Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 101 of 210
Found at i:29561298 original size:52 final size:53
Alignment explanation
Indices: 29561166--29561309 Score: 166
Period size: 52 Copynumber: 2.7 Consensus size: 53
29561156 AGTAAACAGT
* * * *
29561166 TAATTACTTGATACAGATTTACCATAATTAGTTTATC-TAATATAAATTCACCA
1 TAATTACTTAATATACATTTACCATAATTAGTTTA-CATAATATAAATTAACCA
* * * * * *
29561219 TAATCAATTAATATATATTAACCATAATTAGTTCACATAATAT-AATTAATCA
1 TAATTACTTAATATACATTTACCATAATTAGTTTACATAATATAAATTAACCA
*
29561271 TAATTACTTAATATACATTTACTATAATTAGTTTACATA
1 TAATTACTTAATATACATTTACCATAATTAGTTTACATA
29561310 TTTACAATAA
Statistics
Matches: 75, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
52 41 0.55
53 34 0.45
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.41
Consensus pattern (53 bp):
TAATTACTTAATATACATTTACCATAATTAGTTTACATAATATAAATTAACCA
Found at i:29565820 original size:6 final size:6
Alignment explanation
Indices: 29565800--29565831 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
29565790 TACTCGTCGT
29565800 TTTTTA -TTTTA -TTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
29565832 GTTTTATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:29566721 original size:22 final size:22
Alignment explanation
Indices: 29566677--29566735 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
29566667 ATGAATGTTG
*
29566677 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
29566701 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
*
29566723 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
29566736 GTATCATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
24 11 0.33
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:29575671 original size:16 final size:16
Alignment explanation
Indices: 29575650--29575681 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29575640 AATCCATTGG
29575650 AATTGTCCATCAAGTT
1 AATTGTCCATCAAGTT
29575666 AATTGTCCATCAAGTT
1 AATTGTCCATCAAGTT
29575682 TCATCCCCTT
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:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
AATTGTCCATCAAGTT
Found at i:29582901 original size:24 final size:22
Alignment explanation
Indices: 29582860--29582903 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
29582850 CATTATTTAA
*
29582860 ATTTCATATACATGTATCATTC
1 ATTTCATATACATATATCATTC
29582882 ATTTCATATATCAATATATCAT
1 ATTTCATATA-C-ATATATCAT
29582904 GTAACATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTCATATACATATATCATTC
Found at i:29583125 original size:24 final size:25
Alignment explanation
Indices: 29583073--29583133 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
29583063 GTACATGTAT
* * *
29583073 GCTCATACGAGCTTTGAATCGGTAT
1 GCTCATACGAGCTGTGAAACGGTAA
*
29583098 GCTCTTACGAGCTGT-AAACGGTAA
1 GCTCATACGAGCTGTGAAACGGTAA
*
29583122 GCTCATATGAGC
1 GCTCATACGAGC
29583134 CAAATATTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (25 bp):
GCTCATACGAGCTGTGAAACGGTAA
Found at i:29583164 original size:25 final size:25
Alignment explanation
Indices: 29583116--29583175 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
29583106 GAGCTGTAAA
*
29583116 CGGTAAGCTCATATGAGCCAAATAT
1 CGGTAAGCTCATACGAGCCAAATAT
* * **
29583141 TGGTAAGCTCATGCGAGCTGAATAT
1 CGGTAAGCTCATACGAGCCAAATAT
*
29583166 CAGTAAGCTC
1 CGGTAAGCTC
29583176 TCTCGAGTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (25 bp):
CGGTAAGCTCATACGAGCCAAATAT
Found at i:29584028 original size:11 final size:11
Alignment explanation
Indices: 29584012--29584041 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29584002 CTAAATGATA
*
29584012 TTTTAATTTGG
1 TTTTAATTCGG
29584023 TTTTAATTCGG
1 TTTTAATTCGG
29584034 TTTTAATT
1 TTTTAATT
29584042 ACCTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.13, T:0.63
Consensus pattern (11 bp):
TTTTAATTCGG
Found at i:29587902 original size:258 final size:259
Alignment explanation
Indices: 29587434--29587952 Score: 817
Period size: 258 Copynumber: 2.0 Consensus size: 259
29587424 AAACCATAAA
*
29587434 TAATTAAAAATTATAAACCAAAACCAATAGAGACTAATTAATACTTATTAAAAATAGTCCGAGGT
1 TAATTAAAAATTATAAACCAAAACCAATAGAGACTAATTAATACTTATTAAAAATAGTCCGAAGT
* * *
29587499 CAAAGGTGATTCTCCGTATGTCGAGTCTGGCCCTAGTTTCGAGGTTTACCTGAAAAGTTAAACAC
66 CAAAGGTAATTCTCCGTATGTCGAGTCCGGCCCTAGTTTCAAGGTTTACCTGAAAAGTTAAACAC
* * *
29587564 TATGGGGGTGAGCTTATGAAAGCTCAGTGTGAGTCGAACATTTATTTAAACACCCATAAATAGAA
131 TATGGGGGTGAGCTTATGAAAGCTCAGTATGAGTCAAACAATTATTTAAACACCCATAAATAGAA
* *
29587629 AATATAGTTAAGCATATTACCATTAACAAAAGAACACAAACCCATCATTGGAATTTCATATCAT
196 AAAATAGTGAAGCATATTACCATTAACAAAAGAACACAAACCCATCATTGGAATTTCATATCAT
* * *
29587693 TAATTAAAAATTATAAACCAAAACCAATAGAGATTGATTAATACTT-TTAAAAATAGTCTGAAGT
1 TAATTAAAAATTATAAACCAAAACCAATAGAGACTAATTAATACTTATTAAAAATAGTCCGAAGT
* * **
29587757 CCAGGGTAATTCTCCGTAT-TCCGAGTCCGGTTCTAGTTTCAAGGTTTACCTGAAAAGTTAAACA
66 CAAAGGTAATTCTCCGTATGT-CGAGTCCGGCCCTAGTTTCAAGGTTTACCTGAAAAGTTAAACA
* * *
29587821 CTATTGGGGTGAGCTTATGAAATCTCAGTATGAGTCAAACAATTATTTAAGCACCCATAAATAGA
130 CTATGGGGGTGAGCTTATGAAAGCTCAGTATGAGTCAAACAATTATTTAAACACCCATAAATAGA
* * *
29587886 AAAAATAGTGAAGCATATTAGCATTAACAGAAGAACACAGACCCATCATTGGAATTTCATATCAT
195 AAAAATAGTGAAGCATATTACCATTAACAAAAGAACACAAACCCATCATTGGAATTTCATATCAT
29587951 TA
1 TA
29587953 CATAGTAATT
Statistics
Matches: 237, Mismatches: 22, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
257 1 0.00
258 192 0.81
259 44 0.19
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (259 bp):
TAATTAAAAATTATAAACCAAAACCAATAGAGACTAATTAATACTTATTAAAAATAGTCCGAAGT
CAAAGGTAATTCTCCGTATGTCGAGTCCGGCCCTAGTTTCAAGGTTTACCTGAAAAGTTAAACAC
TATGGGGGTGAGCTTATGAAAGCTCAGTATGAGTCAAACAATTATTTAAACACCCATAAATAGAA
AAAATAGTGAAGCATATTACCATTAACAAAAGAACACAAACCCATCATTGGAATTTCATATCAT
Found at i:29588055 original size:5 final size:5
Alignment explanation
Indices: 29588040--29588073 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
29588030 GATACCATTT
*
29588040 AATAC AGTAC AATAC AATAC AATAC AATAC AATA
1 AATAC AATAC AATAC AATAC AATAC AATAC AATA
29588074 TGTAGCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.18, G:0.03, T:0.21
Consensus pattern (5 bp):
AATAC
Found at i:29588268 original size:27 final size:27
Alignment explanation
Indices: 29588210--29588319 Score: 148
Period size: 27 Copynumber: 4.0 Consensus size: 27
29588200 AACTTGATGT
*
29588210 AGTAAAACTACCTAATAAAAAATAATGC
1 AGTAAAACTACCGAAT-AAAAATAATGC
* *
29588238 AGTAAAACTACTGAATAACAATAATGC
1 AGTAAAACTACCGAATAAAAATAATGC
*
29588265 AGTAAAACTACCGAATAAAAATAATGT
1 AGTAAAACTACCGAATAAAAATAATGC
* *
29588292 AGTAAAAGTGCCGAATAACAAATAATGC
1 AGTAAAACTACCGAATAA-AAATAATGC
29588320 GATATAATCG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 50 0.69
28 22 0.31
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.21
Consensus pattern (27 bp):
AGTAAAACTACCGAATAAAAATAATGC
Found at i:29589357 original size:5 final size:5
Alignment explanation
Indices: 29589349--29589379 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
29589339 ATGCATTTAT
*
29589349 TTCAT TTCAA TTCAA TTCAA TTCAA TTCAA T
1 TTCAA TTCAA TTCAA TTCAA TTCAA TTCAA T
29589380 CTAATTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (5 bp):
TTCAA
Found at i:29592362 original size:17 final size:18
Alignment explanation
Indices: 29592340--29592378 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29592330 GTTTTACAAG
29592340 AAAATAAA-TAAACATGC
1 AAAATAAAGTAAACATGC
* *
29592357 AAAATAAAGTGAACATGG
1 AAAATAAAGTAAACATGC
29592375 AAAA
1 AAAA
29592379 CTAATGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15
Consensus pattern (18 bp):
AAAATAAAGTAAACATGC
Found at i:29595432 original size:15 final size:15
Alignment explanation
Indices: 29595412--29595450 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
29595402 TTGGACTGGG
29595412 TATGGGTATTACATT
1 TATGGGTATTACATT
29595427 TATGGGTATTACATT
1 TATGGGTATTACATT
*
29595442 TATTGGTAT
1 TATGGGTAT
29595451 CAGAGCTCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (15 bp):
TATGGGTATTACATT
Found at i:29600515 original size:22 final size:22
Alignment explanation
Indices: 29600490--29600546 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
29600480 TAAAAATTAA
29600490 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTACAAAATCAT
* *
29600512 ATCTTCTAAGATTGC-ATATCAT
1 ATC-TCTAAGATTACAAAATCAT
29600534 A--TCTAAGATTACA
1 ATCTCTAAGATTACA
29600547 TATAATATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 10 0.33
22 10 0.33
23 10 0.33
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (22 bp):
ATCTCTAAGATTACAAAATCAT
Found at i:29600519 original size:23 final size:22
Alignment explanation
Indices: 29600493--29600537 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29600483 AAATTAAATC
29600493 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
29600516 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
29600538 AAGATTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:29600540 original size:19 final size:19
Alignment explanation
Indices: 29600516--29600569 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
29600506 AATCATATCT
29600516 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
29600535 TCTAAGATTACATATAATA
1 TCTAAGATTGCATATCATA
29600554 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
29600570 CTTGAAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:29600540 original size:42 final size:38
Alignment explanation
Indices: 29600493--29600569 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 38
29600483 AAATTAAATC
*
29600493 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-AAAT-A-AT-ATCTAAGATTGCATATCATA
*
29600535 TCTAAGATTACATATAATATCTAAGATTGCATATC
1 TCTAAGATTACAAATAATATCTAAGATTGCATATC
29600570 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 16 0.48
39 2 0.06
40 1 0.03
41 3 0.09
42 11 0.33
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (38 bp):
TCTAAGATTACAAATAATATCTAAGATTGCATATCATA
Found at i:29601175 original size:45 final size:45
Alignment explanation
Indices: 29601118--29601246 Score: 188
Period size: 45 Copynumber: 2.9 Consensus size: 45
29601108 TTGTTTATTT
* * *
29601118 AGTCTGGC-CCACTGCAATTTTAGGGGGATAAGACTTGATTTCTTG
1 AGTCT-GCTCCACTGCAACTTTAGGGAGATAAGACTCGATTTCTTG
*
29601163 AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTCGATTTCTTG
* *
29601208 TGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGAT
1 AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTCGAT
29601247 GCGATCTGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
44 2 0.03
45 74 0.97
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTCGATTTCTTG
Found at i:29601410 original size:132 final size:132
Alignment explanation
Indices: 29601263--29601517 Score: 347
Period size: 132 Copynumber: 1.9 Consensus size: 132
29601253 TGCTTGCTGT
* *
29601263 AACTTTAGAGAGATAAGATTTATGATT-TTA-ATCCACTCCACTGCAACTTCAGTGAGATAGGAT
1 AACTTTAGAGAGATAAG-GTT-TGATTATTAGA-CCACTCCACTGCAACTTCAGGGAGATAGGAT
* * *
29601326 TATTGGCTTTAATC-GCTTCACTGTAACTTCATGGAGATAAAATTCGCCATCTTCAGTCTGCATC
63 TATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAAATTCGCCATCTTCAGTCTGCATC
29601390 ACTAC
128 ACTAC
* ** *
29601395 AACTTTAG-GAGGATAAGGTTTGCTTACTTAGACTGCTCCACTGCGACTTCAGGGAGATAGGATT
1 AACTTTAGAGA-GATAAGGTTTGATTA-TTAGACCACTCCACTGCAACTTCAGGGAGATAGGATT
*
29601459 ATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCT
64 ATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAAATTCGCCATCTTCAGTCT
29601518 TTTAAATTGC
Statistics
Matches: 108, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
130 4 0.04
131 4 0.04
132 58 0.54
133 42 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (132 bp):
AACTTTAGAGAGATAAGGTTTGATTATTAGACCACTCCACTGCAACTTCAGGGAGATAGGATTAT
TGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAAATTCGCCATCTTCAGTCTGCATCACT
AC
Found at i:29601490 original size:44 final size:44
Alignment explanation
Indices: 29601289--29601502 Score: 140
Period size: 44 Copynumber: 4.9 Consensus size: 44
29601279 GATTTATGAT
** *
29601289 TTTAATCCACTCCACTGCAACTTCAGTGAGATAGGATTATTGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGC
* * * * *
29601333 TTTAATC-GCTTCACTGTAACTTCATGGAGATA--A-AATTCGCC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATT-GGC
* * * * * *
29601374 ATCTTCAGTCTGCAT-CACTACAACTTTA-GGAGGATAAGGTTTGCTT-AC
1 -T-TT-AATCTGC-TCCACTGCAACTTCAGGGA-GAT-AGGATT-ATTGGC
*
29601422 -TTAGA-CTGCTCCACTGCGACTTCAGGGAGATAGGATTATTGGC
1 TTTA-ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGC
*
29601465 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATT
29601503 CGCCATCTTC
Statistics
Matches: 128, Mismatches: 24, Indels: 36
0.68 0.13 0.19
Matches are distributed among these distances:
40 3 0.02
41 3 0.02
42 3 0.02
43 30 0.23
44 64 0.50
45 20 0.16
46 2 0.02
48 1 0.01
50 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGC
Found at i:29601916 original size:44 final size:44
Alignment explanation
Indices: 29601866--29601985 Score: 174
Period size: 44 Copynumber: 2.7 Consensus size: 44
29601856 ATCTGTTATT
* *
29601866 TTCAACCTACTCCACTGTTGCTCAGGGAGATAGGA-TTCACAATC
1 TTCAACCTATTCCACTGCTGCTCAGGGAGATAGGACTT-ACAATC
29601910 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGCTG-CTCAGGGAGATAGGACTTACAATC
29601954 TTCAACCTATTCCACTGCTG-TCCAGGGAGATA
1 TTCAACCTATTCCACTGCTGCT-CAGGGAGATA
29601986 AGGTTGGGGT
Statistics
Matches: 70, Mismatches: 2, Indels: 8
0.88 0.03 0.10
Matches are distributed among these distances:
44 67 0.96
45 3 0.04
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGCTCAGGGAGATAGGACTTACAATC
Found at i:29602116 original size:88 final size:88
Alignment explanation
Indices: 29601975--29602649 Score: 953
Period size: 88 Copynumber: 7.7 Consensus size: 88
29601965 CCACTGCTGT
** * * * * * *
29601975 CCAGGGAGATAAGGTTGGGGTCATCGATATGCTTCGCTGTCAGTGCAGAAAGGCAAGATCTGCTA
1 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA
* *
29602040 TTTTTAACCTACTTCACTGCAAC
66 TTTTTAACCTGCTTCACTACAAC
* * * *
29602063 CCAGGGAGGCAAGGCTGGTGTCTTCAATCTGCTTCGTTGTCGGTGCAAGAAGGCAAGATCTGTTA
1 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA
*
29602128 TTTTTAACCTGCTCCACTACAAC
66 TTTTTAACCTGCTTCACTACAAC
* *
29602151 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGTTGTCTGTGCAGGAAGGCAAGATCTGCTA
1 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA
*
29602216 TTTTTAACCTG-TTCCGCTACAAC
66 TTTTTAACCTGCTT-CACTACAAC
* * * *
29602239 CCAAGGAAGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTA
1 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA
*
29602304 TTTTTAACCTGC-TCTGCTACAAC
66 TTTTTAACCTGCTTC-ACTACAAC
* *
29602327 CCAGGGAGACAAGGCTGGTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTG-TA
1 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCT-
*
29602391 ATTTTTAACCTGC-TCTACTGCAAC
65 ATTTTTAACCTGCTTC-ACTACAAC
*
29602415 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTA
1 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA
* *
29602480 TTTTTAACCTGCTCCACTGCAAC
66 TTTTTAACCTGCTTCACTACAAC
* *
29602503 CCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTA
1 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA
* * *
29602568 TTTTTACCCTGCTCCGCTACAAC
66 TTTTTAACCTGCTTCACTACAAC
* * *
29602591 CCAGGGAGGCAAGGTTGGTGTCTTCGATCTTCTTCGCTATCGGTGCAGGAAGGCAAGAT
1 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGAT
29602650 ATGTTATCTT
Statistics
Matches: 534, Mismatches: 47, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
87 3 0.01
88 529 0.99
89 2 0.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.28
Consensus pattern (88 bp):
CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA
TTTTTAACCTGCTTCACTACAAC
Found at i:29602469 original size:44 final size:44
Alignment explanation
Indices: 29602416--29602559 Score: 119
Period size: 44 Copynumber: 3.3 Consensus size: 44
29602406 TACTGCAACC
*
29602416 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTGGTG
* * * * ** * * * *****
29602460 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTG-CAACC
1 CAGGAAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTTGGTG
* *
29602504 CAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTTGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTGGTG
29602548 CAGGAAGGCAAG
1 CAGGAAGGCAAG
29602560 ATCTGCTATT
Statistics
Matches: 66, Mismatches: 32, Indels: 4
0.65 0.31 0.04
Matches are distributed among these distances:
43 16 0.24
44 33 0.50
45 17 0.26
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTGGTG
Found at i:29603989 original size:14 final size:15
Alignment explanation
Indices: 29603966--29603998 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29603956 ATCGACGCCT
29603966 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
29603980 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
29603995 TTCC
1 TTCC
29603999 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:29604878 original size:25 final size:25
Alignment explanation
Indices: 29604827--29604896 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
29604817 AAGAAAATCC
* **
29604827 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAAT-ATTAGCTCA
*
29604853 AAAAGAATGAAAAAATATTGGCTCA
1 AAAAGAATGAAAAAATATTAGCTCA
* *
29604878 AAAATGAATGCAAAGATAT
1 AAAA-GAATGAAAAAATAT
29604897 ATTTTATTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 10 0.27
26 27 0.73
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.23
Consensus pattern (25 bp):
AAAAGAATGAAAAAATATTAGCTCA
Found at i:29609638 original size:19 final size:19
Alignment explanation
Indices: 29609606--29609678 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
29609596 AATCATATCT
* *
29609606 TCTAACATTGCATATCATA
1 TCTAAGATTACATATCATA
29609625 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
29609644 TCTAAGATTACATATCATG
1 TCTAAGATTACATATCATA
* *
29609663 TCTAAAATTGCATATC
1 TCTAAGATTACATATC
29609679 CTTGAAGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:29614362 original size:22 final size:22
Alignment explanation
Indices: 29614318--29614369 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
29614308 TATCAGCATT
*
29614318 ATCAGTGGCGGTTTATCCATAA
1 ATCAGTGGCAGTTTATCCATAA
* **
29614340 ATTAGTGGCAGTTTATCTGTAA
1 ATCAGTGGCAGTTTATCCATAA
29614362 ATCAGTGG
1 ATCAGTGG
29614370 TGGCATGTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (22 bp):
ATCAGTGGCAGTTTATCCATAA
Found at i:29622677 original size:33 final size:32
Alignment explanation
Indices: 29622640--29622701 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
29622630 ATGCTCATAT
* *
29622640 TGTCATAACTCAGTTATGGTCTTATCATTAGAA
1 TGTCATAACCCAGCTATGGTCTTAT-ATTAGAA
*
29622673 TGTCATAGCCCAGCTATGGTCTTATATTA
1 TGTCATAACCCAGCTATGGTCTTATATTA
29622702 TATATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 4 0.15
33 22 0.85
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTCATAACCCAGCTATGGTCTTATATTAGAA
Found at i:29622707 original size:2 final size:2
Alignment explanation
Indices: 29622695--29622724 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29622685 GCTATGGTCT
29622695 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29622725 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:29622834 original size:2 final size:2
Alignment explanation
Indices: 29622827--29622855 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29622817 NNNNNNNNCT
29622827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29622856 GTATGTATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29631417 original size:24 final size:24
Alignment explanation
Indices: 29631345--29631417 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
29631335 TTAAATAATT
*
29631345 TTTTAAAA-ATTTAAAAATTCAAAAA
1 TTTTAAAATATTTTAAAATT--AAAA
*
29631370 TTTTAAAATATATATTTAAA--AAAA
1 TTTTAAAATAT-T-TTAAAATTAAAA
29631394 TTTTAAAATATTTTAAAATTAAAA
1 TTTTAAAATATTTTAAAATTAAAA
29631418 AAATTACTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
22 5 0.12
23 1 0.03
24 19 0.47
25 8 0.20
26 2 0.05
27 1 0.03
28 4 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTTAAAATATTTTAAAATTAAAA
Found at i:29633521 original size:27 final size:27
Alignment explanation
Indices: 29633483--29633549 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
29633473 CAAGAGACTG
29633483 ATAGGCGGCACCAAAGGTGCCATTCCC
1 ATAGGCGGCACCAAAGGTGCCATTCCC
* * *
29633510 ATAGGCAGCACCGATGGTGCCATTCCC
1 ATAGGCGGCACCAAAGGTGCCATTCCC
*
29633537 ATGGGCGGCACCA
1 ATAGGCGGCACCA
29633550 CTCGTGTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.24, C:0.33, G:0.28, T:0.15
Consensus pattern (27 bp):
ATAGGCGGCACCAAAGGTGCCATTCCC
Found at i:29633912 original size:40 final size:36
Alignment explanation
Indices: 29633852--29633937 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
29633842 AAACTAGTAT
* * *
29633852 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATTGTTAGTTATTATTTTGAGTATAAA-AC
29633888 TAATTATTATTGTTAGTTACTATTATTTTGAGTATAAAAC
1 T-ATTATTATTGTTAG-T--TATTATTTTGAGTATAAAAC
29633928 TATTATTATT
1 TATTATTATT
29633938 TTTATTGAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.31
38 1 0.02
39 9 0.21
40 15 0.36
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTATTATTGTTAGTTATTATTTTGAGTATAAAAC
Found at i:29636608 original size:159 final size:154
Alignment explanation
Indices: 29636248--29636660 Score: 412
Period size: 159 Copynumber: 2.6 Consensus size: 154
29636238 GAAAAAAAAG
*
29636248 TTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCGTTTTATTA-TTTTAA
1 TTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTTAA
* *
29636312 AAAATATCATAATTTCTAATTTTATAATTTTACATTATTTAAGTGCATTATGTTTGAAATTTATT
66 AAAAAATCATAATTTCTAATTTTATAATTTTACATTATTTAAGTACATTATGTTTGAAATTTATT
* *
29636377 ATTTTAGTGTATTTTTTAAATTAAT
131 ATTTTACTGTAATTTTTAAA-TAAT
* * * * * * *
29636402 TTAGTGTCAAAAAAACCCTTA-TTCCTGCCCTTTGC-TCATATTATTTTC-CCGAATTTTATTAC
1 TTA--GT--AAAACACTCTTACTT-CGGCCATTT-CTTCGTATTTTTTTCTCCGCATTTTATTAC
* * * * *
29636464 TTTTAATAAAAAAT-ATTATTTTCGT-ATTTTATTATTTTATATTATTTCAGTACATTTTGTTTG
60 TTTTAA-AAAAAATCA-TAATTTC-TAATTTTATAATTTTACATTATTTAAGTACATTATGTTTG
*
29636527 AAATATTTGTATTAATTATTTCTG-AATTTTTAAA-AATT
122 -AA-A-TT-TATT-ATT-TTACTGTAATTTTTAAATAA-T
* *
29636565 TTAGTAAAACACTATTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATT-CCTTTAA
1 TTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTTAA
* *
29636629 AAAATATCATAATTTCTAATTTTATAAATTTA
66 AAAAAATCATAATTTCTAATTTTATAATTTTA
29636661 TTAATTTAGT
Statistics
Matches: 206, Mismatches: 31, Indels: 40
0.74 0.11 0.14
Matches are distributed among these distances:
154 3 0.01
156 2 0.01
157 14 0.07
158 60 0.29
159 80 0.39
160 16 0.08
161 3 0.01
162 4 0.02
163 8 0.04
164 12 0.06
165 4 0.02
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.51
Consensus pattern (154 bp):
TTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTACTTTTAA
AAAAAATCATAATTTCTAATTTTATAATTTTACATTATTTAAGTACATTATGTTTGAAATTTATT
ATTTTACTGTAATTTTTAAATAAT
Found at i:29636879 original size:285 final size:286
Alignment explanation
Indices: 29636368--29636945 Score: 989
Period size: 285 Copynumber: 2.0 Consensus size: 286
29636358 ATTATGTTTG
* * *
29636368 AAATTTATTATTTTAGTGTATTTTTTAAATTAATTTAGTGTCAAAAAAACCCTTATTCCTGCCCT
1 AAATTTATTAATTTAGTGTATTTTTTAAATTAATTTAGTGTCAAAAAAACACTTATTCCTACCCT
*
29636433 TTGCTCATATTATTTTCCCGAATTTTATTACTTTTAATAAAAAATATTATTTTCGTATTTTATTA
66 TTGCTCATATTATTTTCCCGAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTA
*
29636498 TTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAA
131 TTTTATATTATTTCAGTACATATTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAA
* * * *
29636563 TTTTAGTAAAACACTATTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTCCTTTA
196 ATTTAGTAAAACACTATTACTCCGGCCATTTCTTCGTATTTTTTTCTCCGCATCTTATTACTTTA
29636628 AAAAATATCATAATTTCTAATTTTAT
261 AAAAATATCATAATTTCTAATTTTAT
*
29636654 AAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGT-AAAAAAACACTTATTCCTACCCT
1 AAATTTATTAATTTAGTGTATTTTTTAAATTAATTTAGTGTCAAAAAAACACTTATTCCTACCCT
* *
29636718 TTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAAATATTATTTTTGTATTTTATT
66 TTGCTCATATTATTTTCCCGAATTTTATTACTTTCAAT-AAAAAATATTATTTTCGTATTTTATT
*
29636783 ATTTTATATTATTTCAGTACATATT-TTTGAAATATTTGTATTAATTATTTTTGAATTTTTAAAA
130 ATTTTATATTATTTCAGTACATATTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAA
* *
29636847 AATTTAGTAAAACACTCTTACTCCGGCCATTTCTTCGTATTTTTTTCTTCGCATCTTATTACTTT
195 AATTTAGTAAAACACTATTACTCCGGCCATTTCTTCGTATTTTTTTCTCCGCATCTTATTACTTT
29636912 AAAAAATATCATAATTTCTAATTTTAT
260 AAAAAATATCATAATTTCTAATTTTAT
*
29636939 AATTTTA
1 AAATTTA
29636946 CTTTATTTCA
Statistics
Matches: 275, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
285 187 0.68
286 88 0.32
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (286 bp):
AAATTTATTAATTTAGTGTATTTTTTAAATTAATTTAGTGTCAAAAAAACACTTATTCCTACCCT
TTGCTCATATTATTTTCCCGAATTTTATTACTTTCAATAAAAAATATTATTTTCGTATTTTATTA
TTTTATATTATTTCAGTACATATTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAA
ATTTAGTAAAACACTATTACTCCGGCCATTTCTTCGTATTTTTTTCTCCGCATCTTATTACTTTA
AAAAATATCATAATTTCTAATTTTAT
Found at i:29637330 original size:10 final size:10
Alignment explanation
Indices: 29637315--29637480 Score: 67
Period size: 10 Copynumber: 16.0 Consensus size: 10
29637305 AATTACATTT
29637315 TTTTTCTTTC
1 TTTTTCTTTC
29637325 TTTTTCCTTTC
1 TTTTT-CTTTC
***
29637336 -TCCCCTCTTC
1 TTTTTCT-TTC
*
29637346 TTCTTCTTT-
1 TTTTTCTTTC
29637355 TTTTT-TTCTC
1 TTTTTCTT-TC
29637365 TTCTTTCCTTTTC
1 TT-TTT-C-TTTC
29637378 TTTCCTTCTTT-
1 TTT--TTCTTTC
*
29637389 TTCTTCTTCTC
1 TTTTTCTT-TC
* *
29637400 CTTTCCTTT-
1 TTTTTCTTTC
* *
29637409 TCTTTCCTTC
1 TTTTTCTTTC
29637419 TTTTTCTTTC
1 TTTTTCTTTC
29637429 TTTCCTCTCATTTC
1 TTT--T-TC-TTTC
*
29637443 CTTTTCTTTC
1 TTTTTCTTTC
29637453 TTTTTCTTTC
1 TTTTTCTTTC
29637463 --TTTCTTTC
1 TTTTTCTTTC
*
29637471 TTCTTCTTTC
1 TTTTTCTTTC
29637481 CCTCTCTTTC
Statistics
Matches: 117, Mismatches: 19, Indels: 40
0.66 0.11 0.23
Matches are distributed among these distances:
8 10 0.09
9 17 0.15
10 46 0.39
11 21 0.18
12 6 0.05
13 7 0.06
14 10 0.09
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:29637393 original size:43 final size:43
Alignment explanation
Indices: 29637312--29637431 Score: 106
Period size: 43 Copynumber: 2.9 Consensus size: 43
29637302 AAAAATTACA
* * *
29637312 TTTTTTTTCTT-TCTT-TTTCC-TTTC-TCCCCTCTTCTTCTTC
1 TTTTTTTT-TTCTCTTCTTTCCTTTTCTTTCCTTCTTTTTCTTC
29637352 TTTTTTTTTTCTCTTCTTTCCTTTTCTTTCCTTCTTTTTCTTC
1 TTTTTTTTTTCTCTTCTTTCCTTTTCTTTCCTTCTTTTTCTTC
* ** * * *
29637395 TTCTCCTTTCCTTTTCTTTCCTTCTT-TTTCTTTCTTT
1 TTTTTTTTTTCTCTTCTTTCCTT-TTCTTTCCTTCTTT
29637432 CCTCTCATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
39 2 0.03
40 12 0.18
41 5 0.08
42 4 0.06
43 41 0.62
44 2 0.03
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (43 bp):
TTTTTTTTTTCTCTTCTTTCCTTTTCTTTCCTTCTTTTTCTTC
Found at i:29637404 original size:33 final size:33
Alignment explanation
Indices: 29637348--29637495 Score: 137
Period size: 33 Copynumber: 4.5 Consensus size: 33
29637338 CCCTCTTCTT
*
29637348 CTTCTTTTT-TTTTTCTCTTCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTCTTCTC--CTTTCCTTTTCTTTC
29637382 CTTCTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
* * *
29637415 CTTCTTTTTCTTTCTT-TCCTCTCATTTCCTTTTC
1 CTTCTTTTTC-TTCTTCTCCTTTCCTTTTC-TTTC
*
29637449 TTTCTTTTTCTTTCTT-T-CTTT-CTTCTTCTTTC
1 CTTCTTTTTC-TTCTTCTCCTTTCCTT-TTCTTTC
* *
29637481 CCTCTCTTTC-TCTTC
1 CTTCTTTTTCTTCTTC
29637496 CCCCCACCCA
Statistics
Matches: 98, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
30 4 0.04
32 13 0.13
33 40 0.41
34 34 0.35
35 7 0.07
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (33 bp):
CTTCTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
Found at i:29637444 original size:38 final size:36
Alignment explanation
Indices: 29637345--29637470 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 36
29637335 CTCCCCTCTT
* *
29637345 CTTCTTCTTT-TTTTTTTCTCTTCTTTCCTTTTCTTTC
1 CTTCTT-TTTCTTTCTTTC-CTCCTTTCCTTTTCTTTC
29637382 CTTCTTTTTC-TTC-TT-CTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTCCTCCTTTCCTTTTCTTTC
29637415 CTTCTTTTTCTTTCTTTCCTCTCATTTCCTTTTCTTT-
1 CTTCTTTTTCTTTCTTTCCTC-C-TTTCCTTTTCTTTC
*
29637452 CTTTTTCTTTCTTTCTTTC
1 CTTCTT-TTTCTTTCTTTC
29637471 TTCTTCTTTC
Statistics
Matches: 79, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
33 27 0.34
34 3 0.04
35 4 0.05
36 8 0.10
37 12 0.15
38 25 0.32
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (36 bp):
CTTCTTTTTCTTTCTTTCCTCCTTTCCTTTTCTTTC
Found at i:29637481 original size:38 final size:37
Alignment explanation
Indices: 29637343--29637495 Score: 160
Period size: 38 Copynumber: 4.2 Consensus size: 37
29637333 TTCTCCCCTC
*
29637343 TTCTTCTTCTTTTTTTTTTC-TCTTCTTTCCTTTTCT
1 TTCTTCTTCTTTTTTCTTTCTTCTTCTTTCCTTTTCT
*
29637379 TTC--CTTC-TTTTTC-TTCTTCTCCTTTCCTTTTCT
1 TTCTTCTTCTTTTTTCTTTCTTCTTCTTTCCTTTTCT
*
29637412 TTCCTTCTT-TTTCTTTCTTTCCTC-TCATTTCCTTTTCT
1 TT-CTTCTTCTTT-TTTCTTTCTTCTTC-TTTCCTTTTCT
* * *
29637450 TTCTTTTTCTTTCTTTCTTTCTTCTTCTTTCCCTCTCT
1 TTCTTCTTCTTT-TTTCTTTCTTCTTCTTTCCTTTTCT
29637488 TTC-TCTTC
1 TTCTTCTTC
29637496 CCCCCACCCA
Statistics
Matches: 98, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
32 3 0.03
33 22 0.22
34 5 0.05
36 8 0.08
37 14 0.14
38 44 0.45
39 2 0.02
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.69
Consensus pattern (37 bp):
TTCTTCTTCTTTTTTCTTTCTTCTTCTTTCCTTTTCT
Found at i:29639975 original size:39 final size:39
Alignment explanation
Indices: 29639932--29640018 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 39
29639922 ACCTATATCA
* *
29639932 TATATTACCCGAGAATTCGCA-ACAAATG-TTGAATCTCGT
1 TATATTACCCGAGAATCCGCATA-AAATGCTAG-ATCTCGT
* * *
29639971 TATATTGCCGGAGGATCCGCATAAAATGCTAGATCTCGT
1 TATATTACCCGAGAATCCGCATAAAATGCTAGATCTCGT
29640010 TATATTACC
1 TATATTACC
29640019 TAAGGATCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
39 37 0.93
40 3 0.08
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (39 bp):
TATATTACCCGAGAATCCGCATAAAATGCTAGATCTCGT
Found at i:29640369 original size:15 final size:15
Alignment explanation
Indices: 29640349--29640377 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29640339 GTCAAAATTC
29640349 ACAACAATTTTCACT
1 ACAACAATTTTCACT
29640364 ACAACAATTTTCAC
1 ACAACAATTTTCAC
29640378 ATAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (15 bp):
ACAACAATTTTCACT
Found at i:29650306 original size:9 final size:9
Alignment explanation
Indices: 29650294--29650388 Score: 138
Period size: 9 Copynumber: 10.4 Consensus size: 9
29650284 AAATAAAAAA
29650294 AATTCGGGT
1 AATTCGGGT
29650303 AATTCGGGT
1 AATTCGGGT
*
29650312 ATTTTTC-GGT
1 A--ATTCGGGT
*
29650322 AATTCGGTT
1 AATTCGGGT
29650331 AATTCGGGT
1 AATTCGGGT
*
29650340 AATTCGGTT
1 AATTCGGGT
29650349 AATTCGGGT
1 AATTCGGGT
29650358 AATTCGGGT
1 AATTCGGGT
29650367 AATTCGGGT
1 AATTCGGGT
29650376 AATTCGGGT
1 AATTCGGGT
29650385 AATT
1 AATT
29650389 TTTAACCAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
8 3 0.04
9 67 0.87
10 4 0.05
11 3 0.04
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (9 bp):
AATTCGGGT
Found at i:29654757 original size:44 final size:42
Alignment explanation
Indices: 29654700--29655010 Score: 158
Period size: 44 Copynumber: 7.1 Consensus size: 42
29654690 GTGGCAAATC
*
29654700 TTATCTCCCTGAAGTTACAGTGAAGCAGATTAAAGCCACAAA
1 TTATCTCCCTGAAGTTACAGTGAAGCAGATTAAAGCTACAAA
** * * *
29654742 TTAGATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATAGCAAA
1 TT--ATCTCCCTGAAGTTACAGTGAAGCAGATTAAAGCTA-CAAA
* * *
29654787 TCTTATCTCCCTGAAGTTGCAGT-AGAGTAGATTAAAGCTATAAA
1 --TTATCTCCCTGAAGTTACAGTGA-AGCAGATTAAAGCTACAAA
** * * * *
29654831 CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAAGTTACAAGTC
1 --TTATCTCCCTGAAGTTACAGTGAAGCAGATTAAAGCTACAA--A
** * ** * * *
29654877 TTATCTCCCAAAAGTTGCAGTGGGGCAGATTGAAGTTACAAG
1 TTATCTCCCTGAAGTTACAGTGAAGCAGATTAAAGCTACAAA
* * * * * * *
29654919 TCTAATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATC
1 T-T-ATCTCCCTGAAGTTACAGTGAAGCAGATTAAAGCTA-C-AA-A
* * * *
29654966 TTATTTCCCTGAAGTTGCAGTAGAA-TAGATTAAGGCTACAAA
1 TTATCTCCCTGAAGTTACAGT-GAAGCAGATTAAAGCTACAAA
29655008 TTA
1 TTA
29655011 CAAATCGGAT
Statistics
Matches: 211, Mismatches: 43, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
42 6 0.03
43 3 0.01
44 134 0.64
45 60 0.28
46 5 0.02
47 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (42 bp):
TTATCTCCCTGAAGTTACAGTGAAGCAGATTAAAGCTACAAA
Found at i:29654799 original size:89 final size:88
Alignment explanation
Indices: 29654693--29655819 Score: 547
Period size: 89 Copynumber: 12.4 Consensus size: 88
29654683 AGTCATCGTG
* *
29654693 GCAAATCTTATCTCCCTGAAGTTACAGTGAAGCAGATTAAAGCCACAAATTAGATCTCCCTGAAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCTACAAATTA-ATCTCCCTGAAG
* *
29654758 TTGTAGTGGAGCAGACTAAAGATA
65 TTGCAGTGGAGCAGACTGAAGATA
* *
29654782 GCAAATCTTATCTCCCTGAAGTTGCAGT-AGAGTAGATTAAAGCTATAAACCTT-ATCTCCCTGA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAGCTACAAA--TTAATCTCCCTGA
* * ** *
29654845 AGTTACAGTGGGGCAGGTTGAAGTTA
63 AGTTGCAGTGGAGCAGACTGAAGATA
* ** ** * * * *
29654871 -CAAGTCTTATCTCCCAAAAGTTGCAGTGGGGCAGATTGAAGTTACAAGTCTAATCCCCCTGAAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCTACAAAT-TAATCTCCCTGAAG
29654935 TTGCAGTGGAGCAGACTGAAGATA
65 TTGCAGTGGAGCAGACTGAAGATA
* * * *
29654959 GCGAATCTTATTTCCCTGAAGTTGCAGTAGAA-TAGATTAAGGCTACAAATTACAAATCGGATCC
1 GCAAATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAGCTACAAATT---AATC---T-C
* * * * *
29655023 CCTTGAAGTTGTAGTGGGGAAGATTGAAGTTA
58 CC-TGAAGTTGCAGTGGAGCAGACTGAAGATA
* * ** * * ** * *
29655055 -CGAGTCTTATCTCCCTGAAGTTGTTGTGGAA-CAGACTAAAGATAGCAAATCTTGTTTCCCTAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAGCTA-CAAAT-TAATCTCCCTGA
* * * * * *
29655118 AGTTGCAGTAGA-AAAAATTAAGGCTA
63 AGTTGCAGTGGAGCAGACTGAA-GATA
* * * ** * * * *
29655144 -CAAATTACAATCGGATCTCCTTGAAGTTGTAGTGGGGCAGATTGAAGATACAAGTCTTATCTCC
1 GCAAA-T-C--T--TATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCTACAAAT-TAATCTCC
*
29655208 CTGAAGTTGCAGTGGAGCAGACTAAAGATA
59 CTGAAGTTGCAGTGGAGCAGACTGAAGATA
* * * *
29655238 GCAAATCTTATCTCTCTGAAGTTACAGT-AGAGCAAATTAAAGCTATAAACCTT-ATCTCCCTGA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAGCTACAAA--TTAATCTCCCTGA
* ** *
29655301 AGTTACAGTAGG-GCAGGTTGAAGTTA
63 AGTTGCAGT-GGAGCAGACTGAAGATA
* ** ** * ** * * *
29655327 -CAAGTCTTATCTCCCAAAAGTTGCAGTGGGGCAGATTGAATTTACAAGTCTTATAC-CCCTAAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCTACAAAT-TAAT-CTCCCTGAA
29655390 GTTGCAGTGGAGCAGACTGAAGATA
64 GTTGCAGTGGAGCAGACTGAAGATA
* * * * *
29655415 G-AGAACCTTATTTCCTTGAAGTTGCAGTGGAA-TAGATTAAGGCTACAAATTACAAATCGGATC
1 GCA-AATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAGCTACAAATT---AATC---T-
* * **
29655478 CCCTTGAAGTTGCAGTGGGGCAGATTGAATTTA
57 CCC-TGAAGTTGCAGTGGAGCAGACTGAAGATA
* * * * * * *
29655511 -CGAGTCTTATCTCCCTGAAGTTGCAGTGGAA-CAGACTAAAGATAGCAAATCTTATTTCCCTAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAGCTA-CAAAT-TAATCTCCCTGA
* * * *
29655574 AGTTGCAGTGGAACA-AATTAAGGCTA
63 AGTTGCAGTGGAGCAGACTGAA-GATA
* * * ** * ** * * *
29655600 -CAAATTACAATCGGATCTCCTTGAAGTTGTAGTGGGGCAAATCCAAGATACAAGTCTTATCTCC
1 GCAAA-T-C--T--TATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCTACAAAT-TAATCTCC
29655664 CTGAAGTTGCAGTGGAGCAGACTGAAGATA
59 CTGAAGTTGCAGTGGAGCAGACTGAAGATA
* * * *
29655694 GCAAATCTTATCTCTCTGAAGTTGCAGT-AGAGGAAATTAAAGCTATAAACCTT-ATCTCCCTGA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAGCTACAAA--TTAATCTCCCTGA
* *
29655757 AGATGCAGTGGAGCAGGA-TGAAG-TT
63 AGTTGCAGTGGAGCA-GACTGAAGATA
* * *
29655782 GCTAATCTTATCTCCATGAAGATGCAGT-AGAGCAGATT
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATT
29655820 GAATATACTA
Statistics
Matches: 777, Mismatches: 195, Indels: 133
0.70 0.18 0.12
Matches are distributed among these distances:
86 2 0.00
87 4 0.01
88 174 0.22
89 287 0.37
90 17 0.02
91 16 0.02
93 4 0.01
94 67 0.09
95 146 0.19
96 58 0.07
97 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (88 bp):
GCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCTACAAATTAATCTCCCTGAAGT
TGCAGTGGAGCAGACTGAAGATA
Found at i:29654969 original size:133 final size:133
Alignment explanation
Indices: 29654693--29655405 Score: 626
Period size: 133 Copynumber: 5.3 Consensus size: 133
29654683 AGTCATCGTG
* *
29654693 GCAAATCTTATCTCCCTGAAGTTACAGTGAAGCAGATTAAAGCCACAAAT-TAGATCTCCCTGAA
1 GCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAATCT-GATCTCCCTGAA
* * * * * * * *
29654757 GTTGTAGTGGAGCAGACTAAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAA
65 GTTGTAGTGGGGCAGATTGAAGTTA-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
*
29654822 AGCTA
129 AGATA
* * * * * * * * **
29654827 -TAAACCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAAGTTACAAGTCTTATCTCCCAAAAG
1 GCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTGATCTCCCTGAAG
* * * *
29654891 TTGCAGTGGGGCAGATTGAAGTTACAAGTCTAATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAG
66 TTGTAGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG
29654956 ATA
131 ATA
* * * * ** *
29654959 GCGAATCTTATTTCCCTGAAGTTGCAGTAGAATAGATTAAGGCTACAAATTACAAATCGGATC-C
1 GCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAA-T-C---T--GATCTC
* * ** *
29655023 CCTTGAAGTTGTAGTGGGGAAGATTGAAGTTACGAGTCTTATCTCCCTGAAGTTGTTGTGGAACA
59 CC-TGAAGTTGTAGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
29655088 GACTAAAGATA
123 GACTAAAGATA
* * * * * ** * *
29655099 GCAAATCTTGTTTCCCTAAAGTTGCAGTAGAAAAAATTAAGGCTACAAATTACAATCGGATCTCC
1 GCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAA-T-C--T--GATCTCC
* *
29655164 TTGAAGTTGTAGTGGGGCAGATTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
60 CTGAAGTTGTAGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
29655229 CTAAAGATA
125 CTAAAGATA
* * * * * *
29655238 GCAAATCTTATCTCTCTGAAGTTACAGTAGAGCAAATTAAAGCTATAAACCTTATCTCCCTGAAG
1 GCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTGATCTCCCTGAAG
** * * ** * * * *
29655303 TTACAGTAGGGCAGGTTGAAGTTACAAGTCTTATCTCCCAAAAGTTGCAGTGGGGCAGATTGAAT
66 TTGTAGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG
*
29655368 TTA
131 ATA
* * *
29655371 -CAAGTCTTATAC-CCCTAAAGTTGCAGTGGAGCAGA
1 GCAAATCTTAT-CTCCCTGAAGTTACAGTGGAGCAGA
29655406 CTGAAGATAG
Statistics
Matches: 474, Mismatches: 93, Indels: 26
0.80 0.16 0.04
Matches are distributed among these distances:
132 63 0.13
133 171 0.36
134 2 0.00
135 2 0.00
137 1 0.00
138 1 0.00
139 119 0.25
140 115 0.24
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (133 bp):
GCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTGATCTCCCTGAAG
TTGTAGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG
ATA
Found at i:29655104 original size:96 final size:96
Alignment explanation
Indices: 29654923--29655104 Score: 213
Period size: 95 Copynumber: 1.9 Consensus size: 96
29654913 TACAAGTCTA
* *
29654923 ATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTA
1 ATCCCCCTGAAGTTGCAGTGGAGAAGACTGAAGATAGCGAATCTTATCTCCCTGAAGTTGCAGTA
* * * *
29654988 GAATAGATTAAGGCTACAAATTACAAATCGG
66 GAACAGACTAAAGATACAAATTACAAATCGG
* * * * * * ** *
29655019 ATCCCCTTGAAGTTGTAGTGGGGAAGATTGAAGTTA-CGAGTCTTATCTCCCTGAAGTTGTTGTG
1 ATCCCCCTGAAGTTGCAGTGGAGAAGACTGAAGATAGCGAATCTTATCTCCCTGAAGTTGCAGTA
29655083 GAACAGACTAAAGATAGCAAAT
66 GAACAGACTAAAGATA-CAAAT
29655105 CTTGTTTCCC
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
95 35 0.50
96 35 0.50
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (96 bp):
ATCCCCCTGAAGTTGCAGTGGAGAAGACTGAAGATAGCGAATCTTATCTCCCTGAAGTTGCAGTA
GAACAGACTAAAGATACAAATTACAAATCGG
Found at i:29655213 original size:44 final size:44
Alignment explanation
Indices: 29655009--29655867 Score: 481
Period size: 44 Copynumber: 19.0 Consensus size: 44
29654999 GGCTACAAAT
** * * * *
29655009 TACAAATCGGATC-CCCTTGAAGTTGTAGTGGGGAAGATTGAAGT
1 TACAAATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATTGAAGA
* * ** * * *
29655053 TACGAGTCTTATCTCCCTGAAGTTGTTGTGGAACAGACTAAAGA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * * * ** * *
29655097 TAGCAAATCTTGTTTCCCTAAAGTTGCAGTAGAAAAAATT-AAGGC
1 TA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-GA
* * * *
29655142 TACAAATTACAATCGGATCTCCTTGAAGTTGTAGTGGGGCAGATTGAAGA
1 TACAAA-T-C--T--TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * *
29655192 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * * * * *
29655236 TAGCAAATCTTATCTCTCTGAAGTTACAGTAGAGCAAATTAAAGC
1 TA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * * * *
29655281 TATAAACCTTATCTCCCTGAAGTTACAGTAGG-GCAGGTTGAAGT
1 TACAAATCTTATCTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGA
* ** * **
29655325 TACAAGTCTTATCTCCCAAAAGTTGCAGTGGGGCAGATTGAATT
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * *
29655369 TACAAGTCTTATAC-CCCTAAAGTTGCAGTGGAGCAGACTGAAGA
1 TACAAATCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * * * ** *
29655413 TAGAGAACCTTATTTCCTTGAAGTTGCAGTGGAATAGATT-AAGGC
1 TACA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-GA
** * **
29655458 TACAAATTACAAATCGGATCCCCTTGAAGTTGCAGTGGGGCAGATTGAATT
1 TACAAA-T-CTTATC---T-CCC-TGAAGTTGCAGTGGAGCAGATTGAAGA
* * * * *
29655509 TACGAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAGA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * * * *
29655553 TAGCAAATCTTATTTCCCTAAAGTTGCAGTGGAACAAATT-AAGGC
1 TA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-GA
* * * * * **
29655598 TACAAATTACAATCGGATCTCCTTGAAGTTGTAGTGGGGCAAATCCAAGA
1 TACAAA-T-C--T--TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* *
29655648 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * * * * *
29655692 TAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGGAAATTAAAGC
1 TA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * * *
29655737 TATAAACCTTATCTCCCTGAAGATGCAGTGGAGCAGGA-TGAAGT
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTGAAGA
* * * * * *
29655781 TGCTAATCTTATCTCCATGAAGATGCAGTAGAGCAGATTGAATA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* ** * * *
29655825 TACTAATCTTATCTCCCCAAAGTTCCAGTAGAGTAGATTGAAG
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
29655868 CGACAAATTC
Statistics
Matches: 619, Mismatches: 159, Indels: 74
0.73 0.19 0.09
Matches are distributed among these distances:
43 4 0.01
44 334 0.54
45 177 0.29
46 8 0.01
48 4 0.01
49 7 0.01
50 56 0.09
51 27 0.04
52 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
Found at i:29655229 original size:139 final size:139
Alignment explanation
Indices: 29654888--29655361 Score: 600
Period size: 139 Copynumber: 3.4 Consensus size: 139
29654878 TATCTCCCAA
* * *
29654888 AAGTTGCAGTGGGGCAGATTGAAGTTACAAGTCTAATCCCCCTGAAGTTGCAGTGGAGCAGACTG
1 AAGTTGCAGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
* * *
29654953 AAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTAGAATAGATTAAGGCTACAAATTACAAATCG
66 AAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTAGAAAAAATTAAGGCTACAAATTAC-AATCG
*
29655018 GATCCCCTTG
130 GATCTCCTTG
* * * ** *
29655028 AAGTTGTAGTGGGGAAGATTGAAGTTACGAGTCTTATCTCCCTGAAGTTGTTGTGGAACAGACTA
1 AAGTTGCAGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
* *
29655093 AAGATAGCAAATCTTGTTTCCCTAAAGTTGCAGTAGAAAAAATTAAGGCTACAAATTACAATCGG
66 AAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTAGAAAAAATTAAGGCTACAAATTACAATCGG
29655158 ATCTCCTTG
131 ATCTCCTTG
* *
29655167 AAGTTGTAGTGGGGCAGATTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
1 AAGTTGCAGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
* * * ** * * **
29655232 AAGATAGCAAATCTTATCTCTCTGAAGTTACAGTAGAGCAAATTAAAGCT----A-TA-AACCTT
66 AAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTAGAAAAAATTAAGGCTACAAATTACAATCGG
*
29655291 ATCTCCCTG
131 ATCTCCTTG
* * * ** *
29655300 AAGTTACAGTAGGGCAGGTTGAAGTTACAAGTCTTATCTCCCAAAAGTTGCAGTGGGGCAGA
1 AAGTTGCAGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
29655362 TTGAATTTAC
Statistics
Matches: 293, Mismatches: 41, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
133 65 0.22
134 2 0.01
135 1 0.00
139 115 0.39
140 110 0.38
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (139 bp):
AAGTTGCAGTGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
AAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTAGAAAAAATTAAGGCTACAAATTACAATCGG
ATCTCCTTG
Found at i:29655497 original size:456 final size:454
Alignment explanation
Indices: 29654746--29655867 Score: 1791
Period size: 456 Copynumber: 2.5 Consensus size: 454
29654736 CACAAATTAG
* *
29654746 ATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTA
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTA
* *
29654811 GAGTAGATTAAAGCTATAAACCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAAGTTACAAGT
66 GAGCAAATTAAAGCTATAAACCTTATCTCCCTGAAGTTACAGT-GGGCAGGTTGAAGTTACAAGT
* * *
29654876 CTTATCTCCCAAAAGTTGCAGTGGGGCAGATTGAAGTTACAAGTCTAATCCCCCTGAAGTTGCAG
130 CTTATCTCCCAAAAGTTGCAGTGGGGCAGATTGAATTTACAAGTCTTAT-CCCCTAAAGTTGCAG
* *
29654941 TGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTAGAATAGATTAAGGCTACA
194 TGGAGCAGACTGAAGATAGAGAACCTTATTTCCCTGAAGTTGCAGTAGAATAGATTAAGGCTACA
*
29655006 AATTACAAATCGGATCCCCTTGAAGTTGTAGTGGGGAAGATTGAAGTTACGAGTCTTATCTCCCT
259 AATTACAAATCGGATCCCCTTGAAGTTGCAGTGGGGAAGATTGAAGTTACGAGTCTTATCTCCCT
** *
29655071 GAAGTTGTTGTGGAACAGACTAAAGATAGCAAATCTTGTTTCCCTAAAGTTGCAGTAGAAAAAAT
324 GAAGTTGCAGTGGAACAGACTAAAGATAGCAAATCTTATTTCCCTAAAGTTGCAGTAGAAAAAAT
* **
29655136 TAAGGCTACAAATTACAATCGGATCTCCTTGAAGTTGTAGTGGGGCAGATTGAAGATACAAGTCT
389 TAAGGCTACAAATTACAATCGGATCTCCTTGAAGTTGTAGTGGGGCAAATCCAAGATACAAGTCT
29655201 T
454 T
*
29655202 ATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATCTCTCTGAAGTTACAGTA
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTA
29655267 GAGCAAATTAAAGCTATAAACCTTATCTCCCTGAAGTTACAGTAGGGCAGGTTGAAGTTACAAGT
66 GAGCAAATTAAAGCTATAAACCTTATCTCCCTGAAGTTACAGT-GGGCAGGTTGAAGTTACAAGT
29655332 CTTATCTCCCAAAAGTTGCAGTGGGGCAGATTGAATTTACAAGTCTTATACCCCTAAAGTTGCAG
130 CTTATCTCCCAAAAGTTGCAGTGGGGCAGATTGAATTTACAAGTCTTAT-CCCCTAAAGTTGCAG
* *
29655397 TGGAGCAGACTGAAGATAGAGAACCTTATTTCCTTGAAGTTGCAGTGGAATAGATTAAGGCTACA
194 TGGAGCAGACTGAAGATAGAGAACCTTATTTCCCTGAAGTTGCAGTAGAATAGATTAAGGCTACA
* *
29655462 AATTACAAATCGGATCCCCTTGAAGTTGCAGTGGGGCAGATTGAATTTACGAGTCTTATCTCCCT
259 AATTACAAATCGGATCCCCTTGAAGTTGCAGTGGGGAAGATTGAAGTTACGAGTCTTATCTCCCT
* *
29655527 GAAGTTGCAGTGGAACAGACTAAAGATAGCAAATCTTATTTCCCTAAAGTTGCAGTGGAACAAAT
324 GAAGTTGCAGTGGAACAGACTAAAGATAGCAAATCTTATTTCCCTAAAGTTGCAGTAGAAAAAAT
29655592 TAAGGCTACAAATTACAATCGGATCTCCTTGAAGTTGTAGTGGGGCAAATCCAAGATACAAGTCT
389 TAAGGCTACAAATTACAATCGGATCTCCTTGAAGTTGTAGTGGGGCAAATCCAAGATACAAGTCT
29655657 T
454 T
*
29655658 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTA
1 ATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTA
* * * * *
29655723 GAGGAAATTAAAGCTATAAACCTTATCTCCCTGAAGATGCAGTGGAGCAGGATGAAGTTGCTAA-
66 GAGCAAATTAAAGCTATAAACCTTATCTCCCTGAAGTTACAGTGG-GCAGGTTGAAGTTAC-AAG
* * * * * * *
29655787 TCTTATCT-CCATGAAGATGCAGTAGAGCAGATTGAATATACTAA-TCTTATCTCCCCAAAGTTC
129 TCTTATCTCCCA-AAAGTTGCAGTGGGGCAGATTGAATTTAC-AAGTCTTATC-CCCTAAAGTTG
* * *
29655850 CAGTAGAGTAGATTGAAG
191 CAGTGGAGCAGACTGAAG
29655868 CGACAAATTC
Statistics
Matches: 619, Mismatches: 42, Indels: 10
0.92 0.06 0.01
Matches are distributed among these distances:
455 6 0.01
456 609 0.98
457 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (454 bp):
ATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTA
GAGCAAATTAAAGCTATAAACCTTATCTCCCTGAAGTTACAGTGGGCAGGTTGAAGTTACAAGTC
TTATCTCCCAAAAGTTGCAGTGGGGCAGATTGAATTTACAAGTCTTATCCCCTAAAGTTGCAGTG
GAGCAGACTGAAGATAGAGAACCTTATTTCCCTGAAGTTGCAGTAGAATAGATTAAGGCTACAAA
TTACAAATCGGATCCCCTTGAAGTTGCAGTGGGGAAGATTGAAGTTACGAGTCTTATCTCCCTGA
AGTTGCAGTGGAACAGACTAAAGATAGCAAATCTTATTTCCCTAAAGTTGCAGTAGAAAAAATTA
AGGCTACAAATTACAATCGGATCTCCTTGAAGTTGTAGTGGGGCAAATCCAAGATACAAGTCTT
Found at i:29655500 original size:140 final size:139
Alignment explanation
Indices: 29655344--29655721 Score: 546
Period size: 140 Copynumber: 2.7 Consensus size: 139
29655334 TATCTCCCAA
*
29655344 AAGTTGCAGTGGGGCAGATTGAATTTACAAGTCTTATAC-CCCTAAAGTTGCAGTGGAGCAGACT
1 AAGTTGCAGTGGGGCAGATTGAATTTACAAGTCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACT
* * *
29655408 GAAGATAG-AGAACCTTATTTCCTTGAAGTTGCAGTGGAATAGATTAAGGCTACAAATTACAAAT
65 GAAGATAGCA-AATCTTATTTCCTTGAAGTTGCAGTGGAACAAATTAAGGCTACAAATTAC-AAT
29655472 CGGATCCCCTTG
128 CGGATCCCCTTG
* * *
29655484 AAGTTGCAGTGGGGCAGATTGAATTTACGAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTA
1 AAGTTGCAGTGGGGCAGATTGAATTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG
* *
29655549 AAGATAGCAAATCTTATTTCCCTAAAGTTGCAGTGGAACAAATTAAGGCTACAAATTACAATCGG
66 AAGATAGCAAATCTTATTTCCTTGAAGTTGCAGTGGAACAAATTAAGGCTACAAATTACAATCGG
*
29655614 ATCTCCTTG
131 ATCCCCTTG
* * ** **
29655623 AAGTTGTAGTGGGGCAAATCCAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG
1 AAGTTGCAGTGGGGCAGATTGAATTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG
*
29655688 AAGATAGCAAATCTTATCT-CTCTGAAGTTGCAGT
66 AAGATAGCAAATCTTATTTCCT-TGAAGTTGCAGT
29655722 AGAGGAAATT
Statistics
Matches: 213, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
138 1 0.00
139 100 0.47
140 111 0.52
141 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (139 bp):
AAGTTGCAGTGGGGCAGATTGAATTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG
AAGATAGCAAATCTTATTTCCTTGAAGTTGCAGTGGAACAAATTAAGGCTACAAATTACAATCGG
ATCCCCTTG
Found at i:29657643 original size:73 final size:72
Alignment explanation
Indices: 29657558--29657751 Score: 230
Period size: 73 Copynumber: 2.7 Consensus size: 72
29657548 TTAATACTAT
* *
29657558 ATATTTATTTTATTTATTTACTCATTTATTTATCATTCTTTTACTTTTAAAATAATTAAATTTCA
1 ATATTTATTTTATCTATTTACTCATTTATTTAT-ATTCTTTTACTTTTAAAATAATTAAATTTAA
29657623 TATTATGA
65 TATTATGA
* * * **
29657631 ATATTTACTTTATCTATTTACTTATTTATTTATTATTCTTTTACTTTTCAAATGCTTAAATTTAA
1 ATATTTATTTTATCTATTTACTCATTTATTTA-TATTCTTTTACTTTTAAAATAATTAAATTTAA
* **
29657696 TATTGTTT
65 TATTATGA
* * * *
29657704 ACATTTGTTTTATCTATTTATTCACTTA-TT-TATTCTTTTACTTTTAAA
1 ATATTTATTTTATCTATTTACTCATTTATTTATATTCTTTTACTTTTAAA
29657752 GAAATTTTAA
Statistics
Matches: 103, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
70 17 0.17
72 2 0.02
73 83 0.81
74 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (72 bp):
ATATTTATTTTATCTATTTACTCATTTATTTATATTCTTTTACTTTTAAAATAATTAAATTTAAT
ATTATGA
Found at i:29658055 original size:19 final size:19
Alignment explanation
Indices: 29658031--29658077 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
29658021 TCATCCTCTT
*
29658031 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
29658050 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
29658069 TATGCATTA
1 TTTGCATTA
29658078 AATTTTACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:29666212 original size:73 final size:73
Alignment explanation
Indices: 29666112--29666305 Score: 205
Period size: 73 Copynumber: 2.7 Consensus size: 73
29666102 TTAATACTAT
** * *
29666112 ATATTTATTTTATTTATTTACTCATTTATTTATCATTCTTTTACTTTTAAAATATTTAAATTTAA
1 ATATTTACGTTATCTATTTACTCATTTATTTATCATTCTTTTACTTTTAAAATACTTAAATTTAA
29666177 TATTATGA
66 TATTATGA
* * * * *
29666185 ATATTTACGTTATCTATTTACTTATTTATTTATTATTCTTTTATTTTTCAAATGCTTAAATTTAA
1 ATATTTACGTTATCTATTTACTCATTTATTTATCATTCTTTTACTTTTAAAATACTTAAATTTAA
* **
29666250 TATTGTTT
66 TATTATGA
* *** * *
29666258 ACATTTGTTTTATCTATTTATTCACTTA-TT-T-ATTCTTTTACTTTTAAA
1 ATATTTACGTTATCTATTTACTCATTTATTTATCATTCTTTTACTTTTAAA
29666306 GAAATTTTAA
Statistics
Matches: 100, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
70 15 0.15
71 1 0.01
72 2 0.02
73 82 0.82
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.60
Consensus pattern (73 bp):
ATATTTACGTTATCTATTTACTCATTTATTTATCATTCTTTTACTTTTAAAATACTTAAATTTAA
TATTATGA
Found at i:29666482 original size:12 final size:12
Alignment explanation
Indices: 29666465--29666511 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
29666455 ATTAAGCACC
29666465 TTTCATTTTGAT
1 TTTCATTTTGAT
29666477 TTTCATTTTGAT
1 TTTCATTTTGAT
*
29666489 TTTCATTTTCAT
1 TTTCATTTTGAT
29666501 TTTCATTTTGA
1 TTTCATTTTGA
29666512 ATTATGTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (12 bp):
TTTCATTTTGAT
Found at i:29666484 original size:6 final size:6
Alignment explanation
Indices: 29666465--29666509 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
29666455 ATTAAGCACC
* *
29666465 TTTCAT TTTGAT TTTCAT TTTGAT TTTCAT TTTCAT TTTCAT TTT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTT
29666510 GAATTATGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (6 bp):
TTTCAT
Found at i:29667619 original size:31 final size:31
Alignment explanation
Indices: 29667578--29667638 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
29667568 AACAACCCAA
*
29667578 TGACATAAATAAAAGCTTATGAATAATTTAG
1 TGACATAAATAAAAACTTATGAATAATTTAG
* *
29667609 TGACTTAAATAAAAACTTTTGAATAATTTA
1 TGACATAAATAAAAACTTATGAATAATTTA
29667639 ATAACCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (31 bp):
TGACATAAATAAAAACTTATGAATAATTTAG
Found at i:29672620 original size:11 final size:11
Alignment explanation
Indices: 29672606--29672703 Score: 93
Period size: 11 Copynumber: 9.4 Consensus size: 11
29672596 TATTTTTTAA
29672606 TTTTAAAATAT
1 TTTTAAAATAT
29672617 TTTTAAAATACT
1 TTTTAAAATA-T
*
29672629 TTTTAAACT-T
1 TTTTAAAATAT
*
29672639 TTTT----TAA
1 TTTTAAAATAT
29672646 TTTTAAAATAT
1 TTTTAAAATAT
29672657 TTTTAAAATAT
1 TTTTAAAATAT
29672668 TTTTAAAATACT
1 TTTTAAAATA-T
**
29672680 TTTT-TTA-AT
1 TTTTAAAATAT
29672689 TTTTAAAATAT
1 TTTTAAAATAT
29672700 TTTT
1 TTTT
29672704 TTGGTATTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
6 1 0.01
7 4 0.06
9 5 0.07
10 7 0.10
11 40 0.56
12 14 0.20
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:29672649 original size:29 final size:28
Alignment explanation
Indices: 29672617--29672673 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
29672607 TTTAAAATAT
* *
29672617 TTTTAAAATACTTTTTAAACTTTTTTTAA
1 TTTTAAAATA-TTTTTAAAATATTTTTAA
29672646 TTTTAAAATATTTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAAAATATTTTTAA
29672674 AATACTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTAAAATATTTTTAAAATATTTTTAA
Found at i:29672653 original size:40 final size:41
Alignment explanation
Indices: 29672598--29672703 Score: 171
Period size: 40 Copynumber: 2.6 Consensus size: 41
29672588 CTTTTTTTTA
29672598 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTT-AA-ACT
1 TTTTTTAATTTTAAAATATTTTTAAAATA-TTTTTAAATACT
29672638 TTTTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATATTTTT-AAATACT
29672680 TTTTTTAATTTTTAAAATATTTTT
1 TTTTTTAA-TTTTAAAATATTTTT
29672704 TTGGTATTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
39 5 0.08
40 29 0.47
41 2 0.03
42 11 0.18
43 15 0.24
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (41 bp):
TTTTTTAATTTTAAAATATTTTTAAAATATTTTTAAATACT
Found at i:29672704 original size:21 final size:21
Alignment explanation
Indices: 29672637--29672705 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
29672627 CTTTTTAAAC
29672637 TTTTTTTAA-TTTTAAAATAT
1 TTTTTTTAATTTTTAAAATAT
*** *
29672657 TTTTAAAATATTTTTAAAATAC
1 TTTTTTTA-ATTTTTAAAATAT
29672679 TTTTTTTAATTTTTAAAATAT
1 TTTTTTTAATTTTTAAAATAT
29672700 TTTTTT
1 TTTTTT
29672706 GGTATTTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 5 0.13
21 19 0.49
22 15 0.38
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTTAATTTTTAAAATAT
Found at i:29672712 original size:22 final size:20
Alignment explanation
Indices: 29672637--29672719 Score: 76
Period size: 22 Copynumber: 3.9 Consensus size: 20
29672627 CTTTTTAAAC
*
29672637 TTTTTTTAATTTTAAAATAT
1 TTTTTTTATTTTTAAAATAT
**
29672657 TTTTAAAATATTTTTAAAATACT
1 TTTT--TTTATTTTTAAAATA-T
*
29672680 TTTTTTAATTTTTAAAATAT
1 TTTTTTTATTTTTAAAATAT
29672700 TTTTTTGGTATTTATTAAAA
1 TTTTTT--TATTT-TTAAAA
29672720 AATGGGCTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
20 11 0.22
21 12 0.24
22 16 0.32
23 11 0.22
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTTTATTTTTAAAATAT
Found at i:29672713 original size:20 final size:21
Alignment explanation
Indices: 29672598--29672705 Score: 84
Period size: 21 Copynumber: 5.3 Consensus size: 21
29672588 CTTTTTTTTA
29672598 TTTTTTAAT-TTTAAAATA-T
1 TTTTTTAATATTTAAAATACT
** **
29672617 TTTTAAAATACTTTTTAA-ACT
1 TTTTTTAATA-TTTAAAATACT
29672638 TTTTTTAAT-TTTAAAATA-T
1 TTTTTTAATATTTAAAATACT
**
29672657 TTTTAAAATATTTTTAAAATACT
1 TTTTTTAATA--TTTAAAATACT
*
29672680 TTTTTTAATTTTTAAAATA-T
1 TTTTTTAATATTTAAAATACT
29672700 TTTTTT
1 TTTTTT
29672706 GGTATTTATT
Statistics
Matches: 68, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
19 20 0.29
20 9 0.13
21 22 0.32
22 9 0.13
23 8 0.12
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTAATATTTAAAATACT
Found at i:29674365 original size:22 final size:22
Alignment explanation
Indices: 29674317--29674369 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
29674307 TGCACAATGA
*
29674317 ATAAAAATAGTAGTAAAGCATTG
1 ATAAAAA-AGTAGTAAAGAATTG
* * *
29674340 ATAAAAAAGTAGTATATAATTT
1 ATAAAAAAGTAGTAAAGAATTG
29674362 ATAAAAAA
1 ATAAAAAA
29674370 AAGTTGAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.28
Consensus pattern (22 bp):
ATAAAAAAGTAGTAAAGAATTG
Found at i:29675395 original size:21 final size:22
Alignment explanation
Indices: 29675354--29675397 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29675344 GCAATATAAT
*
29675354 ATCAAAATGACAGCAAAACAAC
1 ATCAAAATGACAACAAAACAAC
*
29675376 ATCAAAATTACAAC-AAACAAC
1 ATCAAAATGACAACAAAACAAC
29675397 A
1 A
29675398 AAAAACAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.61, C:0.23, G:0.05, T:0.11
Consensus pattern (22 bp):
ATCAAAATGACAACAAAACAAC
Found at i:29680712 original size:3 final size:3
Alignment explanation
Indices: 29680697--29680761 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
29680687 TAATCACTTA
* ** * * *
29680697 ATT ATT TTT ATT ATT ATT GCT ATT ATT -TT TTT ATC AAT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
*
29680742 ATT GTT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
29680762 ATTTGATTAT
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:29684240 original size:4 final size:4
Alignment explanation
Indices: 29684231--29684257 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29684221 TAATGGACAC
29684231 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
29684258 TCAAGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:29685913 original size:29 final size:28
Alignment explanation
Indices: 29685881--29685941 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
29685871 AAAAGCCCTC
29685881 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** * *
29685910 TTTTTTGATTATTTACCGGAATGGTCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
29685938 TTTT
1 TTTT
29685942 CTGGGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:29686199 original size:22 final size:22
Alignment explanation
Indices: 29686172--29686222 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
29686162 CTCTCTAATC
*
29686172 CTCTCAATTTCCTTCGAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29686194 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29686216 CTCTCAA
1 CTCTCAA
29686223 ACTCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:29686301 original size:11 final size:11
Alignment explanation
Indices: 29686281--29686331 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 11
29686271 TTTAAAATAA
29686281 TTATAATTTTT
1 TTATAATTTTT
29686292 TTAT-ATTTTT
1 TTATAATTTTT
* **
29686302 TTAAAATAATT
1 TTATAATTTTT
29686313 TTA-AATTTTT
1 TTATAATTTTT
29686323 TTAT-ATTTT
1 TTATAATTTT
29686332 CATCAATGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 22 0.67
11 11 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATAATTTTT
Found at i:29686304 original size:30 final size:31
Alignment explanation
Indices: 29686268--29686331 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
29686258 CTCAAATCCA
29686268 TTTTTTAAAATAATTAT-AATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
*
29686298 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
29686329 TTT
1 TTT
29686332 CATCAATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTTTTAAAATAATTATAAATTTTTTTATAT
Found at i:29686444 original size:15 final size:16
Alignment explanation
Indices: 29686424--29686454 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
29686414 TTTGTAATTA
29686424 TTATTTAAG-ATTTTT
1 TTATTTAAGTATTTTT
29686439 TTATTTAAGTATTTTT
1 TTATTTAAGTATTTTT
29686455 AGATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTATTTAAGTATTTTT
Found at i:29687423 original size:7 final size:7
Alignment explanation
Indices: 29687411--29687435 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29687401 AGTCGATTGA
29687411 TATTTAG
1 TATTTAG
29687418 TATTTAG
1 TATTTAG
29687425 TATTTAG
1 TATTTAG
29687432 TATT
1 TATT
29687436 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:29688413 original size:24 final size:24
Alignment explanation
Indices: 29688380--29688435 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
29688370 ATGCAGAACC
*
29688380 GGAAGAACCACAACCACCACTGGA
1 GGAAGAACCACAACCACCACTAGA
* *
29688404 GGAAGGACCACAATCACCACTAGA
1 GGAAGAACCACAACCACCACTAGA
29688428 GGAAGAAC
1 GGAAGAAC
29688436 AACCGCCGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.29, G:0.23, T:0.05
Consensus pattern (24 bp):
GGAAGAACCACAACCACCACTAGA
Found at i:29688674 original size:28 final size:28
Alignment explanation
Indices: 29688643--29689061 Score: 489
Period size: 28 Copynumber: 14.4 Consensus size: 28
29688633 AATAAAAACC
29688643 CTAACCTAAATTAACTAAAAACCCTAAT
1 CTAACCTAAATTAACTAAAAACCCTAAT
* *
29688671 CTAACCTAAATTAATTTAAAA-CCTAAT
1 CTAACCTAAATTAACTAAAAACCCTAAT
29688698 CTAACCTAAATTAACTAAAAACCCTAACCT
1 CTAACCTAAATTAACTAAAAACCCTAA--T
29688728 AACCCTAACCTAAATTAACTAAAAACCCTAAT
1 ----CTAACCTAAATTAACTAAAAACCCTAAT
* * *
29688760 CTAACCTAAATTAATTTAAAACCCTAACC
1 CTAACCTAAATTAACTAAAAACCCTAA-T
* *
29688789 CTAACCTAAATTAATTAAAAAACCTAAT
1 CTAACCTAAATTAACTAAAAACCCTAAT
29688817 CTAACCTAAATTAACTAAAAACCCTAACCT
1 CTAACCTAAATTAACTAAAAACCCTAA--T
29688847 AACCCTAACCTAAATTAACTAAAAAACCCTAAT
1 ----CTAACCTAAATTAACT-AAAAACCCTAAT
*
29688880 CTAACCTAAATTAACTAAAAACCATAAT
1 CTAACCTAAATTAACTAAAAACCCTAAT
*
29688908 CTAACTTAAATTAACTAAAAACCCTAAT
1 CTAACCTAAATTAACTAAAAACCCTAAT
* * **
29688936 TTAATCTAAATTAACTAAAAACCCTAGGG
1 CTAACCTAAATTAACTAAAAACCCTA-AT
* * *
29688965 GTAACCTAAATTAATTTAAAACCCTAAT
1 CTAACCTAAATTAACTAAAAACCCTAAT
* * *
29688993 CTAACCAAAATTAATTAAAAACCCTAAAC
1 CTAACCTAAATTAACTAAAAACCCT-AAT
* * *
29689022 CTAACCTAAATTAATTAAAAACCCAAAA
1 CTAACCTAAATTAACTAAAAACCCTAAT
29689050 CTAACCTAAATT
1 CTAACCTAAATT
29689062 TTTTTGGCTT
Statistics
Matches: 341, Mismatches: 33, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
27 25 0.07
28 170 0.50
29 88 0.26
30 2 0.01
32 1 0.00
33 1 0.00
34 43 0.13
35 11 0.03
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.26
Consensus pattern (28 bp):
CTAACCTAAATTAACTAAAAACCCTAAT
Found at i:29688815 original size:57 final size:57
Alignment explanation
Indices: 29688643--29689061 Score: 511
Period size: 57 Copynumber: 7.2 Consensus size: 57
29688633 AATAAAAACC
* *
29688643 CTAACCTAAATTAACTAAAAACCCTAA-TCTAACCTAAATTAATTTAAAA-CCTAAT
1 CTAACCTAAATTAACTAAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCTAAT
*
29688698 CTAACCTAAATTAACTAAAAACCCTAACCTAACCCTAACCTAAATTAACTAAAAACCCTAAT
1 CTAACCTAAATTAACTAAAAA--C---CCTAACCCTAACCTAAATTAATTAAAAACCCTAAT
* * *
29688760 CTAACCTAAATTAATTTAAAACCCTAACCCTAACCTAAATTAATTAAAAAACCTAAT
1 CTAACCTAAATTAACTAAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCTAAT
*
29688817 CTAACCTAAATTAACTAAAAACCCTAACCTAACCCTAACCTAAATTAACTAAAAAACCCTAAT
1 CTAACCTAAATTAACTAAAAA--C---CCTAACCCTAACCTAAATTAA-TTAAAAACCCTAAT
* * * *
29688880 CTAACCTAAATTAACTAAAAACCATAA-TCTAACTTAAATTAACTAAAAACCCTAAT
1 CTAACCTAAATTAACTAAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCTAAT
* * **** *
29688936 TTAATCTAAATTAACTAAAAACCCTAGGGGTAACCTAAATTAATTTAAAACCCTAAT
1 CTAACCTAAATTAACTAAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCTAAT
* * * * *
29688993 CTAACCAAAATTAATTAAAAACCCTAAACCTAACCTAAATTAATTAAAAACCCAAAA
1 CTAACCTAAATTAACTAAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCTAAT
29689050 CTAACCTAAATT
1 CTAACCTAAATT
29689062 TTTTTGGCTT
Statistics
Matches: 313, Mismatches: 37, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
55 21 0.07
56 35 0.11
57 147 0.47
58 4 0.01
59 1 0.00
60 6 0.02
61 20 0.06
62 46 0.15
63 33 0.11
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.26
Consensus pattern (57 bp):
CTAACCTAAATTAACTAAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCTAAT
Found at i:29688841 original size:119 final size:118
Alignment explanation
Indices: 29688643--29689061 Score: 571
Period size: 119 Copynumber: 3.6 Consensus size: 118
29688633 AATAAAAACC
* *
29688643 CTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATT-TAAAACCTAATCTAACCTAA
1 CTAACCTAAATTAACTAAAAACCCTAACCTAACCTAAATTAATTAAAAAACCTAATCTAACCTAA
29688707 ATTAACTAAAAACCCTAACCTAACCCTAACCTAAATTAACTAAAAACCCTAAT
66 ATTAACTAAAAACCCTAACCTAACCCTAACCTAAATTAACTAAAAACCCTAAT
* *
29688760 CTAACCTAAATTAATTTAAAACCCTAACCCTAACCTAAATTAATTAAAAAACCTAATCTAACCTA
1 CTAACCTAAATTAACTAAAAACCCTAA-CCTAACCTAAATTAATTAAAAAACCTAATCTAACCTA
29688825 AATTAACTAAAAACCCTAACCTAACCCTAACCTAAATTAACTAAAAAACCCTAAT
65 AATTAACTAAAAACCCTAACCTAACCCTAACCTAAATTAACT-AAAAACCCTAAT
* * * * * * *
29688880 CTAACCTAAATTAACTAAAAACCATAATCTAACTTAAATTAACTAAAAACCCTAATTTAATCTAA
1 CTAACCTAAATTAACTAAAAACCCTAACCTAACCTAAATTAATTAAAAAACCTAATCTAACCTAA
**** * *
29688945 ATTAACTAAAAA--C---CCTAGGGGTAACCTAAATTAATTTAAAACCCTAAT
66 ATTAACTAAAAACCCTAACCTAACCCTAACCTAAATTAACTAAAAACCCTAAT
* * * * *
29688993 CTAACCAAAATTAATTAAAAACCCTAAACCTAACCTAAATTAATTAAAAACCCAAAACTAACCTA
1 CTAACCTAAATTAACTAAAAACCCT-AACCTAACCTAAATTAATTAAAAAACCTAATCTAACCTA
29689058 AATT
65 AATT
29689062 TTTTTGGCTT
Statistics
Matches: 269, Mismatches: 29, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
113 33 0.12
114 54 0.20
117 26 0.10
118 16 0.06
119 104 0.39
120 36 0.13
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.26
Consensus pattern (118 bp):
CTAACCTAAATTAACTAAAAACCCTAACCTAACCTAAATTAATTAAAAAACCTAATCTAACCTAA
ATTAACTAAAAACCCTAACCTAACCCTAACCTAAATTAACTAAAAACCCTAAT
Found at i:29689200 original size:10 final size:10
Alignment explanation
Indices: 29689185--29689209 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29689175 TTTTGGCTTA
29689185 ATAATTTTAC
1 ATAATTTTAC
29689195 ATAATTTTAC
1 ATAATTTTAC
29689205 ATAAT
1 ATAAT
29689210 GTTAGATCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:29699998 original size:17 final size:18
Alignment explanation
Indices: 29699971--29700004 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29699961 AAAAAAACAA
29699971 AAAATATATGAAAATTAG
1 AAAATATATGAAAATTAG
29699989 AAAATA-ATGAAAATTA
1 AAAATATATGAAAATTA
29700005 AAATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
AAAATATATGAAAATTAG
Found at i:29702170 original size:123 final size:123
Alignment explanation
Indices: 29701975--29702199 Score: 396
Period size: 123 Copynumber: 1.8 Consensus size: 123
29701965 TAATTTCGAG
* * * *
29701975 TTGACGTTTCTAATCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTCAGAACAATTTGTA
*
29702040 AAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCATGGAAGAAATATTGTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATATTGTTT
*
29702098 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTCAGAACAATTTGTA
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTCAGAACAATTTGTA
29702163 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
29702200 CAAGTTTGGG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 96 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (123 bp):
TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTCAGAACAATTTGTA
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATATTGTTT
Found at i:29704896 original size:19 final size:19
Alignment explanation
Indices: 29704871--29704917 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
29704861 TCCCAAGCAG
*
29704871 TTTTATTTATGATT-TTGT
1 TTTTATTTATGATTATTAT
*
29704889 TATTTATTTATTATTATTAT
1 T-TTTATTTATGATTATTAT
29704909 TTTTATTTA
1 TTTTATTTA
29704918 CGTCACCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 20 0.80
20 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (19 bp):
TTTTATTTATGATTATTAT
Found at i:29704898 original size:23 final size:23
Alignment explanation
Indices: 29704872--29704917 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
29704862 CCCAAGCAGT
29704872 TTTATTTATGATT-TTGTTATTTA
1 TTTA-TTATGATTATTGTTATTTA
* *
29704895 TTTATTATTATTATTTTTATTTA
1 TTTATTATGATTATTGTTATTTA
29704918 CGTCACCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTATTATGATTATTGTTATTTA
Found at i:29717251 original size:40 final size:40
Alignment explanation
Indices: 29717204--29717519 Score: 356
Period size: 40 Copynumber: 7.8 Consensus size: 40
29717194 AAAAAATAGA
* *
29717204 TCTTATCTTCCTAAGTAGTAGTGGAGCAGATCGCCTCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAG
* * *
29717244 TTTTATCTCCCTAAGCAGTATTGGAGCAGA-CAGAAC-CACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-G-CCTCA-AG
29717285 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAG
* * * *
29717326 TCTTATCTTCCTAAGTAGTAGTGGAACAGA-CAGAAC-CACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-G-CCTCA-AG
29717367 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAG
* *
29717408 TCTTATCTCCCTAAGCAGTAGTGGAGTAGA-CAGAAC-CACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-G-CCTCA-AG
* *
29717449 ATCTTATCTCTCTAAGCAGTAATGGAGCAGATCGCCTCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAG
*
29717490 TCTTATCTCCCTAAGCAGTAGCGGAGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
29717520 CTATAGATAG
Statistics
Matches: 233, Mismatches: 25, Indels: 36
0.79 0.09 0.12
Matches are distributed among these distances:
39 3 0.01
40 118 0.51
41 18 0.08
42 91 0.39
43 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAG
Found at i:29717299 original size:82 final size:82
Alignment explanation
Indices: 29717201--29717520 Score: 541
Period size: 82 Copynumber: 3.9 Consensus size: 82
29717191 CGAAAAAAAT
* * * *
29717201 AGATCTTATCTTCCTAAGTAGTAGTGGAGCAGATCGCCTCAAGTTTTATCTCCCTAAGCAGTATT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGCAGTAGT
29717266 GGAGCAGACAGAACCAC
66 GGAGCAGACAGAACCAC
* *
29717283 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTTCCTAAGTAGTAGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGCAGTAGT
*
29717348 GGAACAGACAGAACCAC
66 GGAGCAGACAGAACCAC
29717365 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGCAGTAGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGCAGTAGT
*
29717430 GGAGTAGACAGAACCAC
66 GGAGCAGACAGAACCAC
* * *
29717447 AGATCTTATCTCTCTAAGCAGTAATGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGCAGTAGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGCAGTAGT
29717512 GGAGCAGAC
66 GGAGCAGAC
29717521 TATAGATAGC
Statistics
Matches: 223, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 223 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (82 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGCAGTAGT
GGAGCAGACAGAACCAC
Found at i:29722078 original size:116 final size:116
Alignment explanation
Indices: 29721871--29722231 Score: 625
Period size: 116 Copynumber: 3.1 Consensus size: 116
29721861 TAAGTTTGTG
29721871 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
* * *
29721936 TTGTTAGTACCAGTCAAAACAGTTTTCCAAATCTAAAATTATGTGAATGTA
66 TTGTTAGTACCAATCAAAACATTTTTCCAAATCTAACATTATGTGAATGTA
29721987 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
*
29722052 TTGTTAATACCAATCAAAACATTTTTCCAAATCTAACATTATGTGAATGTA
66 TTGTTAGTACCAATCAAAACATTTTTCCAAATCTAACATTATGTGAATGTA
*
29722103 AAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
** *
29722167 TTGTTAGTACCAGGAAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
66 TTGTTAGTACCA--ATCAAAACATTTTTCCAAATCTAACATTATGTGAATGTA
29722220 AAATTATTAATT
1 AAATTATTAATT
29722232 TAGTTTAGGG
Statistics
Matches: 234, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
115 40 0.17
116 146 0.62
117 48 0.21
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
TTGTTAGTACCAATCAAAACATTTTTCCAAATCTAACATTATGTGAATGTA
Found at i:29722168 original size:17 final size:17
Alignment explanation
Indices: 29722101--29722168 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
29722091 TATGTGAATG
*
29722101 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
29722117 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
29722136 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
29722155 TAAAATTATTAATT
1 TAAAATTATTAATT
29722169 GTTAGTACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:29722257 original size:23 final size:22
Alignment explanation
Indices: 29722225--29722781 Score: 415
Period size: 23 Copynumber: 25.1 Consensus size: 22
29722215 AAGTAAAATT
*
29722225 ATTAATTTAGTTTAGGGTTTTTA
1 ATTAA-TTAGGTTAGGGTTTTTA
29722248 ATTAAATTAGGTTAGGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
*
29722271 ATTTAATTAGGTTAGAG-----A
1 A-TTAATTAGGTTAGGGTTTTTA
* *
29722289 TTTAATTAGGTTAGAGTTTTTA
1 ATTAATTAGGTTAGGGTTTTTA
*
29722311 AGTTAAATAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
***
29722334 AGTTAAGGGGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
* * *
29722357 AGT--TTAGGGTTTAAGATTTTTA
1 ATTAATTA-GG-TTAGGGTTTTTA
29722379 ATTAAATTAGGTTAGGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
* *
29722402 AGT--TTAGGGTTTA-GGATTTTA
1 ATTAATTA-GG-TTAGGGTTTTTA
29722423 ATTAAATTAGGTTAGGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
29722446 ATTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
***
29722469 AGTTAAGGGGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
* * * *
29722492 AGTTTA-CAGTTTAGGGTTCTTA
1 A-TTAATTAGGTTAGGGTTTTTA
29722514 ATTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
29722537 ATTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
*
29722560 AGT--TTAGGGTTTAGGGTTTTTA
1 ATTAATTA-GG-TTAGGGTTTTTA
*
29722582 ATTTAATTAAGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
* *
29722605 AGT--TTAGGGTTTAAGGTTTTTA
1 ATTAATTA-GG-TTAGGGTTTTTA
*
29722627 ATTAAATTAGGTTAGAG--TTT-
1 ATT-AATTAGGTTAGGGTTTTTA
*
29722647 -TT-A--AGTTTAGGGTTTTTA
1 ATTAATTAGGTTAGGGTTTTTA
29722665 ATTAAATTAGGTTAGGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
29722688 ATTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
*
29722711 AGTTAATTAGGTTAGGATTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
* * *
29722734 AGT--TTAGGGTTTAAGATTTTTA
1 ATTAATTA-GG-TTAGGGTTTTTA
*
29722756 ATTAAATTAGGTTATGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
29722779 ATT
1 ATT
29722782 TAAGGGTATT
Statistics
Matches: 434, Mismatches: 55, Indels: 90
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.02
17 19 0.04
18 1 0.00
19 4 0.01
20 12 0.03
21 22 0.05
22 78 0.18
23 261 0.60
24 18 0.04
25 12 0.03
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (22 bp):
ATTAATTAGGTTAGGGTTTTTA
Found at i:29722291 original size:17 final size:17
Alignment explanation
Indices: 29722271--29722304 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29722261 AGGGTTTTTA
29722271 ATTTAATTAGGTTAGAG
1 ATTTAATTAGGTTAGAG
29722288 ATTTAATTAGGTTAGAG
1 ATTTAATTAGGTTAGAG
29722305 TTTTTAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (17 bp):
ATTTAATTAGGTTAGAG
Found at i:29722296 original size:45 final size:44
Alignment explanation
Indices: 29722244--29722769 Score: 293
Period size: 45 Copynumber: 11.9 Consensus size: 44
29722234 GTTTAGGGTT
29722244 TTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGAGA
1 TTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAG-GA
* * * *
29722289 --T--TT-AATTAGGTTAGAGTTTTTAAGTTAAATAGGTTAGGG
1 TTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGA
* * *
29722328 TTT--TTAAGTTAAGGGGGTTAGGGTTTTTAAGTTT-A--GGGTTTAAGA
1 TTTAATTAAATT-A---GGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGA
*
29722373 TTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTT-A--GGGTTTAGGA
1 --TTTAATTAAATTAGGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGA
*
29722418 TTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGG
1 -TTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGA
* * * *
29722463 TTT--TTAAGTTAAGGGGGTTAGGGTTTTTAAGTTT-A-CAGTTTAGGGT
1 TTTAATTAAATT-A---GGTTAGGGTTTTTAA-TTTAATTAGGTTA-GGA
* *
29722509 TCTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGG
1 T-TTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGA
* * *
29722554 TTT--TTAAGTTTAGGGTTTAGGGTTTTTAATTTAATTAAGTTAGGG
1 TTTAATTAA-ATTA-GG-TTAGGGTTTTTAATTTAATTAGGTTAGGA
* * *
29722599 TTT--TTAAGTTTAGGGTTTAAGGTTTTTAATTAAATTAGGTTA-GA
1 TTTAATTAA-ATTA-GG-TTAGGGTTTTTAATTTAATTAGGTTAGGA
* * *
29722643 GTTT--TT--A--AGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 -TTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTA-GG-A
* *
29722684 TTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGA
1 TTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGA
* * * *
29722728 TTT--TTAAGTTTAGGGTTTAAGATTTTTAATTAAATTAGGTTA
1 TTTAATTAA-ATTA-GG-TTAGGGTTTTTAATTTAATTAGGTTA
29722770 TGGTTTTTAA
Statistics
Matches: 394, Mismatches: 44, Indels: 86
0.75 0.08 0.16
Matches are distributed among these distances:
38 25 0.06
39 2 0.01
40 36 0.09
41 5 0.01
42 17 0.04
43 12 0.03
44 49 0.12
45 158 0.40
46 67 0.17
47 10 0.03
48 2 0.01
49 11 0.03
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (44 bp):
TTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGA
Found at i:29722605 original size:14 final size:15
Alignment explanation
Indices: 29722588--29722616 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29722578 TTTAATTTAA
29722588 TTAAG-TTAGGGTTT
1 TTAAGTTTAGGGTTT
29722602 TTAAGTTTAGGGTTT
1 TTAAGTTTAGGGTTT
29722617 AAGGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
TTAAGTTTAGGGTTT
Found at i:29722647 original size:68 final size:68
Alignment explanation
Indices: 29722225--29722784 Score: 463
Period size: 68 Copynumber: 8.4 Consensus size: 68
29722215 AAGTAAAATT
* * * *
29722225 ATTAATTTAGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTTA---ATT-AGG-TT
1 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAAGGTTT
**
29722284 AGA
66 TTA
* * * * * * *
29722287 GATTTAATTAGGTTAGAGTTTTTAAGTTAAATAGGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGT
1 -ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTA-GGGTTTAAGGT
29722352 TTTTA
64 TTTTA
* * * * *
29722357 AGT---TTAGGGTTTAAGATTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTT-AGGA
1 ATTAAATTA-GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAAGGT
29722418 TTTTA
64 TTTTA
* * *
29722423 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTT
1 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTA-GGGTTTAAGGTT
29722488 TTTA
65 TTTA
* * * * * *
29722492 AGTT-TA-CAGTTTAGGGTTCTTAATTTAATTAGGTTAGGGTTTTTAA-TTTAATTAGG-TTAGG
1 A-TTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTT-A--GGGTTTAAG
29722553 GTTTTTA
62 GTTTTTA
* *
29722560 AGT---TTAGGGTTTAGGGTTTTTAATTTAATTAAGTTAGGGTTTTTAAGTTTAGGGTTTAAGGT
1 ATTAAATTA-GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAAGGT
29722622 TTTTA
64 TTTTA
* * * *
29722627 ATTAAATTAGGTTAGAGTTTTTAAGTTT-A--GGGTT----TTTAATTAA-ATTA-GG-TTAGGG
1 ATTAAATTAGGTTAGGGTTTTTAA-TTTAATTAGGTTAGGGTTT--TTAAGTTTAGGGTTTAAGG
29722682 TTTTTA
63 TTTTTA
* * * *
29722688 ATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGATTTTTAAGTTTAGGGTTTAAGATTT
1 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAAGGTTT
29722753 TTA
66 TTA
*
29722756 ATTAAATTAGGTTATGGTTTTTAATTTAA
1 ATTAAATTAGGTTAGGGTTTTTAATTTAA
29722785 GGGTATTAAT
Statistics
Matches: 398, Mismatches: 61, Indels: 71
0.75 0.12 0.13
Matches are distributed among these distances:
60 2 0.01
61 34 0.09
62 5 0.01
63 47 0.12
64 7 0.02
65 4 0.01
66 21 0.05
67 66 0.17
68 178 0.45
69 26 0.07
70 8 0.02
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (68 bp):
ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAAGGTTT
TTA
Found at i:29722655 original size:38 final size:38
Alignment explanation
Indices: 29722613--29722693 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
29722603 TAAGTTTAGG
29722613 GTTTAAGGTTTTTAATTAAATTAGGTTAGAGTTTTTAA
1 GTTTAAGGTTTTTAATTAAATTAGGTTAGAGTTTTTAA
* *
29722651 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA
1 GTTTAAGGTTTTTAATTAAATTAGGTTAGAGTTTTTAA
29722689 -TTTAA
1 GTTTAA
29722694 TTAGGTTAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 4 0.10
38 36 0.90
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.51
Consensus pattern (38 bp):
GTTTAAGGTTTTTAATTAAATTAGGTTAGAGTTTTTAA
Found at i:29722777 original size:45 final size:45
Alignment explanation
Indices: 29722438--29722798 Score: 329
Period size: 45 Copynumber: 8.1 Consensus size: 45
29722428 ATTAGGTTAG
* * * *
29722438 GGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGGGTTAG
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTA-GGGTTTAA
* * * * * *
29722484 GGTTTTTAAGTT-TA-CAGTTTAGGGTTCTTAA-TTTAATTAGG-TTAG
1 GGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTT-A--GGGTTTAA
* *
29722529 GGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAG
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAA
* *
29722574 GGTTTTTAATTTAATTAAGTTAGGGTTTTTAAGTTTAGGGTTTAA
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAA
*
29722619 GGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTTA--G-----
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAA
* *
29722657 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTTAATTAGG-TTAG
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTT-A--GGGTTTAA
*
29722703 GGTTTTTAAGTT-AATTAGGTTAGGATTTTTAAGTTTAGGGTTTAA
1 GGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAA
* *
29722748 GATTTTTAATTAAATTAGGTTATGGTTTTTAA-TTTAAGGGTATTAA
1 GGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTT-AGGGT-TTAA
29722794 TGGTT
1 -GGTT
29722799 AGTAGAATTC
Statistics
Matches: 267, Mismatches: 25, Indels: 45
0.79 0.07 0.13
Matches are distributed among these distances:
37 3 0.01
38 32 0.12
42 1 0.00
43 1 0.00
44 13 0.05
45 144 0.54
46 60 0.22
47 13 0.05
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.50
Consensus pattern (45 bp):
GGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAA
Found at i:29722855 original size:25 final size:25
Alignment explanation
Indices: 29722823--29722874 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
29722813 ATAATATAAA
29722823 AAATTTCTATTTTATTACATCAAAT
1 AAATTTCTATTTTATTACATCAAAT
29722848 AAATTTCTATTTTATTACATCAAAT
1 AAATTTCTATTTTATTACATCAAAT
29722873 AA
1 AA
29722875 TATCAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATTTCTATTTTATTACATCAAAT
Found at i:29723721 original size:7 final size:7
Alignment explanation
Indices: 29723711--29723735 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29723701 TTATATACAT
29723711 AATACTA
1 AATACTA
29723718 AATACTA
1 AATACTA
29723725 AATACTA
1 AATACTA
29723732 AATA
1 AATA
29723736 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:29723943 original size:20 final size:20
Alignment explanation
Indices: 29723906--29723943 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29723896 TTTATTTTTA
*
29723906 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
29723926 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
29723944 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:29724857 original size:12 final size:12
Alignment explanation
Indices: 29724822--29724858 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
29724812 ATTTTTACGA
*
29724822 TTTAAAAAAATT
1 TTTAAAAATATT
29724834 TTTAAAAATATT
1 TTTAAAAATATT
*
29724846 TTTAAAATTATT
1 TTTAAAAATATT
29724858 T
1 T
29724859 AAAAAAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTAAAAATATT
Found at i:29724887 original size:11 final size:11
Alignment explanation
Indices: 29724871--29724912 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
29724861 AAAAAGGGAG
29724871 TTAAGAGAAAC
1 TTAAGAGAAAC
*
29724882 TTAAGAGGAAC
1 TTAAGAGAAAC
*
29724893 TTAAGAGTAAC
1 TTAAGAGAAAC
29724904 TTAAGAGAA
1 TTAAGAGAA
29724913 TTTTTGAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:29724959 original size:14 final size:11
Alignment explanation
Indices: 29724916--29724955 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
29724906 AAGAGAATTT
29724916 TTGA-AGGAAA
1 TTGAGAGGAAA
29724926 TTGAGAGGAAA
1 TTGAGAGGAAA
29724937 TTGAGAGGAAA
1 TTGAGAGGAAA
29724948 TTTGAGAG
1 -TTGAGAG
29724956 AGGATTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 17 0.61
12 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:29725942 original size:19 final size:19
Alignment explanation
Indices: 29725920--29725998 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 19
29725910 AAAAATGAAG
29725920 AAAAACTAGAAAATTATTA
1 AAAAACTAGAAAATTATTA
*
29725939 AAAATCATA-AAAATTA--A
1 AAAAAC-TAGAAAATTATTA
* *
29725956 ATAAATCTACGAAAA-TATTC
1 A-AAAACTA-GAAAATTATTA
* *
29725976 AATAACTAGAAAAATATTA
1 AAAAACTAGAAAATTATTA
29725995 AAAA
1 AAAA
29725999 CATTAAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
17 4 0.09
18 12 0.26
19 28 0.60
20 3 0.06
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAAACTAGAAAATTATTA
Found at i:29726334 original size:15 final size:16
Alignment explanation
Indices: 29726314--29726349 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
29726304 TCCTTTATTG
29726314 TTATTTTAAT-AATTT
1 TTATTTTAATGAATTT
29726329 TTATTTTTAATGAATTT
1 TTA-TTTTAATGAATTT
29726346 TTAT
1 TTAT
29726350 GGTTTGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 8 0.42
17 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTATTTTAATGAATTT
Found at i:29726338 original size:16 final size:17
Alignment explanation
Indices: 29726317--29726349 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29726307 TTTATTGTTA
29726317 TTTTAAT-AATTTTTAT
1 TTTTAATGAATTTTTAT
29726333 TTTTAATGAATTTTTAT
1 TTTTAATGAATTTTTAT
29726350 GGTTTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTAATGAATTTTTAT
Found at i:29727215 original size:26 final size:26
Alignment explanation
Indices: 29727186--29727244 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
29727176 TACCCCCAAC
*
29727186 AAAATTTTGACAATTTTACTCC-TGAT
1 AAAATTTTAACAATTTTAC-CCATGAT
* *
29727212 AAAATTTTAACGATTTTACCCATGGT
1 AAAATTTTAACAATTTTACCCATGAT
29727238 AAAATTT
1 AAAATTT
29727245 CGAGAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (26 bp):
AAAATTTTAACAATTTTACCCATGAT
Found at i:29727416 original size:18 final size:18
Alignment explanation
Indices: 29727393--29727429 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29727383 CAAATGAATC
*
29727393 ATTTCCATTTTCATTTTT
1 ATTTCCATTTCCATTTTT
29727411 ATTTCCATTTCCATTTTT
1 ATTTCCATTTCCATTTTT
29727429 A
1 A
29727430 GAAACATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTCCATTTCCATTTTT
Found at i:29730288 original size:22 final size:22
Alignment explanation
Indices: 29730214--29730320 Score: 81
Period size: 22 Copynumber: 4.6 Consensus size: 22
29730204 GACTCTTAGC
*
29730214 GTGCTCTCTGGTTATTAGCACGTTA
1 GTGCTCTCT-G-T-TTAGCACTTTA
* * **
29730239 GTGCTCTCCGATTTTTGCACACTA
1 GTGCTCTCTG--TTTAGCACTTTA
*
29730263 GTGCTCTCGGTTTAGCACATTT-
1 GTGCTCTCTGTTTAGCAC-TTTA
* *
29730285 GTGCTCCCTGTATAGCACTTTA
1 GTGCTCTCTGTTTAGCACTTTA
29730307 GTGCTCTCTGTTTA
1 GTGCTCTCTGTTTA
29730321 ATAGTGCATA
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
21 3 0.05
22 34 0.52
23 1 0.02
24 18 0.27
25 10 0.15
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACTTTA
Found at i:29733030 original size:14 final size:14
Alignment explanation
Indices: 29733011--29733043 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
29733001 TAAGCTGAAG
29733011 AGACACCTGCAATA
1 AGACACCTGCAATA
29733025 AGACACCTGCAATA
1 AGACACCTGCAATA
29733039 A-ACAC
1 AGACAC
29733044 ATTAAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.45, C:0.30, G:0.12, T:0.12
Consensus pattern (14 bp):
AGACACCTGCAATA
Found at i:29733491 original size:50 final size:52
Alignment explanation
Indices: 29733366--29733496 Score: 151
Period size: 50 Copynumber: 2.6 Consensus size: 52
29733356 TGAACAAATG
* * *
29733366 AGTTACTTAATGCA-AGACTTAATTTAATGATGCAGACTTAAACTAACATGGG
1 AGTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGGA
** * * *
29733418 AGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
*
29733468 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATAACTTTATTTAATG
29733497 CAGAACACAC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
50 31 0.48
51 15 0.23
52 19 0.29
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (52 bp):
AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
Found at i:29737247 original size:49 final size:49
Alignment explanation
Indices: 29737194--29737295 Score: 134
Period size: 49 Copynumber: 2.1 Consensus size: 49
29737184 AAATATGGGT
* * *
29737194 CACACGCCCGTGTTGCC-CACACGGCCTACATGAATTTTCCATGTAATCG
1 CACACGCCCATG-TGCCTCACACGGCCTACATGAATTTCCCATGTAACCG
* * *
29737243 CACACGCCCATGTGCCTCACACGGCTTACTTGAATTTCCCGTGTAACCG
1 CACACGCCCATGTGCCTCACACGGCCTACATGAATTTCCCATGTAACCG
29737292 CACA
1 CACA
29737296 TGCTTGTATG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 4 0.09
49 42 0.91
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (49 bp):
CACACGCCCATGTGCCTCACACGGCCTACATGAATTTCCCATGTAACCG
Found at i:29739833 original size:52 final size:52
Alignment explanation
Indices: 29739755--29739911 Score: 269
Period size: 52 Copynumber: 3.0 Consensus size: 52
29739745 GGGTTTTAGG
*
29739755 GTTTAGGGTGCAAGCTTTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTC
1 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTC
* *
29739807 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAAGGGTGCCGAAAAAAATTATTTC
1 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTC
* *
29739859 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGAGTCTCGAAAAAAATTATTTC
1 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTC
29739911 G
1 G
29739912 AGTTGACGTT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 98 1.00
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.37
Consensus pattern (52 bp):
GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTC
Found at i:29740007 original size:28 final size:28
Alignment explanation
Indices: 29739966--29740087 Score: 93
Period size: 29 Copynumber: 4.1 Consensus size: 28
29739956 ATGCGATCAG
29739966 ATTAGGGTTAGGTTTTATAATTAAATTAAA
1 ATTA-GGTTAGGTTTTATAATTAAATT-AA
*
29739996 TTATGTTAGGTTAGGGTTTT-TAATTAAATTAG
1 --A--TTAGGTTA-GGTTTTATAATTAAATTAA
* * *
29740028 GTTAGGTTAGGGTTTTATAATTGAATTAG
1 ATTAGGTTA-GGTTTTATAATTAAATTAA
* * *
29740057 GTTAGGGTTAGGGTTTATAATTAAATCAA
1 ATTA-GGTTAGGTTTTATAATTAAATTAA
29740086 AT
1 AT
29740088 AATATCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
28 15 0.19
29 31 0.40
30 5 0.06
32 2 0.03
33 15 0.19
34 9 0.12
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.44
Consensus pattern (28 bp):
ATTAGGTTAGGTTTTATAATTAAATTAA
Found at i:29740018 original size:29 final size:28
Alignment explanation
Indices: 29739989--29740082 Score: 143
Period size: 28 Copynumber: 3.3 Consensus size: 28
29739979 TTTATAATTA
*
29739989 AATTAAATTATGTTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGTTAGGGTTTTT
29740017 AATTAAATTAGGTTAGGTTAGGGTTTTAT
1 AATTAAATTAGGTTAGGTTAGGGTTTT-T
* *
29740046 AATTGAATTAGGTTAGGGTTAGGGTTTAT
1 AATTAAATTAGGTTA-GGTTAGGGTTTTT
29740075 AATTAAAT
1 AATTAAAT
29740083 CAAATAATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
28 26 0.43
29 23 0.38
30 11 0.18
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (28 bp):
AATTAAATTAGGTTAGGTTAGGGTTTTT
Found at i:29742403 original size:29 final size:30
Alignment explanation
Indices: 29742365--29742422 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
29742355 AGAAAATATT
*
29742365 AAAAATTTTAAAATTAT-TTTAAAAAAATA
1 AAAAAATTTAAAATTATCTTTAAAAAAATA
*
29742394 AAAAAATTTAAAATTTTCTTTAAAAAAAT
1 AAAAAATTTAAAATTATCTTTAAAAAAAT
29742423 GAAATTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAAAATTTAAAATTATCTTTAAAAAAATA
Found at i:29742536 original size:22 final size:22
Alignment explanation
Indices: 29742511--29742579 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
29742501 CGAGAGTTTA
*
29742511 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
**
29742533 AGAGAATTTTTGAAGGACTTTG
1 AGAGAATTTTTGAAGGAAATTG
*
29742555 AGAGAATTTTTGAATGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
29742577 AGA
1 AGA
29742580 TAGGATTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.39, C:0.01, G:0.28, T:0.32
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGAAATTG
Found at i:29742558 original size:52 final size:51
Alignment explanation
Indices: 29742453--29742558 Score: 131
Period size: 52 Copynumber: 2.1 Consensus size: 51
29742443 ATTTAATATG
* * * * *
29742453 GAGTTTAGAGATTTTTTGAAGGAAATTGTGAGGATTTTGGAATGAATTCGA
1 GAGTTTAGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
* * *
29742504 GAGTTTAAGAGAATTTTGGAAGGAAATTGAGAGAATTTTTGAAGGACTTTGA
1 GAGTTT-AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
29742556 GAG
1 GAG
29742559 AATTTTTGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
51 6 0.13
52 40 0.87
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (51 bp):
GAGTTTAGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
Found at i:29743993 original size:177 final size:176
Alignment explanation
Indices: 29743713--29744053 Score: 450
Period size: 177 Copynumber: 1.9 Consensus size: 176
29743703 CTACACTTCA
* * * *
29743713 ATTTTTACATAATTTAGACATCTGCCCGTTCTTTTTTCTTTTCTTTTGACATGAAAAAATAATGG
1 ATTTTGACATAATTTAGACACCTGACCATTCTTTTTTCTTTTCTTTTGACATGAAAAAATAATGG
* *** * * *
29743778 TTAAATTTCAGTTCTAACCCCTCTACCTTCTCAAGATTATATAAGAACGGTTAAATTTTAGTTTT
66 CTAAATTTCAGTTCTAACCCAAATACCTTCTCAAGATTATATAAGAACGATTAAATTTCAGTGTT
*
29743843 GAGT-CCTATATTTCACTCAAATTTGAAATTTAATCTCTATACTTTT
131 GA-TCCCTATATTCCACTCAAATTTGAAATTTAATCTCTATACTTTT
** *
29743889 ATTTTGACATAATTTAGACACCTGATTATTCTTTTTTTCTTTTCTTTTGACATGAGAAAATAATG
1 ATTTTGACATAATTTAGACACCTGACCATTC-TTTTTTCTTTTCTTTTGACATGAAAAAATAATG
* ** * * *
29743954 GCTAAATTTCAGTTCTAATCCAAATATTTTTTTAAGATTATATAAGAATGATTAAATTTCAGTGT
65 GCTAAATTTCAGTTCTAACCCAAATACCTTCTCAAGATTATATAAGAACGATTAAATTTCAGTGT
* *
29744019 TGATCCCTATATTCCACTCGAATTTGAGATTTAAT
130 TGATCCCTATATTCCACTCAAATTTGAAATTTAAT
29744054 TTCTCTAATT
Statistics
Matches: 140, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
176 26 0.19
177 114 0.81
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (176 bp):
ATTTTGACATAATTTAGACACCTGACCATTCTTTTTTCTTTTCTTTTGACATGAAAAAATAATGG
CTAAATTTCAGTTCTAACCCAAATACCTTCTCAAGATTATATAAGAACGATTAAATTTCAGTGTT
GATCCCTATATTCCACTCAAATTTGAAATTTAATCTCTATACTTTT
Found at i:29747271 original size:6 final size:6
Alignment explanation
Indices: 29747253--29747288 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
29747243 AGAAGTGAAT
* *
29747253 TTTTGC TTTTAC TTCTAC TTTTAC TTTTAC TTTTAC
1 TTTTAC TTTTAC TTTTAC TTTTAC TTTTAC TTTTAC
29747289 CAATTCTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.19, G:0.03, T:0.64
Consensus pattern (6 bp):
TTTTAC
Found at i:29747668 original size:20 final size:20
Alignment explanation
Indices: 29747639--29747689 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
29747629 TAATATATAT
* *
29747639 AAATACATAAAT-ATTTTCAA
1 AAATATATAAATAAATTT-AA
29747659 AAATATAT-AATAAATTTAA
1 AAATATATAAATAAATTTAA
*
29747678 ATATATATAAAT
1 AAATATATAAAT
29747690 TATAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATATAAATAAATTTAA
Found at i:29747689 original size:16 final size:17
Alignment explanation
Indices: 29747659--29747704 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
29747649 ATATTTTCAA
29747659 AAATATATAATAAATT-T
1 AAATATAT-ATAAATTAT
29747676 AAATATATATAAATTAT
1 AAATATATATAAATTAT
*
29747693 AAAAAT-TATAAA
1 AAATATATATAAA
29747705 GATAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATATATATAAATTAT
Found at i:29747713 original size:26 final size:25
Alignment explanation
Indices: 29747659--29747722 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
29747649 ATATTTTCAA
* *
29747659 AAATATATAATAAATTTAAATATATAT
1 AAAT-TATAA-AAATTTAAAGATAAAT
29747686 AAATTATAAAAATTATAAAGATAAAT
1 AAATTATAAAAATT-TAAAGATAAAT
29747712 AAA-TA-AAAAAT
1 AAATTATAAAAAT
29747723 AAAAAACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 6 0.18
25 7 0.21
26 17 0.50
27 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATTATAAAAATTTAAAGATAAAT
Done.