Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 29 of 186
Found at i:8558217 original size:3 final size:3
Alignment explanation
Indices: 8558209--8558246 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
8558199 GTAAAAGTAC
* *
8558209 TCT TCT TCT TCT TCT TTT TCT TCC TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
8558247 GACTACTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:8558638 original size:7 final size:7
Alignment explanation
Indices: 8558628--8558659 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
8558618 GGGGCTCTAT
*
8558628 TGAAATG
1 TGAAAGG
8558635 TGAAAGG
1 TGAAAGG
8558642 TGAAAGG
1 TGAAAGG
8558649 TGAAAGG
1 TGAAAGG
8558656 TGAA
1 TGAA
8558660 TGGATCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.19
Consensus pattern (7 bp):
TGAAAGG
Found at i:8563691 original size:29 final size:27
Alignment explanation
Indices: 8563659--8563727 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 27
8563649 AATTAGATCT
*
8563659 TAATTTTAAAATCTAAAAAGTA-AAAACAC
1 TAATTTTAAAA-ATAAAAA-TACAAAA-AC
8563688 TAATTTTCTAAAAATAAAAATACAAAAAC
1 TAA-TTT-TAAAAATAAAAATACAAAAAC
8563717 TAAATTTTAAA
1 T-AATTTTAAA
8563728 TTTATAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
28 4 0.11
29 11 0.31
30 15 0.43
31 5 0.14
ACGTcount: A:0.59, C:0.09, G:0.01, T:0.30
Consensus pattern (27 bp):
TAATTTTAAAAATAAAAATACAAAAAC
Found at i:8564080 original size:27 final size:28
Alignment explanation
Indices: 8564029--8564087 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
8564019 AAAGTTTTTT
*
8564029 TAAATATATCATTAAAATTTAAAAAAAA
1 TAAATATATCATTAAAATATAAAAAAAA
*
8564057 TAAATATAT-ATTAAAA-ATAGAAAAAA
1 TAAATATATCATTAAAATATAAAAAAAA
*
8564083 CAAAT
1 TAAAT
8564088 TTAATCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 12 0.43
27 7 0.25
28 9 0.32
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (28 bp):
TAAATATATCATTAAAATATAAAAAAAA
Found at i:8564080 original size:28 final size:28
Alignment explanation
Indices: 8564029--8564082 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
8564019 AAAGTTTTTT
**
8564029 TAAATATATCATTAAAATTTAAAAAAAA
1 TAAATATATCATTAAAATAGAAAAAAAA
8564057 TAAATATAT-ATTAAAAATAGAAAAAA
1 TAAATATATCATT-AAAATAGAAAAAA
8564083 CAAATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
TAAATATATCATTAAAATAGAAAAAAAA
Found at i:8572854 original size:25 final size:25
Alignment explanation
Indices: 8572803--8572854 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
8572793 TTTGGCTTGA
* **
8572803 CATTTACTATGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
8572828 CATTTATTAAGCAATATCAAATGTT
1 CATTTACTAAGCAATATCAAATATT
8572853 CA
1 CA
8572855 AATTATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:8576458 original size:31 final size:32
Alignment explanation
Indices: 8576410--8576481 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
8576400 GATATTTTGA
*
8576410 TATTTTA-TAATTATTTAATTAGATA-AATAT
1 TATTTTATTAATTATTTAATAAGATATAATAT
**
8576440 TATTTTATTAA-TATTTTAATAAGATATTTTAT
1 TATTTTATTAATTA-TTTAATAAGATATAATAT
8576472 TATTTTATTA
1 TATTTTATTA
8576482 GTATATAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 9 0.25
31 14 0.39
32 13 0.36
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (32 bp):
TATTTTATTAATTATTTAATAAGATATAATAT
Found at i:8578341 original size:46 final size:46
Alignment explanation
Indices: 8578289--8578501 Score: 293
Period size: 46 Copynumber: 4.6 Consensus size: 46
8578279 GCTCTCTGAA
* *
8578289 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
8578335 ATGAAATGTGTAAGACCATGGTTGTAAGATAACATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
8578381 ATGAAAAGAATAAGACCATGGTTGAGAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
8578427 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
8578473 A-GAAAATGAGTAAGACCATAGTTGAAAGA
1 ATG-AAATGAGTAAGACCATGGTTGAAAGA
8578502 CATTATGGCA
Statistics
Matches: 148, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.01
46 147 0.99
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:8580418 original size:23 final size:24
Alignment explanation
Indices: 8580385--8580433 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
8580375 AAATTTCGGA
8580385 ATTTATAATTTTTATA-ACTTATAT
1 ATTTATAATTTTTATAGA-TTATAT
*
8580409 ATTTA-AATTTTTTTAGATTATAT
1 ATTTATAATTTTTATAGATTATAT
8580432 AT
1 AT
8580434 ATATTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
ATTTATAATTTTTATAGATTATAT
Found at i:8585168 original size:30 final size:30
Alignment explanation
Indices: 8585132--8585194 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
8585122 ATTTATTTTA
8585132 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
8585162 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
8585192 TTG
1 TTG
8585195 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:8585297 original size:18 final size:18
Alignment explanation
Indices: 8585276--8585315 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
8585266 GAAATATTTA
*
8585276 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
8585294 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
8585312 TTTT
1 TTTT
8585316 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:8591052 original size:17 final size:18
Alignment explanation
Indices: 8591030--8591064 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
8591020 CCCAATAATA
8591030 TCTTCTGCTTTTT-TTTT
1 TCTTCTGCTTTTTGTTTT
*
8591047 TCTTCTTCTTTTTGTTTT
1 TCTTCTGCTTTTTGTTTT
8591065 GCTCTTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (18 bp):
TCTTCTGCTTTTTGTTTT
Found at i:8599199 original size:69 final size:69
Alignment explanation
Indices: 8599107--8599244 Score: 222
Period size: 69 Copynumber: 2.0 Consensus size: 69
8599097 AATAACCTTT
*
8599107 TAAGTAATACTGCAAGAGATTATCAACAAAATTTAACTTATAATCATATGTATTAATTGTTATTA
1 TAAGCAATACTGCAAGAGATTATCAACAAAATTTAACTTATAATCATATGTATTAATTGTTATTA
8599172 CATA
66 CATA
* * * * *
8599176 TAAGCAATATTGCAAGAGATTATCAACAAAATTTAACTTATAATCATTTGTATTAGTTTTTGTTA
1 TAAGCAATACTGCAAGAGATTATCAACAAAATTTAACTTATAATCATATGTATTAATTGTTATTA
8599241 CATA
66 CATA
8599245 ATATAGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.39
Consensus pattern (69 bp):
TAAGCAATACTGCAAGAGATTATCAACAAAATTTAACTTATAATCATATGTATTAATTGTTATTA
CATA
Found at i:8614732 original size:43 final size:43
Alignment explanation
Indices: 8614577--8614734 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 43
8614567 TATGTTGTCG
* *
8614577 TGTAAGACCACGTTTGGGACGTTGGCATTGAT-TTGAGATTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATTGATATT-TGA-TTACA
* * * ***
8614621 TGTAAGACCATGTCTGGGACATTGGCATTG-TATATGATTTTG
1 TGTAAGACCACGTCTGGGACGTTGGCATTGATATTTGATTACA
*
8614663 TGTAAGACC-CTGTCTGGGATAG-TGGCATTGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGA-CGTTGGCATTGATATTTGATTACA
* *
8614706 TGTAAGACCACGTCTAGGATGTTGGCATT
1 TGTAAGACCACGTCTGGGACGTTGGCATT
8614735 ATACGAGCTT
Statistics
Matches: 91, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
42 28 0.31
43 34 0.37
44 29 0.32
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.35
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATTGATATTTGATTACA
Found at i:8619223 original size:44 final size:44
Alignment explanation
Indices: 8619160--8619247 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
8619150 CATCAAGACT
8619160 GAAGATCTCCCTTCAAATTCCCTCAAG-AGTTTTGGGTTTTCTTA
1 GAAGATCTCCCTTCAAATTCCCT-AAGAAGTTTTGGGTTTTCTTA
*
8619204 GAAGATCTCCCTTCAAATTCCCTTAGAAGTTTTGGGTTTTCTTA
1 GAAGATCTCCCTTCAAATTCCCTAAGAAGTTTTGGGTTTTCTTA
8619248 TGTTTTGTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.40
Consensus pattern (44 bp):
GAAGATCTCCCTTCAAATTCCCTAAGAAGTTTTGGGTTTTCTTA
Found at i:8620462 original size:20 final size:20
Alignment explanation
Indices: 8620437--8620476 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
8620427 CTCGTAGCTG
8620437 ATGCATGTCCCAGACATGTC
1 ATGCATGTCCCAGACATGTC
*
8620457 ATGCATGTCCCAGACCTGTC
1 ATGCATGTCCCAGACATGTC
8620477 TTACACTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.25
Consensus pattern (20 bp):
ATGCATGTCCCAGACATGTC
Found at i:8622983 original size:23 final size:22
Alignment explanation
Indices: 8622939--8622980 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
8622929 TATTTTAAAA
8622939 AAAAAGGAAAATTATATATATT
1 AAAAAGGAAAATTATATATATT
*
8622961 AAAAA-GAAAAGTATATATAT
1 AAAAAGGAAAATTATATATAT
8622981 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (22 bp):
AAAAAGGAAAATTATATATATT
Found at i:8624655 original size:104 final size:105
Alignment explanation
Indices: 8624457--8624718 Score: 305
Period size: 104 Copynumber: 2.4 Consensus size: 105
8624447 TTTTTAACTT
* * *
8624457 TAAATCCAATCAAAATTAAATATGACAAATTTAAAAGAAAAGCAGTTGTAAATGCACCTTTCAAT
1 TAAATCCAATCGAAATTAAATATG----ATTTAAAAGAAAAGCAATTGTAAATGCACCTTTCAAC
* * **
8624522 AACTACCATGAAGTTTCTTTTAAATTGTTAAGGGTACTTCACTC
62 AACTACCATGAAGTTTATTTGAAATTGTTAAAAGTACTTCACTC
* * * *
8624566 TAAATCCAATCGAAATTAAATATGA-TTAAAGGAAAATCAATTGTAAATGTACCTTTCAACAGCT
1 TAAATCCAATCGAAATTAAATATGATTTAAAAGAAAAGCAATTGTAAATGCACCTTTCAACAACT
*
8624630 ACCATGAAGTTTATTTGAAGA-TGTTAAAAGTACTTCATTC
66 ACCATGAAGTTTATTTGAA-ATTGTTAAAAGTACTTCACTC
*
8624670 TAAAT-CAATCGAAATTAAATATGACGTATTTAAAAGAAAATCAATTGTA
1 TAAATCCAATCGAAATTAAATAT---G-ATTTAAAAGAAAAGCAATTGTA
8624719 TAGTAAATGT
Statistics
Matches: 134, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
103 17 0.13
104 71 0.53
105 2 0.01
106 1 0.01
107 1 0.01
108 19 0.14
109 23 0.17
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.32
Consensus pattern (105 bp):
TAAATCCAATCGAAATTAAATATGATTTAAAAGAAAAGCAATTGTAAATGCACCTTTCAACAACT
ACCATGAAGTTTATTTGAAATTGTTAAAAGTACTTCACTC
Found at i:8625054 original size:29 final size:29
Alignment explanation
Indices: 8625031--8625087 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
8625021 TATTATTGTT
*
8625031 ATTATTTTATTATATTAT-AAATTAAATTG
1 ATTATATTATTATATTATGAAATT-AATTG
*
8625060 ATTATATTATTATATTATGAAATAAATT
1 ATTATATTATTATATTATGAAATTAATT
8625088 AAGAAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (29 bp):
ATTATATTATTATATTATGAAATTAATTG
Found at i:8625188 original size:33 final size:32
Alignment explanation
Indices: 8625146--8625217 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 32
8625136 AAATGAGTAC
8625146 ATTTGTATTATTTA-TATATAATTAGTAAAGAGAT
1 ATTT-TATTATTTATTAT-TAATTAGTAAA-AGAT
8625180 ATTTTATTATTTATTATTAATTAGTAAAAGAT
1 ATTTTATTATTTATTATTAATTAGTAAAAGAT
8625212 -TTTTAT
1 ATTTTAT
8625218 ATGATAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.16
32 4 0.11
33 20 0.54
34 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (32 bp):
ATTTTATTATTTATTATTAATTAGTAAAAGAT
Found at i:8625227 original size:144 final size:142
Alignment explanation
Indices: 8625069--8625340 Score: 307
Period size: 144 Copynumber: 1.9 Consensus size: 142
8625059 GATTATATTA
* * * *
8625069 TTATATTATGAAATAAATTAAGAAA-A-GACAAGTGTAAGGTAAAAATAAAATACAAGTGTATTA
1 TTATATGATGAAATAAATT--GAAATATGACAAGTGGAAGGTAAAAATAAAATACAAATGTA-AA
* * * *
8625132 ATTTAAATGAGTACATTTGTATTATTTATATATAATTAGTAAAGAGATATTTTATTATTTATTAT
63 ATATAAATGAGTACATTTGTAATATTTATAT-TAATTAGTAAAGAAATATTTAATTA-TTATTAT
8625197 TAATTAGTAAAAGATTT
126 TAATTAGTAAAAGATTT
* * * *
8625214 TTATATGAT-AAATAAATTGAAATTATGATAAGTGGATGGTGATAATAAAATACAAATGTAAAAT
1 TTATATGATGAAATAAATTGAAA-TATGACAAGTGGAAGGTAAAAATAAAATACAAATGTAAAAT
* * ** * *
8625278 ATATATGTGTACATTTGTAATATTTATATTTGTTATTAAATAAATATTTAATTATTATTATTA
65 ATAAATGAGTACATTTGTAATATTTATATTAATTAGTAAAGAAATATTTAATTATTATTATTA
8625341 TTTATTTGAT
Statistics
Matches: 106, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
142 13 0.12
143 19 0.18
144 38 0.36
145 36 0.34
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (142 bp):
TTATATGATGAAATAAATTGAAATATGACAAGTGGAAGGTAAAAATAAAATACAAATGTAAAATA
TAAATGAGTACATTTGTAATATTTATATTAATTAGTAAAGAAATATTTAATTATTATTATTAATT
AGTAAAAGATTT
Found at i:8626432 original size:44 final size:44
Alignment explanation
Indices: 8626364--8626453 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
8626354 TGTTCAGAGA
* *
8626364 TACTTCGACCTCGAGTCGATGAGGCA-CTATAG-GTGTCGTACTGT
1 TACTTCGACCTCAAGTCGACGAGGCACCT-T-GTGTGTCGTACTGT
*
8626408 TACTTCGACTTCAAGTCGACGAGGCACCTTGTGTGTCGTACTGT
1 TACTTCGACCTCAAGTCGACGAGGCACCTTGTGTGTCGTACTGT
8626452 TA
1 TA
8626454 TTATTACTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 38 0.93
45 2 0.05
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (44 bp):
TACTTCGACCTCAAGTCGACGAGGCACCTTGTGTGTCGTACTGT
Found at i:8626705 original size:18 final size:18
Alignment explanation
Indices: 8626611--8626707 Score: 67
Period size: 18 Copynumber: 5.4 Consensus size: 18
8626601 ACTACTGTAC
* *
8626611 TGAATAATTGATAGTTAT
1 TGAATAACTGATTGTTAT
* * *
8626629 TGAATAACTAAATTACTGTAC
1 TGAATAACT-GATT-GT-TAT
8626650 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
* * *
8626668 TG-AT---TGTTTGATAC
1 TGAATAACTGATTGTTAT
8626682 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
8626700 TGAATAAC
1 TGAATAAC
8626708 AATAAGCAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
14 9 0.16
15 2 0.03
17 2 0.03
18 27 0.47
19 3 0.05
20 4 0.07
21 11 0.19
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.41
Consensus pattern (18 bp):
TGAATAACTGATTGTTAT
Found at i:8628033 original size:30 final size:30
Alignment explanation
Indices: 8627999--8628061 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
8627989 ACTTAACAAG
8627999 CAAATGCCTCTAAAATAATAAC-AAAATTAA
1 CAAATGCCTCTAAAATAAT-ACTAAAATTAA
*
8628029 CAAATGCCTTTAAAATAATACTAAAATTAA
1 CAAATGCCTCTAAAATAATACTAAAATTAA
8628059 CAA
1 CAA
8628062 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATACTAAAATTAA
Found at i:8632980 original size:31 final size:31
Alignment explanation
Indices: 8632945--8633019 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
8632935 TTTAACGACC
* **
8632945 TAGTGACTTAAATAAAAACTTTTGAGTGGTT
1 TAGTGACTTAAATAAAAACTTTTGAATAATT
**
8632976 TAGTGACTTAAATAAAATTTTTTGAATAATT
1 TAGTGACTTAAATAAAAACTTTTGAATAATT
*
8633007 TAATGACTTAAAT
1 TAGTGACTTAAAT
8633020 GAAACATTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.41
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTTTGAATAATT
Found at i:8635747 original size:3 final size:3
Alignment explanation
Indices: 8635739--8635778 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
8635729 TAGTTTACTC
8635739 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
8635779 AAGCTTGATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:8636131 original size:3 final size:3
Alignment explanation
Indices: 8636123--8636165 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
8636113 CGTATCCTTC
8636123 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
8636166 GTCATATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:8636473 original size:29 final size:29
Alignment explanation
Indices: 8636378--8636474 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
8636368 CACATGCCCA
*
8636378 TGTTTTCATAGTTATATGTATCTCAT-CT
1 TGTTTTCATAGTTATATTTATCTCATGCT
* * * * * * *
8636406 TGGTTACATTAGCTTTTATTAATTTAAATGACCA
1 TGTTTTCA-TAG-TTATATTTATCT-CATG--CT
8636440 TGTTTTCATAGTTATATTTATCTCATGCT
1 TGTTTTCATAGTTATATTTATCTCATGCT
8636469 TGTTTT
1 TGTTTT
8636475 TAAAAAAGGA
Statistics
Matches: 48, Mismatches: 15, Indels: 11
0.65 0.20 0.15
Matches are distributed among these distances:
28 6 0.12
29 10 0.21
30 8 0.17
31 5 0.10
32 9 0.19
33 3 0.06
34 7 0.15
ACGTcount: A:0.24, C:0.12, G:0.11, T:0.53
Consensus pattern (29 bp):
TGTTTTCATAGTTATATTTATCTCATGCT
Found at i:8642150 original size:18 final size:18
Alignment explanation
Indices: 8642127--8642188 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
8642117 ATATAGATAT
8642127 ATATATAATAAGATATAA
1 ATATATAATAAGATATAA
* *
8642145 ATATATGATAAGATGATAT
1 ATATATAATAAGAT-ATAA
*
8642164 ATATA-AAT-AGTTAT-A
1 ATATATAATAAGATATAA
8642179 ATA-ATAATAA
1 ATATATAATAA
8642189 TAATAATAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 3 0.08
17 3 0.08
18 15 0.42
19 8 0.22
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (18 bp):
ATATATAATAAGATATAA
Found at i:8656636 original size:41 final size:40
Alignment explanation
Indices: 8656591--8656702 Score: 118
Period size: 41 Copynumber: 2.8 Consensus size: 40
8656581 AGGTAAAACG
8656591 GTAGCGACGTTTATGAGAAAAATGCCGCAAAAGGTCAAGCA
1 GTAGCGACGTTTATGAGAAAAATGCCGCAAAAGGT-AAGCA
** * *
8656632 GTAGCGGTGTTTATGAGAAAAATGCTGTAAAAGGTAAGCA
1 GTAGCGACGTTTATGAGAAAAATGCCGCAAAAGGTAAGCA
* * * * *
8656672 ATAGC-AGCATTTTTGATAAAAACGCCGCAAA
1 GTAGCGA-CGTTTATGAGAAAAATGCCGCAAA
8656703 GTATCATTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
40 26 0.46
41 31 0.54
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (40 bp):
GTAGCGACGTTTATGAGAAAAATGCCGCAAAAGGTAAGCA
Found at i:8656693 original size:40 final size:41
Alignment explanation
Indices: 8656600--8656702 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 41
8656590 GGTAGCGACG
* * **
8656600 TTTATGAGAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGTG
1 TTTATGAGAAAAATGCCGCAAAAGGTCAAGCAATAGCAGCA
* *
8656641 TTTATGAGAAAAATGCTGTAAAAGGT-AAGCAATAGCAGCA
1 TTTATGAGAAAAATGCCGCAAAAGGTCAAGCAATAGCAGCA
* * *
8656681 TTTTTGATAAAAACGCCGCAAA
1 TTTATGAGAAAAATGCCGCAAA
8656703 GTATCATTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 27 0.53
41 24 0.47
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (41 bp):
TTTATGAGAAAAATGCCGCAAAAGGTCAAGCAATAGCAGCA
Found at i:8657902 original size:25 final size:25
Alignment explanation
Indices: 8657873--8657920 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
8657863 TATTAGCTCA
8657873 ATTTTTATTATTTCATTTAACAATT
1 ATTTTTATTATTTCATTTAACAATT
*
8657898 ATTTTTATTATTTCATTTTACAA
1 ATTTTTATTATTTCATTTAACAA
8657921 AATCCTGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTTATTATTTCATTTAACAATT
Found at i:8663606 original size:36 final size:36
Alignment explanation
Indices: 8663565--8663641 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
8663555 AACTTTAGAT
*
8663565 CATAACTTATATAAATATATATCATATCATAACTTA
1 CATAACTTACATAAATATATATCATATCATAACTTA
8663601 CATAACTTACATAAATATATATCATATCATAACTTA
1 CATAACTTACATAAATATATATCATATCATAACTTA
8663637 CATAA
1 CATAA
8663642 AACTTTGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (36 bp):
CATAACTTACATAAATATATATCATATCATAACTTA
Found at i:8677109 original size:18 final size:18
Alignment explanation
Indices: 8677058--8677110 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
8677048 CAGTTACTCT
*
8677058 ATAACAGTCAATTATACA
1 ATAACAGTCAATTATTCA
*
8677076 ATAACAGTCATTTATTCA
1 ATAACAGTCAATTATTCA
* *
8677094 GTAACAGTCACTTATTC
1 ATAACAGTCAATTATTC
8677111 TGCAGCAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (18 bp):
ATAACAGTCAATTATTCA
Found at i:8678434 original size:32 final size:31
Alignment explanation
Indices: 8678387--8678450 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
8678377 TCTACATTTT
* *
8678387 TCATAATTAATTTATTTACTTATATAATTATC
1 TCATAATTAATTTATTTAATTA-ATAAATATC
8678419 TCATAATATAA-TTATTTAATTAATAAATATC
1 TCATAAT-TAATTTATTTAATTAATAAATATC
8678450 T
1 T
8678451 AGTAATACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 9 0.31
32 17 0.59
33 3 0.10
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (31 bp):
TCATAATTAATTTATTTAATTAATAAATATC
Found at i:8688675 original size:19 final size:19
Alignment explanation
Indices: 8688653--8688689 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
8688643 AGACTTATGA
8688653 CATGTTTTAACTTTTATTG
1 CATGTTTTAACTTTTATTG
8688672 CATGTTTTAACTTTTATT
1 CATGTTTTAACTTTTATT
8688690 TTCTTTTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.59
Consensus pattern (19 bp):
CATGTTTTAACTTTTATTG
Found at i:8690676 original size:30 final size:30
Alignment explanation
Indices: 8690630--8690689 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
8690620 TTCCCGAGCC
*
8690630 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
8690660 TAGGGGTAAAAATGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
8690690 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:8695409 original size:31 final size:31
Alignment explanation
Indices: 8695351--8695432 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 31
8695341 TAGTTGATGA
* * **
8695351 AAAAAAATTGAA-TATCAATTTGGGATAAA-
1 AAAAAAATTCAAGTAACAATTTAAGATAAAT
* *
8695380 AAAAAAACTTTAAGTACCAATTTAAGATAAAT
1 AAAAAAA-TTCAAGTAACAATTTAAGATAAAT
*
8695412 AAACAAATTCAAGTAACAATT
1 AAAAAAATTCAAGTAACAATT
8695433 ATATATTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 7 0.16
30 4 0.09
31 26 0.60
32 6 0.14
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.27
Consensus pattern (31 bp):
AAAAAAATTCAAGTAACAATTTAAGATAAAT
Found at i:8696904 original size:25 final size:25
Alignment explanation
Indices: 8696876--8696994 Score: 95
Period size: 25 Copynumber: 4.7 Consensus size: 25
8696866 ATCGGATTAT
*
8696876 TTTTATATATATTTATTTTAACTTG
1 TTTTATATATATTTATTTTAAATTG
* **
8696901 TTTTATGTACT-TTTATTCGAAATTG
1 TTTTATATA-TATTTATTTTAAATTG
8696926 TTTTAT-TATA--TATTTTAAATTG
1 TTTTATATATATTTATTTTAAATTG
* *
8696948 CCTTATATATATTTATTTATTTCTAAATTA
1 --TT-T-TATATATATTTATTT-TAAATTG
8696978 TTTTATATATA-TTATTT
1 TTTTATATATATTTATTT
8696995 ATTTTAGATT
Statistics
Matches: 75, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
22 10 0.13
23 1 0.01
24 4 0.05
25 32 0.43
26 11 0.15
27 4 0.05
28 2 0.03
29 5 0.07
30 6 0.08
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTTATATATATTTATTTTAAATTG
Found at i:8696968 original size:29 final size:28
Alignment explanation
Indices: 8696929--8697000 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
8696919 GAAATTGTTT
* *
8696929 TATTATATATTTTAAATTGCCTTATATA
1 TATTATTTATTTTAAATTACCTTATATA
**
8696957 TATTTATTTATTTCTAAATTATTTTATATA
1 TA-TTATTTATTT-TAAATTACCTTATATA
8696987 TATTATTTATTTTA
1 TATTATTTATTTTA
8697001 GATTCTTTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 4 0.11
29 19 0.50
30 15 0.39
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (28 bp):
TATTATTTATTTTAAATTACCTTATATA
Found at i:8697163 original size:24 final size:25
Alignment explanation
Indices: 8697132--8697189 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
8697122 TAGTATATAA
*
8697132 ATTTTAAACTAACTT-ATATTACTT
1 ATTTTAAACTAACTTCATATGACTT
* * *
8697156 ATTTTAAA-TTATTTCATATGCCTT
1 ATTTTAAACTAACTTCATATGACTT
8697180 ATTTTAAACT
1 ATTTTAAACT
8697190 CTTTTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 4 0.14
24 23 0.82
25 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTTAAACTAACTTCATATGACTT
Found at i:8697254 original size:24 final size:25
Alignment explanation
Indices: 8697196--8697254 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
8697186 AACTCTTTTC
* *
8697196 ATTTATTTTAAATTTTATTATTATT
1 ATTTATTTTAAATTCTATTATTAAT
*
8697221 ATTTACTTTAATATTCT-TTA-TAAT
1 ATTTATTTTAA-ATTCTATTATTAAT
8697245 ATTTATTTTA
1 ATTTATTTTA
8697255 CACTTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 12 0.41
25 13 0.45
26 4 0.14
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTATTTTAAATTCTATTATTAAT
Found at i:8697284 original size:30 final size:31
Alignment explanation
Indices: 8697225--8697284 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
8697215 ATTATTATTT
* *
8697225 ACTTTAATATTCTTTATAATATTTATTTTAC
1 ACTTTAATATTCTATATAATATCTATTTTAC
* *
8697256 ACTTTTATATT-TATATATTATCTATTTTA
1 ACTTTAATATTCTATATAATATCTATTTTA
8697285 AAATTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (31 bp):
ACTTTAATATTCTATATAATATCTATTTTAC
Found at i:8697291 original size:28 final size:26
Alignment explanation
Indices: 8697260--8697321 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 26
8697250 TTTTACACTT
8697260 TTATATTTATATATTATCTATTTTAAAA
1 TTATATTTATATA--ATCTATTTTAAAA
*
8697288 TTATA--TATATAATCTATTTTTAAA
1 TTATATTTATATAATCTATTTTAAAA
*
8697312 TCAT-TTTATA
1 TTATATTTATA
8697322 CATAGTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 15 0.50
25 4 0.13
26 6 0.20
28 5 0.17
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATATTTATATAATCTATTTTAAAA
Found at i:8697302 original size:24 final size:24
Alignment explanation
Indices: 8697267--8697312 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
8697257 CTTTTATATT
*
8697267 TATATATTATCTATTTTAAAATTA
1 TATATATAATCTATTTTAAAATTA
*
8697291 TATATATAATCTATTTTTAAAT
1 TATATATAATCTATTTTAAAAT
8697313 CATTTTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
TATATATAATCTATTTTAAAATTA
Found at i:8700669 original size:6 final size:6
Alignment explanation
Indices: 8700658--8700687 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
8700648 TGCAAGTTAT
*
8700658 TTGTAA TTGTAA TTGTAA TTGTAA TAGTAA
1 TTGTAA TTGTAA TTGTAA TTGTAA TTGTAA
8700688 AAAGGAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.47
Consensus pattern (6 bp):
TTGTAA
Found at i:8701104 original size:17 final size:18
Alignment explanation
Indices: 8701064--8701104 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
8701054 CTTTTAATTT
*
8701064 TTTAAC-AAAAATTATGA
1 TTTAACAAAAAAATATGA
8701081 TTT-ACAAAAAAATAT-A
1 TTTAACAAAAAAATATGA
8701097 TTTAACAA
1 TTTAACAA
8701105 TAGAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (18 bp):
TTTAACAAAAAAATATGA
Found at i:8704928 original size:37 final size:38
Alignment explanation
Indices: 8704877--8704961 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 38
8704867 GAATTCGAAT
8704877 TATTTAAATCATCGTTGTACT-AAAATATATAAACATA
1 TATTTAAATCATCGTTGTACTAAAAATATATAAACATA
*
8704914 TATTTAAATTATCGTTGTACTAAAAAATATATAAACATA
1 TATTTAAATCATCGTTGTACT-AAAAATATATAAACATA
8704953 TATTTAAAT
1 TATTTAAAT
8704962 ATTAAAATGC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 20 0.44
39 25 0.56
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (38 bp):
TATTTAAATCATCGTTGTACTAAAAATATATAAACATA
Found at i:8711639 original size:17 final size:16
Alignment explanation
Indices: 8711617--8711649 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
8711607 TGTACTTGGT
8711617 AGAAAATAAAAGTGAGA
1 AGAAAATAAAA-TGAGA
8711634 AGAAAATAAAATGAGA
1 AGAAAATAAAATGAGA
8711650 GATCATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (16 bp):
AGAAAATAAAATGAGA
Found at i:8716850 original size:13 final size:15
Alignment explanation
Indices: 8716819--8716854 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
8716809 GTATTTAGTC
8716819 TTATTTTTATATATT
1 TTATTTTTATATATT
8716834 TTATTTTTAT-T-TT
1 TTATTTTTATATATT
8716847 TTATTTTT
1 TTATTTTT
8716855 GGGAATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
14 1 0.05
15 10 0.48
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TTATTTTTATATATT
Found at i:8722684 original size:13 final size:13
Alignment explanation
Indices: 8722666--8722691 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8722656 CTATAAATGT
8722666 TTTTGCAATGTTG
1 TTTTGCAATGTTG
8722679 TTTTGCAATGTTG
1 TTTTGCAATGTTG
8722692 GGTAGTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (13 bp):
TTTTGCAATGTTG
Found at i:8723376 original size:30 final size:31
Alignment explanation
Indices: 8723342--8723443 Score: 131
Period size: 30 Copynumber: 3.4 Consensus size: 31
8723332 TAAAAAATAA
*
8723342 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
8723372 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
*
8723402 AAATTTCATTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
8723432 AAATTTCATTTT
1 AAATTTCATTTT
8723444 AATCATAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
29 4 0.06
30 59 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:8723826 original size:3 final size:3
Alignment explanation
Indices: 8723818--8723889 Score: 90
Period size: 3 Copynumber: 22.0 Consensus size: 3
8723808 GCTCGGTTTT
8723818 GAA GAA GAA GAA GAA GGAA GAA GAA GAA GGAA GAA GAA GAA GAA GAAA
1 GAA GAA GAA GAA GAA -GAA GAA GAA GAA -GAA GAA GAA GAA GAA G-AA
8723866 GAAA GAGA GAA GAA GAAA GAA GAA
1 G-AA GA-A GAA GAA G-AA GAA GAA
8723890 AAAAAAAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
3 45 0.70
4 19 0.30
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:8723839 original size:10 final size:9
Alignment explanation
Indices: 8723818--8723889 Score: 90
Period size: 10 Copynumber: 7.3 Consensus size: 9
8723808 GCTCGGTTTT
8723818 GAAGAAGAA
1 GAAGAAGAA
8723827 GAAGAAGGAA
1 GAAGAA-GAA
8723837 GAAGAAGAA
1 GAAGAAGAA
8723846 GGAAGAAGAA
1 -GAAGAAGAA
8723856 GAAGAAGAAA
1 GAAGAAG-AA
8723866 GAAAGAGAGAA
1 G-AAGA-AGAA
8723877 GAAGAAAGAA
1 GAAG-AAGAA
8723887 GAA
1 GAA
8723890 AAAAAAAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
9 16 0.28
10 31 0.54
11 8 0.14
12 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (9 bp):
GAAGAAGAA
Found at i:8723839 original size:13 final size:13
Alignment explanation
Indices: 8723819--8723889 Score: 94
Period size: 13 Copynumber: 5.6 Consensus size: 13
8723809 CTCGGTTTTG
8723819 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
*
8723832 AGGAAGAAGAAGA
1 AAGAAGAAGAAGA
*
8723845 AGGAAGAAGAAG-
1 AAGAAGAAGAAGA
8723857 AAGAAG-A-AAGA
1 AAGAAGAAGAAGA
8723868 AAGAGAGAAGAAGA
1 AAGA-AGAAGAAGA
8723882 AAGAAGAA
1 AAGAAGAA
8723890 AAAAAAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
10 3 0.06
11 5 0.10
12 7 0.13
13 29 0.56
14 8 0.15
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:8723979 original size:18 final size:18
Alignment explanation
Indices: 8723942--8723984 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
8723932 AACCGGGTAT
* * *
8723942 AACCCGACCCGATCCGGC
1 AACCCAACCCGACCCAGC
8723960 AACCCAACCCGACCCAGC
1 AACCCAACCCGACCCAGC
8723978 AAGCCCA
1 AA-CCCA
8723985 TTAGCCAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.30, C:0.51, G:0.16, T:0.02
Consensus pattern (18 bp):
AACCCAACCCGACCCAGC
Found at i:8724030 original size:11 final size:11
Alignment explanation
Indices: 8724009--8724041 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
8723999 AGTAGCCCAA
8724009 CAAAAAAAAAG
1 CAAAAAAAAAG
8724020 -AAAAAACAAAG
1 CAAAAAA-AAAG
8724031 CAAAAAAAAAG
1 CAAAAAAAAAG
8724042 GGGAAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.30
11 8 0.40
12 6 0.30
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAG
Found at i:8724206 original size:11 final size:10
Alignment explanation
Indices: 8724170--8724208 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
8724160 CAGCCCAGCA
8724170 AAAAAAAAAGG
1 AAAAAAAAA-G
8724181 AAGAAAAAAAG
1 AA-AAAAAAAG
*
8724192 AAAAAACAAG
1 AAAAAAAAAG
8724202 AAAAAAA
1 AAAAAAA
8724209 GGGGTTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 13 0.52
11 5 0.20
12 7 0.28
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:8724370 original size:5 final size:5
Alignment explanation
Indices: 8724360--8724392 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
8724350 CATTTATATT
8724360 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
8724393 TTATTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:8724405 original size:6 final size:6
Alignment explanation
Indices: 8724389--8724421 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
8724379 ATTTAATTTA
8724389 ATTTTT A-TTTT ATTTTT ATTTTT A-TTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
8724422 AAATACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:8724422 original size:10 final size:10
Alignment explanation
Indices: 8724359--8724420 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 10
8724349 GCATTTATAT
8724359 TTTTAATTTAA
1 TTTT-ATTTAA
*
8724370 TTTAATTTAA
1 TTTTATTTAA
*
8724380 TTTAATTTAA
1 TTTTATTTAA
*
8724390 TTTTTATTTTAT
1 -TTTTA-TTTAA
*
8724402 TTTTATTTTTA
1 TTTTA-TTTAA
8724413 TTTTATTT
1 TTTTATTT
8724421 TAAATACTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
10 19 0.43
11 21 0.48
12 4 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:8725732 original size:55 final size:55
Alignment explanation
Indices: 8725661--8725825 Score: 321
Period size: 55 Copynumber: 3.0 Consensus size: 55
8725651 TTGCAATCAT
*
8725661 TTTATTCTTAAGTAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTG
1 TTTATTCTTAAATAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTG
8725716 TTTATTCTTAAATAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTG
1 TTTATTCTTAAATAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTG
8725771 TTTATTCTTAAATAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTG
1 TTTATTCTTAAATAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTG
8725826 CTTAATTTTC
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 109 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (55 bp):
TTTATTCTTAAATAATACAATACATTTGAGAGTATTTATTCAAATACGTGGTGTG
Found at i:8743760 original size:9 final size:9
Alignment explanation
Indices: 8743743--8743779 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
8743733 TGAGTTTTCG
8743743 AATTCGAAT
1 AATTCGAAT
*
8743752 AACTCGAAT
1 AATTCGAAT
8743761 AATTCGAAT
1 AATTCGAAT
8743770 AATTCGAAT
1 AATTCGAAT
8743779 A
1 A
8743780 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:8745048 original size:25 final size:25
Alignment explanation
Indices: 8745014--8745065 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
8745004 TGATTTGGAG
*
8745014 AATGACTATTTCTTGGTAAAGTTCC
1 AATGAATATTTCTTGGTAAAGTTCC
*
8745039 AATGAATATTTCTTGGTCAAGTTCC
1 AATGAATATTTCTTGGTAAAGTTCC
8745064 AA
1 AA
8745066 AATGATGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (25 bp):
AATGAATATTTCTTGGTAAAGTTCC
Found at i:8749230 original size:46 final size:46
Alignment explanation
Indices: 8749049--8749230 Score: 249
Period size: 46 Copynumber: 4.0 Consensus size: 46
8749039 TTTGACATGA
* * * *
8749049 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT
* ** * *
8749095 TGCCATGGTATCTTTCAACTATGGTCTTGTTCATTTCATATTACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
8749141 TGCCATGGTATCTTTCAACCATGGTCTTACGCATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
8749187 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
8749231 AGAGCACACT
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
45 4 0.03
46 118 0.97
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
Found at i:8750410 original size:17 final size:17
Alignment explanation
Indices: 8750385--8750418 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
8750375 ATAGGACTCC
*
8750385 AAAATTTTAAGAATTTT
1 AAAACTTTAAGAATTTT
8750402 AAAACTTTAAGAATTTT
1 AAAACTTTAAGAATTTT
8750419 TGGTTTATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
AAAACTTTAAGAATTTT
Found at i:8754530 original size:25 final size:26
Alignment explanation
Indices: 8754502--8754567 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 26
8754492 CACTACCGAT
8754502 CAGGATGCTCGTAGGA-ACCATATAA
1 CAGGATGCTCGTAGGAGACCATATAA
* ** *
8754527 CAGGAAGCTCG-A-GAGGGCTTATAA
1 CAGGATGCTCGTAGGAGACCATATAA
8754551 CAGGATGCTCGTAGGAG
1 CAGGATGCTCGTAGGAG
8754568 TTATGGTGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
23 2 0.06
24 17 0.52
25 11 0.33
26 3 0.09
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (26 bp):
CAGGATGCTCGTAGGAGACCATATAA
Found at i:8754904 original size:21 final size:21
Alignment explanation
Indices: 8754880--8754921 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8754870 AACTTAACAC
* *
8754880 CAATTTAATAAAATTCACATT
1 CAATTCAACAAAATTCACATT
*
8754901 CAATTCAACCAAATTCACATT
1 CAATTCAACAAAATTCACATT
8754922 TAGGCAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (21 bp):
CAATTCAACAAAATTCACATT
Found at i:8757300 original size:18 final size:19
Alignment explanation
Indices: 8757259--8757309 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
8757249 TTTTAGAATT
* *
8757259 ATTTTATATATTTTTTAGA
1 ATTTTATATATTTTTAAAA
*
8757278 TTTTTA-ATATTTTTAAAA
1 ATTTTATATATTTTTAAAA
8757296 ATTTTATA-ATTTTT
1 ATTTTATATATTTTT
8757310 TTCAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTATATATTTTTAAAA
Found at i:8757339 original size:18 final size:19
Alignment explanation
Indices: 8757318--8757354 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
8757308 TTTTCAAAAA
8757318 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
8757336 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
8757355 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:8767267 original size:19 final size:19
Alignment explanation
Indices: 8767243--8767282 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
8767233 TAGGTCTCAA
8767243 CAACATGAAGAGGCAAAAG
1 CAACATGAAGAGGCAAAAG
*
8767262 CAACATGAAGAGGTAAAAG
1 CAACATGAAGAGGCAAAAG
8767281 CA
1 CA
8767283 TTTATTGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.15, G:0.25, T:0.07
Consensus pattern (19 bp):
CAACATGAAGAGGCAAAAG
Found at i:8772567 original size:13 final size:12
Alignment explanation
Indices: 8772513--8772573 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
8772503 TTGGCTATGT
8772513 TTTTGAAAAGTAG
1 TTTTGAAAAGT-G
*
8772526 TTTTGAGAAGTG
1 TTTTGAAAAGTG
* *
8772538 TTGTGGAAAATTG
1 TT-TTGAAAAGTG
*
8772551 CTTTTGAGAAGTG
1 -TTTTGAAAAGTG
8772564 CTTTTGAAAA
1 -TTTTGAAAA
8772574 CTTTAGTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
12 3 0.08
13 33 0.87
14 2 0.05
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.39
Consensus pattern (12 bp):
TTTTGAAAAGTG
Found at i:8772572 original size:26 final size:25
Alignment explanation
Indices: 8772513--8772573 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
8772503 TTGGCTATGT
8772513 TTTTGAAAAGTAGTTTTGAGAAGTG
1 TTTTGAAAAGTAGTTTTGAGAAGTG
* *
8772538 TTGTGGAAAA-TTGCTTTTGAGAAGTG
1 TT-TTGAAAAGTAG-TTTTGAGAAGTG
8772564 CTTTTGAAAA
1 -TTTTGAAAA
8772574 CTTTAGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.13
26 24 0.80
27 2 0.07
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.39
Consensus pattern (25 bp):
TTTTGAAAAGTAGTTTTGAGAAGTG
Found at i:8781992 original size:14 final size:14
Alignment explanation
Indices: 8781968--8782004 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
8781958 TGCTACCACT
8781968 AAAAT-ATTTTTCA
1 AAAATAATTTTTCA
*
8781981 AAAATAATTTTTGA
1 AAAATAATTTTTCA
8781995 AAAATAATTT
1 AAAATAATTT
8782005 ATTTTTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (14 bp):
AAAATAATTTTTCA
Found at i:8782139 original size:20 final size:20
Alignment explanation
Indices: 8782116--8782155 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
8782106 CTATTTTTAA
8782116 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
8782136 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
8782156 TTTAAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:8782160 original size:16 final size:18
Alignment explanation
Indices: 8782111--8782155 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
8782101 AAAAACTATT
* *
8782111 TTTAAATATATTAATAAA
1 TTTATATATTTTAATAAA
8782129 TTTATATATATATTAATAAA
1 TTTATATAT-T-TTAATAAA
8782149 TTTATAT
1 TTTATAT
8782156 TTTAAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATTTTAATAAA
Found at i:8783015 original size:15 final size:15
Alignment explanation
Indices: 8782995--8783046 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
8782985 ACCAGAAAAC
8782995 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
8783010 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
8783029 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
8783044 ATT
1 ATT
8783047 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:8783117 original size:13 final size:13
Alignment explanation
Indices: 8783075--8783120 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
8783065 TAATAGATCA
*
8783075 AAAATATTATTTA
1 AAAATATTATTTT
8783088 AAAATATTATTTCT
1 AAAATATTATTT-T
8783102 AAAAT-TTATTATT
1 AAAATATTATT-TT
8783115 AAAATA
1 AAAATA
8783121 AAATTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 23 0.79
14 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATATTATTTT
Found at i:8783148 original size:20 final size:20
Alignment explanation
Indices: 8783123--8783162 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
8783113 TTAAAATAAA
*
8783123 ATTAAAATATTAAATAATTT
1 ATTAAAATAATAAATAATTT
*
8783143 ATTAAAATAATAAATTATTT
1 ATTAAAATAATAAATAATTT
8783163 TAATAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAAATAATAAATAATTT
Found at i:8783155 original size:34 final size:33
Alignment explanation
Indices: 8783110--8783248 Score: 91
Period size: 29 Copynumber: 4.3 Consensus size: 33
8783100 CTAAAATTTA
8783110 TTATTAAAAT-A-AAATTAAAATATTAAATAAT
1 TTATTAAAATAATAAATTAAAATATTAAATAAT
*
8783141 TTATTAAAATAATAAATT---AT-TTTAATAAT
1 TTATTAAAATAATAAATTAAAATATTAAATAAT
*
8783170 TTATT-ATATGAATAAA-TATAAATAATTAAATATAT
1 TTATTAAAAT-AATAAATTA-AAAT-ATTAAATA-AT
* * *
8783205 ATTTTTAATAATATTTTAAATTAAAATTTTAAAT-AT
1 -TTATTAA-AATA--ATAAATTAAAATATTAAATAAT
8783241 TT-TTAAAA
1 TTATTAAAA
8783249 ATAAAAGTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 30
0.70 0.06 0.25
Matches are distributed among these distances:
28 4 0.05
29 19 0.22
30 2 0.02
31 10 0.12
32 3 0.04
33 7 0.08
34 10 0.12
35 4 0.05
36 6 0.07
37 2 0.02
38 8 0.09
39 8 0.09
40 2 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
TTATTAAAATAATAAATTAAAATATTAAATAAT
Found at i:8783183 original size:16 final size:15
Alignment explanation
Indices: 8783135--8783184 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
8783125 TAAAATATTA
*
8783135 AATAATTTATTAAAAT
1 AATAATTTATT-ATAT
*
8783151 AATAAATTATT-T-T
1 AATAATTTATTATAT
8783164 AATAATTTATTATAT
1 AATAATTTATTATAT
8783179 GAATAA
1 -AATAA
8783185 ATATAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
15 1 0.04
16 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
AATAATTTATTATAT
Found at i:8788511 original size:18 final size:20
Alignment explanation
Indices: 8788476--8788514 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
8788466 AAATTTTATC
*
8788476 AATTTGTAAAACATTATTAA
1 AATTTATAAAACATTATTAA
8788496 AATTTATAAAA-A-TATTAA
1 AATTTATAAAACATTATTAA
8788514 A
1 A
8788515 TAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AATTTATAAAACATTATTAA
Found at i:8788519 original size:13 final size:13
Alignment explanation
Indices: 8788501--8788541 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
8788491 ATTAAAATTT
*
8788501 ATAAAAATATTAA
1 ATAAAAATAATAA
*
8788514 ATAAAATTAATAA
1 ATAAAAATAATAA
8788527 ATAATAAATAATAA
1 ATAA-AAATAATAA
8788541 A
1 A
8788542 AATCATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAAAAATAATAA
Found at i:8788531 original size:7 final size:7
Alignment explanation
Indices: 8788501--8788541 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
8788491 ATTAAAATTT
8788501 ATAA-AA
1 ATAATAA
*
8788507 ATATTAA
1 ATAATAA
8788514 ATAA-AA
1 ATAATAA
*
8788520 TTAATAA
1 ATAATAA
8788527 ATAATAA
1 ATAATAA
8788534 ATAATAA
1 ATAATAA
8788541 A
1 A
8788542 AATCATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 8 0.28
7 21 0.72
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAATAA
Found at i:8790148 original size:21 final size:21
Alignment explanation
Indices: 8790113--8790189 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
8790103 GTGTGGATCT
**
8790113 ACACGCCCATGTGAAGGCAAC
1 ACACGCCTGTGTGAAGGCAAC
* *
8790134 ACATGCCTGTGTGAAGGCCAC
1 ACACGCCTGTGTGAAGGCAAC
* *
8790155 ACACGCCCGTGTGGAGAG-AAC
1 ACACGCCTGTGTGAAG-GCAAC
*
8790176 ACACGCCTATGTGA
1 ACACGCCTGTGTGA
8790190 GCAGCCCGTG
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 43 0.98
22 1 0.02
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (21 bp):
ACACGCCTGTGTGAAGGCAAC
Found at i:8793046 original size:25 final size:26
Alignment explanation
Indices: 8792997--8793051 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
8792987 AATAATGACG
8792997 AAAACAATAATAATATCAATAGTA-T
1 AAAACAATAATAATATCAATAGTATT
* *
8793022 AAAACGATAATAATA-CATATGGTATT
1 AAAACAATAATAATATCA-ATAGTATT
8793048 AAAA
1 AAAA
8793052 TATCTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 2 0.08
25 19 0.73
26 5 0.19
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.27
Consensus pattern (26 bp):
AAAACAATAATAATATCAATAGTATT
Found at i:8798265 original size:10 final size:10
Alignment explanation
Indices: 8798250--8798276 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
8798240 TTTTATAAAT
8798250 TTATAAAGCA
1 TTATAAAGCA
8798260 TTATAAAGCA
1 TTATAAAGCA
8798270 TTATAAA
1 TTATAAA
8798277 AATATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (10 bp):
TTATAAAGCA
Found at i:8799951 original size:55 final size:55
Alignment explanation
Indices: 8799862--8799968 Score: 196
Period size: 55 Copynumber: 1.9 Consensus size: 55
8799852 CTCTTTTAGA
*
8799862 AAAAAATAGACTTTTATTTCTTAGTTGATATATCGATTTCTTATTTCTAATGTCT
1 AAAAAATAGAATTTTATTTCTTAGTTGATATATCGATTTCTTATTTCTAATGTCT
*
8799917 AAAAGATAGAATTTTATTTCTTAGTTGATATATCGATTTCTTATTTCTAATG
1 AAAAAATAGAATTTTATTTCTTAGTTGATATATCGATTTCTTATTTCTAATG
8799969 ATTTGATTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (55 bp):
AAAAAATAGAATTTTATTTCTTAGTTGATATATCGATTTCTTATTTCTAATGTCT
Found at i:8804233 original size:23 final size:23
Alignment explanation
Indices: 8804205--8804250 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
8804195 ACAACAGGCA
8804205 TTTCAACAATATCTTTTTTTTAT
1 TTTCAACAATATCTTTTTTTTAT
8804228 TTTCAACAATATCTTTTTTTTAT
1 TTTCAACAATATCTTTTTTTTAT
8804251 ATACAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTCAACAATATCTTTTTTTTAT
Found at i:8805190 original size:23 final size:23
Alignment explanation
Indices: 8805140--8805200 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
8805130 TGCCTTTAGA
* *
8805140 TTAAATTAATTAATGATTAATGT
1 TTAATTTAATTAATAATTAATGT
8805163 TTAATTTAATTAATTAATTAA-GT
1 TTAATTTAATTAA-TAATTAATGT
8805186 TTAATTATAAATTAA
1 TTAATT-T-AATTAA
8805201 ACTAATCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 20 0.61
24 7 0.21
25 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
TTAATTTAATTAATAATTAATGT
Found at i:8805198 original size:17 final size:17
Alignment explanation
Indices: 8805163--8805200 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
8805153 TGATTAATGT
*
8805163 TTAATTTAATTAATTAA
1 TTAATTTAATTAATAAA
8805180 TTAAGTTTAATT-ATAAA
1 TTAA-TTTAATTAATAAA
8805197 TTAA
1 TTAA
8805201 ACTAATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTAATTTAATTAATAAA
Found at i:8811280 original size:18 final size:18
Alignment explanation
Indices: 8811257--8811292 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
8811247 GTTAGAAGTT
8811257 GAATGCGTTTTTAGATTC
1 GAATGCGTTTTTAGATTC
8811275 GAATGCGTTTTTAGATTC
1 GAATGCGTTTTTAGATTC
8811293 AAATATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (18 bp):
GAATGCGTTTTTAGATTC
Found at i:8812151 original size:50 final size:50
Alignment explanation
Indices: 8812093--8812194 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
8812083 TGTTAAATTT
8812093 AATACCCCTTAACCTACCCTTGAGTCGTGCAAATCGAATCAAACCCCTCG
1 AATACCCCTTAACCTACCCTTGAGTCGTGCAAATCGAATCAAACCCCTCG
*
8812143 AATACCCCTTAACCTACTCTTGAGTCGTGCAAATCGAATCAAACCCCTCG
1 AATACCCCTTAACCTACCCTTGAGTCGTGCAAATCGAATCAAACCCCTCG
8812193 AA
1 AA
8812195 ACACTTCAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.31, C:0.34, G:0.12, T:0.23
Consensus pattern (50 bp):
AATACCCCTTAACCTACCCTTGAGTCGTGCAAATCGAATCAAACCCCTCG
Found at i:8813161 original size:33 final size:33
Alignment explanation
Indices: 8813123--8813188 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
8813113 TTTCCACGTA
8813123 AAGGAATTATAGCTCTTATCTTTTTCCTCTTTC
1 AAGGAATTATAGCTCTTATCTTTTTCCTCTTTC
8813156 AAGGAATTATAGCTCTTATCTTTTTCCTCTTTC
1 AAGGAATTATAGCTCTTATCTTTTTCCTCTTTC
8813189 CCTCACTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.48
Consensus pattern (33 bp):
AAGGAATTATAGCTCTTATCTTTTTCCTCTTTC
Found at i:8814701 original size:23 final size:25
Alignment explanation
Indices: 8814675--8814721 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
8814665 TATCATTCAT
*
8814675 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
8814698 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
8814722 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:8815044 original size:46 final size:46
Alignment explanation
Indices: 8814992--8815377 Score: 446
Period size: 46 Copynumber: 8.7 Consensus size: 46
8814982 TGTCATAGTG
* ** * *
8814992 TCTTTCAACTATGGTCTTACTTATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTA
**** * *
8815038 TCTTTCAACCATGGTCTTATTTTTTTCATGTCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
* *
8815084 TCTTTCAACCATGGTCATACACATCTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
**** * *
8815130 TCTTTCAACCATGGTCTTATTTTTTTCATGTCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
8815176 TCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
8815222 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGATA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
8815268 TCTTTCAATCATGGTCTT--ACA---C--A-CAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
8815306 TCTTTCAACCATGGTCTT--ACA---C--A-CAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
8815344 TCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TCTTTCAACCATGGTCTTACACATTTCATATCAG
8815378 AGAGCACACT
Statistics
Matches: 299, Mismatches: 32, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
38 69 0.23
39 1 0.00
40 3 0.01
41 1 0.00
43 1 0.00
44 3 0.01
45 5 0.02
46 216 0.72
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
Found at i:8815308 original size:38 final size:38
Alignment explanation
Indices: 8815253--8815366 Score: 210
Period size: 38 Copynumber: 3.0 Consensus size: 38
8815243 CATTTCATAT
* *
8815253 CAGGTTGCCATGATATCTTTCAATCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
8815291 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
8815329 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
8815367 TTTCATATCA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 74 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:8818213 original size:43 final size:43
Alignment explanation
Indices: 8818165--8818250 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
8818155 TTTCTAAGAA
8818165 AAAAACAAAAGCTTTTGAAACTTTTATACATTTGACTATCAAT
1 AAAAACAAAAGCTTTTGAAACTTTTATACATTTGACTATCAAT
8818208 AAAAACAAAAGCTTTTGAAACTTTTATACATTTGACTATCAAT
1 AAAAACAAAAGCTTTTGAAACTTTTATACATTTGACTATCAAT
8818251 TACAAGTAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (43 bp):
AAAAACAAAAGCTTTTGAAACTTTTATACATTTGACTATCAAT
Found at i:8834310 original size:16 final size:16
Alignment explanation
Indices: 8834289--8834319 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8834279 TATTCCAATT
8834289 TTGTCCATAAAATTTC
1 TTGTCCATAAAATTTC
8834305 TTGTCCATAAAATTT
1 TTGTCCATAAAATTT
8834320 TAGATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGTCCATAAAATTTC
Found at i:8838987 original size:32 final size:32
Alignment explanation
Indices: 8838929--8838999 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
8838919 TCGTTGGATT
*
8838929 TTGAAATTATTATGTCTTGAATTTGTTACATA
1 TTGAAATTATTATGTCTTGAACTTGTTACATA
* * **
8838961 TTGAATTTATTATGT-TTTAAGCTTGTTGGATA
1 TTGAAATTATTATGTCTTGAA-CTTGTTACATA
8838993 TTGAAAT
1 TTGAAAT
8839000 GATTGACAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 4 0.12
32 28 0.88
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (32 bp):
TTGAAATTATTATGTCTTGAACTTGTTACATA
Found at i:8840222 original size:14 final size:14
Alignment explanation
Indices: 8840203--8840236 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8840193 AACAATTTAA
8840203 AATATAAACTTATT
1 AATATAAACTTATT
* *
8840217 AATATATATTTATT
1 AATATAAACTTATT
8840231 AATATA
1 AATATA
8840237 TGTAAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATAAACTTATT
Found at i:8844588 original size:14 final size:14
Alignment explanation
Indices: 8844569--8844596 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8844559 TAAATACTTG
8844569 ATTTGTTCTTAATT
1 ATTTGTTCTTAATT
8844583 ATTTGTTCTTAATT
1 ATTTGTTCTTAATT
8844597 CTTGTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (14 bp):
ATTTGTTCTTAATT
Found at i:8848846 original size:45 final size:45
Alignment explanation
Indices: 8848790--8848882 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
8848780 CCCACTGCGA
* *
8848790 ATCACATAGCCTCACTGCCCACGCCAGTGATTGACCCACATCACC
1 ATCACAAAGCCTCACTGCCCACGCCAGTGACTGACCCACATCACC
*
8848835 ATCACAAAGCCTCACTGCCCACGCCAGTGGCTGACCCACATCACC
1 ATCACAAAGCCTCACTGCCCACGCCAGTGACTGACCCACATCACC
8848880 ATC
1 ATC
8848883 CTCGACGATC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.43, G:0.14, T:0.16
Consensus pattern (45 bp):
ATCACAAAGCCTCACTGCCCACGCCAGTGACTGACCCACATCACC
Found at i:8855655 original size:21 final size:21
Alignment explanation
Indices: 8855626--8855666 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
8855616 TTTTTTTGCC
* * *
8855626 TCTGTTTCCCTTGCTGCTGCG
1 TCTGCTTCCCTCGCTACTGCG
8855647 TCTGCTTCCCTCGCTACTGC
1 TCTGCTTCCCTCGCTACTGC
8855667 TTTTATTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.39, G:0.20, T:0.39
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTACTGCG
Found at i:8869676 original size:34 final size:34
Alignment explanation
Indices: 8869638--8869704 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
8869628 GAAGAAAAGA
8869638 TGTTTGATAAACCATAATATATACATATTTTTAC
1 TGTTTGATAAACCATAATATATACATATTTTTAC
*
8869672 TGTTTGATCAACCATAATATATACATATTTTTA
1 TGTTTGATAAACCATAATATATACATATTTTTA
8869705 TCCCATGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (34 bp):
TGTTTGATAAACCATAATATATACATATTTTTAC
Found at i:8871116 original size:27 final size:29
Alignment explanation
Indices: 8871071--8871125 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
8871061 CTTTAGCCAT
8871071 TTTTATTTTTATTGCAATT-C-AATTTTG
1 TTTTATTTTTATTGCAATTACTAATTTTG
* **
8871098 TTTTGTTTTTATTTTAATTACTAATTTT
1 TTTTATTTTTATTGCAATTACTAATTTT
8871126 TCTTTTACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.70
28 1 0.04
29 6 0.26
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTTATTTTTATTGCAATTACTAATTTTG
Found at i:8876835 original size:21 final size:21
Alignment explanation
Indices: 8876807--8876854 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
8876797 TGTATTTACT
8876807 TAAT-ATTTAAGAA-ATAATAA
1 TAATAATTTAA-AATATAATAA
*
8876827 TTATAATTTAAAATATAATAA
1 TAATAATTTAAAATATAATAA
8876848 TAATAAT
1 TAATAAT
8876855 AGTGATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TAATAATTTAAAATATAATAA
Found at i:8876885 original size:16 final size:16
Alignment explanation
Indices: 8876844--8876894 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
8876834 TTAAAATATA
8876844 ATAATAATAATAGTGAT
1 ATAATAATAATAGT-AT
8876861 ATAAT-ATAATAGT-T
1 ATAATAATAATAGTAT
*
8876875 ATAATGAATAAAAG-AT
1 ATAAT-AATAATAGTAT
8876891 ATAA
1 ATAA
8876895 AAACATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.20
16 19 0.63
17 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (16 bp):
ATAATAATAATAGTAT
Found at i:8876963 original size:16 final size:17
Alignment explanation
Indices: 8876935--8876978 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 17
8876925 CACGATTAGC
8876935 AGGGAAAGAAAGAAGGAAAA
1 AGGGAAAGAAA-AA-G-AAA
8876955 AGGGAAAGAAAAAGAAA
1 AGGGAAAGAAAAAGAAA
8876972 AGGGAAA
1 AGGGAAA
8876979 ATTAGGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.42
18 1 0.04
19 2 0.08
20 11 0.46
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
AGGGAAAGAAAAAGAAA
Found at i:8884605 original size:18 final size:17
Alignment explanation
Indices: 8884581--8884624 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
8884571 TCGCCATATG
8884581 TTTTATTTTTTTGT-ATA
1 TTTTATTTTTTT-TAATA
*
8884598 TATTTATTTATTTTAATA
1 T-TTTATTTTTTTTAATA
8884616 TTTTATTTT
1 TTTTATTTT
8884625 AACTTATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTATTTTTTTTAATA
Found at i:8889107 original size:5 final size:5
Alignment explanation
Indices: 8889097--8889128 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
8889087 CAATTTGTGA
8889097 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
8889129 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:8889122 original size:9 final size:9
Alignment explanation
Indices: 8889098--8889128 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
8889088 AATTTGTGAA
8889098 AAATAAAAT
1 AAATAAAAT
8889107 AAAATAAAAT
1 -AAATAAAAT
8889117 AAATAAAAT
1 AAATAAAAT
8889126 AAA
1 AAA
8889129 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:8890566 original size:22 final size:23
Alignment explanation
Indices: 8890541--8890591 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
8890531 TTTTAATTTT
8890541 AAAAAATAAAAAT-AATATGATC
1 AAAAAATAAAAATAAATATGATC
8890563 AAAAAATAAAAATAACAATATGATC
1 AAAAAATAAAAAT-A-AATATGATC
8890588 AAAA
1 AAAA
8890592 TTTTCATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.50
25 13 0.50
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAAAATAAAAATAAATATGATC
Found at i:8890790 original size:29 final size:29
Alignment explanation
Indices: 8890756--8890872 Score: 234
Period size: 29 Copynumber: 4.0 Consensus size: 29
8890746 TTATTAATTG
8890756 AATCTTATTTCAGTTGATACATTATTGTC
1 AATCTTATTTCAGTTGATACATTATTGTC
8890785 AATCTTATTTCAGTTGATACATTATTGTC
1 AATCTTATTTCAGTTGATACATTATTGTC
8890814 AATCTTATTTCAGTTGATACATTATTGTC
1 AATCTTATTTCAGTTGATACATTATTGTC
8890843 AATCTTATTTCAGTTGATACATTATTGTC
1 AATCTTATTTCAGTTGATACATTATTGTC
8890872 A
1 A
8890873 GAAAGGGATA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 88 1.00
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (29 bp):
AATCTTATTTCAGTTGATACATTATTGTC
Found at i:8896096 original size:3 final size:3
Alignment explanation
Indices: 8896084--8896123 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
8896074 TCATATTGGC
*
8896084 CTT C-T CTT CTT CTT CTT CTT ATT CTT CTT CTT CTTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT C
8896124 AAACCTATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:8900984 original size:56 final size:58
Alignment explanation
Indices: 8900912--8901025 Score: 151
Period size: 56 Copynumber: 2.0 Consensus size: 58
8900902 TTATTTTTAT
*
8900912 TTTTCATTTTGAAGAAAACCACATTCATTTCCAAAT-ATTC-CATTTCTCCATTTTCA
1 TTTTCATTTTGAAGAAAACCACAATCATTTCCAAATGATTCTCATTTCTCCATTTTCA
* * * * * *
8900968 TTTTCATTTTGGAGAAAATCATAATCATTTCCAATTGTTTCTCATTTCTTCATTTTCA
1 TTTTCATTTTGAAGAAAACCACAATCATTTCCAAATGATTCTCATTTCTCCATTTTCA
8901026 CCATTTTTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
56 31 0.63
57 3 0.06
58 15 0.31
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.46
Consensus pattern (58 bp):
TTTTCATTTTGAAGAAAACCACAATCATTTCCAAATGATTCTCATTTCTCCATTTTCA
Found at i:8905198 original size:24 final size:24
Alignment explanation
Indices: 8905171--8905217 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
8905161 AAATATGAAT
*
8905171 AAAAATTT-TAAAATTTATATTTTA
1 AAAAATTTCTAAAA-TAATATTTTA
*
8905195 AAAATTTTCTAAAATAATATTTT
1 AAAAATTTCTAAAATAATATTTT
8905218 TTAGACCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
AAAAATTTCTAAAATAATATTTTA
Found at i:8908569 original size:24 final size:25
Alignment explanation
Indices: 8908515--8908563 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
8908505 TAAACTTATG
* *
8908515 CTAAATATATAATGCTATTCTAATTA
1 CTAAATATATAATACTACTCTAA-TA
8908541 CTAAATATATAATACTACTCTAA
1 CTAAATATATAATACTACTCTAA
8908564 CGTAAACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (25 bp):
CTAAATATATAATACTACTCTAATA
Found at i:8909178 original size:125 final size:125
Alignment explanation
Indices: 8909045--8909347 Score: 419
Period size: 125 Copynumber: 2.4 Consensus size: 125
8909035 GCCAAACGGT
* *
8909045 AAATCGAAACCCAGCACGATTGGGCACGATTTATCGAACTTCCAAATACGAAATATTGTCTCATT
1 AAATCGAAACCCAGCACGATTGGGCACGATTTATCGAACTTCCAAATACGAAATATTGCCTCACT
* * * *
8909110 TTAATTTCAA-AAAATATGGATGAAATTCCAAAAAGATATTCCATATTTTAGTCGAATGAA
66 TTAATTT-AAGAAAACATAGACGAAATTCCAAAAAGATATTCCATATTTTAGTCAAATGAA
* * * *
8909170 CAATCGAAACCTAGCTCAATTGGGCACGATTTATCGAACTTCCAAATACGAAATATTGCCTCACT
1 AAATCGAAACCCAGCACGATTGGGCACGATTTATCGAACTTCCAAATACGAAATATTGCCTCACT
* * * **
8909235 TTAATTTAAGAGAACATAGACGAAATTTCAAAAGGATATTCTGTATTTTAGTCAAATGAA
66 TTAATTTAAGAAAACATAGACGAAATTCCAAAAAGATATTCCATATTTTAGTCAAATGAA
* * * *
8909295 AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCAAACACGAAA
1 AAATCGAAACCCAGCACGATTGGGCACGATTTATCGAACTTCCAAATACGAAA
8909348 GATTTCTTTA
Statistics
Matches: 154, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
124 2 0.01
125 152 0.99
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.27
Consensus pattern (125 bp):
AAATCGAAACCCAGCACGATTGGGCACGATTTATCGAACTTCCAAATACGAAATATTGCCTCACT
TTAATTTAAGAAAACATAGACGAAATTCCAAAAAGATATTCCATATTTTAGTCAAATGAA
Found at i:8909969 original size:29 final size:26
Alignment explanation
Indices: 8909905--8909956 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
8909895 AGTCAAATTG
* *
8909905 TACATAAATAAATTTTAAAGAAAATA
1 TACATAAATAAATCTAAAAGAAAATA
*
8909931 TATAT-AATAAATCTAAAAGAAAATA
1 TACATAAATAAATCTAAAAGAAAATA
8909956 T
1 T
8909957 TTACATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (26 bp):
TACATAAATAAATCTAAAAGAAAATA
Done.