Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 103 of 141
Found at i:29221074 original size:30 final size:30
Alignment explanation
Indices: 29221003--29221074 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
29220993 TGATAGGGGG
* * *
29221003 ATGGAAAATGGCAGCTCCGTTAAGTTTGTA
1 ATGGAAAATGGTAGCTCCGTTAAGTCTATA
* * *
29221033 ACGGAAAATGGTAGCTTCGTTACGTCTATA
1 ATGGAAAATGGTAGCTCCGTTAAGTCTATA
29221063 ATGGAAAATGGT
1 ATGGAAAATGGT
29221075 TAGTGGCAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (30 bp):
ATGGAAAATGGTAGCTCCGTTAAGTCTATA
Found at i:29221410 original size:9 final size:9
Alignment explanation
Indices: 29221396--29221429 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
29221386 ATTTTCGAAT
*
29221396 TCGAATAAC
1 TCGAATAAA
*
29221405 TCGAATAAT
1 TCGAATAAA
29221414 TCGAATAAA
1 TCGAATAAA
29221423 TCGAATA
1 TCGAATA
29221430 CCAAACTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (9 bp):
TCGAATAAA
Found at i:29221414 original size:18 final size:18
Alignment explanation
Indices: 29221393--29221429 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29221383 TTAATTTTCG
*
29221393 AATTCGAATAACTCGAAT
1 AATTCGAATAAATCGAAT
29221411 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCGAAT
29221429 A
1 A
29221430 CCAAACTATA
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:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCGAAT
Found at i:29221489 original size:23 final size:23
Alignment explanation
Indices: 29221443--29221489 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
29221433 AACTATAATA
*
29221443 TTTTACATTTTACCCCAATTTTT
1 TTTTACATTTTACCCCAATCTTT
*
29221466 TTTTAC-TTTTCCCCCAATACTTT
1 TTTTACATTTTACCCCAAT-CTTT
29221489 T
1 T
29221490 ACTCCCTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTACATTTTACCCCAATCTTT
Found at i:29222072 original size:19 final size:19
Alignment explanation
Indices: 29222048--29222085 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29222038 AAGTTAATAA
29222048 CAAATTTGATTACGATGGG
1 CAAATTTGATTACGATGGG
29222067 CAAATTTGATTACGATGGG
1 CAAATTTGATTACGATGGG
29222086 TGACAGTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
CAAATTTGATTACGATGGG
Found at i:29223933 original size:23 final size:23
Alignment explanation
Indices: 29223902--29223945 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
29223892 TTATAATTGG
*
29223902 AGGGTAAAATGCAAAGGCTTTGT
1 AGGGAAAAATGCAAAGGCTTTGT
29223925 AGGGAAAAATGCAAAGGCTTT
1 AGGGAAAAATGCAAAGGCTTT
29223946 TTGATATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.23
Consensus pattern (23 bp):
AGGGAAAAATGCAAAGGCTTTGT
Found at i:29224571 original size:6 final size:6
Alignment explanation
Indices: 29224560--29224586 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29224550 TCAGGGCCTG
29224560 AAACAC AAACAC AAACAC AAACAC AAA
1 AAACAC AAACAC AAACAC AAACAC AAA
29224587 TAAATTGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAC
Found at i:29230039 original size:24 final size:24
Alignment explanation
Indices: 29229977--29230044 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
29229967 TTCAGGCTCT
* * *
29229977 TCAACAACAGTTTGAGTAGGTGCC
1 TCAACAATAGCTTGAGTGGGTGCC
* * *
29230001 TCGACAATAGGTTGAGTGGGTGCT
1 TCAACAATAGCTTGAGTGGGTGCC
* *
29230025 TCAACAGTAGCTTGAATGGG
1 TCAACAATAGCTTGAGTGGG
29230045 CTCCTTGGCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.26
Consensus pattern (24 bp):
TCAACAATAGCTTGAGTGGGTGCC
Found at i:29232108 original size:22 final size:23
Alignment explanation
Indices: 29232058--29232120 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 23
29232048 GTGCTTAAAA
*
29232058 TAAATATGT-TATATATATTAACT
1 TAAA-ATGTATATATATAATAACT
*
29232081 T-TAATGTATATATATAATAA-T
1 TAAAATGTATATATATAATAACT
*
29232102 TAAAATG-A-ATGTATAATAA
1 TAAAATGTATATATATAATAA
29232121 AAGAAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 10 0.29
21 7 0.21
22 16 0.47
23 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (23 bp):
TAAAATGTATATATATAATAACT
Found at i:29237045 original size:44 final size:44
Alignment explanation
Indices: 29236994--29237418 Score: 214
Period size: 44 Copynumber: 9.7 Consensus size: 44
29236984 ATTACAGATA
29236994 TTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATC
* * ** **
29237038 CTATCTCCTTGAGATTACAGTGGAGCAGATT-AAAATAAAAGATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTA-ATC
* * * * * * * *
29237082 TTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATC-AG--GTC
1 TTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGTAATC
** ** * *
29237123 TTATCTCCCTGAGATTACAGTGGAATAGACCGAAG-AATTTCAGATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTA-GT-A-ATC
*
29237169 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATC
* * ** *
29237213 CTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAG-GATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCT--AGTAATC
* * * * * * * *
29237257 TTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATC-AG--GTC
1 TTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGTAATC
* ** * **
29237298 TTATCTTCCTGAGATTACAGTGGA--ATGAACCGAAGAATTTTAGATC
1 TTATCTCCCTGAGATTACAGTGGAGCA-G-ATTGAAG-CTAGTA-ATC
*
29237344 TTATCTCCTTGAGATTACA-TCGGAGCAGATTGAAGCTAGTAATC
1 TTATCTCCCTGAGATTACAGT-GGAGCAGATTGAAGCTAGTAATC
* ** * *
29237388 CTATCTGTCTGATATTACAGTGGAGCGGATT
1 TTATCTCCCTGAGATTACAGTGGAGCAGATT
29237419 AAAATAAAGG
Statistics
Matches: 279, Mismatches: 75, Indels: 54
0.68 0.18 0.13
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 51 0.18
42 6 0.02
43 12 0.04
44 135 0.48
45 10 0.04
46 60 0.22
47 2 0.01
48 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
TTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATC
Found at i:29237270 original size:175 final size:175
Alignment explanation
Indices: 29236979--29237524 Score: 893
Period size: 175 Copynumber: 3.1 Consensus size: 175
29236969 ACAGATCAGT
* * *
29236979 GAAGAATTACAGATATTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCCTATCT
1 GAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCT
* * *
29237044 CCTTGAGATTACAGTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTAAAGTTACAGTAGAGTA
66 CCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTA
29237109 GATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACC
131 GATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACC
29237154 GAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCT
1 GAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCT
29237219 CCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTA
66 CCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTA
*
29237284 GATCGCATCAGGTCTTATCTTCCTGAGATTACAGTGGAAT-GAACC
131 GATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAG-ACC
* * *
29237329 GAAGAATTTTAGATCTTATCTCCTTGAGATTACATCGGAGCAGATTGAAGCTAGTAATCCTATCT
1 GAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCT
** * *
29237394 GTCTGATATTACAGTGGAGCGGATTAAAATAAAGGATCTTA--TCTCTAAAGTTACAGTAGAGCA
66 CCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTA
* *
29237457 GATCGTATCAGGTCTTATTTCCCTGAGATTACAGTGGAATAGACC
131 GATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACC
* *
29237502 GAAGAATGTCAGACCTTA-CTCCC
1 GAAGAATTTCAGATCTTATCTCCC
29237525 CCAGCGGTGC
Statistics
Matches: 348, Mismatches: 21, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
172 4 0.01
173 76 0.22
174 2 0.01
175 266 0.76
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (175 bp):
GAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCT
CCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTA
GATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACC
Found at i:29239345 original size:17 final size:16
Alignment explanation
Indices: 29239320--29239360 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
29239310 TTCAAAAGGC
29239320 TTTTAATAAATCAAAT
1 TTTTAATAAATCAAAT
* *
29239336 TTTATAATAATTCATAT
1 TTT-TAATAAATCAAAT
29239353 TTTTAATA
1 TTTTAATA
29239361 TCATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTAATAAATCAAAT
Found at i:29239391 original size:21 final size:22
Alignment explanation
Indices: 29239356--29239396 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
29239346 TTCATATTTT
**
29239356 TAATATCATTTTAA-TATTGGC
1 TAATATCATCATAATTATTGGC
29239377 TAATATCATCATAATTATTG
1 TAATATCATCATAATTATTG
29239397 CTATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (22 bp):
TAATATCATCATAATTATTGGC
Found at i:29241395 original size:43 final size:43
Alignment explanation
Indices: 29241348--29241433 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
29241338 TATGTGATTG
*
29241348 ATATTGAAATGGA-AAAAATGAGAAATGA-ATATGAGATGAGAAA
1 ATATTGAAAT-GACAAAAATGAGAAACGATA-ATGAGATGAGAAA
*
29241391 ATATTGAAATGACAAATATGAGAAACGATAATGAGATGAGAAA
1 ATATTGAAATGACAAAAATGAGAAACGATAATGAGATGAGAAA
29241434 TGAAATATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 2 0.05
43 36 0.92
44 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.21
Consensus pattern (43 bp):
ATATTGAAATGACAAAAATGAGAAACGATAATGAGATGAGAAA
Found at i:29246629 original size:138 final size:138
Alignment explanation
Indices: 29246381--29246658 Score: 448
Period size: 138 Copynumber: 2.0 Consensus size: 138
29246371 CTGTTTTTTG
* *
29246381 AGACAAAATCAACATAAGCAATTGGAAAATTCCTACTTGAAGTAAGTCTAAACATACATAAAGAT
1 AGACAAAATCAACAAAAGCAATTGGAAAAATCCTACTTGAAGTAAGTCTAAACATACATAAAGAT
* *
29246446 CAGCATCCATTTACAAGCTTTTTAACAGTAAAGAACAAAATCAAGCTTCTGTTAATAGAGAAAAC
66 CAGCATCCATTTACAAGCTTTTTAACAGTAAACAACAAAATCAAGCTGCTGTTAATAGAGAAAAC
29246511 ATTCTATA
131 ATTCTATA
**
29246519 AGACAAAATCAACAAAAGCAATTGGAAAAATCCTACTTTTAGTAAGTCTAAACATACATAAAGAT
1 AGACAAAATCAACAAAAGCAATTGGAAAAATCCTACTTGAAGTAAGTCTAAACATACATAAAGAT
* * * * * *
29246584 CAGCATCCGTTTACAAGCTTTTTGACATTGAACAATAAAATCAAGCTGCTGTTAATAGAGAAATC
66 CAGCATCCATTTACAAGCTTTTTAACAGTAAACAACAAAATCAAGCTGCTGTTAATAGAGAAAAC
29246649 ATTCTATA
131 ATTCTATA
29246657 AG
1 AG
29246659 CGATGCAATA
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 128 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.27
Consensus pattern (138 bp):
AGACAAAATCAACAAAAGCAATTGGAAAAATCCTACTTGAAGTAAGTCTAAACATACATAAAGAT
CAGCATCCATTTACAAGCTTTTTAACAGTAAACAACAAAATCAAGCTGCTGTTAATAGAGAAAAC
ATTCTATA
Found at i:29256250 original size:30 final size:30
Alignment explanation
Indices: 29256216--29256282 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
29256206 GTGTCTCAGC
*
29256216 CGTGTTTGACACACGGCCACGCGATACGGA
1 CGTGTGTGACACACGGCCACGCGATACGGA
* * *
29256246 CGTGTGTGACACACGTCCATGCGATACGGT
1 CGTGTGTGACACACGGCCACGCGATACGGA
29256276 CGTGTGT
1 CGTGTGT
29256283 CCCTCGTAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.22
Consensus pattern (30 bp):
CGTGTGTGACACACGGCCACGCGATACGGA
Found at i:29261261 original size:27 final size:27
Alignment explanation
Indices: 29261231--29261324 Score: 113
Period size: 27 Copynumber: 3.4 Consensus size: 27
29261221 CAATTTCGAT
29261231 TAGTTGGGTGACCAA-AAAAATGGGCAA
1 TAGTTGGGTGACCAATAAAAA-GGGCAA
**
29261258 TAGTTGGGTGACCAAATTAAAAAAATG--A
1 TAGTTGGGTGACC-AA-T-AAAAAGGGCAA
29261286 TAGTTGGGTGACCAATAAAAAGGGCAA
1 TAGTTGGGTGACCAATAAAAAGGGCAA
29261313 TAGTTGGGTGAC
1 TAGTTGGGTGAC
29261325 ATGTGGTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
25 6 0.11
26 1 0.02
27 28 0.49
28 16 0.28
30 1 0.02
31 5 0.09
ACGTcount: A:0.39, C:0.10, G:0.29, T:0.22
Consensus pattern (27 bp):
TAGTTGGGTGACCAATAAAAAGGGCAA
Found at i:29263996 original size:33 final size:33
Alignment explanation
Indices: 29263950--29264063 Score: 146
Period size: 33 Copynumber: 3.5 Consensus size: 33
29263940 TCTTGACAAA
29263950 CTCT-TTCTGTGTTTACTATCCCAGCGAGCTAT
1 CTCTGTTCTGTGTTTACTATCCCAGCGAGCTAT
29263982 CTCTGTTCTGTGTTTACTATCCCAGC-AGACTAT
1 CTCTGTTCTGTGTTTACTATCCCAGCGAG-CTAT
* *
29264015 CTCTATTTTGTGTTTACTATCCCAATG-GA-CTAT
1 CTCTGTTCTGTGTTTACTATCCC-A-GCGAGCTAT
*
29264048 CTATGTTCTGTGTTTA
1 CTCTGTTCTGTGTTTA
29264064 AGTCCTAGCA
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
32 6 0.08
33 63 0.88
34 1 0.01
35 2 0.03
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (33 bp):
CTCTGTTCTGTGTTTACTATCCCAGCGAGCTAT
Found at i:29264063 original size:66 final size:65
Alignment explanation
Indices: 29263957--29264085 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 65
29263947 AAACTCTTTC
*
29263957 TGTGTTTACTATCCCAGCGAGCTATCTCTGTTCTGTGTTTACTA-TCCCAGCAGACTATCTCTAT
1 TGTGTTTACTATCCCAGCGAGCTATCTATGTTCTGTGTTTA--AGTCCCAGCAGACTATCTCTAT
29264021 TT
64 TT
*
29264023 TGTGTTTACTATCCCAATG-GA-CTATCTATGTTCTGTGTTTAAGTCCTAGCAGACTATCTCTAT
1 TGTGTTTACTATCCC-A-GCGAGCTATCTATGTTCTGTGTTTAAGTCCCAGCAGACTATCTCTAT
29264086 GGATGCCATG
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
64 1 0.02
65 19 0.33
66 34 0.59
67 3 0.05
68 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (65 bp):
TGTGTTTACTATCCCAGCGAGCTATCTATGTTCTGTGTTTAAGTCCCAGCAGACTATCTCTATTT
Found at i:29281540 original size:16 final size:16
Alignment explanation
Indices: 29281532--29281609 Score: 50
Period size: 16 Copynumber: 4.6 Consensus size: 16
29281522 AAAGTACAAG
29281532 AAAATAAAAATAAAAC
1 AAAATAAAAATAAAAC
*
29281548 AAAATAACTAAAAATAAAAAT
1 --AA-AA-TAAAAAT-AAAAC
* **
29281569 AAACATAAAATTAAATT
1 AAA-ATAAAAATAAAAC
*
29281586 AAATTAAAAATAAAAC
1 AAAATAAAAATAAAAC
29281602 -AAATAAAA
1 AAAATAAAA
29281610 TCAATTATCC
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
15 7 0.15
16 9 0.19
17 7 0.15
18 9 0.19
19 5 0.10
20 7 0.15
21 4 0.08
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAAAAATAAAAC
Found at i:29281543 original size:6 final size:6
Alignment explanation
Indices: 29281532--29281600 Score: 54
Period size: 6 Copynumber: 11.5 Consensus size: 6
29281522 AAAGTACAAG
*
29281532 AAAATA AAAATA AAACA-A AATAACTA AAAATA AAAATA AACAT- AAAAT-
1 AAAATA AAAATA AAA-ATA AA-AA-TA AAAATA AAAATA AAAATA AAAATA
* * *
29281580 TAAATT AAATTA AAAATA AAA
1 AAAATA AAAATA AAAATA AAA
29281601 CAAATAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
5 8 0.16
6 36 0.71
7 4 0.08
8 3 0.06
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:29283089 original size:15 final size:16
Alignment explanation
Indices: 29283059--29283090 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29283049 AACTACTAAG
29283059 AAATAATAAGGAAGAA
1 AAATAATAAGGAAGAA
29283075 AAATAATAA-GAAGAA
1 AAATAATAAGGAAGAA
29283090 A
1 A
29283091 CGAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (16 bp):
AAATAATAAGGAAGAA
Found at i:29283294 original size:17 final size:18
Alignment explanation
Indices: 29283258--29283296 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29283248 TAAACTAATG
*
29283258 ATAAGAAAAGTAAGAATA
1 ATAAGAAAAATAAGAATA
*
29283276 ATAAGAAAAATGA-AATA
1 ATAAGAAAAATAAGAATA
29283293 ATAA
1 ATAA
29283297 TAATGATAGT
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:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (18 bp):
ATAAGAAAAATAAGAATA
Found at i:29283360 original size:22 final size:23
Alignment explanation
Indices: 29283316--29283361 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
29283306 TAATGACAAG
29283316 AAATAATTACAACTAGAAAAATA
1 AAATAATTACAACTAGAAAAATA
*
29283339 AAATAA-TATAACTA-AAATAATA
1 AAATAATTACAACTAGAAA-AATA
29283361 A
1 A
29283362 TATTAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 12 0.57
23 6 0.29
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (23 bp):
AAATAATTACAACTAGAAAAATA
Found at i:29291036 original size:22 final size:21
Alignment explanation
Indices: 29291003--29291045 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
29290993 AAATTTATAT
29291003 ATATTTTATAAAGCTATAAAAA
1 ATATTTTATAAAGC-ATAAAAA
*
29291025 ATATTATT-TAAATCATAAAAA
1 ATATT-TTATAAAGCATAAAAA
29291046 TTTCTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTTATAAAGCATAAAAA
Found at i:29291062 original size:20 final size:20
Alignment explanation
Indices: 29291021--29291080 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
29291011 TAAAGCTATA
** *
29291021 AAAAATATTATTTAAATCAT
1 AAAAATATTATAAAAATAAT
*
29291041 AAAAAT-TTCTAAAATATAAT
1 AAAAATATTATAAAA-ATAAT
29291061 AAAAATATTATAAAAATAAT
1 AAAAATATTATAAAAATAAT
29291081 TTGCATGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 5 0.15
20 21 0.64
21 7 0.21
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATATTATAAAAATAAT
Found at i:29291359 original size:8 final size:8
Alignment explanation
Indices: 29291325--29291369 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
29291315 TAAAACATTT
29291325 TTTTTATAA
1 TTTTTAT-A
*
29291334 ATTTTATA
1 TTTTTATA
29291342 -TTTTATA
1 TTTTTATA
*
29291349 TTTTTACA
1 TTTTTATA
29291357 TTTTTATA
1 TTTTTATA
29291365 TTTTT
1 TTTTT
29291370 TTAACTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
7 7 0.22
8 19 0.59
9 6 0.19
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTATA
Found at i:29291993 original size:13 final size:13
Alignment explanation
Indices: 29291977--29292016 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
29291967 TTTAAACCAA
29291977 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
29291990 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
29292003 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
29292016 A
1 A
29292017 TTGTCAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 5 0.22
13 13 0.57
14 5 0.22
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:29294479 original size:28 final size:30
Alignment explanation
Indices: 29294421--29294485 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 30
29294411 ACCATAAACT
29294421 CTTTCTTTTTGGTTACATGAACCAATTAATTAA
1 CTTTCTTTTTGGTTACATGAACC-A--AATTAA
*
29294454 CTTT-TTTTTTGTTACATGAACC-AATTAA
1 CTTTCTTTTTGGTTACATGAACCAAATTAA
29294482 CTTT
1 CTTT
29294486 GATTCATTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 10 0.32
32 17 0.55
33 4 0.13
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (30 bp):
CTTTCTTTTTGGTTACATGAACCAAATTAA
Found at i:29294618 original size:27 final size:27
Alignment explanation
Indices: 29294569--29294633 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
29294559 AAATATTCTC
*
29294569 TAAATTAATAA-ATATTAATTTATCGA
1 TAAATTAATAAGATATTAATTTATCAA
*
29294595 TAAATTAATAAGATATTCATTTATCAA
1 TAAATTAATAAGATATTAATTTATCAA
*
29294622 TAAACTAATAAG
1 TAAATTAATAAG
29294634 CTCAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 11 0.31
27 24 0.69
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (27 bp):
TAAATTAATAAGATATTAATTTATCAA
Found at i:29304023 original size:24 final size:24
Alignment explanation
Indices: 29303965--29304039 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
29303955 GCTTTACATA
*
29303965 TTTTTGTT-AATTTGATATTT-AT
1 TTTTTATTAAATTTGATATTTAAT
*
29303987 TTTTTAATTAAATTTGATTTTTAAT
1 TTTTT-ATTAAATTTGATATTTAAT
*
29304012 TTTTT-TTCAAATTTAATCA-TTAAT
1 TTTTTATT-AAATTTGAT-ATTTAAT
29304036 TTTT
1 TTTT
29304040 GAAAAATAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 5 0.11
23 4 0.09
24 28 0.64
25 7 0.16
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTTATTAAATTTGATATTTAAT
Found at i:29304148 original size:19 final size:19
Alignment explanation
Indices: 29304126--29304165 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29304116 TTCATGCTAA
29304126 TTTTT-TAATTTTTATGAAT
1 TTTTTATAATTTTTAT-AAT
*
29304145 TTTTTATATTTTTTATAAT
1 TTTTTATAATTTTTATAAT
29304164 TT
1 TT
29304166 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAT
Found at i:29304150 original size:11 final size:10
Alignment explanation
Indices: 29304126--29304165 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
29304116 TTCATGCTAA
29304126 TTTTT-TAA-
1 TTTTTATAAT
29304134 TTTTTATGAAT
1 TTTTTAT-AAT
29304145 TTTTTAT-AT
1 TTTTTATAAT
29304154 TTTTTATAAT
1 TTTTTATAAT
29304164 TT
1 TT
29304166 ATATTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.18
9 10 0.36
10 6 0.21
11 7 0.25
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:29304589 original size:18 final size:18
Alignment explanation
Indices: 29304563--29304632 Score: 52
Period size: 18 Copynumber: 3.7 Consensus size: 18
29304553 AAATAAAAGT
*
29304563 AATAAAAAAATCTA-GAAA
1 AATATAAAAAT-TATGAAA
*
29304581 AATATAAAAATTATTAAA
1 AATATAAAAATTATGAAA
* *
29304599 AATTTAAAAATATATAAAGAA
1 AATATAAAAAT-TAT-GA-AA
*
29304620 AATATCAAAATTA
1 AATATAAAAATTA
29304633 ATTAAAAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.05
18 23 0.55
19 3 0.07
20 3 0.07
21 11 0.26
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (18 bp):
AATATAAAAATTATGAAA
Found at i:29304598 original size:10 final size:10
Alignment explanation
Indices: 29304585--29304716 Score: 51
Period size: 10 Copynumber: 12.9 Consensus size: 10
29304575 TAGAAAAATA
29304585 TAAAAATTAT
1 TAAAAATTAT
29304595 TAAAAA-T-T
1 TAAAAATTAT
29304603 TAAAAATATAT
1 TAAAAAT-TAT
* *
29304614 AAAGAAAATA-
1 TAA-AAATTAT
*
29304624 TCAAAATTAAT
1 TAAAAATT-AT
29304635 TAAAAAGTTA-
1 TAAAAA-TTAT
* **
29304645 GAAAAAGAAT
1 TAAAAATTAT
29304655 ATAAAAA-TAT
1 -TAAAAATTAT
*
29304665 AAGAAAATTAT
1 TA-AAAATTAT
*
29304676 TTAAAA-TAT
1 TAAAAATTAT
*
29304685 ATACAAATTTTAT
1 -TA-AAA-ATTAT
29304698 TAAAAATTAT
1 TAAAAATTAT
*
29304708 AAAAAATTA
1 TAAAAATTA
29304717 AAAAATTCCT
Statistics
Matches: 89, Mismatches: 18, Indels: 30
0.65 0.13 0.22
Matches are distributed among these distances:
8 7 0.08
9 10 0.11
10 37 0.42
11 25 0.28
12 7 0.08
13 3 0.03
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:29304599 original size:39 final size:40
Alignment explanation
Indices: 29304564--29304687 Score: 103
Period size: 42 Copynumber: 3.1 Consensus size: 40
29304554 AATAAAAGTA
* *
29304564 ATAAAAAAATCTAGA-AAAATATAAAAATT-ATTAAAAAT
1 ATAAAAAAATATAAAGAAAATATAAAAATTAATTAAAAAT
* * *
29304602 TTAAAAATATATAAAGAAAATATCAAAATTAATTAAAAAGTT
1 ATAAAAAAATATAAAGAAAATATAAAAATTAATTAAAAA--T
* * *
29304644 AGAAAAAGAATATAAA-AATATA-AGAAAATTATTTAAAATAT
1 ATAAAAA-AATATAAAGAAAATATA-AAAATTAATTAAAA-AT
29304685 ATA
1 ATA
29304688 CAAATTTTAT
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
38 11 0.16
39 13 0.19
40 8 0.12
41 3 0.04
42 24 0.36
43 8 0.12
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (40 bp):
ATAAAAAAATATAAAGAAAATATAAAAATTAATTAAAAAT
Found at i:29304662 original size:40 final size:38
Alignment explanation
Indices: 29304578--29304681 Score: 102
Period size: 40 Copynumber: 2.6 Consensus size: 38
29304568 AAAAATCTAG
* *
29304578 AAAAATATAAAAATTATTAAAAATTTAAAAATATATAA
1 AAAAATATAAAAATTATTAAAAAGTTAAAAATAAATAA
* *
29304616 AGAAAATATCAAAATTAATTAAAAAGTTAGAAAA-AGAATAT
1 A-AAAATATAAAAATT-ATTAAAAAGTTA-AAAATA-AATAA
*
29304657 AAAAATATAAGAAAATTATTTAAAA
1 AAAAATAT-A-AAAATTATTAAAAA
29304682 TATATACAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
38 1 0.02
39 13 0.24
40 19 0.35
41 15 0.28
42 6 0.11
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (38 bp):
AAAAATATAAAAATTATTAAAAAGTTAAAAATAAATAA
Found at i:29304683 original size:20 final size:19
Alignment explanation
Indices: 29304578--29304716 Score: 79
Period size: 21 Copynumber: 6.9 Consensus size: 19
29304568 AAAAATCTAG
29304578 AAAAATAT-AAAAATTATT
1 AAAAATATAAAAAATTATT
*
29304596 AAAAAT-TTAAAAA-TATAT
1 AAAAATATAAAAAATTAT-T
* *
29304614 AAAGAAAATATCAAAATTAATT
1 AAA-AATATA-AAAAATT-ATT
**
29304636 AAAAAGT-TAGAAAAAGAATAT
1 AAAAA-TATA-AAAAATTAT-T
29304657 AAAAATATAAGAAAATTATTT
1 AAAAATATAA-AAAATTA-TT
**
29304678 AAAATATATACAAATTTTATT
1 AAAA-ATATA-AAAAATTATT
29304699 AAAAATTATAAAAAATTA
1 AAAAA-TATAAAAAATTA
29304717 AAAAATTCCT
Statistics
Matches: 92, Mismatches: 14, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
17 4 0.04
18 15 0.16
19 2 0.02
20 12 0.13
21 40 0.43
22 16 0.17
23 3 0.03
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAAATATAAAAAATTATT
Found at i:29304686 original size:22 final size:21
Alignment explanation
Indices: 29304656--29304716 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
29304646 AAAAAGAATA
29304656 TAAAA-ATATAAGAAAATTATT
1 TAAAATATATAA-AAAATTATT
**
29304677 TAAAATATATACAAATTTTATT
1 TAAAATATATA-AAAAATTATT
*
29304699 AAAAAT-TATAAAAAATTA
1 TAAAATATATAAAAAATTA
29304717 AAAAATTCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 6 0.18
21 9 0.27
22 17 0.52
23 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAATATATAAAAAATTATT
Found at i:29304846 original size:17 final size:17
Alignment explanation
Indices: 29304808--29304846 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
29304798 AAGTATAAAA
*
29304808 TTTATTAAAATATTGAT
1 TTTATTAAAATATTAAT
29304825 TTTATTAAAATA-TAAT
1 TTTATTAAAATATTAAT
29304841 TATTAT
1 T-TTAT
29304847 AATTATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTATTAAAATATTAAT
Found at i:29308056 original size:13 final size:14
Alignment explanation
Indices: 29308030--29308062 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
29308020 CATTAATTAA
29308030 AACTAAAGTTAACT
1 AACTAAAGTTAACT
29308044 AACTAAA-TTAACT
1 AACTAAAGTTAACT
29308057 AACTAA
1 AACTAA
29308063 TGCATTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.27
Consensus pattern (14 bp):
AACTAAAGTTAACT
Found at i:29309906 original size:20 final size:20
Alignment explanation
Indices: 29309863--29309947 Score: 82
Period size: 20 Copynumber: 4.2 Consensus size: 20
29309853 AATTTGTTTG
*
29309863 AAAATAATTTTGA-TGTATT
1 AAAATAATTTTGACTTTATT
*
29309882 AAAATAATTTTAACTTTATT
1 AAAATAATTTTGACTTTATT
* **
29309902 GAAATAATTTTGACTTGGTT
1 AAAATAATTTTGACTTTATT
* * *
29309922 AAAATCATTTTCACTTGATTT
1 AAAATAATTTTGACTTTA-TT
29309943 AAAAT
1 AAAAT
29309948 TGTTTCAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.22
20 35 0.65
21 7 0.13
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (20 bp):
AAAATAATTTTGACTTTATT
Found at i:29310652 original size:92 final size:92
Alignment explanation
Indices: 29310495--29310666 Score: 299
Period size: 92 Copynumber: 1.9 Consensus size: 92
29310485 ATATGACCTG
* * *
29310495 ACGTCATCTTTACCTACGTACAATAATTCAATTATAGAAACGATATTAGTTTTCACCCGATCACA
1 ACGTCATCTTTACCTACATACAATAATTCAAGTATAGAAACGATATTAGTTTTCACCCAATCACA
29310560 TGAAAAACACATAATTAGGATGAACCA
66 TGAAAAACACATAATTAGGATGAACCA
* *
29310587 ACGTCATCTTTAGCTACATACGATAATTCAAGTATAGAAACGATATTAGTTTTCACCCAATCACA
1 ACGTCATCTTTACCTACATACAATAATTCAAGTATAGAAACGATATTAGTTTTCACCCAATCACA
29310652 TGAAAAACACATAAT
66 TGAAAAACACATAAT
29310667 CATGAAAACA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.28
Consensus pattern (92 bp):
ACGTCATCTTTACCTACATACAATAATTCAAGTATAGAAACGATATTAGTTTTCACCCAATCACA
TGAAAAACACATAATTAGGATGAACCA
Found at i:29315173 original size:12 final size:12
Alignment explanation
Indices: 29315164--29315188 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29315154 TTCCTCTTTG
29315164 TCATTTTCTTCT
1 TCATTTTCTTCT
29315176 TCATTTTCTTCT
1 TCATTTTCTTCT
29315188 T
1 T
29315189 ATCTCTTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (12 bp):
TCATTTTCTTCT
Found at i:29315188 original size:27 final size:27
Alignment explanation
Indices: 29315153--29315213 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
29315143 TCATCTTCTA
* *
29315153 TTTCCTCTT-TGTCATTTTCTTCTTCAT
1 TTTCCTCTTATCTC-TTCTCTTCTTCAT
* *
29315180 TTTCTTCTTATCTCTTCTCTTCTTCCT
1 TTTCCTCTTATCTCTTCTCTTCTTCAT
29315207 TTTCCTC
1 TTTCCTC
29315214 ACCTCCCGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.05, C:0.31, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTCCTCTTATCTCTTCTCTTCTTCAT
Found at i:29329359 original size:14 final size:14
Alignment explanation
Indices: 29329340--29329366 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29329330 CATTTCTTGG
29329340 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
29329354 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
29329367 ACTGGACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:29330809 original size:28 final size:28
Alignment explanation
Indices: 29330741--29330810 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
29330731 GCATAATCTA
* *
29330741 GTGGAAGTCCTTCAGGACTATCGTATTT
1 GTGGAAGTCCATCAGGACTATCATATTT
* * *
29330769 TTTGAAGTTCATCAGGACTATCATATTT
1 GTGGAAGTCCATCAGGACTATCATATTT
*
29330797 GTGGAAATCCATCA
1 GTGGAAGTCCATCA
29330811 AGACCCTCGT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (28 bp):
GTGGAAGTCCATCAGGACTATCATATTT
Found at i:29332909 original size:51 final size:50
Alignment explanation
Indices: 29332848--29332959 Score: 152
Period size: 51 Copynumber: 2.2 Consensus size: 50
29332838 ATAACATCCA
* * * * * *
29332848 AGAATACACCTGGGCACTGTGTGCCAAGCCCGTAGGCTATACATCCCTCT
1 AGAACACACCTGAGCACTGAGTGCCAAGCCCGTAGGCTACACATCCCCCC
*
29332898 AGAAACACACCTGAGCACTGAGTGCCAAGCCTGTAGGCTACACATCCCCCC
1 AG-AACACACCTGAGCACTGAGTGCCAAGCCCGTAGGCTACACATCCCCCC
29332949 AGAACACACCT
1 AGAACACACCT
29332960 AAATCTCCGT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 11 0.20
51 43 0.80
ACGTcount: A:0.29, C:0.35, G:0.20, T:0.17
Consensus pattern (50 bp):
AGAACACACCTGAGCACTGAGTGCCAAGCCCGTAGGCTACACATCCCCCC
Found at i:29336127 original size:32 final size:32
Alignment explanation
Indices: 29336090--29336161 Score: 119
Period size: 32 Copynumber: 2.2 Consensus size: 32
29336080 GAACATGATA
29336090 AATTTT-AATTAATTTTATAGTTAATTTTGACT
1 AATTTTGAA-TAATTTTATAGTTAATTTTGACT
*
29336122 AATTTTGAATAATTTTATAGTTAATTTTGATT
1 AATTTTGAATAATTTTATAGTTAATTTTGACT
29336154 AATTTTGA
1 AATTTTGA
29336162 CTATTTTCGA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 36 0.95
33 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (32 bp):
AATTTTGAATAATTTTATAGTTAATTTTGACT
Found at i:29336160 original size:10 final size:10
Alignment explanation
Indices: 29336085--29336161 Score: 64
Period size: 10 Copynumber: 7.3 Consensus size: 10
29336075 AATATGAACA
*
29336085 TGATAAATTT
1 TGATTAATTT
*
29336095 TAATTAATTT
1 TGATTAATTT
*
29336105 TATAGTTAATTT
1 T-GA-TTAATTT
*
29336117 TGACTAATTT
1 TGATTAATTT
*
29336127 TGAATAATTT
1 TGATTAATTT
*
29336137 TATAGTTAATTT
1 T-GA-TTAATTT
29336149 TGATTAATTT
1 TGATTAATTT
29336159 TGA
1 TGA
29336162 CTATTTTCGA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
10 35 0.65
11 4 0.07
12 15 0.28
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.55
Consensus pattern (10 bp):
TGATTAATTT
Found at i:29346311 original size:44 final size:44
Alignment explanation
Indices: 29346243--29346330 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
29346233 CTTCCCTACA
* * *
29346243 AGGAATAAGGAAATAATTGTATCTTCAAAGCGTCATCAGGAATG
1 AGGAAAAAGGAAATAATTGCATCTTCAAAGCATCATCAGGAATG
*
29346287 AGGAAAAAGGAAATAATTGCATCTTCAAAGCATCATTAGGAATG
1 AGGAAAAAGGAAATAATTGCATCTTCAAAGCATCATCAGGAATG
29346331 CCTTGTTGAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (44 bp):
AGGAAAAAGGAAATAATTGCATCTTCAAAGCATCATCAGGAATG
Found at i:29354030 original size:25 final size:25
Alignment explanation
Indices: 29354001--29354080 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
29353991 ATAACACACA
*
29354001 ACAAAGGTTTTCCAAAGAATTCTCC
1 ACAAAGGTTTTCCAGAGAATTCTCC
* * *
29354026 ACAAAGGTGTTCCAGAGGATTCGCC
1 ACAAAGGTTTTCCAGAGAATTCTCC
29354051 ACAAAGGCTTTT-CAGAGAATT-TGCC
1 ACAAAGG-TTTTCCAGAGAATTCT-CC
29354076 ACAAA
1 ACAAA
29354081 TGCGTTTACT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
25 43 0.93
26 3 0.07
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (25 bp):
ACAAAGGTTTTCCAGAGAATTCTCC
Found at i:29369809 original size:21 final size:21
Alignment explanation
Indices: 29369769--29369819 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
29369759 TTTAACAACT
29369769 TTAATT-AATCAATTTATTTAA
1 TTAATTAAATCAATTTATTT-A
29369790 TTAATTAAATCCAA-TT-TTTA
1 TTAATTAAAT-CAATTTATTTA
*
29369810 TTAATGAAAT
1 TTAATTAAAT
29369820 ATTTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 10 0.37
21 9 0.33
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (21 bp):
TTAATTAAATCAATTTATTTA
Found at i:29373325 original size:19 final size:21
Alignment explanation
Indices: 29373287--29373328 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 21
29373277 TTTTCATGGC
29373287 ATAAATTTTAAAATTAAAATTA
1 ATAAATTTT-AAATTAAAATTA
29373309 ATAAATTTT-AA-TAAAATTA
1 ATAAATTTTAAATTAAAATTA
29373328 A
1 A
29373329 ATATTTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
22 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAATTTTAAATTAAAATTA
Found at i:29374456 original size:22 final size:22
Alignment explanation
Indices: 29374431--29374485 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
29374421 ATTTTATTCT
29374431 AATTGTGATTCGTTATATGATA
1 AATTGTGATTCGTTATATGATA
29374453 AATTGTGATTCGTTATATGATA
1 AATTGTGATTCGTTATATGATA
29374475 AATTGTGATTC
1 AATTGTGATTC
29374486 TAAATGACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.45
Consensus pattern (22 bp):
AATTGTGATTCGTTATATGATA
Found at i:29381239 original size:17 final size:17
Alignment explanation
Indices: 29381185--29381243 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
29381175 TTATATCTAA
*
29381185 TATTTATATTATTAAAT
1 TATTTATATTATTGAAT
* *
29381202 TAAATTTCAAATT-TTGTAT
1 T--ATTT-ATATTATTGAAT
29381221 TATTTATATTATTGAAT
1 TATTTATATTATTGAAT
29381238 TATTTA
1 TATTTA
29381244 ATCATATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 16 0.48
19 9 0.27
20 4 0.12
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (17 bp):
TATTTATATTATTGAAT
Found at i:29381796 original size:23 final size:22
Alignment explanation
Indices: 29381744--29381798 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
29381734 CACCCCTAAT
29381744 TATTATATATAAGTAAATTACGA
1 TATTATA-ATAAGTAAATTACGA
* *
29381767 -ATGTATAATAATTACAATTATGA
1 TAT-TATAATAAGTA-AATTACGA
29381790 TATTATAAT
1 TATTATAAT
29381799 GTACTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 8 0.30
23 17 0.63
24 2 0.07
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (22 bp):
TATTATAATAAGTAAATTACGA
Found at i:29387085 original size:29 final size:29
Alignment explanation
Indices: 29387048--29387108 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
29387038 ACGGCTTGGG
*
29387048 ACACAGGCTGTCACACGGCCGTGTCTCAC
1 ACACAGGCTGTCACACGGCCATGTCTCAC
* * * *
29387077 ACACGGGCTGTTACACGGTCATGTGTCAC
1 ACACAGGCTGTCACACGGCCATGTCTCAC
29387106 ACA
1 ACA
29387109 TGGGTAGCCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (29 bp):
ACACAGGCTGTCACACGGCCATGTCTCAC
Found at i:29387316 original size:19 final size:19
Alignment explanation
Indices: 29387252--29387320 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
29387242 GCGTGTGAGG
* *
29387252 TAGCCACACAGGTGTGGGA
1 TAGCCACACAAGTATGGGA
**
29387271 TAGCCACACAACCATGTTTGG-
1 TAGCCACACAAGTATG---GGA
29387292 -AGCCACACAAGTATGGGA
1 TAGCCACACAAGTATGGGA
29387310 TAGCCACACAA
1 TAGCCACACAA
29387321 CCAAGTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
17 2 0.05
19 22 0.56
20 13 0.33
22 2 0.05
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (19 bp):
TAGCCACACAAGTATGGGA
Found at i:29392649 original size:16 final size:15
Alignment explanation
Indices: 29392626--29392659 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
29392616 GTAAATGTCA
29392626 AAATAGTAATTAAAC
1 AAATAGTAATTAAAC
29392641 AAATAAGTAATTAAAC
1 AAAT-AGTAATTAAAC
29392657 AAA
1 AAA
29392660 AAGATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (15 bp):
AAATAGTAATTAAAC
Found at i:29395596 original size:27 final size:26
Alignment explanation
Indices: 29395565--29395742 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
29395555 TAAATTGTAC
29395565 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
29395592 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
29395618 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
29395646 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
29395674 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
29395701 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
29395728 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29395743 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 103 0.80
28 25 0.19
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:29395681 original size:82 final size:81
Alignment explanation
Indices: 29395566--29395721 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
29395556 AAATTGTACA
* *
29395566 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
29395630 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
29395647 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
29395712 TGCGAGTTGA
65 TGCGAATTGA
29395722 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29395733 original size:82 final size:81
Alignment explanation
Indices: 29395562--29395742 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
29395552 GATTAAATTG
* *
29395562 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
29395627 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
29395643 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29395707 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29395725 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29395743 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29395753 original size:27 final size:27
Alignment explanation
Indices: 29395647--29395753 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
29395637 TGACCATGCG
* * * *
29395647 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
29395675 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
29395702 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
29395729 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
29395754 CATTCGTGGA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:29397214 original size:23 final size:21
Alignment explanation
Indices: 29397196--29397261 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
29397186 CAGTTTCTCC
29397196 CCCTCGTTCTTGCTGGTTTCT
1 CCCTCGTTCTTGCTGGTTTCT
* * *
29397217 CCCTTGTTCTTGCTGGCTTGT
1 CCCTCGTTCTTGCTGGTTTCT
* * * *
29397238 CCATCATTTTTGCTAGTTTCT
1 CCCTCGTTCTTGCTGGTTTCT
29397259 CCC
1 CCC
29397262 CTCTTTTTTG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.05, C:0.32, G:0.17, T:0.47
Consensus pattern (21 bp):
CCCTCGTTCTTGCTGGTTTCT
Found at i:29400349 original size:17 final size:17
Alignment explanation
Indices: 29400327--29400386 Score: 99
Period size: 17 Copynumber: 3.7 Consensus size: 17
29400317 GAGGGCACGG
29400327 TGGAAGAGGGGAATCGA
1 TGGAAGAGGGGAATCGA
29400344 TGGAAGAGGGG-A--GA
1 TGGAAGAGGGGAATCGA
29400358 TGGAAGAGGGGAATCGA
1 TGGAAGAGGGGAATCGA
29400375 TGGAAGAGGGGA
1 TGGAAGAGGGGA
29400387 GATGGGAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
14 13 0.32
15 1 0.03
16 1 0.03
17 25 0.62
ACGTcount: A:0.35, C:0.03, G:0.52, T:0.10
Consensus pattern (17 bp):
TGGAAGAGGGGAATCGA
Found at i:29400362 original size:31 final size:31
Alignment explanation
Indices: 29400327--29400458 Score: 131
Period size: 31 Copynumber: 4.1 Consensus size: 31
29400317 GAGGGCACGG
29400327 TGGAAGAGGGGAATCGATGGAAGAGGGGAGA
1 TGGAAGAGGGGAATCGATGGAAGAGGGGAGA
29400358 TGGAAGAGGGGAATCGATGGAAGAGGGGAGA
1 TGGAAGAGGGGAATCGATGGAAGAGGGGAGA
* * * * * *
29400389 TGGGAA-TGGGAAATGGGAAATGGGAGGAGGGCACGG
1 T-GGAAGAGGGGAAT-CG--AT-GGAAGAGGGGA-GA
* *
29400425 TGGAAGAGGGGAATCGATGGAAAAGGGAAGA
1 TGGAAGAGGGGAATCGATGGAAGAGGGGAGA
29400456 TGG
1 TGG
29400459 GAATGGGGAA
Statistics
Matches: 81, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
31 42 0.52
32 13 0.16
33 2 0.02
34 2 0.02
35 14 0.17
36 8 0.10
ACGTcount: A:0.35, C:0.04, G:0.51, T:0.11
Consensus pattern (31 bp):
TGGAAGAGGGGAATCGATGGAAGAGGGGAGA
Found at i:29400518 original size:30 final size:30
Alignment explanation
Indices: 29400483--29400609 Score: 236
Period size: 30 Copynumber: 4.2 Consensus size: 30
29400473 CATTGTATTT
29400483 GTGTATTTTAAAAATAAAAAAATATATGTA
1 GTGTATTTTAAAAATAAAAAAATATATGTA
* *
29400513 ATGTATTTTAAAAATAAAGAAATATATGTA
1 GTGTATTTTAAAAATAAAAAAATATATGTA
29400543 GTGTATTTTAAAAATAAAAAAATATATGTA
1 GTGTATTTTAAAAATAAAAAAATATATGTA
29400573 GTGTATTTTAAAAATAAAAAAATATATGTA
1 GTGTATTTTAAAAATAAAAAAATATATGTA
29400603 GTGTATT
1 GTGTATT
29400610 CGATTTATTC
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 93 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (30 bp):
GTGTATTTTAAAAATAAAAAAATATATGTA
Found at i:29400961 original size:39 final size:39
Alignment explanation
Indices: 29400918--29401076 Score: 318
Period size: 39 Copynumber: 4.1 Consensus size: 39
29400908 ACTAAAGTGA
29400918 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
1 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
29400957 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
1 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
29400996 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
1 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
29401035 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
1 AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
29401074 AAA
1 AAA
29401077 TCGATTGAAT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 120 1.00
ACGTcount: A:0.55, C:0.10, G:0.15, T:0.20
Consensus pattern (39 bp):
AAAGAAAACAATAGTTCAAGTAAAGCTTTAAAGATGAAC
Found at i:29404557 original size:21 final size:21
Alignment explanation
Indices: 29404533--29404585 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
29404523 CATTGTTTCT
*
29404533 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
29404554 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
29404575 AATCTCACCGC
1 AATCTCACCGC
29404586 CACCACTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:29405537 original size:29 final size:29
Alignment explanation
Indices: 29405504--29405569 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
29405494 ACAACCTGGG
29405504 ACACGGGCTGTCACACGACCATGTATCAC
1 ACACGGGCTGTCACACGACCATGTATCAC
* *
29405533 ACACGGGCTGTCACACGACCGTGTGTCAC
1 ACACGGGCTGTCACACGACCATGTATCAC
29405562 ACACGGGC
1 ACACGGGC
29405570 ATGTGCGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.24, C:0.35, G:0.26, T:0.15
Consensus pattern (29 bp):
ACACGGGCTGTCACACGACCATGTATCAC
Found at i:29405561 original size:15 final size:15
Alignment explanation
Indices: 29405512--29405563 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
29405502 GGACACGGGC
*
29405512 TGTCACACGACCATG
1 TGTCACACGACCGTG
* *
29405527 TATCACAC-A-CGGG
1 TGTCACACGACCGTG
29405540 CTGTCACACGACCGTG
1 -TGTCACACGACCGTG
29405556 TGTCACAC
1 TGTCACAC
29405564 ACGGGCATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.28
15 16 0.55
16 3 0.10
ACGTcount: A:0.25, C:0.35, G:0.21, T:0.19
Consensus pattern (15 bp):
TGTCACACGACCGTG
Found at i:29421178 original size:3 final size:3
Alignment explanation
Indices: 29421170--29421242 Score: 87
Period size: 3 Copynumber: 24.3 Consensus size: 3
29421160 ACATGTGTAT
*
29421170 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GGA GAA GAA GAA GAA GATA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A
* *
29421219 -AA GGA -AA GAAA GAA GAT GAA GAA G
1 GAA GAA GAA G-AA GAA GAA GAA GAA G
29421243 GAAAATAAGG
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.03
3 54 0.90
4 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:29421243 original size:21 final size:20
Alignment explanation
Indices: 29421170--29421246 Score: 97
Period size: 21 Copynumber: 3.9 Consensus size: 20
29421160 ACATGTGTAT
29421170 GAAGAAGAAGAA-G-AAGAA
1 GAAGAAGAAGAAGGAAAGAA
29421188 GAAGAAGAAGAAGGAGAAGAA
1 GAAGAAGAAGAAGGA-AAGAA
29421209 GAAGAAGATA-AAGGAAAGAAA
1 GAAGAAGA-AGAAGGAAAG-AA
*
29421230 GAAGATGAAGAAGGAAA
1 GAAGAAGAAGAAGGAAA
29421247 ATAAGGAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
18 12 0.23
19 1 0.02
20 4 0.08
21 34 0.65
22 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.03
Consensus pattern (20 bp):
GAAGAAGAAGAAGGAAAGAA
Found at i:29426838 original size:25 final size:26
Alignment explanation
Indices: 29426790--29426843 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
29426780 CATAATTGAA
* * *
29426790 ATGAAATGGATTGATTTTGTATAT-T
1 ATGAAATAGATTGATTATGAATATAT
*
29426815 ATGAAATATATTGATTATGAATATAT
1 ATGAAATAGATTGATTATGAATATAT
29426841 ATG
1 ATG
29426844 TATTAAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (26 bp):
ATGAAATAGATTGATTATGAATATAT
Found at i:29426848 original size:17 final size:15
Alignment explanation
Indices: 29426811--29426853 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
29426801 TGATTTTGTA
29426811 TATTATGAAATATAT
1 TATTATGAAATATAT
29426826 TGATTATGAATATATAT
1 T-ATTATGAA-ATATAT
*
29426843 GTATTAAGAAA
1 -TATTATGAAA
29426854 AATGTGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 9 0.38
17 13 0.54
18 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (15 bp):
TATTATGAAATATAT
Found at i:29430394 original size:43 final size:41
Alignment explanation
Indices: 29430332--29430413 Score: 119
Period size: 43 Copynumber: 2.0 Consensus size: 41
29430322 TTTATCCTAG
* *
29430332 AAAAAAATTAAAAAGAGGAGAAGATAATCTTGGGTTGTTCA
1 AAAAAAATTAAAAAGAGGAGAAGATAAACATGGGTTGTTCA
*
29430373 AAAAAGAATTTAAAAATAGGAGAAGATAAACATGGGTTGTT
1 AAAAA-AA-TTAAAAAGAGGAGAAGATAAACATGGGTTGTT
29430414 GGATATACCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 5 0.14
42 2 0.06
43 29 0.81
ACGTcount: A:0.50, C:0.04, G:0.22, T:0.24
Consensus pattern (41 bp):
AAAAAAATTAAAAAGAGGAGAAGATAAACATGGGTTGTTCA
Found at i:29436156 original size:43 final size:42
Alignment explanation
Indices: 29436074--29436157 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
29436064 TTTATCCTAG
* * *
29436074 AAAAAATAATTTAAAAAGAGGAGAAGATAATCTTGGTTGTTC
1 AAAAAAGAATTTAAAAAGAGGAGAAGATAAACTGGGTTGTTC
*
29436116 AAAAAAGAATTTAAAAAGAGGAGAATATAAACATGGGTTGTT
1 AAAAAAGAATTTAAAAAGAGGAGAAGATAAAC-TGGGTTGTT
29436158 GGATTTACCC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 29 0.78
43 8 0.22
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAAAAGAATTTAAAAAGAGGAGAAGATAAACTGGGTTGTTC
Found at i:29446131 original size:13 final size:13
Alignment explanation
Indices: 29446109--29446140 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
29446099 GCGCATGAAT
29446109 ATAA-AAATAATA
1 ATAATAAATAATA
29446121 ATAATAAATAATA
1 ATAATAAATAATA
29446134 ATAATAA
1 ATAATAA
29446141 TGATACAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAATAAATAATA
Found at i:29446638 original size:19 final size:19
Alignment explanation
Indices: 29446614--29446686 Score: 137
Period size: 19 Copynumber: 3.8 Consensus size: 19
29446604 AATCATATCT
29446614 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
29446633 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
29446652 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
29446671 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
29446687 CTTGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:29447579 original size:32 final size:32
Alignment explanation
Indices: 29447488--29447580 Score: 125
Period size: 32 Copynumber: 2.9 Consensus size: 32
29447478 AACATGACCA
* *
29447488 TGTGGCCCACACGGCCCAAATATCCCAAATCG
1 TGTGGCCCACACAGCCCAAATATCCCAGATCG
*
29447520 TGTGGCCCACACA-TCCAGAATATCCCAGATCG
1 TGTGGCCCACACAGCCCA-AATATCCCAGATCG
* *
29447552 TGTGGCCTACACAGCCCAAATAGCCCAGA
1 TGTGGCCCACACAGCCCAAATATCCCAGA
29447581 CCGTTTGGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 3 0.06
32 47 0.89
33 3 0.06
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (32 bp):
TGTGGCCCACACAGCCCAAATATCCCAGATCG
Found at i:29452502 original size:3 final size:3
Alignment explanation
Indices: 29452494--29452528 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29452484 AGGGTTTTAA
29452494 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29452529 AAGCTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29453066 original size:18 final size:19
Alignment explanation
Indices: 29453031--29453096 Score: 75
Period size: 18 Copynumber: 3.5 Consensus size: 19
29453021 TTTTTCAACC
29453031 TAAT-ATTTTAAATATTTT
1 TAATAATTTTAAATATTTT
*
29453049 TAATAATTTTACAT-TTTT
1 TAATAATTTTAAATATTTT
*
29453067 TTATAATTTTAAAAATATTTT
1 TAATAATTTT--AAATATTTT
29453088 T-ATAATTTT
1 TAATAATTTT
29453097 TTTGAAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 17 0.41
19 8 0.20
20 11 0.27
21 5 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TAATAATTTTAAATATTTT
Found at i:29453087 original size:20 final size:18
Alignment explanation
Indices: 29453035--29453096 Score: 79
Period size: 20 Copynumber: 3.3 Consensus size: 18
29453025 TCAACCTAAT
29453035 ATTTTAAATATTTTTAATA
1 ATTTTAAATATTTTT-ATA
* *
29453054 ATTTTACATTTTTTTATA
1 ATTTTAAATATTTTTATA
29453072 ATTTTAAAAATATTTTTATA
1 ATTTT--AAATATTTTTATA
29453092 ATTTT
1 ATTTT
29453097 TTTGAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 8 0.22
19 13 0.35
20 16 0.43
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTAAATATTTTTATA
Found at i:29453432 original size:19 final size:18
Alignment explanation
Indices: 29453385--29453433 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
29453375 TTTTATCTAA
*
29453385 TTTATTTTTCTATAATTT
1 TTTATTTTTTTATAATTT
* *
29453403 TTTAATTTTTTATTCATTT
1 TTTATTTTTTTA-TAATTT
29453422 TTTATTTTTTTA
1 TTTATTTTTTTA
29453434 CTTTCTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTTTTATAATTT
Found at i:29454444 original size:106 final size:106
Alignment explanation
Indices: 29454259--29454470 Score: 361
Period size: 106 Copynumber: 2.0 Consensus size: 106
29454249 CATACGTAAT
* * *
29454259 TTGCAACCTGCAAGTTAGTGGCAATGGTTTATCTTCCTGGAATGCAAGGGGTAAGAACAACAAAT
1 TTGCAACCTGCAAGTTAATGGCAACGGTTCATCTTCCTGGAATGCAAGGGGTAAGAACAACAAAT
* *
29454324 AGAAAAATGACAAGCAAGAATAATTTAAAATCATGCAATGG
66 AGAAAAACGACAAGCAAGAATAATATAAAATCATGCAATGG
29454365 TTGCAACCTGCAAGTTAATGGCAACGGTTCATCTTCCTGGAATGCAAGGGGTAAGAACAACAAAT
1 TTGCAACCTGCAAGTTAATGGCAACGGTTCATCTTCCTGGAATGCAAGGGGTAAGAACAACAAAT
* *
29454430 AGAAAGACGACAAGCAAGAATCATATAAAATCATGCAATGG
66 AGAAAAACGACAAGCAAGAATAATATAAAATCATGCAATGG
29454471 CAAATGTGAT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (106 bp):
TTGCAACCTGCAAGTTAATGGCAACGGTTCATCTTCCTGGAATGCAAGGGGTAAGAACAACAAAT
AGAAAAACGACAAGCAAGAATAATATAAAATCATGCAATGG
Found at i:29458240 original size:97 final size:97
Alignment explanation
Indices: 29458087--29458376 Score: 541
Period size: 97 Copynumber: 3.0 Consensus size: 97
29458077 TGAGCAGACA
*
29458087 CTAGCTCATATTGGA-GA-A-GTAAAGTTTCAGTAAAAAAATGAAAAATTAAAGATTCTTAAAGT
1 CTAGCTCATATTGGAGGAGAGGTAAAGTTTCAGT-AAAAAATGAAAAATTGAAGATTCTTAAAGT
29458149 AGCAAAAAAAGGAAATCCTACAGAAATAGGGCC
65 AGCAAAAAAAGGAAATCCTACAGAAATAGGGCC
29458182 CTAGCTCATATTGGAGGAGAGGTAAAGTTTCAGTAAAAAATGAAAAATTGAAGATTCTTAAAGTA
1 CTAGCTCATATTGGAGGAGAGGTAAAGTTTCAGTAAAAAATGAAAAATTGAAGATTCTTAAAGTA
29458247 GCAAAAAAAGGAAATCCTACAGAAATAGGGCC
66 GCAAAAAAAGGAAATCCTACAGAAATAGGGCC
29458279 CTAGCTCATATTGGAGGAGAGGTAAAGTTTCAGTAAAAAATGAAAAATTGAAGATTCTTAAAGTA
1 CTAGCTCATATTGGAGGAGAGGTAAAGTTTCAGTAAAAAATGAAAAATTGAAGATTCTTAAAGTA
29458344 GCAAAAAAAGGAAATCCTACAGAAATAGGGCC
66 GCAAAAAAAGGAAATCCTACAGAAATAGGGCC
29458376 C
1 C
29458377 CCTAAAAACA
Statistics
Matches: 191, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
95 15 0.08
96 2 0.01
97 161 0.84
98 13 0.07
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (97 bp):
CTAGCTCATATTGGAGGAGAGGTAAAGTTTCAGTAAAAAATGAAAAATTGAAGATTCTTAAAGTA
GCAAAAAAAGGAAATCCTACAGAAATAGGGCC
Found at i:29463104 original size:196 final size:194
Alignment explanation
Indices: 29462770--29463160 Score: 545
Period size: 196 Copynumber: 2.0 Consensus size: 194
29462760 TACAACCACC
*
29462770 CTAGAGAAAATTAATAAAATGCAGAACAAAAGCACAAACCAAATAAGCAACAAAAACTTAAAAAG
1 CTAGAGAAAATTAATAAAATGCAGAACAAAAGCACAAACCAAATAAACAACAAAAACTTAAAAAG
* *
29462835 CAGAAGTTTAATGCACTTCATTATCTTATGACTTAAGAGAAGGGGGACTTCTAATAAATTGTACC
66 CAGAAGTTTAATGCACTTCATTATCTTATGACTTAAGAAAAAGGGGACTTCTAATAAATTGTACC
* * *
29462900 AACAGATTCACATTTCAAAAAGGATCAATTTAC-AGGATTAG-CCTTTGGATAGAAGATTAAGCT
131 AACAGATTCACATTTCAAAAAGGATCAATTTACTAGAATT-GCCCCTTGAATAGAAGATTAAGCT
* * ** *
29462963 CTAGAGAGAATTAATAAAATGTAGAACAACAAAAGTGCAAACCAAATAAACGAA-AAAAACTTTA
1 CTAGAGAAAATTAATAAAATGCAG---AACAAAAGCACAAACCAAATAAAC-AACAAAAACTTAA
* ** *
29463027 TATTCAGAAGTTTAATGTACTTCATTATCTTATGACTTAAGAAAAAGGGGACTTCTAATAAATTG
62 AAAGCAGAAGTTTAATGCACTTCATTATCTTATGACTTAAGAAAAAGGGGACTTCTAATAAATTG
*** *
29463092 TACGTCCAGATTCACATTTCAAAAAGGATCAATTTACTTGAATTGCCCCTTGAATAGAAGATTAA
127 TACCAACAGATTCACATTTCAAAAAGGATCAATTTACTAGAATTGCCCCTTGAATAGAAGATTAA
29463157 GCT
192 GCT
29463160 C
1 C
29463161 CATAGTTGCA
Statistics
Matches: 173, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
193 22 0.13
196 124 0.72
197 27 0.16
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (194 bp):
CTAGAGAAAATTAATAAAATGCAGAACAAAAGCACAAACCAAATAAACAACAAAAACTTAAAAAG
CAGAAGTTTAATGCACTTCATTATCTTATGACTTAAGAAAAAGGGGACTTCTAATAAATTGTACC
AACAGATTCACATTTCAAAAAGGATCAATTTACTAGAATTGCCCCTTGAATAGAAGATTAAGCT
Found at i:29464381 original size:34 final size:34
Alignment explanation
Indices: 29464321--29464426 Score: 115
Period size: 35 Copynumber: 3.0 Consensus size: 34
29464311 TTTAACAATC
*
29464321 ATTTGTACTACCACTTAAAAAGGCCGTAATTAGGG
1 ATTTGGACTACCACTT-AAAAGGCCGTAATTAGGG
29464356 ATTTGGACTACCACTTAAAAGGCCGTAATTAAGGAG
1 ATTTGGACTACCACTTAAAAGGCCGTAATT-AGG-G
* ** * *
29464392 GTAACGGACTACCACTTAAGA-GCCGTGATTAGGG
1 AT-TTGGACTACCACTTAAAAGGCCGTAATTAGGG
29464426 A
1 A
29464427 GGTAACTGAG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
34 15 0.25
35 21 0.34
36 10 0.16
37 15 0.25
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.25
Consensus pattern (34 bp):
ATTTGGACTACCACTTAAAAGGCCGTAATTAGGG
Found at i:29464428 original size:36 final size:37
Alignment explanation
Indices: 29464327--29464432 Score: 121
Period size: 36 Copynumber: 2.9 Consensus size: 37
29464317 AATCATTTGT
* **
29464327 ACTACCACTTAAAAAGGCCGTAATT-AGG-GAT-TTGG
1 ACTACCACTT-AAAAGGCCGTAATTAAGGAGGTAACGG
29464362 ACTACCACTTAAAAGGCCGTAATTAAGGAGGTAACGG
1 ACTACCACTTAAAAGGCCGTAATTAAGGAGGTAACGG
* * *
29464399 ACTACCACTTAAGA-GCCGTGATTAGGGAGGTAAC
1 ACTACCACTTAAAAGGCCGTAATTAAGGAGGTAAC
29464433 TGAGTTTAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
34 14 0.23
35 13 0.21
36 20 0.32
37 15 0.24
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.22
Consensus pattern (37 bp):
ACTACCACTTAAAAGGCCGTAATTAAGGAGGTAACGG
Found at i:29466978 original size:16 final size:19
Alignment explanation
Indices: 29466930--29466979 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
29466920 TTTATTCATA
29466930 TAATAAATTATTGATATAAT
1 TAATAAATTATTGATAT-AT
29466950 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTGATATAT
29466968 TAATAAATTATT
1 TAATAAATTATT
29466980 TAATATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.18
17 2 0.07
18 6 0.21
20 6 0.21
21 4 0.14
22 5 0.18
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTGATATAT
Found at i:29467027 original size:14 final size:14
Alignment explanation
Indices: 29466995--29467035 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
29466985 TTTCAATTTT
29466995 ATTTTAACAATAA-A
1 ATTTTAA-AATAATA
*
29467009 TTTTTAAAATAATA
1 ATTTTAAAATAATA
29467023 ATTTT-AAATAATA
1 ATTTTAAAATAATA
29467036 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTAAAATAATA
Found at i:29469890 original size:16 final size:16
Alignment explanation
Indices: 29469869--29469922 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
29469859 TTTGGTTCGC
29469869 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
29469885 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGG
29469901 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
29469917 CGTAAT
1 TGTAAT
29469923 AGTAATTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:29469956 original size:45 final size:44
Alignment explanation
Indices: 29469904--29469997 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
29469894 ATAGAGCTGT
* *
29469904 AATGGAATAGAGGC-GTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGA-ACTGTAATAAT-ATTC-ATGTGTTTGGTTGAATGG
* *
29469949 CATGGAATAGAACTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAATATTCATGTGTTTGGTTGAATGG
29469993 AATGG
1 AATGG
29469998 TGTTGTAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
43 1 0.02
44 24 0.57
45 17 0.40
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:29473656 original size:18 final size:18
Alignment explanation
Indices: 29473623--29473675 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
29473613 ACTCATGTAT
* *
29473623 TTATGCTAACTCATGTTA
1 TTATGCGAACCCATGTTA
* *
29473641 TTCTGCGAACCTATGTTA
1 TTATGCGAACCCATGTTA
29473659 TTATGCGAACCCATGTT
1 TTATGCGAACCCATGTT
29473676 GTATGTTATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (18 bp):
TTATGCGAACCCATGTTA
Found at i:29473680 original size:25 final size:25
Alignment explanation
Indices: 29473652--29473702 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
29473642 TCTGCGAACC
*
29473652 TATGTTATTATGCGAACCCATGTTG
1 TATGTTATCATGCGAACCCATGTTG
* * *
29473677 TATGTTATCATGTGGACCTATGTTG
1 TATGTTATCATGCGAACCCATGTTG
29473702 T
1 T
29473703 TGTGCAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.43
Consensus pattern (25 bp):
TATGTTATCATGCGAACCCATGTTG
Found at i:29474111 original size:20 final size:20
Alignment explanation
Indices: 29474051--29474112 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
29474041 GGGCATCTAA
* *
29474051 TTGCACATTTGTGCCTCTGA
1 TTGCACATTCGTGCCTCTGT
* *
29474071 TTGCACATTCATGCCTTTGT
1 TTGCACATTCGTGCCTCTGT
29474091 TTGCAC-TTCGGTGCCTCTGT
1 TTGCACATTC-GTGCCTCTGT
29474111 TT
1 TT
29474113 AGCATTTCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.11, C:0.26, G:0.19, T:0.44
Consensus pattern (20 bp):
TTGCACATTCGTGCCTCTGT
Found at i:29474468 original size:43 final size:43
Alignment explanation
Indices: 29474352--29474521 Score: 193
Period size: 43 Copynumber: 3.9 Consensus size: 43
29474342 TAAAATATAT
* * * * *
29474352 GATGATGCAC-TGTGTGTGCCAATATATTTGCTTTGGTTTATCC
1 GATGATGCACTTGTATGTGCCAGTATAGTTGC-TTCGTTTATTC
29474395 GATGATGCACTGTGTATGTGCCAGTATAGTTGCTTCGATTTATTC
1 GATGATGCACT-TGTATGTGCCAGTATAGTTGCTTCG-TTTATTC
*
29474440 GATGATGCA-TTGTATGTGTCAGTATAGTTGCTTCTGTTTATTC
1 GATGATGCACTTGTATGTGCCAGTATAGTTGCTTC-GTTTATTC
* * *
29474483 GATGATGCACAT-TATGTGCTAGTATAGTTACTTCAGTTT
1 GATGATGCACTTGTATGTGCCAGTATAGTTGCTTC-GTTT
29474522 TACCCGATGA
Statistics
Matches: 111, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
43 72 0.65
44 6 0.05
45 33 0.30
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (43 bp):
GATGATGCACTTGTATGTGCCAGTATAGTTGCTTCGTTTATTC
Found at i:29480062 original size:17 final size:18
Alignment explanation
Indices: 29480040--29480074 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29480030 AACATAATGC
29480040 AAAA-TTGGTATCAATAT
1 AAAATTTGGTATCAATAT
29480057 AAAATTTTGGTATCAATA
1 AAAA-TTTGGTATCAATA
29480075 AAATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
19 12 0.75
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (18 bp):
AAAATTTGGTATCAATAT
Found at i:29480493 original size:22 final size:22
Alignment explanation
Indices: 29480468--29480514 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
29480458 TAGTTCAATA
*
29480468 GAACAGTAAAATTCTCTTGCAT
1 GAACAGTAAAATTCTCTGGCAT
*
29480490 GAACAGTGAAATTCTCTGGCAT
1 GAACAGTAAAATTCTCTGGCAT
29480512 GAA
1 GAA
29480515 TAGAGAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (22 bp):
GAACAGTAAAATTCTCTGGCAT
Found at i:29480529 original size:23 final size:22
Alignment explanation
Indices: 29480478--29480572 Score: 111
Period size: 23 Copynumber: 4.2 Consensus size: 22
29480468 GAACAGTAAA
*
29480478 ATTCTCTTGCATGAACAGTGAA-
1 ATTCTC-TGCATGAATAGTGAAG
*
29480500 ATTCTCTGGCATGAATAGAGAAG
1 ATTCTCT-GCATGAATAGTGAAG
29480523 ATTCTCTGCAATGAATAGTGAAG
1 ATTCTCTGC-ATGAATAGTGAAG
* *
29480546 ATTCTCTACAATGGATAGTGAAG
1 ATTCTCTGC-ATGAATAGTGAAG
29480569 ATTC
1 ATTC
29480573 CTTGAAAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
21 1 0.02
22 20 0.31
23 44 0.68
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (22 bp):
ATTCTCTGCATGAATAGTGAAG
Found at i:29497082 original size:7 final size:7
Alignment explanation
Indices: 29497070--29497095 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29497060 TTCATTAAAT
29497070 ATTTAAC
1 ATTTAAC
29497077 ATTTAAC
1 ATTTAAC
29497084 ATTTAAC
1 ATTTAAC
29497091 ATTTA
1 ATTTA
29497096 CTAATATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTTAAC
Found at i:29505500 original size:9 final size:9
Alignment explanation
Indices: 29505478--29505518 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
29505468 GGGTTATAGT
*
29505478 TTATTATTA
1 TTATTATGA
*
29505487 CTATTATGA
1 TTATTATGA
29505496 TTATTATGA
1 TTATTATGA
29505505 TTATTATGA
1 TTATTATGA
29505514 TTATT
1 TTATT
29505519 TTGGGTAGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (9 bp):
TTATTATGA
Found at i:29512721 original size:20 final size:20
Alignment explanation
Indices: 29512698--29512743 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
29512688 TAGGGAGCTT
* *
29512698 GCACTGGTATATGCAGCTAG
1 GCACCGGTATATGCAACTAG
*
29512718 GCACCGGTATCTGCAACTAG
1 GCACCGGTATATGCAACTAG
29512738 GCACCG
1 GCACCG
29512744 TGAGGACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.20
Consensus pattern (20 bp):
GCACCGGTATATGCAACTAG
Found at i:29516820 original size:16 final size:16
Alignment explanation
Indices: 29516799--29516832 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29516789 CAATTCAAGT
29516799 TTTTGTTGTCGAATTC
1 TTTTGTTGTCGAATTC
*
29516815 TTTTGTTTTCGAATTC
1 TTTTGTTGTCGAATTC
29516831 TT
1 TT
29516833 CTATTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.62
Consensus pattern (16 bp):
TTTTGTTGTCGAATTC
Found at i:29522242 original size:10 final size:10
Alignment explanation
Indices: 29522229--29522373 Score: 53
Period size: 10 Copynumber: 14.1 Consensus size: 10
29522219 ATTTTTTTTA
29522229 ATTTTAAAAT
1 ATTTTAAAAT
* *
29522239 ATTTTTTACAT
1 A-TTTTAAAAT
**
29522250 ACTTTTTTAAT
1 A-TTTTAAAAT
* *
29522261 TTTTTTAAAT
1 ATTTTAAAAT
*
29522271 -TTTAAAAAT
1 ATTTTAAAAT
*
29522280 TTTTTAAAAT
1 ATTTTAAAAT
* *
29522290 TTTTTTAAAT
1 ATTTTAAAAT
* ***
29522300 TTTTTTTTA-
1 ATTTTAAAAT
29522309 ATTTTAAAAT
1 ATTTTAAAAT
29522319 ATTTTTAAAAT
1 A-TTTTAAAAT
29522330 ATTTTTAAAAT
1 A-TTTTAAAAT
**
29522341 ACTTTTTTTTAAT
1 A---TTTTAAAAT
*
29522354 TTTTTAAAAT
1 ATTTTAAAAT
29522364 -TTTTAAAAT
1 ATTTTAAAAT
29522373 A
1 A
29522374 AAAATGGGTC
Statistics
Matches: 106, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
9 21 0.20
10 41 0.39
11 36 0.34
13 8 0.08
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:29522282 original size:39 final size:40
Alignment explanation
Indices: 29522219--29522356 Score: 158
Period size: 40 Copynumber: 3.4 Consensus size: 40
29522209 ATAAATATAT
*
29522219 ATTTTTTTTAATTTTAAAATATTTTTTACATACTTTTTT-A
1 ATTTTTTTTAATTTTAAAATATTTTTTA-AAACTTTTTTAA
* *
29522259 ATTTTTTTAAATTTTAAAA-ATTTTTTAAAATTTTTTTAA
1 ATTTTTTTTAATTTTAAAATATTTTTTAAAACTTTTTTAA
29522298 ATTTTTTTTTAATTTTAAAATA-TTTTTAAAA-TATTTTTAAAA
1 A-TTTTTTTTAATTTTAAAATATTTTTTAAAACT-TTTTT--AA
29522340 TACTTTTTTTTAATTTT
1 -A-TTTTTTTTAATTTT
29522357 TTAAAATTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
38 8 0.09
39 11 0.13
40 49 0.57
41 1 0.01
42 2 0.02
43 15 0.17
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (40 bp):
ATTTTTTTTAATTTTAAAATATTTTTTAAAACTTTTTTAA
Found at i:29522284 original size:11 final size:10
Alignment explanation
Indices: 29522258--29522372 Score: 85
Period size: 10 Copynumber: 11.3 Consensus size: 10
29522248 ATACTTTTTT
*
29522258 AATTTTTTTA
1 AATTTTTTAA
*
29522268 AA-TTTTAAA
1 AATTTTTTAA
29522277 AATTTTTTAA
1 AATTTTTTAA
29522287 AATTTTTTTAA
1 AA-TTTTTTAA
* **
29522298 ATTTTTTTTT
1 AATTTTTTAA
29522308 AA--TTTTAA
1 AATTTTTTAA
29522316 AATATTTTTAA
1 AAT-TTTTTAA
29522327 AATATTTTTAAA
1 AAT-TTTTT-AA
**
29522339 ATACTTTTTTTT
1 A-A-TTTTTTAA
29522351 AATTTTTTAA
1 AATTTTTTAA
29522361 AA-TTTTTAA
1 AATTTTTTAA
29522370 AAT
1 AAT
29522373 AAAAATGGGT
Statistics
Matches: 83, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
8 6 0.07
9 16 0.19
10 25 0.30
11 25 0.30
12 4 0.05
13 6 0.07
14 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:29527158 original size:13 final size:14
Alignment explanation
Indices: 29527126--29527162 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
29527116 GCCATACAAT
29527126 TTATGATATATGTA
1 TTATGATATATGTA
29527140 TGTATGATATATG-A
1 T-TATGATATATGTA
29527154 TTATGATAT
1 TTATGATAT
29527163 GCTTGTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
14 3 0.14
15 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
TTATGATATATGTA
Found at i:29527436 original size:20 final size:20
Alignment explanation
Indices: 29527413--29527457 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29527403 GTTATGATTC
* *
29527413 GATATAATATGATATGTTAT
1 GATATAATATAATATGTTAA
* *
29527433 GATACATTATAATATGTTAA
1 GATATAATATAATATGTTAA
29527453 GATAT
1 GATAT
29527458 GGTCTATATG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.42
Consensus pattern (20 bp):
GATATAATATAATATGTTAA
Found at i:29529104 original size:24 final size:24
Alignment explanation
Indices: 29529068--29529139 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
29529058 GGATCTATGA
* *
29529068 TTGCATCTATATCAGAATTTGCAT
1 TTGCATCTGTATCTGAATTTGCAT
*
29529092 TTGCATTTGTATCTGAATTTG-AT
1 TTGCATCTGTATCTGAATTTGCAT
* *
29529115 TATGCATCTGAATCTGAATATGCAT
1 T-TGCATCTGTATCTGAATTTGCAT
29529140 ATGTATCCGA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.08
24 35 0.88
25 2 0.05
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (24 bp):
TTGCATCTGTATCTGAATTTGCAT
Found at i:29529123 original size:18 final size:18
Alignment explanation
Indices: 29529102--29529139 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29529092 TTGCATTTGT
* *
29529102 ATCTGAATTTGATTATGC
1 ATCTGAATCTGAATATGC
29529120 ATCTGAATCTGAATATGC
1 ATCTGAATCTGAATATGC
29529138 AT
1 AT
29529140 ATGTATCCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (18 bp):
ATCTGAATCTGAATATGC
Found at i:29529154 original size:18 final size:18
Alignment explanation
Indices: 29529112--29529154 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
29529102 ATCTGAATTT
* *
29529112 GATTATGCATCTGAATCT
1 GATTATGCATATGAATCC
* *
29529130 GAATATGCATATGTATCC
1 GATTATGCATATGAATCC
29529148 GATTATG
1 GATTATG
29529155 AAATACACTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (18 bp):
GATTATGCATATGAATCC
Found at i:29533026 original size:18 final size:18
Alignment explanation
Indices: 29533003--29533039 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29532993 GTCTGTAGCG
29533003 GATGGTATTTACATTTGT
1 GATGGTATTTACATTTGT
29533021 GATGGTATTTACATTTGT
1 GATGGTATTTACATTTGT
29533039 G
1 G
29533040 TTTGTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (18 bp):
GATGGTATTTACATTTGT
Found at i:29535416 original size:16 final size:16
Alignment explanation
Indices: 29535395--29535430 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
29535385 TTTGGTTCGC
29535395 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
29535411 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
29535427 TGTA
1 TGTA
29535431 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:29535495 original size:44 final size:45
Alignment explanation
Indices: 29535411--29535501 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
29535401 GGATTAGAGG
* * *
29535411 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
29535456 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
29535500 TG
1 TG
29535502 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:29535687 original size:18 final size:17
Alignment explanation
Indices: 29535666--29535700 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
29535656 TTATTATTAA
29535666 ATATATTTTAATTAAAAT
1 ATATATTTTAA-TAAAAT
29535684 ATATATTTTAATAAAAT
1 ATATATTTTAATAAAAT
29535701 TATTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATTTTAATAAAAT
Found at i:29535837 original size:156 final size:157
Alignment explanation
Indices: 29535553--29535868 Score: 544
Period size: 156 Copynumber: 2.0 Consensus size: 157
29535543 TAGAATACCC
29535553 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
29535618 TTGTCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAA
*
29535683 TATATATTTTAATAAAATTATT-ATAA
131 TATATAATTTAATAAAATTATTAATAA
*
29535709 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
29535774 TTATCAATAATAAATAATTTAATCATATTTAAACATATTTTTTATTAAACATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAA
*
29535839 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTATTAATAA
29535866 TTA
1 TTA
29535869 ATATTCTTAT
Statistics
Matches: 150, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
156 143 0.95
157 7 0.05
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (157 bp):
TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAA
TATATAATTTAATAAAATTATTAATAA
Found at i:29535841 original size:14 final size:15
Alignment explanation
Indices: 29535802--29535841 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
29535792 TTAATCATAT
*
29535802 TTAAACATATTTTTTA
1 TTAAACATA-TTTTAA
29535818 TTAAACATATTTTAA
1 TTAAACATATTTTAA
29535833 TTAAA-ATAT
1 TTAAACATAT
29535842 ATAATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.17
15 10 0.43
16 9 0.39
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAACATATTTTAA
Found at i:29535985 original size:26 final size:27
Alignment explanation
Indices: 29535911--29535991 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 27
29535901 ATATGATACT
* *
29535911 ATAATTAATATT-AATATATTTTAATTA
1 ATAATTATTATTAAATATAATTTAA-TA
* *
29535938 A-AATATATGATTAAATACAATTTAA-A
1 ATAAT-TATTATTAAATATAATTTAATA
*
29535964 ATAATTATTATTAAATATAATTTCATA
1 ATAATTATTATTAAATATAATTTAATA
29535991 A
1 A
29535992 AATGTTCTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
26 22 0.51
27 11 0.26
28 10 0.23
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (27 bp):
ATAATTATTATTAAATATAATTTAATA
Done.