Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 41 of 228
Found at i:12489981 original size:19 final size:19
Alignment explanation
Indices: 12489957--12490002 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
12489947 AGCCGCCCCT
* *
12489957 TTTATTTTATTTTATTTTA
1 TTTATTTTATGTTATATTA
12489976 TTTATTATT-TGTTATATTA
1 TTTATT-TTATGTTATATTA
12489995 -TTATTTTA
1 TTTATTTTA
12490003 CTAATTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 5 0.22
19 14 0.61
20 2 0.09
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTATTTTATGTTATATTA
Found at i:12490016 original size:26 final size:26
Alignment explanation
Indices: 12489964--12490017 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
12489954 CCTTTTATTT
* * *
12489964 TATTTTATTTTATTTATTATTTGTTA
1 TATTTTATTTTACTAATTATTTCTTA
12489990 TATTATTATTTTACTAATT-TTTCTTA
1 TATT-TTATTTTACTAATTATTTCTTA
12490016 TA
1 TA
12490018 CTTAGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (26 bp):
TATTTTATTTTACTAATTATTTCTTA
Found at i:12490131 original size:3 final size:3
Alignment explanation
Indices: 12490123--12490171 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
12490113 ATCATTGAGT
* *
12490123 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TT- TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12490170 TT
1 TT
12490172 TATCTTTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:12490342 original size:32 final size:32
Alignment explanation
Indices: 12490298--12490360 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
12490288 CTTAATCTTC
12490298 TCTATTACTTGTGTTTATTTTCTTATTAGTTA
1 TCTATTACTTGTGTTTATTTTCTTATTAGTTA
*
12490330 TCTATTATTTGTGTTTATTTTCTTATTAGTT
1 TCTATTACTTGTGTTTATTTTCTTATTAGTT
12490361 TGCTCGGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.17, C:0.08, G:0.10, T:0.65
Consensus pattern (32 bp):
TCTATTACTTGTGTTTATTTTCTTATTAGTTA
Found at i:12493545 original size:23 final size:23
Alignment explanation
Indices: 12493518--12493565 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
12493508 TGAAAGTGTA
12493518 AACTTTAGTTATTTATTTGGGAT
1 AACTTTAGTTATTTATTTGGGAT
12493541 AACTTTAGTTATTTATTTGGGAT
1 AACTTTAGTTATTTATTTGGGAT
12493564 AA
1 AA
12493566 TATAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.50
Consensus pattern (23 bp):
AACTTTAGTTATTTATTTGGGAT
Found at i:12493573 original size:19 final size:21
Alignment explanation
Indices: 12493522--12493573 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
12493512 AGTGTAAACT
*
12493522 TTAGTTATTTATTTGGGATAA
1 TTAGTAATTTATTTGGGATAA
*
12493543 CTTTAGTTATTTATTTGGGATAA
1 --TTAGTAATTTATTTGGGATAA
12493566 -TA-TAATTT
1 TTAGTAATTT
12493574 TTAGCTCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.18
20 2 0.07
23 21 0.75
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (21 bp):
TTAGTAATTTATTTGGGATAA
Found at i:12496047 original size:6 final size:6
Alignment explanation
Indices: 12496036--12496066 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12496026 TTTGTGGTGG
*
12496036 ATTAAA ATTAAA ATTAAA ATTAAG ATTAAA A
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA A
12496067 AAAAACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (6 bp):
ATTAAA
Found at i:12496830 original size:22 final size:24
Alignment explanation
Indices: 12496778--12496831 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
12496768 TTTTTTATAA
12496778 TTAAATTATTGTTATTAAATATGCT
1 TTAAATTATTGTTATTAAATAT-CT
* *
12496803 TGAAATTATTG-TATTATATAT-T
1 TTAAATTATTGTTATTAAATATCT
12496825 TTAAATT
1 TTAAATT
12496832 GAATTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 7 0.27
24 9 0.35
25 10 0.38
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (24 bp):
TTAAATTATTGTTATTAAATATCT
Found at i:12500103 original size:15 final size:15
Alignment explanation
Indices: 12500083--12500113 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12500073 TTAGATGTTT
12500083 TGAATGTATTGAAGA
1 TGAATGTATTGAAGA
12500098 TGAATGTATTGAAGA
1 TGAATGTATTGAAGA
12500113 T
1 T
12500114 TCAATTATGA
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:0.39, C:0.00, G:0.26, T:0.35
Consensus pattern (15 bp):
TGAATGTATTGAAGA
Found at i:12501075 original size:13 final size:13
Alignment explanation
Indices: 12501057--12501120 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
12501047 TCTTCATTAT
*
12501057 TTTTGAAAAGTGC
1 TTTTGAAAAGTAC
*
12501070 TTTTGAAAAAGTAA
1 TTTTG-AAAAGTAC
* *
12501084 TGTGGAAAAGTAC
1 TTTTGAAAAGTAC
* **
12501097 TTTTGAGAAGTGT
1 TTTTGAAAAGTAC
12501110 TTTTGAAAAGT
1 TTTTGAAAAGT
12501121 TTGGTTTAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
13 30 0.77
14 9 0.23
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (13 bp):
TTTTGAAAAGTAC
Found at i:12509923 original size:22 final size:21
Alignment explanation
Indices: 12509883--12509923 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12509873 TATTCAAAAA
* *
12509883 TAAAATAATAATTATAAAACT
1 TAAAATAATAATAAAAAAACT
12509904 TAAAACTAATAATAAAAAAA
1 TAAAA-TAATAATAAAAAAA
12509924 TTCAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAAATAATAATAAAAAAACT
Found at i:12510588 original size:124 final size:123
Alignment explanation
Indices: 12510437--12510734 Score: 375
Period size: 124 Copynumber: 2.4 Consensus size: 123
12510427 TCAATTTTTT
* * *
12510437 CCCTTTTATTTGTTGAATGATTGTACCAAAAGATTCTATTGTAGTTTTTCAATTTTTTCAAATAC
1 CCCTTTTATTTGTTGAATGATTGTACCAAAAGATTCTATCGTAGTTTTTCAATTTGTTCAAACAC
* * **
12510502 TT-CAAAACAAAATTTACACGGTTTACTTTAGCCCTTTACTTACATTTTACCCATTTCCC
66 TTCCAAAACAAAATTTACACGATTTACTTTAGCCATTTACTTACATACTACCCATTT--C
* ** * *
12510561 CCCTTTTATTTGTTGAATGATTATACCAAAAGATTCTATCACAGTTTTCCAATTTGTTCAAGCAC
1 CCCTTTTATTTGTTGAATGATTGTACCAAAAGATTCTATCGTAGTTTTTCAATTTGTTCAAACAC
* * * *
12510626 TTCCAAAACAAAATTTACACTATTTACTTTAGTCATTTACTTACATACTACCCCTTTT
66 TTCCAAAACAAAATTTACACGATTTACTTTAGCCATTTACTTACATACTACCCATTTC
** * * *
12510684 TTC-TGTATTTTTTGAATGATTGTGCCAAAAGATTCTATCGTAGTTTTTCAA
1 CCCTTTTATTTGTTGAATGATTGTACCAAAAGATTCTATCGTAGTTTTTCAA
12510735 ACACTTCAAA
Statistics
Matches: 148, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
122 41 0.28
123 1 0.01
124 59 0.40
125 47 0.32
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (123 bp):
CCCTTTTATTTGTTGAATGATTGTACCAAAAGATTCTATCGTAGTTTTTCAATTTGTTCAAACAC
TTCCAAAACAAAATTTACACGATTTACTTTAGCCATTTACTTACATACTACCCATTTC
Found at i:12512701 original size:36 final size:36
Alignment explanation
Indices: 12512658--12512730 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
12512648 TTACACTGAT
*
12512658 TATAGGGAGAAGCCCGACAATTTTTCTCTATGATTA
1 TATAGGGAGAAGCCCCACAATTTTTCTCTATGATTA
12512694 TATAGGGAGAAGCCCCACAATTTTTCTCTATGATTA
1 TATAGGGAGAAGCCCCACAATTTTTCTCTATGATTA
12512730 T
1 T
12512731 GCCCTCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (36 bp):
TATAGGGAGAAGCCCCACAATTTTTCTCTATGATTA
Found at i:12512995 original size:24 final size:24
Alignment explanation
Indices: 12512968--12513019 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12512958 AATCAAAGTC
* *
12512968 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
12512992 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
12513016 AAAT
1 AAAT
12513020 CTTCTGCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:12516407 original size:23 final size:23
Alignment explanation
Indices: 12516381--12516456 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
12516371 ATAAGTACAA
12516381 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
12516404 CACTGTTATGTAGCCGAAACTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
12516427 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12516450 CACTGAT
1 CACTGAT
12516457 CAATAACACT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:12519985 original size:24 final size:24
Alignment explanation
Indices: 12519943--12519994 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
12519933 AATCAAAGTC
** *
12519943 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
12519967 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
12519991 AAAT
1 AAAT
12519995 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:12521265 original size:19 final size:19
Alignment explanation
Indices: 12521241--12521278 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
12521231 GGACACGACA
12521241 TTCAA-CCAGTGTGTTTGAT
1 TTCAACCCAGTG-GTTTGAT
12521260 TTCAACTCCAGTGGTTTGA
1 TTCAAC-CCAGTGGTTTGA
12521279 AATTTTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (19 bp):
TTCAACCCAGTGGTTTGAT
Found at i:12523228 original size:20 final size:20
Alignment explanation
Indices: 12523203--12523240 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12523193 GCTGACAAAA
12523203 CAGTCACTCAACTTTCAATT
1 CAGTCACTCAACTTTCAATT
*
12523223 CAGTCATTCAACTTTCAA
1 CAGTCACTCAACTTTCAA
12523241 AAAATAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (20 bp):
CAGTCACTCAACTTTCAATT
Found at i:12525432 original size:15 final size:17
Alignment explanation
Indices: 12525406--12525440 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
12525396 AAATAGTTGT
12525406 TATTTCAATTGTTTA-A
1 TATTTCAATTGTTTATA
12525422 TATTT-AATTGTTTATA
1 TATTTCAATTGTTTATA
12525438 TAT
1 TAT
12525441 GAATCGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (17 bp):
TATTTCAATTGTTTATA
Found at i:12525619 original size:41 final size:41
Alignment explanation
Indices: 12525562--12525639 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
12525552 TTCTGTCGAG
*
12525562 TAAGACCATAGCTGAAAGACCTTATCG-CATCACGATTGTAT
1 TAAGACCATAACTGAAAGACCTTAT-GTCATCACGATTGTAT
**
12525603 TAAGACCATAACTGAAAGATGTTATGTCATCACGATT
1 TAAGACCATAACTGAAAGACCTTATGTCATCACGATT
12525640 CTATCAAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 32 0.97
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (41 bp):
TAAGACCATAACTGAAAGACCTTATGTCATCACGATTGTAT
Found at i:12525668 original size:45 final size:44
Alignment explanation
Indices: 12525515--12525666 Score: 159
Period size: 45 Copynumber: 3.5 Consensus size: 44
12525505 ACTAGAAATG
* ** *
12525515 AGTAAGACCTTAGCTGAAAGACGTTATAGCATCAAAATTCTGTC
1 AGTAAGACCATAGCTGAAAGACGTTATAGCATCACGATTCTATC
* * *
12525559 GAGTAAGACCATAGCTGAAAGACCTTATCGCATCACGATTGTAT-
1 -AGTAAGACCATAGCTGAAAGACGTTATAGCATCACGATTCTATC
* *
12525603 --TAAGACCATAACTGAAAGATGTTAT-GTCATCACGATTCTATC
1 AGTAAGACCATAGCTGAAAGACGTTATAG-CATCACGATTCTATC
*
12525645 AAGTAAGGCCATAGCTGAAAGA
1 -AGTAAGACCATAGCTGAAAGA
12525667 TGCTATGACA
Statistics
Matches: 89, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
40 1 0.01
41 35 0.39
45 53 0.60
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (44 bp):
AGTAAGACCATAGCTGAAAGACGTTATAGCATCACGATTCTATC
Found at i:12525702 original size:45 final size:45
Alignment explanation
Indices: 12525603--12525711 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
12525593 ACGATTGTAT
* * * * * * *
12525603 TAAGACCATAACTGAAAGATGTTATGTCATCACGATTCTATCAAG
1 TAAGACCATAGCTGAAAGATGCTATGACATCACGAATCAAACAAA
* * *
12525648 TAAGGCCATAGCTGAAAGATGCTATGACATTACGAATCAAAGAAA
1 TAAGACCATAGCTGAAAGATGCTATGACATCACGAATCAAACAAA
*
12525693 TAAGACCATAGTTGAAAGA
1 TAAGACCATAGCTGAAAGA
12525712 CACTATGGCA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (45 bp):
TAAGACCATAGCTGAAAGATGCTATGACATCACGAATCAAACAAA
Found at i:12525718 original size:45 final size:44
Alignment explanation
Indices: 12525648--12525804 Score: 129
Period size: 45 Copynumber: 3.5 Consensus size: 44
12525638 TTCTATCAAG
* * ** *
12525648 TAAGGCCATAGCTGAAAGATGCTATGACATTACGAATCAAAGAAA
1 TAAGACCATAGTTGAAAGACACTATGACATCACGAAT-AAAGAAA
* *
12525693 TAAGACCATAGTTGAAAGACACTATGGCAACATGACGGAA-AATG-AA
1 TAAGACCATAGTTGAAAGACACTAT-G--ACATCAC-GAATAAAGAAA
* * * * *
12525739 TATGACCATGGTTGAAAGACACTATGGCATCAAGAATAGAATAAA
1 TAAGACCATAGTTGAAAGACACTATGACATCACGAATA-AAGAAA
*
12525784 TAAGACCATGGTTGAAAGACA
1 TAAGACCATAGTTGAAAGACA
12525805 TCATGGCACT
Statistics
Matches: 91, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
44 1 0.01
45 44 0.48
46 26 0.29
47 3 0.03
48 6 0.07
49 3 0.03
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.20
Consensus pattern (44 bp):
TAAGACCATAGTTGAAAGACACTATGACATCACGAATAAAGAAA
Found at i:12525811 original size:45 final size:46
Alignment explanation
Indices: 12525690--12525812 Score: 151
Period size: 46 Copynumber: 2.7 Consensus size: 46
12525680 CGAATCAAAG
* * *
12525690 AAATAAGACCATAGTTGAAAGACACTATGGCAACATGACGGAAAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACAGAAAAT
* * * * *
12525736 GAATATGACCATGGTTGAAAGACACTATGGCATCAAGA-ATAGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACAGAAAAT
12525781 AAATAAGACCATGGTTGAAAGACA-TCATGGCA
1 AAATAAGACCATGGTTGAAAGACACT-ATGGCA
12525813 CTGTCCGATT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 32 0.48
46 33 0.50
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.20
Consensus pattern (46 bp):
AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACAGAAAAT
Found at i:12527530 original size:42 final size:42
Alignment explanation
Indices: 12527451--12527532 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
12527441 TAGACACAAG
* **
12527451 GGCTGGAACACGACCGTGTGTCTCAATTCAGTGAGTTACACA
1 GGCTGGAACACGACCGTGTGTCCCAATTCAGAAAGTTACACA
* * **
12527493 GGCTGGAACACGGCTGTGTGTCCCAATTTTGAAAGTTACA
1 GGCTGGAACACGACCGTGTGTCCCAATTCAGAAAGTTACA
12527533 AGGTCTAGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (42 bp):
GGCTGGAACACGACCGTGTGTCCCAATTCAGAAAGTTACACA
Found at i:12528822 original size:17 final size:17
Alignment explanation
Indices: 12528796--12528879 Score: 64
Period size: 17 Copynumber: 4.9 Consensus size: 17
12528786 ATCGTAGGAT
* *
12528796 TGCGAACTCACCAAATG
1 TGCGAGCTCACCAAATC
*
12528813 TGCGAGCTCACCCAAAAC
1 TGCGAGCTCA-CCAAATC
* *
12528831 TGTGAGCTCATCAAGA-C
1 TGCGAGCTCACCAA-ATC
* *
12528848 TGCGAGCTCTCC-AATAG
1 TGCGAGCTCACCAAAT-C
12528865 TGCGAGCTCACCAAA
1 TGCGAGCTCACCAAA
12528880 GCTTCGTAGT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
15 1 0.02
16 1 0.02
17 33 0.63
18 17 0.33
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (17 bp):
TGCGAGCTCACCAAATC
Found at i:12532542 original size:4 final size:4
Alignment explanation
Indices: 12532533--12532571 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
12532523 CTACATATAG
12532533 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
12532572 TGTATGTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:12538807 original size:23 final size:23
Alignment explanation
Indices: 12538764--12538809 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12538754 CTTGCCTGTG
* *
12538764 TGGCGCACACGGCCTAGCTTGTA
1 TGGCCCACACGGCCTAACTTGTA
12538787 TGGCCCACACGGCC-ACACTTGTA
1 TGGCCCACACGGCCTA-ACTTGTA
12538810 CCGTCACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.20, C:0.35, G:0.26, T:0.20
Consensus pattern (23 bp):
TGGCCCACACGGCCTAACTTGTA
Found at i:12541316 original size:21 final size:21
Alignment explanation
Indices: 12541300--12541460 Score: 121
Period size: 21 Copynumber: 7.8 Consensus size: 21
12541290 TTAGCTTTTT
12541300 TGAGCTTCTATTCAGCTCTTA
1 TGAGCTTCTATTCAGCTCTTA
** *
12541321 CAAGCTTCTATTCAACTCTTA
1 TGAGCTTCTATTCAGCTCTTA
*
12541342 TGAG-TTCTATTAAGCTCTTA
1 TGAGCTTCTATTCAGCTCTTA
* * * *
12541362 CGAGCTTATGTTCAACTCTTA
1 TGAGCTTCTATTCAGCTCTTA
* * *
12541383 TGAGATTCTGTTCAGCTCTGA
1 TGAGCTTCTATTCAGCTCTTA
* * * *
12541404 CGAGCTTTTGTTCAACT-TT-
1 TGAGCTTCTATTCAGCTCTTA
* * * *
12541423 TGAGTTTCTGTTTAACTCTTA
1 TGAGCTTCTATTCAGCTCTTA
*
12541444 TGAGCTTCTATTTAGCT
1 TGAGCTTCTATTCAGCT
12541461 TTCGAGCTTA
Statistics
Matches: 108, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
19 13 0.12
20 20 0.19
21 75 0.69
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.43
Consensus pattern (21 bp):
TGAGCTTCTATTCAGCTCTTA
Found at i:12541362 original size:41 final size:42
Alignment explanation
Indices: 12541300--12541455 Score: 158
Period size: 41 Copynumber: 3.8 Consensus size: 42
12541290 TTAGCTTTTT
* * *
12541300 TGAGCTTCTATTCAGCTCTTACAAGCTTCTATTCAACTCTTA
1 TGAGATTCTATTAAGCTCTTACGAGCTTCTATTCAACTCTTA
* *
12541342 TGAG-TTCTATTAAGCTCTTACGAGCTTATGTTCAACTCTTA
1 TGAGATTCTATTAAGCTCTTACGAGCTTCTATTCAACTCTTA
* * * * *
12541383 TGAGATTCTGTTCAGCTCTGACGAGCTTTTGTTCAACT-TT-
1 TGAGATTCTATTAAGCTCTTACGAGCTTCTATTCAACTCTTA
* * *
12541423 TGAGTTTCTGTTTAA-CTCTTATGAGCTTCTATT
1 TGAGATTCT-ATTAAGCTCTTACGAGCTTCTATT
12541456 TAGCTTTCGA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 22 0.23
41 42 0.43
42 33 0.34
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (42 bp):
TGAGATTCTATTAAGCTCTTACGAGCTTCTATTCAACTCTTA
Found at i:12553036 original size:232 final size:231
Alignment explanation
Indices: 12552617--12553045 Score: 597
Period size: 232 Copynumber: 1.9 Consensus size: 231
12552607 TCATAAATAA
*
12552617 GTGAACTCTTAATGAACTGTTCATGATAACAAATCAATAAACTGAAATTGTGATCATAAATCAGC
1 GTGAACTCTTAATGAACTGTTCATCATAACAAATCAATAAACTGAAATTGTGATCATAAATCAGC
* * * **
12552682 AAGCTTTAAAATTACAATTGTGATCGTAAATCAATGAATTGTTTAAGTGGAGTCGCGATCGTAAA
66 AAGCTTTAAAATAACAATTGTGATCGTAAATCAATGAACTATTTAAGTAAAGTCGCGATCGTAAA
* * * *
12552747 TCAACAAACTCTTAATGAATTGTTCATGATCGTAAATTAATGAACTGAAACTGTGATCGTAAATT
131 TCAACAAAATCTTAATGAATTATTCATGATCATAAATCAATGAACTGAAACTGTGATCGTAAATT
12552812 AGCAAACTGTTTAAGTAGAGTAGCAATCGTAAATTG
196 AGCAAACTGTTTAAGTAGAGTAGCAATCGTAAATTG
* *** * * * * *
12552848 GTGAACTCTTAATGAATTGTTCATCATCGTAAATCAATGAACTGAAGTTGTGGTCTTAAATCATC
1 GTGAACTCTTAATGAACTGTTCATCATAACAAATCAATAAACTGAAATTGTGATCATAAATCAGC
* * * * * *
12552913 GAGCTTTAAAAATAACAGTTGTGATCGTGAATCAATGAACTATTTACGTAAAGTCGCGATCTTAG
66 AAGCTTT-AAAATAACAATTGTGATCGTAAATCAATGAACTATTTAAGTAAAGTCGCGATCGTAA
* **
12552978 ATCTACAAAATCTTAATGAATTATTCATGATCATAAATCAATGAACTGAAGTTGTGATCGTAAAT
130 ATCAACAAAATCTTAATGAATTATTCATGATCATAAATCAATGAACTGAAACTGTGATCGTAAAT
12553043 TAG
195 TAG
12553046 TGAGCTTTGA
Statistics
Matches: 169, Mismatches: 28, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
231 61 0.36
232 108 0.64
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (231 bp):
GTGAACTCTTAATGAACTGTTCATCATAACAAATCAATAAACTGAAATTGTGATCATAAATCAGC
AAGCTTTAAAATAACAATTGTGATCGTAAATCAATGAACTATTTAAGTAAAGTCGCGATCGTAAA
TCAACAAAATCTTAATGAATTATTCATGATCATAAATCAATGAACTGAAACTGTGATCGTAAATT
AGCAAACTGTTTAAGTAGAGTAGCAATCGTAAATTG
Found at i:12553042 original size:134 final size:134
Alignment explanation
Indices: 12552798--12553190 Score: 430
Period size: 134 Copynumber: 2.9 Consensus size: 134
12552788 GAACTGAAAC
* * * * * * *** *
12552798 TGTGATCGTAAATTAGCAAACTGTTTAAGTAGAGTAGCAATCGTAAATTGGTGAACTCTTAATGA
1 TGTGATCATAAATCAACAAACTATTTAAGTAAAGTAGCGATCGTAAATTGACAAAATCTTAATGA
* * *
12552863 ATTGTTCATCATCGTAAATCAATGAACTGAAGTTGTGGTCTTAAATCA-TCGAGCTTTAAAAATA
66 ATTGTTCATGATCGTAAATCAATGAACTGAAGTTGTGATCGTAAATCAGT-GAGCTTTAAAAATA
12552927 ACAGT
130 ACAGT
* * ** * * * *
12552932 TGTGATCGTGAATCAATGAACTATTTACGTAAAGTCGCGATCTTAGATCT-ACAAAATCTTAATG
1 TGTGATCATAAATCAACAAACTATTTAAGTAAAGTAGCGATCGTAAAT-TGACAAAATCTTAATG
* * * * *
12552996 AATTATTCATGATCATAAATCAATGAACTGAAGTTGTGATCGTAAATTAGTGAGCTTTGAAAATG
65 AATTGTTCATGATCGTAAATCAATGAACTGAAGTTGTGATCGTAAATCAGTGAGCTTTAAAAATA
12553061 ACAGT
130 ACAGT
** * *
12553066 TGTGATCATAAATCAACAAACTATTTAAGTGGAGTAGTGATCGTAAATTGACGAAATCTTAATGA
1 TGTGATCATAAATCAACAAACTATTTAAGTAAAGTAGCGATCGTAAATTGACAAAATCTTAATGA
* * * * * *
12553131 ATTGCTCATGATCGTAAATCAATGAACTGAAGTTATGATTGTAAATTAGAGAGTTTTAAA
66 ATTGTTCATGATCGTAAATCAATGAACTGAAGTTGTGATCGTAAATCAGTGAGCTTTAAA
12553191 TTTGGTTCAT
Statistics
Matches: 212, Mismatches: 44, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
133 1 0.00
134 209 0.99
135 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (134 bp):
TGTGATCATAAATCAACAAACTATTTAAGTAAAGTAGCGATCGTAAATTGACAAAATCTTAATGA
ATTGTTCATGATCGTAAATCAATGAACTGAAGTTGTGATCGTAAATCAGTGAGCTTTAAAAATAA
CAGT
Found at i:12556431 original size:84 final size:84
Alignment explanation
Indices: 12556325--12556484 Score: 302
Period size: 84 Copynumber: 1.9 Consensus size: 84
12556315 TTTTATGTAT
12556325 GCGCCGCTATTGGTTAGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
1 GCGCCGCTATTGGTTAGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
12556390 TAGCGGCGTTTCTATCCTA
66 TAGCGGCGTTTCTATCCTA
*
12556409 GCGCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
1 GCGCCGCTATTGGTTAGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
*
12556474 TAGTGGCGTTT
66 TAGCGGCGTTT
12556485 GGTTTTAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.17, C:0.16, G:0.32, T:0.35
Consensus pattern (84 bp):
GCGCCGCTATTGGTTAGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
TAGCGGCGTTTCTATCCTA
Found at i:12556479 original size:42 final size:42
Alignment explanation
Indices: 12556348--12556482 Score: 125
Period size: 42 Copynumber: 3.2 Consensus size: 42
12556338 TTAGGGGTGA
12556348 TAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
1 TAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
* * * * * * * **
12556390 TAGCGGCGT-TTCT-ATCCTAGCGCCGCTATTGGTTGGGGGTGA--
1 TAGTGGCGTGTTTTGGT-CAATCGCCACTAAT-GTT-AAGGT-ATT
12556432 TAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
1 TAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
12556474 TAGTGGCGT
1 TAGTGGCGT
12556483 TTGGTTTTAA
Statistics
Matches: 67, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
40 2 0.03
41 16 0.24
42 31 0.46
43 16 0.24
44 2 0.03
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.36
Consensus pattern (42 bp):
TAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATT
Found at i:12557321 original size:20 final size:20
Alignment explanation
Indices: 12557296--12557343 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
12557286 CGGGTATGGA
12557296 TTAGGGTTTG-GGATTAAGGT
1 TTAGGGTTTGAGG-TTAAGGT
* *
12557316 TTAGGGGTTGAGGTTAGGGT
1 TTAGGGTTTGAGGTTAAGGT
*
12557336 CTAGGGTT
1 TTAGGGTT
12557344 AGGGGTTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.17, C:0.02, G:0.44, T:0.38
Consensus pattern (20 bp):
TTAGGGTTTGAGGTTAAGGT
Found at i:12557353 original size:13 final size:13
Alignment explanation
Indices: 12557296--12557354 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
12557286 CGGGTATGGA
* *
12557296 TTAGGGTTTGGGA
1 TTAGGGTTAGGGG
*
12557309 TTAAGGTTTAGGGG
1 TT-AGGGTTAGGGG
12557323 TT-GAGGTTA-GGG
1 TTAG-GGTTAGGGG
12557335 TCTAGGGTTAGGGG
1 T-TAGGGTTAGGGG
12557349 TTAGGG
1 TTAGGG
12557355 GTTAAGGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
12 5 0.14
13 17 0.46
14 15 0.41
ACGTcount: A:0.17, C:0.02, G:0.47, T:0.34
Consensus pattern (13 bp):
TTAGGGTTAGGGG
Found at i:12557378 original size:28 final size:28
Alignment explanation
Indices: 12557347--12557429 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
12557337 TAGGGTTAGG
12557347 GGTTAGGGGTTAAGGATTTGGGGTTTGT
1 GGTTAGGGGTTAAGGATTTGGGGTTTGT
** *
12557375 GGTT-GGTGGTTTGGGGTTTGGGGTTTGT
1 GGTTAGG-GGTTAAGGATTTGGGGTTTGT
* * * *
12557403 GATTTAGGGTTTAAGGTTTTAGGGTTT
1 G-GTTAGGGGTTAAGGATTTGGGGTTT
12557430 TAGGGTTTGG
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
27 2 0.05
28 23 0.53
29 16 0.37
30 2 0.05
ACGTcount: A:0.11, C:0.00, G:0.45, T:0.45
Consensus pattern (28 bp):
GGTTAGGGGTTAAGGATTTGGGGTTTGT
Found at i:12557387 original size:21 final size:21
Alignment explanation
Indices: 12557361--12557414 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
12557351 AGGGGTTAAG
*
12557361 GATTTGGGGTTTGTGGTTGGT
1 GATTTGGGGTTTGGGGTTGGT
* *
12557382 GGTTTGGGGTTTGGGGTTTGT
1 GATTTGGGGTTTGGGGTTGGT
*
12557403 GATTTAGGGTTT
1 GATTTGGGGTTT
12557415 AAGGTTTTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.06, C:0.00, G:0.46, T:0.48
Consensus pattern (21 bp):
GATTTGGGGTTTGGGGTTGGT
Found at i:12557415 original size:7 final size:7
Alignment explanation
Indices: 12557296--12557454 Score: 64
Period size: 7 Copynumber: 22.9 Consensus size: 7
12557286 CGGGTATGGA
12557296 TTAGGGT
1 TTAGGGT
*
12557303 TT-GGGA
1 TTAGGGT
*
12557309 TTAAGGT
1 TTAGGGT
*
12557316 TTAGGGG
1 TTAGGGT
12557323 TT-GAGG-
1 TTAG-GGT
12557329 TTAGGGT
1 TTAGGGT
*
12557336 CTAGGG-
1 TTAGGGT
*
12557342 TTAGGGG
1 TTAGGGT
12557349 TTAGGGGT
1 TTA-GGGT
* *
12557357 TAAGGAT
1 TTAGGGT
*
12557364 TTGGGGT
1 TTAGGGT
12557371 TT-GTGG-
1 TTAG-GGT
*
12557377 TTGGTGGT
1 TTAG-GGT
*
12557385 TTGGGGT
1 TTAGGGT
*
12557392 TTGGGGT
1 TTAGGGT
*
12557399 TT-GTGAT
1 TTAG-GGT
12557406 TTAGGGT
1 TTAGGGT
*
12557413 TTAAGGTT
1 TT-AGGGT
12557421 TTAGGGTT
1 TTAGGG-T
12557429 TTAGGGT
1 TTAGGGT
*
12557436 TT-GGGA
1 TTAGGGT
*
12557442 TTAAGGT
1 TTAGGGT
12557449 TTAGGG
1 TTAGGG
12557455 GTTAAGGACT
Statistics
Matches: 117, Mismatches: 21, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
6 24 0.21
7 70 0.60
8 23 0.20
ACGTcount: A:0.14, C:0.01, G:0.45, T:0.40
Consensus pattern (7 bp):
TTAGGGT
Found at i:12557428 original size:8 final size:8
Alignment explanation
Indices: 12557405--12557437 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
12557395 GGGTTTGTGA
12557405 TTTAGGG-
1 TTTAGGGT
*
12557412 TTTAAGGT
1 TTTAGGGT
12557420 TTTAGGGT
1 TTTAGGGT
12557428 TTTAGGGT
1 TTTAGGGT
12557436 TT
1 TT
12557438 GGGATTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (8 bp):
TTTAGGGT
Found at i:12557461 original size:14 final size:14
Alignment explanation
Indices: 12557405--12557461 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
12557395 GGGTTTGTGA
12557405 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
*
12557419 TTTTAGGGTTTTAGGG
1 -TTTAGGG-TTTAAGG
*
12557435 TTT-GGGATTAAGG
1 TTTAGGGTTTAAGG
*
12557448 TTTAGGGGTTAAGG
1 TTTAGGGTTTAAGG
12557462 ACTTAGGAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 8 0.22
14 12 0.33
15 10 0.28
16 6 0.17
ACGTcount: A:0.19, C:0.00, G:0.39, T:0.42
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:12558013 original size:16 final size:16
Alignment explanation
Indices: 12557992--12558027 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12557982 ACTTAGTAAT
* *
12557992 TAAAAGATACAATTAA
1 TAAAAGATAAAATAAA
12558008 TAAAAGATAAAATAAA
1 TAAAAGATAAAATAAA
12558024 TAAA
1 TAAA
12558028 GAAATGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (16 bp):
TAAAAGATAAAATAAA
Found at i:12558349 original size:23 final size:23
Alignment explanation
Indices: 12558323--12558371 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
12558313 CACTTAGCTG
*
12558323 AAATTTCCCCCAAATTATCCCCA
1 AAATTCCCCCCAAATTATCCCCA
* *
12558346 AAATTCCCCCCGAATTTTCCCCA
1 AAATTCCCCCCAAATTATCCCCA
12558369 AAA
1 AAA
12558372 AATCCCTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.39, G:0.02, T:0.24
Consensus pattern (23 bp):
AAATTCCCCCCAAATTATCCCCA
Found at i:12558858 original size:22 final size:23
Alignment explanation
Indices: 12558833--12558892 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
12558823 TTTTGCAGGC
12558833 TTGTAATACTGTTTGTTCATAA-
1 TTGTAATACTGTTTGTTCATAAG
* *
12558855 TTGTTACTAAT-TTTGTTCATAAG
1 TTG-TAATACTGTTTGTTCATAAG
12558878 TT-TGAA-ACTGTTTGT
1 TTGT-AATACTGTTTGT
12558893 ATTACAGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
21 3 0.10
22 20 0.67
23 7 0.23
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (23 bp):
TTGTAATACTGTTTGTTCATAAG
Found at i:12559089 original size:14 final size:14
Alignment explanation
Indices: 12559057--12559083 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12559047 TTGAAACTTT
12559057 AAATTTAAATTTTA
1 AAATTTAAATTTTA
12559071 AAATTTAAATTTT
1 AAATTTAAATTTT
12559084 GTAATTATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTTAAATTTTA
Found at i:12560259 original size:27 final size:25
Alignment explanation
Indices: 12560229--12560338 Score: 58
Period size: 27 Copynumber: 4.5 Consensus size: 25
12560219 ATAATAAATT
12560229 TTATATTTTTAAAACTAATTGTACATG
1 TTATATTTTTAAAA-TAATT-TACATG
*
12560256 TTAT-TTTTCT-AAAT-ATTAACAT-
1 TTATATTTT-TAAAATAATTTACATG
* * * *
12560278 ATATA-TTTT-CAATAA--TAAATT
1 TTATATTTTTAAAATAATTTACATG
12560299 TTATATTTTTAAAACTAATTGTACATG
1 TTATATTTTTAAAA-TAATT-TACATG
12560326 TTAT-TTTTCTAAA
1 TTATATTTT-TAAA
12560339 TATTAACATA
Statistics
Matches: 63, Mismatches: 9, Indels: 22
0.67 0.10 0.23
Matches are distributed among these distances:
20 3 0.05
21 8 0.13
22 11 0.17
23 6 0.10
24 6 0.10
25 1 0.02
26 11 0.17
27 17 0.27
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (25 bp):
TTATATTTTTAAAATAATTTACATG
Found at i:12560284 original size:24 final size:24
Alignment explanation
Indices: 12560257--12560356 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 24
12560247 TTGTACATGT
12560257 TATTTTTCTAAATATTAACATATA
1 TATTTTTCTAAATATTAACATATA
* *
12560281 TA-TTTTC--AATAATAA-ATTTTA
1 TATTTTTCTAAATATTAACA-TATA
* * *
12560302 TATTTTT-AAAACTAATTGTACATGT-
1 TATTTTTCTAAA-T-ATT-AACATATA
12560327 TATTTTTCTAAATATTAACATATA
1 TATTTTTCTAAATATTAACATATA
12560351 TATTTT
1 TATTTT
12560357 CAATAGTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
20 1 0.02
21 12 0.21
22 4 0.07
23 12 0.21
24 12 0.21
25 10 0.17
26 6 0.10
27 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTTTTCTAAATATTAACATATA
Found at i:12560436 original size:69 final size:70
Alignment explanation
Indices: 12560210--12560532 Score: 494
Period size: 69 Copynumber: 4.6 Consensus size: 70
12560200 TTATATTTAA
* *
12560210 ATATTGTT-AATAATAAATTTTATATTTTTA-AAACTAATTGTACATGTTATTTTTCTAAATATT
1 ATATT-TTCAATAATAAATTTTATAATTTTAGAAA-TAATTGTAAATGTTATTTTTCTAAATATT
12560273 AACATAT
64 AACATAT
* *
12560280 ATATTTTCAATAATAAATTTTATATTTTTA-AAACTAATTGTACATGTTATTTTTCTAAATATTA
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAA-TAATTGTAAATGTTATTTTTCTAAATATTA
12560344 ACATAT
65 ACATAT
* *
12560350 ATATTTTCAATAGTAAATTTTATAATTTTAGAAATTATTGTAAATGTTA-TTTTCTAAATATTAA
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATTAA
*
12560414 CATCT
66 CATAT
*
12560419 ATATTTTCAATAATAAATTTTATAATTTTAGAAATTATTGTAAATGTTA-TTTTCTAAATATTAA
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATTAA
*
12560483 CATCT
66 CATAT
*
12560488 ATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAAT
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAAT
12560533 ATTACATAAT
Statistics
Matches: 243, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
69 132 0.54
70 108 0.44
71 3 0.01
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.49
Consensus pattern (70 bp):
ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATTAA
CATAT
Found at i:12560436 original size:139 final size:139
Alignment explanation
Indices: 12560210--12560532 Score: 492
Period size: 139 Copynumber: 2.3 Consensus size: 139
12560200 TTATATTTAA
* *
12560210 ATATTGTT-AATAATAAATTTTATATTTTTA-AAACTAATTGTACATGTTATTTTTCTAAATATT
1 ATATT-TTCAATAATAAATTTTATAATTTTAGAAA-TAATTGTAAATGTTATTTTTCTAAATATT
* *
12560273 AACATATATATTTTCAATAATAAATTTTATATTTTTA-AAACTAATTGTACATGTTATTTTTCTA
64 AACATATATATTTTCAATAATAAATTTTATAATTTTAGAAA-TAATTGTAAATGTTA-TTTTCTA
12560337 AATATTAACATAT
127 AATATTAACATAT
* *
12560350 ATATTTTCAATAGTAAATTTTATAATTTTAGAAATTATTGTAAATGTTA-TTTTCTAAATATTAA
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATTAA
* *
12560414 CATCTATATTTTCAATAATAAATTTTATAATTTTAGAAATTATTGTAAATGTTATTTTCTAAATA
66 CATATATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATA
*
12560479 TTAACATCT
131 TTAACATAT
*
12560488 ATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAAT
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAAT
12560533 ATTACATAAT
Statistics
Matches: 168, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
138 61 0.36
139 63 0.38
140 41 0.24
141 3 0.02
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.49
Consensus pattern (139 bp):
ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATTAA
CATATATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATA
TTAACATAT
Found at i:12560787 original size:16 final size:16
Alignment explanation
Indices: 12560764--12561231 Score: 122
Period size: 16 Copynumber: 27.9 Consensus size: 16
12560754 GTCGGACTTC
*
12560764 CATAACTTATATAATA
1 CATAACTTACATAATA
*
12560780 CTTAACTTACATAATA
1 CATAACTTACATAATA
12560796 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
12560813 CATAA--TA-AGT--TA
1 CATAACTTACA-TAATA
*
12560825 CATAA--T--ATTATA
1 CATAACTTACATAATA
*
12560837 CATAACTCACATAACTA
1 CATAACTTACATAA-TA
*
12560854 AATGAA-TT-CATATTATA
1 CAT-AACTTACATA--ATA
* ** * *
12560871 CATTAACTTGTCGGACTTG
1 CA-TAACTT-ACATA-ATA
*
12560890 CATAACTTATATAATA
1 CATAACTTACATAATA
*
12560906 CTTAACTTACATAACTTA
1 CATAACTTACATAA--TA
*
12560924 CTTAACTTACATAATA
1 CATAACTTACATAATA
12560940 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
*
12560957 CATAATAAGTTACATAATATTTA
1 C---ATAACTTACAT-A-A--TA
*
12560980 CATAACTCACATAACTA
1 CATAACTTACATAA-TA
*
12560997 AATGAA-TTA-ATATTATA
1 CAT-AACTTACATA--ATA
* ** * *
12561014 CATTAACTTGTCGGACTTG
1 CA-TAACTT-ACATA-ATA
*
12561033 CATAACTTATATAATA
1 CATAACTTACATAATA
*
12561049 CTTAACTTACATAACTTA
1 CATAACTTACATAA--TA
*
12561067 CATAA-TAACATAATA
1 CATAACTTACATAATA
* *
12561082 -AGTTACATA-ATATTATA
1 CA-TAACTTACATA--ATA
*
12561099 CATAACTCACATAACTA
1 CATAACTTACATAA-TA
* * * *
12561116 AATTAATTTATATTATA
1 CA-TAACTTACATAATA
* ** * *
12561133 CATTAACTTGTCGGACTTG
1 CA-TAACTT-ACATA-ATA
*
12561152 CATAACTTATATAATA
1 CATAACTTACATAATA
*
12561168 CTTAACTTACATAACTTA
1 CATAACTTACATAA--TA
12561186 CATAACTTACATAATA
1 CATAACTTACATAATA
*
12561202 CATAACTTACGTAATA
1 CATAACTTACATAATA
*
12561218 CGTAACTTACATAA
1 CATAACTTACATAA
12561232 CTCATATATA
Statistics
Matches: 328, Mismatches: 77, Indels: 94
0.66 0.15 0.19
Matches are distributed among these distances:
10 1 0.00
11 1 0.00
12 14 0.04
13 1 0.00
14 2 0.01
15 10 0.03
16 124 0.38
17 58 0.18
18 80 0.24
19 10 0.03
20 22 0.07
21 1 0.00
22 1 0.00
23 2 0.01
24 1 0.00
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.35
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:12560950 original size:9 final size:9
Alignment explanation
Indices: 12560885--12561233 Score: 87
Period size: 9 Copynumber: 39.3 Consensus size: 9
12560875 AACTTGTCGG
*
12560885 ACTTGCATA
1 ACTTACATA
*
12560894 ACTTATATA
1 ACTTACATA
*
12560903 A--TACTTA
1 ACTTACATA
12560910 ACTTACATA
1 ACTTACATA
*
12560919 ACTTACTTA
1 ACTTACATA
12560928 ACTTACATA
1 ACTTACATA
12560937 A--TACATA
1 ACTTACATA
12560944 ACTTACATA
1 ACTTACATA
*
12560953 A-TAACATAATA
1 ACTTAC---ATA
*
12560964 AGTTACATAA
1 ACTTACAT-A
*
12560974 TATTTACATA
1 -ACTTACATA
*
12560984 ACTCACATA
1 ACTTACATA
*
12560993 AC-TAAATGA
1 ACTTACAT-A
12561002 A-TTA-AT-
1 ACTTACATA
*
12561008 ATTATACATTA
1 ACT-TACA-TA
* **
12561019 ACTTGTC-GG
1 ACTT-ACATA
*
12561028 ACTTGCATA
1 ACTTACATA
*
12561037 ACTTATATA
1 ACTTACATA
*
12561046 A--TACTTA
1 ACTTACATA
12561053 ACTTACATA
1 ACTTACATA
12561062 ACTTACATA
1 ACTTACATA
*
12561071 A-TAACATAATA
1 ACTTAC---ATA
*
12561082 AGTTACATAA
1 ACTTACAT-A
*
12561092 TATTATACATA
1 -ACT-TACATA
*
12561103 ACTCACATA
1 ACTTACATA
*
12561112 AC-TAAATTA
1 ACTTACA-TA
* * *
12561121 ATTTATATT
1 ACTTACATA
12561130 A--TACATTA
1 ACTTACA-TA
* **
12561138 ACTTGTCGGA
1 ACTT-ACATA
*
12561148 -CTTGCATA
1 ACTTACATA
*
12561156 ACTTATATA
1 ACTTACATA
*
12561165 A--TACTTA
1 ACTTACATA
12561172 ACTTACATA
1 ACTTACATA
12561181 ACTTACATA
1 ACTTACATA
12561190 ACTTACATA
1 ACTTACATA
12561199 A--TACATA
1 ACTTACATA
*
12561206 ACTTACGTA
1 ACTTACATA
*
12561215 A--TACGTA
1 ACTTACATA
12561222 ACTTACATA
1 ACTTACATA
12561231 ACT
1 ACT
12561234 CATATATACT
Statistics
Matches: 248, Mismatches: 51, Indels: 82
0.65 0.13 0.22
Matches are distributed among these distances:
6 1 0.00
7 40 0.16
8 20 0.08
9 142 0.57
10 12 0.05
11 22 0.09
12 11 0.04
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.36
Consensus pattern (9 bp):
ACTTACATA
Found at i:12560984 original size:20 final size:21
Alignment explanation
Indices: 12560937--12560993 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
12560927 AACTTACATA
12560937 ATACATAACTTACATAATAAC
1 ATACATAACTTACATAATAAC
* *
12560958 ATA-ATAAGTTACATAAT-AT
1 ATACATAACTTACATAATAAC
* *
12560977 TTACATAACTCACATAA
1 ATACATAACTTACATAA
12560994 CTAAATGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.80
21 3 0.10
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.32
Consensus pattern (21 bp):
ATACATAACTTACATAATAAC
Found at i:12561117 original size:262 final size:266
Alignment explanation
Indices: 12560711--12561217 Score: 896
Period size: 262 Copynumber: 1.9 Consensus size: 266
12560701 TAACAACTTG
*
12560711 CATAACTCACATAACTAAATCAATTTATATTATACATTAACTTGTCGGACTTCCATAACTTATAT
1 CATAACTCACATAACTAAATCAATTAATATTATACATTAACTTGTCGGACTTCCATAACTTATAT
12560776 AATACTTAACTTACATAATACATAACTTACATAATAACATAATAAGTTACATAATATTATACATA
66 AATACTTAA--TACAT-ATACATAACTTACATAATAACATAATAAGTTACATAATATTATACATA
12560841 ACTCACATAACTAAATGAATTCATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATA
128 ACTCACATAACTAAATGAATTCATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATA
*
12560906 CTTAACTTACATAACTTACTTAACTTACATAATACATAACTTACATAATAACATAATAAGTTACA
193 CTTAACTTACATAACTTACATAACTTACATAATACATAACTTACATAATAACATAATAAGTTACA
12560971 TAATATTTA
258 TAATATTTA
* *
12560980 CATAACTCACATAACTAAATGAATTAATATTATACATTAACTTGTCGGACTTGCATAACTTATAT
1 CATAACTCACATAACTAAATCAATTAATATTATACATTAACTTGTCGGACTTCCATAACTTATAT
12561045 AATACTT-A-AC-T-TACATAACTTACATAATAACATAATAAGTTACATAATATTATACATAACT
66 AATACTTAATACATATACATAACTTACATAATAACATAATAAGTTACATAATATTATACATAACT
* *
12561106 CACATAACTAAATTAATTTATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTT
131 CACATAACTAAATGAATTCATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTT
*
12561171 AACTTACATAACTTACATAACTTACATAATACATAACTTACGTAATA
196 AACTTACATAACTTACATAACTTACATAATACATAACTTACATAATA
12561218 CGTAACTTAC
Statistics
Matches: 231, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
262 158 0.68
264 1 0.00
265 2 0.01
268 1 0.00
269 69 0.30
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.36
Consensus pattern (266 bp):
CATAACTCACATAACTAAATCAATTAATATTATACATTAACTTGTCGGACTTCCATAACTTATAT
AATACTTAATACATATACATAACTTACATAATAACATAATAAGTTACATAATATTATACATAACT
CACATAACTAAATGAATTCATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTT
AACTTACATAACTTACATAACTTACATAATACATAACTTACATAATAACATAATAAGTTACATAA
TATTTA
Found at i:12561151 original size:119 final size:118
Alignment explanation
Indices: 12560938--12561201 Score: 483
Period size: 119 Copynumber: 2.2 Consensus size: 118
12560928 ACTTACATAA
12560938 TACATAACTTACATAATAACATAATAAGTTACATAATATTTACATAACTCACATAACTAAATGAA
1 TACATAACTTACATAATAACATAATAAGTTACATAATATTTACATAACTCACATAACTAAATGAA
12561003 TTAATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACT
66 TTAATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACT
*
12561056 TACATAACTTACATAATAACATAATAAGTTACATAATATTATACATAACTCACATAACTAAATTA
1 TACATAACTTACATAATAACATAATAAGTTACATAATATT-TACATAACTCACATAACTAAATGA
*
12561121 ATTTATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACT
65 ATTAATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACT
*
12561175 TACATAACTTACATAACTTACATAATA
1 TACATAACTTACATAA-TAACATAATA
12561202 CATAACTTAC
Statistics
Matches: 141, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
118 40 0.28
119 92 0.65
120 9 0.06
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (118 bp):
TACATAACTTACATAATAACATAATAAGTTACATAATATTTACATAACTCACATAACTAAATGAA
TTAATATTATACATTAACTTGTCGGACTTGCATAACTTATATAATACTTAACT
Found at i:12561181 original size:25 final size:25
Alignment explanation
Indices: 12561147--12561233 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 25
12561137 AACTTGTCGG
* *
12561147 ACTTGCATAACTTATATAATACTTA
1 ACTTACATAACTTACATAATACTTA
*
12561172 ACTTACATAACTTACATAACTTACATA
1 ACTTACATAACTTACATAA--TACTTA
* *
12561199 A--TACATAACTTACGTAATACGTA
1 ACTTACATAACTTACATAATACTTA
12561222 ACTTACATAACT
1 ACTTACATAACT
12561234 CATATATACT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
23 6 0.11
25 41 0.77
27 6 0.11
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.34
Consensus pattern (25 bp):
ACTTACATAACTTACATAATACTTA
Found at i:12561190 original size:34 final size:34
Alignment explanation
Indices: 12561147--12561231 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 34
12561137 AACTTGTCGG
* * *
12561147 ACTTGCATAACTTATATAATACTTAACTTACATA
1 ACTTACATAACTTACATAATACATAACTTACATA
*
12561181 ACTTACATAACTTACATAATACATAACTTACGTA
1 ACTTACATAACTTACATAATACATAACTTACATA
*
12561215 A--TACGTAACTTACATAA
1 ACTTACATAACTTACATAA
12561232 CTCATATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 15 0.33
34 31 0.67
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.34
Consensus pattern (34 bp):
ACTTACATAACTTACATAATACATAACTTACATA
Found at i:12567177 original size:44 final size:43
Alignment explanation
Indices: 12567111--12567212 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 43
12567101 AGGTTAATGC
* ** * **
12567111 ATTTAGTGGCGTTTTTATGAAAAGCGTCGCTAAAAGTCAAGGT
1 ATTTAGCGGCGTTTGCAAGAAAAGCACCGCTAAAAGTCAAGGT
* * * *
12567154 CTTTTTGCGGCGTTTGCAAGAAAATCACCGCTAAAAGTCAGGGT
1 -ATTTAGCGGCGTTTGCAAGAAAAGCACCGCTAAAAGTCAAGGT
12567198 ATTTAGCGGCGTTTG
1 ATTTAGCGGCGTTTG
12567213 TGATTGAAGT
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
43 13 0.28
44 33 0.72
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (43 bp):
ATTTAGCGGCGTTTGCAAGAAAAGCACCGCTAAAAGTCAAGGT
Found at i:12567228 original size:43 final size:42
Alignment explanation
Indices: 12567132--12567340 Score: 143
Period size: 43 Copynumber: 4.9 Consensus size: 42
12567122 TTTTTATGAA
* * * * *
12567132 AAGCGTCGCTAAAAGTCAAGGTCTTTTTGCGGCGTTTGCAAGA-A
1 AAGCGCCGCTAAAAGTCAAGGT-ATTTAGCGGCGTTTG--TGATT
* * *
12567176 AATCACCGCTAAAAGTCAGGGTATTTAGCGGCGTTTGTGATT
1 AAGCGCCGCTAAAAGTCAAGGTATTTAGCGGCGTTTGTGATT
* * * * * *
12567218 GAAGTGCCGCTAAAGGTCAAGGTCTTTAGTGGCGTTTGTAAATC
1 -AAGCGCCGCTAAAAGTCAAGGTATTTAGCGGCGTTTGT-GATT
* * * * *
12567262 AAGCGCCGCT-ATAGGCTAATGTATTTTGCGGCATTTGTGACTT
1 AAGCGCCGCTAAAAGTC-AAGGTATTTAGCGGCGTTTGTGA-TT
* * *
12567305 AAGCGCCGTTAAAAGTCAAGCTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAAGTCAAGGTATTTAGCGGCGTTT
12567341 TATGGTAAAG
Statistics
Matches: 123, Mismatches: 36, Indels: 13
0.72 0.21 0.08
Matches are distributed among these distances:
41 2 0.02
42 4 0.03
43 93 0.76
44 24 0.20
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
AAGCGCCGCTAAAAGTCAAGGTATTTAGCGGCGTTTGTGATT
Found at i:12568837 original size:21 final size:21
Alignment explanation
Indices: 12568813--12568854 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12568803 GAAATGAAGT
12568813 CCTTTGGAAATGACCAAACCG
1 CCTTTGGAAATGACCAAACCG
12568834 CCTTTGGAAATGACCAAACCG
1 CCTTTGGAAATGACCAAACCG
12568855 TCTATATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
CCTTTGGAAATGACCAAACCG
Found at i:12569346 original size:20 final size:20
Alignment explanation
Indices: 12569321--12569361 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
12569311 ACATCTACAC
12569321 CACCTTGAAAGGAAACTCAT
1 CACCTTGAAAGGAAACTCAT
*
12569341 CACCTTGGAAGGAAACTCAT
1 CACCTTGAAAGGAAACTCAT
12569361 C
1 C
12569362 TATATCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (20 bp):
CACCTTGAAAGGAAACTCAT
Found at i:12570448 original size:11 final size:11
Alignment explanation
Indices: 12570432--12570468 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
12570422 TTTCATTCAT
12570432 CATCCCTCAAG
1 CATCCCTCAAG
12570443 CATCCCTCAAG
1 CATCCCTCAAG
*
12570454 CATCCATCAAG
1 CATCCCTCAAG
12570465 CATC
1 CATC
12570469 ATTCTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.30, C:0.43, G:0.08, T:0.19
Consensus pattern (11 bp):
CATCCCTCAAG
Found at i:12574874 original size:27 final size:27
Alignment explanation
Indices: 12574843--12575273 Score: 485
Period size: 27 Copynumber: 16.0 Consensus size: 27
12574833 GGCAAATTAT
*
12574843 CGAAATACCCTTGAAGGGTAAAATGAC
1 CGAAATACCCTCGAAGGGTAAAATGAC
* * *
12574870 CGAAAAACCCTCAAAGGGTAAAATAAC
1 CGAAATACCCTCGAAGGGTAAAATGAC
* *
12574897 CTAAATACCCTCGAAAGGTAAAATGAC
1 CGAAATACCCTCGAAGGGTAAAATGAC
* * * *
12574924 CAAAATACCCTCAAAGGGTAAAATAAT
1 CGAAATACCCTCGAAGGGTAAAATGAC
* *
12574951 CGAAATACCCTCAAAGGGTAAAATGAT
1 CGAAATACCCTCGAAGGGTAAAATGAC
12574978 CGAAATACCCTCGAAGGGTAAAATGAC
1 CGAAATACCCTCGAAGGGTAAAATGAC
*
12575005 CAAAATACCCTCGAAGGGTAAAATGAC
1 CGAAATACCCTCGAAGGGTAAAATGAC
* ** *
12575032 GGAAATACCCTTAAAGGGTAAAATGAT
1 CGAAATACCCTCGAAGGGTAAAATGAC
* **
12575059 CAAAATACCCTTAAAGGGTAAAAT-AGC
1 CGAAATACCCTCGAAGGGTAAAATGA-C
* *
12575086 CGAAATACCCTCAAATGGTAAAATGAC
1 CGAAATACCCTCGAAGGGTAAAATGAC
12575113 TC-AAATACCCTCGAAGGGTAAAATGAC
1 -CGAAATACCCTCGAAGGGTAAAATGAC
** * * *
12575140 TAAAATACCCTCAAAGGATAAAATGAA
1 CGAAATACCCTCGAAGGGTAAAATGAC
* *
12575167 TGAAGTACCCTCGAAGGGTAAAATGAC
1 CGAAATACCCTCGAAGGGTAAAATGAC
*
12575194 CGAAATACCCTCGAAGGGT-AAATGAT
1 CGAAATACCCTCGAAGGGTAAAATGAC
*
12575220 CGAAATACCC-CTGAAGGTTAAAATGAC
1 CGAAATACCCTC-GAAGGGTAAAATGAC
* * *
12575247 TGAAATACCC-CCATAGGATAAAATGAC
1 CGAAATACCCTCGA-AGGGTAAAATGAC
12575274 TGTTATAACC
Statistics
Matches: 348, Mismatches: 49, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
25 1 0.00
26 24 0.07
27 321 0.92
28 2 0.01
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.18
Consensus pattern (27 bp):
CGAAATACCCTCGAAGGGTAAAATGAC
Found at i:12581025 original size:27 final size:27
Alignment explanation
Indices: 12580986--12581286 Score: 243
Period size: 27 Copynumber: 11.1 Consensus size: 27
12580976 GATTCATGAG
* * * *
12580986 AAAATAGCTGAAATACCTTTGAAGGGT
1 AAAATAACCGAAATACCCTCGAAGGGT
* *
12581013 AAAAAAACCGAAAAACCCTCGAAGGGT
1 AAAATAACCGAAATACCCTCGAAGGGT
* * * * *
12581040 AAAATGACCAAAATAACTTCGAAAGGT
1 AAAATAACCGAAATACCCTCGAAGGGT
* **
12581067 AAAATGATTGAAATACCCTCGAAGGGT
1 AAAATAACCGAAATACCCTCGAAGGGT
12581094 AAAATAACCGAAATACCCTCGAA-GGT
1 AAAATAACCGAAATACCCTCGAAGGGT
* ** * *
12581120 GAACATGAA-AAAAATTCCCTCGAATGGT
1 -AAAAT-AACCGAAATACCCTCGAAGGGT
* *
12581148 AAAATGACCGAAATACTCT-GAAAGGGT
1 AAAATAACCGAAATACCCTCG-AAGGGT
** *
12581175 AAAATAATTGAAATACCCTCAAAGGGT
1 AAAATAACCGAAATACCCTCGAAGGGT
*
12581202 AAAATGA-CGAAAATACCCTCGAAGGGT
1 AAAATAACCG-AAATACCCTCGAAGGGT
* * * *
12581229 AAAATGACCAAAATACGCTCGAAGTGT
1 AAAATAACCGAAATACCCTCGAAGGGT
* *
12581256 AAAATAATCGAAATACTCTC-ATAGGGT
1 AAAATAACCGAAATACCCTCGA-AGGGT
12581283 AAAA
1 AAAA
12581287 GGACTGTTAT
Statistics
Matches: 216, Mismatches: 49, Indels: 18
0.76 0.17 0.06
Matches are distributed among these distances:
26 7 0.03
27 203 0.94
28 6 0.03
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.19
Consensus pattern (27 bp):
AAAATAACCGAAATACCCTCGAAGGGT
Found at i:12581134 original size:81 final size:81
Alignment explanation
Indices: 12580995--12581286 Score: 320
Period size: 81 Copynumber: 3.6 Consensus size: 81
12580985 GAAAATAGCT
* * * * * * *
12580995 GAAATACCTTTGAAGGGTAAAAAAACCGAAAAACCCTCGAAGGGTAAAATGACCAAAATAACTTC
1 GAAATACCCTCGAAGGGTAAAATAACCGAAATACCCTCGAAGGGTAAAATGACAAAAATACCCTC
**
12581060 GAAAGGTAAAATGATT
66 GAAAGGTAAAATGACC
* * *
12581076 GAAATACCCTCGAAGGGTAAAATAACCGAAATACCCTCGAA-GGTGAACATGAAAAAAATTCCCT
1 GAAATACCCTCGAAGGGTAAAATAACCGAAATACCCTCGAAGGGT-AAAATGACAAAAATACCCT
*
12581140 CGAATGGTAAAATGACC
65 CGAAAGGTAAAATGACC
* ** * *
12581157 GAAATACTCT-GAAAGGGTAAAATAATTGAAATACCCTCAAAGGGTAAAATGACGAAAATACCCT
1 GAAATACCCTCG-AAGGGTAAAATAACCGAAATACCCTCGAAGGGTAAAATGACAAAAATACCCT
*
12581221 CGAAGGGTAAAATGACC
65 CGAAAGGTAAAATGACC
* * * * *
12581238 AAAATACGCTCGAAGTGTAAAATAATCGAAATACTCTC-ATAGGGTAAAA
1 GAAATACCCTCGAAGGGTAAAATAACCGAAATACCCTCGA-AGGGTAAAA
12581287 GGACTGTTAT
Statistics
Matches: 179, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
80 5 0.03
81 170 0.95
82 4 0.02
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.19
Consensus pattern (81 bp):
GAAATACCCTCGAAGGGTAAAATAACCGAAATACCCTCGAAGGGTAAAATGACAAAAATACCCTC
GAAAGGTAAAATGACC
Found at i:12593853 original size:21 final size:21
Alignment explanation
Indices: 12593815--12593854 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12593805 CCTGCAATTG
*
12593815 AAATTTTTCTGAATTTCTCCT
1 AAATTTTTCTAAATTTCTCCT
12593836 AAATTTTT-TAAATGTTCTC
1 AAATTTTTCTAAAT-TTCTC
12593855 GATTTAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.53
Consensus pattern (21 bp):
AAATTTTTCTAAATTTCTCCT
Found at i:12601451 original size:12 final size:12
Alignment explanation
Indices: 12601434--12601459 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12601424 CGAGCCCAAA
12601434 CTAATTTTGGCT
1 CTAATTTTGGCT
12601446 CTAATTTTGGCT
1 CTAATTTTGGCT
12601458 CT
1 CT
12601460 TATTCCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.50
Consensus pattern (12 bp):
CTAATTTTGGCT
Found at i:12604461 original size:22 final size:21
Alignment explanation
Indices: 12604436--12604479 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12604426 TATTGATACC
*
12604436 TGGTAAAAGGTATCAATACTTT
1 TGGT-AAAGGTATCAACACTTT
* *
12604458 TGGTTAAGGTATCGACACTTT
1 TGGTAAAGGTATCAACACTTT
12604479 T
1 T
12604480 TGTGAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (21 bp):
TGGTAAAGGTATCAACACTTT
Found at i:12604700 original size:22 final size:24
Alignment explanation
Indices: 12604672--12604715 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
12604662 ATTTTATTCA
12604672 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
12604694 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
12604716 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:12605366 original size:38 final size:39
Alignment explanation
Indices: 12605294--12605419 Score: 155
Period size: 40 Copynumber: 3.2 Consensus size: 39
12605284 ATGTGGACAA
* * * *
12605294 GCAGATAATCTACCAATATTATGGTCAAACCACTAGTATT
1 GCAGATAA-CTGCCAATATTGTGGACAAGCCACTAGTATT
* *
12605334 GTAGATAACTGCCAAT-TTGTGGACTAGCCACTAGTATT
1 GCAGATAACTGCCAATATTGTGGACAAGCCACTAGTATT
* *
12605372 GCAGATAAATTGTCAATATTGTGGACAAGCCACTAGTATT
1 GCAGAT-AACTGCCAATATTGTGGACAAGCCACTAGTATT
12605412 GCAGATAA
1 GCAGATAA
12605420 ACTGTCAGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
38 23 0.31
39 17 0.23
40 34 0.46
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (39 bp):
GCAGATAACTGCCAATATTGTGGACAAGCCACTAGTATT
Found at i:12605405 original size:40 final size:40
Alignment explanation
Indices: 12605307--12605426 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 40
12605297 GATAATCTAC
* * * * *
12605307 CAATATTATGGTCAAACCACTAGTATTGTAGAT-AACTGC
1 CAATATTGTGGACAAGCCACTAGTATTGCAGATAAACTGT
* *
12605346 CAAT-TTGTGGACTAGCCACTAGTATTGCAGATAAATTGT
1 CAATATTGTGGACAAGCCACTAGTATTGCAGATAAACTGT
12605385 CAATATTGTGGACAAGCCACTAGTATTGCAGATAAACTGT
1 CAATATTGTGGACAAGCCACTAGTATTGCAGATAAACTGT
12605425 CA
1 CA
12605427 GTACTTCCTC
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 23 0.33
39 12 0.17
40 35 0.50
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (40 bp):
CAATATTGTGGACAAGCCACTAGTATTGCAGATAAACTGT
Found at i:12631999 original size:43 final size:43
Alignment explanation
Indices: 12631952--12632106 Score: 174
Period size: 43 Copynumber: 3.7 Consensus size: 43
12631942 TGTGTTTTTG
*
12631952 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGTGTTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGTGATTACA
* * * *
12631995 TGTAAGACCATGTCTGGGACATTGGCATCG-TATT-TAATT-CG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGTGATTACA
** * *
12632036 TGTAAGACCTTGTTTGGGACAG-TGGCATCGATATGTGATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATCGATTTGTGATTACA
*
12632079 TGTAAGACCACGTCTGGGACGTTAGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
12632107 TGTACGAGCC
Statistics
Matches: 91, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
41 28 0.31
42 10 0.11
43 53 0.58
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGTGATTACA
Found at i:12659847 original size:22 final size:23
Alignment explanation
Indices: 12659819--12659862 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
12659809 ATTAATAATT
12659819 ATGTAT-ATATATTAATTACAAA
1 ATGTATAATATATTAATTACAAA
*
12659841 ATGTATACATATATTTATTACA
1 ATGTATA-ATATATTAATTACA
12659863 CATGTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
24 13 0.68
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (23 bp):
ATGTATAATATATTAATTACAAA
Found at i:12666720 original size:28 final size:28
Alignment explanation
Indices: 12666689--12666754 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
12666679 ATAAAAAATA
*
12666689 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTTATTT
12666717 ACCAAAATATTATAAATTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTTATTT
*
12666745 GCCAAAATAT
1 ACCAAAATAT
12666755 ACCAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAAATTTTTTTTATTT
Found at i:12667075 original size:26 final size:28
Alignment explanation
Indices: 12667042--12667105 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
12667032 ATAAAAAATA
12667042 ACCAAAATATTAT-AA-CTTTTTTATTT
1 ACCAAAATATTATAAATCTTTTTTATTT
*
12667068 ACCAAAATATTATAAATTTTTTTTATTT
1 ACCAAAATATTATAAATCTTTTTTATTT
*
12667096 GCCAAAATAT
1 ACCAAAATAT
12667106 ACCAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 13 0.38
27 2 0.06
28 19 0.56
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.47
Consensus pattern (28 bp):
ACCAAAATATTATAAATCTTTTTTATTT
Found at i:12667773 original size:18 final size:19
Alignment explanation
Indices: 12667744--12667802 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
12667734 TCTAATTAAG
*
12667744 TAATAACTCTATTTTAATT
1 TAATAAATCTATTTTAATT
* *
12667763 TAATAAA-CTATTCTCATT
1 TAATAAATCTATTTTAATT
12667781 TAATAAATCTATTTTAATT
1 TAATAAATCTATTTTAATT
12667800 TAA
1 TAA
12667803 AATATAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 16 0.47
19 18 0.53
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAAATCTATTTTAATT
Found at i:12668074 original size:19 final size:18
Alignment explanation
Indices: 12668017--12668081 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 18
12668007 TTTAATTTTT
12668017 TTAATTAAAATAGAGTTA
1 TTAATTAAAATAGAGTTA
* *
12668035 TTAAATAAGAATAG-TTTA
1 TTAATTAA-AATAGAGTTA
12668053 TTACATTAAAATAGAGTTA
1 TTA-ATTAAAATAGAGTTA
12668072 TTAAATTAAA
1 TT-AATTAAA
12668082 CTATTTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 18 0.46
19 20 0.51
20 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (18 bp):
TTAATTAAAATAGAGTTA
Found at i:12668475 original size:27 final size:27
Alignment explanation
Indices: 12668390--12668466 Score: 145
Period size: 27 Copynumber: 2.9 Consensus size: 27
12668380 TTTTAGTCCT
12668390 TTGGCACCATTGGTGCCGCCAATCACA
1 TTGGCACCATTGGTGCCGCCAATCACA
12668417 TTGGCACCATTGGTGCCGCCAATCACA
1 TTGGCACCATTGGTGCCGCCAATCACA
*
12668444 TTGGCACCTTTGGTGCCGCCAAT
1 TTGGCACCATTGGTGCCGCCAAT
12668467 GTGATTGGCC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.25
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCACA
Found at i:12673314 original size:10 final size:10
Alignment explanation
Indices: 12673299--12673328 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
12673289 GAGATATTAC
12673299 ACCTTTAAAT
1 ACCTTTAAAT
12673309 ACCTTTAAAT
1 ACCTTTAAAT
12673319 ACCTTTAAAT
1 ACCTTTAAAT
12673329 TTACATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (10 bp):
ACCTTTAAAT
Found at i:12675150 original size:20 final size:18
Alignment explanation
Indices: 12675095--12675150 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
12675085 AGATCACTTC
12675095 AAATTATAAAAATT-TTA
1 AAATTATAAAAATTATTA
*
12675112 TAAAATATAAAAA-TATTA
1 -AAATTATAAAAATTATTA
12675130 AATATTATAAAACATTATTA
1 AA-ATTATAAAA-ATTATTA
12675150 A
1 A
12675151 CACACTACGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 3 0.09
18 22 0.69
19 1 0.03
20 6 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATTATAAAAATTATTA
Found at i:12675655 original size:87 final size:86
Alignment explanation
Indices: 12675564--12675729 Score: 217
Period size: 86 Copynumber: 1.9 Consensus size: 86
12675554 ATTAAAATCA
* * * * * *
12675564 AATAAAATATTGCTGATCGGCAAGAATAAATCTCTAAACAGATTTTA-TTTAATTTCAATTTCTC
1 AATAAAAT-TCGCTGAACGGCAAGAATAAATCCCGAAACAGATTTTATTTTAATTTAAATAT-TC
12675628 ATTTTGGAAATAAAATAGAAAAG
64 ATTTTGGAAATAAAATAGAAAAG
* * * *
12675651 AATAAAATTCGTTGAACGGCAGGAATAAGTCCCGAAACAGATTTTATTTTAATTTAAATATTCGT
1 AATAAAATTCGCTGAACGGCAAGAATAAATCCCGAAACAGATTTTATTTTAATTTAAATATTCAT
12675716 TTTGGAAATAAAAT
66 TTTGGAAATAAAAT
12675730 TCATTGAACG
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
86 48 0.71
87 20 0.29
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (86 bp):
AATAAAATTCGCTGAACGGCAAGAATAAATCCCGAAACAGATTTTATTTTAATTTAAATATTCAT
TTTGGAAATAAAATAGAAAAG
Found at i:12676125 original size:18 final size:18
Alignment explanation
Indices: 12676086--12676134 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
12676076 AGAAAATAAG
*
12676086 TATAAAAATTTTATAAAA
1 TATAAAAATATTATAAAA
*
12676104 TATAAAAATATTA-AATA
1 TATAAAAATATTATAAAA
12676121 T-TATAAAATATTAT
1 TATA-AAAATATTAT
12676135 TAACACATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 2 0.07
17 13 0.48
18 12 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAAAATATTATAAAA
Found at i:12691558 original size:15 final size:15
Alignment explanation
Indices: 12691540--12691569 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12691530 TAAGATCACT
*
12691540 ATATATAAAATTATA
1 ATATATAAAAATATA
12691555 ATATATAAAAATATA
1 ATATATAAAAATATA
12691570 TAAATATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATATAAAAATATA
Found at i:12691584 original size:18 final size:17
Alignment explanation
Indices: 12691539--12691611 Score: 57
Period size: 17 Copynumber: 4.3 Consensus size: 17
12691529 ATAAGATCAC
*
12691539 TATATATAAA-ATTATAA
1 TATATAAAAATATTA-AA
12691556 TATATAAAAATATATAAA
1 TATATAAAAATAT-TAAA
12691574 TAT-TAATAAATATTAAA
1 TATATAA-AAATATTAAA
12691591 -ATA-AAATAAT-TATAAA
1 TATATAAA-AATAT-TAAA
12691607 TATAT
1 TATAT
12691612 TTTTTTAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 15
0.75 0.02 0.24
Matches are distributed among these distances:
15 2 0.04
16 11 0.23
17 19 0.40
18 13 0.28
19 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATATAAAAATATTAAA
Found at i:12691608 original size:27 final size:27
Alignment explanation
Indices: 12691552--12691608 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
12691542 ATATAAAATT
* *
12691552 ATAATATATAAAAATATATAAATATTA
1 ATAATATATAAAAATAAATAAATATAA
* *
12691579 ATAA-ATATTAAAATAAAATAATTATAA
1 ATAATATATAAAAAT-AAATAAATATAA
12691606 ATA
1 ATA
12691609 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
ATAATATATAAAAATAAATAAATATAA
Found at i:12692387 original size:23 final size:23
Alignment explanation
Indices: 12692339--12692387 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12692329 TATAACGAGG
* *
12692339 AAAAATATAATTATTTTATAGAA
1 AAAAATATAATTATTTAAAAGAA
*
12692362 AAAAATGTAATTATTTAAAATGAA
1 AAAAATATAATTATTTAAAA-GAA
12692386 AA
1 AA
12692388 TTTTACACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (23 bp):
AAAAATATAATTATTTAAAAGAA
Found at i:12694460 original size:61 final size:61
Alignment explanation
Indices: 12694289--12694476 Score: 157
Period size: 61 Copynumber: 3.1 Consensus size: 61
12694279 AAATAAATGC
* * * * * * *
12694289 GATGATAAAGAGTGTTTAGGGTTTAATAATTGT-GAGGTTTAGGGTTTGGTTTTAAGGATAAT
1 GATGATAAAAAG-GTTTAAGGTTTAATGATT-TAGAGGTTTAGAGTTTGATTTTAAGGTTAAA
* * * * * *
12694351 GATGATAAAAAGGTGTATGGCTTAATGGTTTA-AGGGTTTA-AGGATTGATTTTAGGGTTAAA
1 GATGATAAAAAGGTTTAAGGTTTAATGATTTAGA-GGTTTAGA-GTTTGATTTTAAGGTTAAA
* * * * *
12694412 GATTATAATATGGTTTAAGGTTTAATGATTTAGAGGTTTAGAGTTTGATTTCAAGGTTAAG
1 GATGATAAAAAGGTTTAAGGTTTAATGATTTAGAGGTTTAGAGTTTGATTTTAAGGTTAAA
12694473 GATG
1 GATG
12694477 GTATGTAACA
Statistics
Matches: 97, Mismatches: 24, Indels: 11
0.73 0.18 0.08
Matches are distributed among these distances:
60 2 0.02
61 82 0.85
62 13 0.13
ACGTcount: A:0.31, C:0.01, G:0.29, T:0.39
Consensus pattern (61 bp):
GATGATAAAAAGGTTTAAGGTTTAATGATTTAGAGGTTTAGAGTTTGATTTTAAGGTTAAA
Found at i:12700341 original size:17 final size:18
Alignment explanation
Indices: 12700301--12700342 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
12700291 CTGGTGACAC
12700301 CATACTTAGTAAAGGATTT
1 CATA-TTAGTAAAGGATTT
* *
12700320 AATATTAGTAGA-GATTT
1 CATATTAGTAAAGGATTT
12700337 CATATT
1 CATATT
12700343 TTAAATTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 10 0.50
18 7 0.35
19 3 0.15
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.40
Consensus pattern (18 bp):
CATATTAGTAAAGGATTT
Found at i:12703918 original size:10 final size:9
Alignment explanation
Indices: 12703868--12703921 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 9
12703858 AACTTTATAG
12703868 AATATTTTT
1 AATATTTTT
*
12703877 GAATTTTTTT
1 -AATATTTTT
12703887 ACATATTTTT
1 A-ATATTTTT
*
12703897 ATTAATTTTT
1 AAT-ATTTTT
12703907 AATATTTATT
1 AATATTT-TT
12703917 AATAT
1 AATAT
12703922 AACATGTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
9 6 0.16
10 31 0.84
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:12704102 original size:15 final size:15
Alignment explanation
Indices: 12704075--12704111 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12704065 ATAATAAATA
12704075 AATAAAAATTAATTT
1 AATAAAAATTAATTT
12704090 AACTAAAAA-TAATTT
1 AA-TAAAAATTAATTT
12704105 AATAAAA
1 AATAAAA
12704112 TATATAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 10 0.48
16 6 0.29
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAAAATTAATTT
Found at i:12706762 original size:41 final size:41
Alignment explanation
Indices: 12706705--12706788 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
12706695 ATCCAAAGAA
12706705 AGGGTCAAAATAAGTGAAGTTTCCTCTTTTTAACGACAATG
1 AGGGTCAAAATAAGTGAAGTTTCCTCTTTTTAACGACAATG
12706746 AGGGTCAAAATAAGTGAAGTTTCCTCTTTTTAACGACAATG
1 AGGGTCAAAATAAGTGAAGTTTCCTCTTTTTAACGACAATG
12706787 AG
1 AG
12706789 TATGTAGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (41 bp):
AGGGTCAAAATAAGTGAAGTTTCCTCTTTTTAACGACAATG
Found at i:12708030 original size:15 final size:15
Alignment explanation
Indices: 12707973--12708033 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 15
12707963 TATTTGATAA
* *
12707973 ATTAAAAAACTAAAT
1 ATTAAAAAATTAAGT
* * *
12707988 ACTAAAAAAATATGT
1 ATTAAAAAATTAAGT
12708003 ATTAAAAAATTAAGT
1 ATTAAAAAATTAAGT
* *
12708018 ATTGAAAATTTAAGT
1 ATTAAAAAATTAAGT
12708033 A
1 A
12708034 CCAAATGAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (15 bp):
ATTAAAAAATTAAGT
Found at i:12708152 original size:14 final size:15
Alignment explanation
Indices: 12708118--12708147 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12708108 ATATAATTTT
*
12708118 AAAATTTTTAAAAGA
1 AAAATCTTTAAAAGA
12708133 AAAATCTTTAAAAGA
1 AAAATCTTTAAAAGA
12708148 TAATCATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAATCTTTAAAAGA
Found at i:12708911 original size:21 final size:20
Alignment explanation
Indices: 12708887--12708936 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
12708877 TCAAATTTTA
*
12708887 TATATAATTTCTAAAAAAAAT
1 TATATAATATCT-AAAAAAAT
*
12708908 TATATAAAATCTAAAAAAAT
1 TATATAATATCTAAAAAAAT
*
12708928 TATGTAATA
1 TATATAATA
12708937 AATCATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (20 bp):
TATATAATATCTAAAAAAAT
Found at i:12712092 original size:25 final size:25
Alignment explanation
Indices: 12712052--12712127 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
12712042 AAACAAACGA
* * *
12712052 TATACAGAATATGCCATAAGGC-CT
1 TATATAGAATACGCCATAAGGCAAT
*
12712076 TATTATAGAATACGCCACAAAGGCAAT
1 TA-TATAGAATACGCCA-TAAGGCAAT
*
12712103 TATATAGAATTCGCCATAAGGCAAT
1 TATATAGAATACGCCATAAGGCAAT
12712128 CCATTCAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 2 0.05
25 20 0.47
26 18 0.42
27 3 0.07
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (25 bp):
TATATAGAATACGCCATAAGGCAAT
Found at i:12712108 original size:26 final size:27
Alignment explanation
Indices: 12712079--12712158 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 27
12712069 AAGGCCTTAT
*
12712079 TATAGAATACGCCACAAAGGCAAT-TA
1 TATAGAATACGCCACAAAGGCAATCCA
* *
12712105 TATAGAATTCGCCA-TAAGGCAATCCA
1 TATAGAATACGCCACAAAGGCAATCCA
* *
12712131 T-TCAGAGTATGCCACAAAGGCAATCCA
1 TAT-AGAATACGCCACAAAGGCAATCCA
12712158 T
1 T
12712159 TCAAAGTACA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
25 9 0.20
26 23 0.52
27 12 0.27
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (27 bp):
TATAGAATACGCCACAAAGGCAATCCA
Found at i:12712176 original size:27 final size:27
Alignment explanation
Indices: 12712116--12712178 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
12712106 ATAGAATTCG
* **
12712116 CCAT-AAGGCAATCCATTCAGAGTATG
1 CCATAAAGGCAATCCATTCAAAGTACA
*
12712142 CCACAAAGGCAATCCATTCAAAGTACA
1 CCATAAAGGCAATCCATTCAAAGTACA
12712169 CCATAAAGGC
1 CCATAAAGGC
12712179 TCACATGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.17
Consensus pattern (27 bp):
CCATAAAGGCAATCCATTCAAAGTACA
Found at i:12721494 original size:25 final size:25
Alignment explanation
Indices: 12721461--12721525 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
12721451 AAAGGACATT
12721461 AAATTAAAATAAATATATATAATAA
1 AAATTAAAATAAATATATATAATAA
* *
12721486 AAATTAAAA-AATATATGTATATTAA
1 AAATTAAAATAA-ATATATATAATAA
12721511 ATAA-TAAATATAAAT
1 A-AATTAAA-ATAAAT
12721526 TAAATTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 2 0.06
25 25 0.74
26 5 0.15
27 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (25 bp):
AAATTAAAATAAATATATATAATAA
Found at i:12721527 original size:18 final size:18
Alignment explanation
Indices: 12721460--12721530 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
12721450 TAAAGGACAT
*
12721460 TAAAT-TAAAATAAATATA
1 TAAATATAAATTAAATA-A
* *
12721478 TATAATAAAAATTAAAAAA
1 TA-AATATAAATTAAATAA
* * *
12721497 TATATGTATATTAAATAA
1 TAAATATAAATTAAATAA
12721515 TAAATATAAATTAAAT
1 TAAATATAAATTAAAT
12721531 TTATATCAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
18 26 0.65
19 6 0.15
20 8 0.20
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (18 bp):
TAAATATAAATTAAATAA
Found at i:12725579 original size:3 final size:3
Alignment explanation
Indices: 12725573--12725599 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12725563 ATTATCTTTT
12725573 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
12725600 GTAGTAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12726052 original size:18 final size:20
Alignment explanation
Indices: 12726029--12726068 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
12726019 CCCCTTTTAC
12726029 ATATATTA-TTATA-TAAAT
1 ATATATTATTTATATTAAAT
12726047 ATATATTATTTATATTAAAT
1 ATATATTATTTATATTAAAT
12726067 AT
1 AT
12726069 TTCATTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTATTTATATTAAAT
Found at i:12729962 original size:25 final size:25
Alignment explanation
Indices: 12729923--12730044 Score: 96
Period size: 23 Copynumber: 5.1 Consensus size: 25
12729913 ACGCCAAGCA
* * * *
12729923 TTATAAAATATGCCACACAAATGTG
1 TTATAATATACGCCACACAAAGGCG
12729948 TTATAATATACG-C-CACAAAGGCG
1 TTATAATATACGCCACACAAAGGCG
*
12729971 TTATAGA-ATACACCACACAAAGGCG
1 TTATA-ATATACGCCACACAAAGGCG
* *
12729996 TTACAATATACG-C-CACAAAGGTG
1 TTATAATATACGCCACACAAAGGCG
* * *
12730019 TTACAAAATACG--TCACAAAGGCG
1 TTATAATATACGCCACACAAAGGCG
12730042 TTA
1 TTA
12730045 CAGAATATGA
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
23 49 0.60
24 5 0.06
25 28 0.34
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (25 bp):
TTATAATATACGCCACACAAAGGCG
Found at i:12729964 original size:23 final size:23
Alignment explanation
Indices: 12729938--12730046 Score: 112
Period size: 23 Copynumber: 4.7 Consensus size: 23
12729928 AAATATGCCA
* * *
12729938 CACAAATGTGTTATAATATACGC
1 CACAAAGGCGTTACAATATACGC
* *
12729961 CACAAAGGCGTTATAGA-ATACACC
1 CACAAAGGCGTTACA-ATATAC-GC
12729985 ACACAAAGGCGTTACAATATACGC
1 -CACAAAGGCGTTACAATATACGC
* * *
12730009 CACAAAGGTGTTACAAAATACGT
1 CACAAAGGCGTTACAATATACGC
12730032 CACAAAGGCGTTACA
1 CACAAAGGCGTTACA
12730047 GAATATGACA
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
23 51 0.70
24 4 0.05
25 18 0.25
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (23 bp):
CACAAAGGCGTTACAATATACGC
Found at i:12730029 original size:48 final size:46
Alignment explanation
Indices: 12729935--12730063 Score: 134
Period size: 48 Copynumber: 2.8 Consensus size: 46
12729925 ATAAAATATG
* * * * * *
12729935 CCACACAAATGTGTTATAATATACGCCACAAAGGCGTTATAGAATACA
1 CCACACAAAGGCGTTACAATATACGCCACAAAGGTGTTACA-AA-ATA
12729983 CCACACAAAGGCGTTACAATATACGCCACAAAGGTGTTACAAAATA
1 CCACACAAAGGCGTTACAATATACGCCACAAAGGTGTTACAAAATA
** * *
12730029 CGTCACAAAGGCGTTACAGA-ATATGACACAAAGGT
1 CCACACAAAGGCGTTACA-ATATACGCCACAAAGGT
12730064 TTCATAGAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 31 0.44
47 3 0.04
48 36 0.51
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (46 bp):
CCACACAAAGGCGTTACAATATACGCCACAAAGGTGTTACAAAATA
Found at i:12730051 original size:23 final size:23
Alignment explanation
Indices: 12729955--12730062 Score: 110
Period size: 23 Copynumber: 4.6 Consensus size: 23
12729945 GTGTTATAAT
* *
12729955 ATACGCCACAAAGGCGTTATAGA
1 ATACGACACAAAGGCGTTACAGA
*
12729978 ATACACCACACAAAGGCGTTACA-A
1 AT--ACGACACAAAGGCGTTACAGA
* * *
12730002 TATACGCCACAAAGGTGTTACAAA
1 -ATACGACACAAAGGCGTTACAGA
*
12730026 ATACGTCACAAAGGCGTTACAGA
1 ATACGACACAAAGGCGTTACAGA
*
12730049 ATATGACACAAAGG
1 ATACGACACAAAGG
12730063 TTTCATAGAG
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
23 50 0.71
24 2 0.03
25 18 0.26
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.17
Consensus pattern (23 bp):
ATACGACACAAAGGCGTTACAGA
Found at i:12740323 original size:23 final size:23
Alignment explanation
Indices: 12740284--12740328 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12740274 GTATAAAATA
* *
12740284 TATATATATAAGCATATGTATAC
1 TATATATATAAACATATATATAC
12740307 TATATATA-AAACAATATATATA
1 TATATATATAAAC-ATATATATA
12740329 TTACATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (23 bp):
TATATATATAAACATATATATAC
Found at i:12740368 original size:3 final size:3
Alignment explanation
Indices: 12740355--12740387 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
12740345 CATGCGCATG
12740355 AAT AA- AAT AAT AAT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
12740388 GATACAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:12740377 original size:13 final size:13
Alignment explanation
Indices: 12740359--12740386 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12740349 CGCATGAATA
12740359 AAATAATAATAAT
1 AAATAATAATAAT
12740372 AAATAATAATAAT
1 AAATAATAATAAT
12740385 AA
1 AA
12740387 TGATACAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:12740891 original size:19 final size:19
Alignment explanation
Indices: 12740867--12740920 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
12740857 AATCATAACT
12740867 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
12740886 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
12740905 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
12740921 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:12740916 original size:38 final size:41
Alignment explanation
Indices: 12740844--12740920 Score: 115
Period size: 38 Copynumber: 1.9 Consensus size: 41
12740834 AAATTAAATC
12740844 TCTAAGATTACAAAATCATAACTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATAAC-TCTAAGATTGCATATCATA
*
12740886 TCTAAGATTAC-ATATCAT-A-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATAACTCTAAGATTGCATATC
12740921 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
40 1 0.03
41 6 0.18
42 11 0.32
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (41 bp):
TCTAAGATTACAAAATCATAACTCTAAGATTGCATATCATA
Found at i:12750798 original size:3 final size:3
Alignment explanation
Indices: 12750792--12750824 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12750782 AAAAAAAGGG
12750792 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
12750825 AACAGAGACT
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:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12753309 original size:29 final size:29
Alignment explanation
Indices: 12753241--12753309 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
12753231 TGGAAGACTT
12753241 ATTGATTTTT-TTATTTTACAAGGATTTA
1 ATTGATTTTTATTATTTTACAAGGATTTA
* *
12753269 ATT-ATTTTT-TTATTTTTTACGAGGGTTTA
1 ATTGATTTTTATTA--TTTTACAAGGATTTA
12753298 ATTGATTATTTA
1 ATTGATT-TTTA
12753310 AGTACAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 9 0.26
28 3 0.09
29 16 0.47
30 3 0.09
31 3 0.09
ACGTcount: A:0.26, C:0.03, G:0.12, T:0.59
Consensus pattern (29 bp):
ATTGATTTTTATTATTTTACAAGGATTTA
Found at i:12753455 original size:20 final size:20
Alignment explanation
Indices: 12753426--12753463 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12753416 TAAGAAAATA
*
12753426 TAAAAAATTATTAAAATTGT
1 TAAAAAATTATAAAAATTGT
*
12753446 TAAAATATTATAAAAATT
1 TAAAAAATTATAAAAATT
12753464 AAAAATTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
TAAAAAATTATAAAAATTGT
Found at i:12753468 original size:18 final size:20
Alignment explanation
Indices: 12753420--12753469 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
12753410 GTTTTTTAAG
12753420 AAAATATAAAAA-ATTATTA
1 AAAATATAAAAATATTATTA
* * *
12753439 AAATTGTTAAAATATTA-TA
1 AAAATATAAAAATATTATTA
12753458 AAAAT-TAAAAAT
1 AAAATATAAAAAT
12753470 TACTAGACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAATATAAAAATATTATTA
Found at i:12754899 original size:17 final size:18
Alignment explanation
Indices: 12754859--12754891 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12754849 ATTTTTATTT
12754859 AAAT-TTAATTATAAAAA
1 AAATATTAATTATAAAAA
12754876 AAATATTAA-TATAAAA
1 AAATATTAATTATAAAA
12754892 TTAATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATTAATTATAAAAA
Found at i:12755374 original size:3 final size:3
Alignment explanation
Indices: 12755366--12755398 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12755356 AAACATTTGG
12755366 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12755399 GAGAATGCCA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12760684 original size:3 final size:3
Alignment explanation
Indices: 12760676--12760713 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
12760666 ATGTATTAGT
*
12760676 TAA TAA TAA TAA CAA TATA TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA
12760714 TTTAATTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12760892 original size:28 final size:28
Alignment explanation
Indices: 12760846--12760907 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
12760836 TTTCCTATAA
*
12760846 TATAATATCTTAACTTTAATTAATATAATT
1 TATAATATCTTAAC-TTAAATAATAT-ATT
* *
12760876 TATAATATTTTAA-TTAAATAATATTTT
1 TATAATATCTTAACTTAAATAATATATT
12760903 TATAA
1 TATAA
12760908 GAAAAATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 10 0.34
30 12 0.41
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TATAATATCTTAACTTAAATAATATATT
Found at i:12763653 original size:12 final size:11
Alignment explanation
Indices: 12763638--12763707 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
12763628 AAAAAATTAA
12763638 AAAAAGTATTTT
1 AAAAA-TATTTT
12763650 AAAAATATTTT
1 AAAAATATTTT
*
12763661 --AAA-A-TTA
1 AAAAATATTTT
* *
12763668 AAAAATA-ATA
1 AAAAATATTTT
12763678 AAAAAGTATTTT
1 AAAAA-TATTTT
12763690 AAAAATATTTT
1 AAAAATATTTT
12763701 AAAAATA
1 AAAAATA
12763708 AAAAAAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 6 0.12
10 8 0.16
11 21 0.43
12 11 0.22
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:12763682 original size:40 final size:40
Alignment explanation
Indices: 12763628--12763722 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
12763618 AATTTTTTAA
* *
12763628 AAAAAATTA-AAAAAAGTATTTTAAAAATATTTTAAAATT
1 AAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAAAT
12763667 AAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAAAT
1 AAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAAAT
12763707 AAAAAA-AATTAAAAAA
1 AAAAAATAA-TAAAAAA
12763723 TAAATATATT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 10 0.19
40 42 0.81
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (40 bp):
AAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAAAT
Found at i:12763711 original size:17 final size:17
Alignment explanation
Indices: 12763689--12763734 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
12763679 AAAAGTATTT
*
12763689 TAAAAATATTTTAAAAA
1 TAAAAATATTTAAAAAA
* *
12763706 TAAAAAAAATTAAAAAA
1 TAAAAATATTTAAAAAA
*
12763723 TAAATATATTTA
1 TAAAAATATTTA
12763735 TTATATCGGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAATATTTAAAAAA
Done.