--T-T
1 TTTGTTTGAATTGC-ATGGTGC
29404042 TTTGTTTGAATTGCATGGTGC
1 TTTGTTTGAATTGCATGGTGC
29404063 TTTG
1 TTTG
29404067 ATTATGTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
16 4 0.13
17 2 0.07
18 7 0.23
19 7 0.23
20 2 0.07
21 8 0.27
ACGTcount: A:0.16, C:0.08, G:0.23, T:0.53
Consensus pattern (21 bp):
TTTGTTTGAATTGCATGGTGC
Found at i:29404036 original size:37 final size:37
Alignment explanation
Indices: 29403995--29404068 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
29403985 TCTCGACAAA
29403995 AATTCTATTTTTTGTTTGAATTGCATGGTGCTTTGAT
1 AATTCTATTTTTTGTTTGAATTGCATGGTGCTTTGAT
29404032 AATTCTATTTTTTGTTTGAATTGCATGGTGCTTTGAT
1 AATTCTATTTTTTGTTTGAATTGCATGGTGCTTTGAT
29404069 TATGTTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (37 bp):
AATTCTATTTTTTGTTTGAATTGCATGGTGCTTTGAT
Found at i:29404091 original size:37 final size:37
Alignment explanation
Indices: 29403995--29404091 Score: 99
Period size: 37 Copynumber: 2.6 Consensus size: 37
29403985 TCTCGACAAA
* **
29403995 AATTCTATTTTTTGTTTGAATTGCATGGTGCTTTGAT
1 AATTCTATTTTGTGACTGAATTGCATGGTGCTTTGAT
* **
29404032 AATTCTATTTTTTGTTTGAATTGCATGGTGCTTTGAT
1 AATTCTATTTTGTGACTGAATTGCATGGTGCTTTGAT
*
29404069 TATGT-TATTATTGTGACT-AATTG
1 AAT-TCTATT-TTGTGACTGAATTG
29404092 ATTGAGAATC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
37 48 0.89
38 6 0.11
ACGTcount: A:0.21, C:0.07, G:0.19, T:0.54
Consensus pattern (37 bp):
AATTCTATTTTGTGACTGAATTGCATGGTGCTTTGAT
Found at i:29405554 original size:30 final size:29
Alignment explanation
Indices: 29405498--29405565 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
29405488 TTTAAGAACG
29405498 CCTTTATGGCAAATCTCTACAAGGAAATA
1 CCTTTATGGCAAATCTCTACAAGGAAATA
* *
29405527 CCTTTGTGGC-AATCTCTATCAAAGGAAA-G
1 CCTTTATGGCAAATCTCTA-C-AAGGAAATA
29405556 CCTTTATGGC
1 CCTTTATGGC
29405566 GCAAAGGACA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.24
29 19 0.56
30 7 0.21
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (29 bp):
CCTTTATGGCAAATCTCTACAAGGAAATA
Found at i:29409022 original size:19 final size:19
Alignment explanation
Indices: 29408998--29409034 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29408988 ATGCTAGAAT
*
29408998 CATGTTGGAATCAGATTTA
1 CATGTTAGAATCAGATTTA
*
29409017 CATGTTAGAATTAGATTT
1 CATGTTAGAATCAGATTT
29409035 GCATTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (19 bp):
CATGTTAGAATCAGATTTA
Found at i:29430341 original size:21 final size:23
Alignment explanation
Indices: 29430294--29430342 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
29430284 TTAAATGACT
**
29430294 TTTAATTTTTTATCATAATTATT
1 TTTAATTTTTTATCATAATTACA
*
29430317 TTTAA-TTTTTCT-ATAATTACA
1 TTTAATTTTTTATCATAATTACA
29430338 TTTAA
1 TTTAA
29430343 AATTAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 12 0.52
22 6 0.26
23 5 0.22
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTAATTTTTTATCATAATTACA
Found at i:29430420 original size:16 final size:17
Alignment explanation
Indices: 29430399--29430436 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
29430389 TTTTAAAACT
29430399 TATATTTACATATA-AA
1 TATATTTACATATATAA
* *
29430415 TATATTTGCATGTATAA
1 TATATTTACATATATAA
29430432 TATAT
1 TATAT
29430437 AATTTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (17 bp):
TATATTTACATATATAA
Found at i:29436900 original size:3 final size:3
Alignment explanation
Indices: 29436892--29436936 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
29436882 TCTATTTCTC
* *
29436892 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT TTT AAT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT AT
29436937 AGTTTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29436942 original size:19 final size:19
Alignment explanation
Indices: 29436894--29436950 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
29436884 TATTTCTCAT
* *
29436894 TATTATTA-TTATTATTAT
1 TATTATTATTTATTTTTAA
29436912 TATTATTATTTATTTTTAA
1 TATTATTATTTATTTTTAA
29436931 TATTA-TAGTTTATTTTTAA
1 TATTATTA-TTTATTTTTAA
29436950 T
1 T
29436951 CTATTTACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
18 10 0.29
19 25 0.71
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTATTATTTATTTTTAA
Found at i:29437425 original size:10 final size:10
Alignment explanation
Indices: 29437399--29437429 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
29437389 GTCAAGAAAT
29437399 ATTTTAAAAA
1 ATTTTAAAAA
29437409 ATCTTTAAAAA
1 AT-TTTAAAAA
29437420 ATTTTAAAAA
1 ATTTTAAAAA
29437430 TCATAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTTTAAAAA
Done.