Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 42 of 199
Found at i:12645570 original size:16 final size:16
Alignment explanation
Indices: 12645542--12645578 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
12645532 GTGTTTTGTG
12645542 ATTTTTTATTAATGTA
1 ATTTTTTATTAATGTA
12645558 ACTTTTTTA-TAATGTA
1 A-TTTTTTATTAATGTA
12645574 ATTTT
1 ATTTT
12645579 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 9 0.45
17 7 0.35
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTTTTTATTAATGTA
Found at i:12645576 original size:106 final size:102
Alignment explanation
Indices: 12645322--12645580 Score: 319
Period size: 106 Copynumber: 2.5 Consensus size: 102
12645312 TTACAAATTG
** * *
12645322 TTAGTGTTTTGTGATTTAATAGTAATGTAAATTCTTTT-T--TTTAATGTTATAGTTATTTTGTT
1 TTAGTGTTTTGTGATTTTTTAGTAATGT-AATT-TTTTATAATATAATTTTATAGTTATTTTGTT
*
12645384 AGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTAGT
64 AGTAATTAATGATTAGTTTATAAATTGTTAGTGTTTAGT
* * * *
12645423 TTA-TGGTTTTGTGATTTTTTAGTAATTTAATTTTTAAAAATAATAATTTTATAGTTTTTTTTGT
1 TTAGT-GTTTTGTGATTTTTTAGTAATGTAATTTTTTATAAT-ATAATTTTATAG-TTATTTTGT
12645487 TAGTAATTAATGATTAGGTTATATAAATTGTTAGTGTTTAGT
63 TAGTAATTAATGATTA-GTT-TATAAATTGTTAGTGTTTAGT
* *
12645529 TTAGTGTTTTGTGATTTTTTATTAATGTAACTTTTTTATAATGTAATTTTAT
1 TTAGTGTTTTGTGATTTTTTAGTAATGTAA-TTTTTTATAATATAATTTTAT
12645581 TTTTATTTGA
Statistics
Matches: 134, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
99 3 0.02
100 5 0.04
101 23 0.17
102 1 0.01
103 10 0.07
104 23 0.17
105 3 0.02
106 56 0.42
107 10 0.07
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (102 bp):
TTAGTGTTTTGTGATTTTTTAGTAATGTAATTTTTTATAATATAATTTTATAGTTATTTTGTTAG
TAATTAATGATTAGTTTATAAATTGTTAGTGTTTAGT
Found at i:12649094 original size:9 final size:8
Alignment explanation
Indices: 12649073--12649097 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12649063 ATGTAGATTA
12649073 CTTTTTGT
1 CTTTTTGT
12649081 CTTTTTGT
1 CTTTTTGT
12649089 CTTTTTGT
1 CTTTTTGT
12649097 C
1 C
12649098 AAAAATCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.12, T:0.72
Consensus pattern (8 bp):
CTTTTTGT
Found at i:12653240 original size:3 final size:3
Alignment explanation
Indices: 12653232--12653265 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12653222 AGCTCACAAA
12653232 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
12653266 GTTTGCCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12653508 original size:17 final size:18
Alignment explanation
Indices: 12653486--12653529 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
12653476 AATTAGGAAC
12653486 GAAAAGAA-AA-AAGAAAA
1 GAAAAGAAGAACAA-AAAA
12653503 GAAAAGAAGAACAAAAAA
1 GAAAAGAAGAACAAAAAA
12653521 GAAAA-AAGA
1 GAAAAGAAGA
12653530 GAGGTCAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.48
18 11 0.44
19 2 0.08
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (18 bp):
GAAAAGAAGAACAAAAAA
Found at i:12653520 original size:13 final size:13
Alignment explanation
Indices: 12653486--12653529 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
12653476 AATTAGGAAC
12653486 GAAAAGAAAA-AA
1 GAAAAGAAAAGAA
12653498 GAAAAGAAAAGAA
1 GAAAAGAAAAGAA
12653511 GAACAA-AAAAGAA
1 GAA-AAGAAAAGAA
12653524 -AAAAGA
1 GAAAAGA
12653530 GAGGTCAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.07
12 13 0.45
13 12 0.41
14 2 0.07
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAAGAA
Found at i:12654931 original size:44 final size:43
Alignment explanation
Indices: 12654883--12655232 Score: 249
Period size: 45 Copynumber: 7.9 Consensus size: 43
12654873 AAAGCAAATC
*
12654883 GAAGACACTAGCCTTGTCTTCCTGTACTGACAGCGAAGCAGACT
1 GAAGACAC-AGCCTTGCCTTCCTGTACTGACAGCGAAGCAGACT
* * * * *
12654927 GAAGATAGCAGATCTTGCCTTTCTGTACTGACAGCGAAGTA-AAT
1 GAAGACA-CAG-CCTTGCCTTCCTGTACTGACAGCGAAGCAGACT
* *
12654971 CGAAGACATCAGCCTTGCATTCCTGTACTGACAGCGGAGCAGACT
1 -GAAGACA-CAGCCTTGCCTTCCTGTACTGACAGCGAAGCAGACT
* * * * * *
12655016 AAAGATAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGTAG-GT
1 GAAGACA-CAG-CCTTGCCTTCCTGTACTGACAGCGAAGCAGACT
* * *
12655060 CGAAGACACCAGCCTTGCATTCCTGTACTGACAG-TAGGGCAGACT
1 -GAAGACA-CAGCCTTGCCTTCCTGTACTGACAGCGA-AGCAGACT
* * * *
12655105 GAAGATAACAGATCTTGCCTTCCTGCACTGATAGCGAAGCAGA-T
1 GAAGA-CACAG-CCTTGCCTTCCTGTACTGACAGCGAAGCAGACT
* *** *
12655149 CAAAGACACCAAAATTGCCTTCCTGTACTGACAGCGGAGCAGACT
1 -GAAGACA-CAGCCTTGCCTTCCTGTACTGACAGCGAAGCAGACT
* ** * *
12655194 GAAGATAGCAAATCTTGCCTTCCTGTACTGGCAGTGAAG
1 GAAGACA-C-AGCCTTGCCTTCCTGTACTGACAGCGAAG
12655233 TAGATCGGAA
Statistics
Matches: 235, Mismatches: 56, Indels: 29
0.73 0.17 0.09
Matches are distributed among these distances:
43 1 0.00
44 107 0.46
45 126 0.54
46 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.23
Consensus pattern (43 bp):
GAAGACACAGCCTTGCCTTCCTGTACTGACAGCGAAGCAGACT
Found at i:12654971 original size:89 final size:89
Alignment explanation
Indices: 12654844--12655253 Score: 470
Period size: 89 Copynumber: 4.6 Consensus size: 89
12654834 GACTAAAAAC
* * ** * *
12654844 AGCAGATCTTGCCTTTTTGTACTAACAGTAAAGCAAATCGAAGACACTAGCCTTGTC-TTCCTGT
1 AGCAGATCTTGCCTTTCTGTACTGACAGCGAAGTAGATCGAAGACACTAGCCTTG-CATTCCTGT
12654908 ACTGACAGCGAAGCAGACTGAAGAT
65 ACTGACAGCGAAGCAGACTGAAGAT
*
12654933 AGCAGATCTTGCCTTTCTGTACTGACAGCGAAGTAAATCGAAGACA-TCAGCCTTGCATTCCTGT
1 AGCAGATCTTGCCTTTCTGTACTGACAGCGAAGTAGATCGAAGACACT-AGCCTTGCATTCCTGT
* *
12654997 ACTGACAGCGGAGCAGACTAAAGAT
65 ACTGACAGCGAAGCAGACTGAAGAT
* *
12655022 AGCAGATCTTGCC-TTCTTGTACTGACAGCGAAGTAGGTCGAAGACACCAGCCTTGCATTCCTGT
1 AGCAGATCTTGCCTTTC-TGTACTGACAGCGAAGTAGATCGAAGACACTAGCCTTGCATTCCTGT
* *
12655086 ACTGACAG-TAGGGCAGACTGAAGAT
65 ACTGACAGCGA-AGCAGACTGAAGAT
* * * * * * * *** *
12655111 AACAGATCTTGCCTTCCTGCACTGATAGCGAAGCAGATCAAAGACACCAAAATTGCCTTCCTGTA
1 AGCAGATCTTGCCTTTCTGTACTGACAGCGAAGTAGATCGAAGACACTAGCCTTGCATTCCTGTA
*
12655176 CTGACAGCGGAGCAGACTGAAGAT
66 CTGACAGCGAAGCAGACTGAAGAT
* * * * *
12655200 AGCAAATCTTGCCTTCCTGTACTGGCAGTGAAGTAGATCGGAAG-CAATAGCCTT
1 AGCAGATCTTGCCTTTCTGTACTGACAGCGAAGTAGATC-GAAGACACTAGCCTT
12655254 ATCTCCTTGA
Statistics
Matches: 272, Mismatches: 41, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
88 5 0.02
89 262 0.96
90 5 0.02
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (89 bp):
AGCAGATCTTGCCTTTCTGTACTGACAGCGAAGTAGATCGAAGACACTAGCCTTGCATTCCTGTA
CTGACAGCGAAGCAGACTGAAGAT
Found at i:12655143 original size:178 final size:178
Alignment explanation
Indices: 12654823--12655239 Score: 532
Period size: 178 Copynumber: 2.3 Consensus size: 178
12654813 CCTTGAAATT
* * * * * * * * *
12654823 ACAGTGGAGTAGACTAAAAACAGCAGATCTTGCCTTTTTGTACTAACAGTAAAGCAAATCGAAGA
1 ACAGCGGAGCAGACTAAAGATAGCAGATCTTGCCTTCTTGTACTGACAGTGAAGTAGATCGAAGA
* * * * *
12654888 CACTAGCCTTGTCTTCCTGTACTGACAGCGAAGCAGACTGAAGATAGCAGATCTTGCCTTTCTGT
66 CACCAGCCTTGTCTTCCTGTACTGACAGAGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGC
* * * ***
12654953 ACTGACAGCGAAGTAAATCGAAGACATCAGCCTTGCATTCCTGTACTG
131 ACTGACAGCGAAGCAAATCAAAGACACCAAAATTGCATTCCTGTACTG
* *
12655001 ACAGCGGAGCAGACTAAAGATAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGTAGGTCGAAGA
1 ACAGCGGAGCAGACTAAAGATAGCAGATCTTGCCTTCTTGTACTGACAGTGAAGTAGATCGAAGA
*
12655066 CACCAGCCTTG-CATTCCTGTACTGACAGTAG-GGCAGACTGAAGATAACAGATCTTGCCTTCCT
66 CACCAGCCTTGTC-TTCCTGTACTGACAG-AGAAGCAGACTGAAGATAACAGATCTTGCCTTCCT
* * *
12655129 GCACTGATAGCGAAGCAGATCAAAGACACCAAAATTGCCTTCCTGTACTG
129 GCACTGACAGCGAAGCAAATCAAAGACACCAAAATTGCATTCCTGTACTG
* * * *
12655179 ACAGCGGAGCAGACTGAAGATAGCAAATCTTGCCTTCCTGTACTGGCAGTGAAGTAGATCG
1 ACAGCGGAGCAGACTAAAGATAGCAGATCTTGCCTTCTTGTACTGACAGTGAAGTAGATCG
12655240 GAAGCAATAG
Statistics
Matches: 205, Mismatches: 32, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
177 1 0.00
178 203 0.99
179 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (178 bp):
ACAGCGGAGCAGACTAAAGATAGCAGATCTTGCCTTCTTGTACTGACAGTGAAGTAGATCGAAGA
CACCAGCCTTGTCTTCCTGTACTGACAGAGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGC
ACTGACAGCGAAGCAAATCAAAGACACCAAAATTGCATTCCTGTACTG
Found at i:12655508 original size:50 final size:50
Alignment explanation
Indices: 12655456--12655719 Score: 190
Period size: 50 Copynumber: 5.3 Consensus size: 50
12655446 CCGCAACAGT
* * *
12655456 GAATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGT
1 GAATCTTACTTCCTTGGCGGTGCAATGGAAAAGATTGAAGCTACAATGGC
* ** * ** * ** *
12655506 GAATCTTGCTTCCCCGACATTACAATTAAAAAGATTGAAG-TCGCAATGGC
1 GAATCTTACTTCCTTGGCGGTGCAATGGAAAAGATTGAAGCT-ACAATGGC
* * * ***
12655556 GAATCTTACTTCTTTGGTGGTGCAATGGAATAGATTGAAGCTACAACAAC
1 GAATCTTACTTCCTTGGCGGTGCAATGGAAAAGATTGAAGCTACAATGGC
* **** * * * *
12655606 GAATCTTGCTTCCCCAAC-ATTCTAATTGAAAAGATTGAAGCCACAATGGC
1 GAATCTTACTTCCTTGGCGGTGC-AATGGAAAAGATTGAAGCTACAATGGC
* * * * * *
12655656 GAATCTTACTTCCTTGGCGGTGTAGTGGAACAGATTGAACCTACAATAGT
1 GAATCTTACTTCCTTGGCGGTGCAATGGAAAAGATTGAAGCTACAATGGC
12655706 GAATCTTACTTCCT
1 GAATCTTACTTCCT
12655720 CGACATTGTA
Statistics
Matches: 151, Mismatches: 59, Indels: 8
0.69 0.27 0.04
Matches are distributed among these distances:
49 3 0.02
50 146 0.97
51 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (50 bp):
GAATCTTACTTCCTTGGCGGTGCAATGGAAAAGATTGAAGCTACAATGGC
Found at i:12655611 original size:100 final size:100
Alignment explanation
Indices: 12655438--12655726 Score: 391
Period size: 100 Copynumber: 2.9 Consensus size: 100
12655428 ACAGTGAAAC
** *
12655438 GATTGAAGCCGCAACAGTGAATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACAAT
1 GATTGAAGCCGCAATGGCGAATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACAAT
*
12655503 GGTGAATCTTGCTTCCCCGACATTAC-AATTAAAAA
66 AGTGAATCTTGCTTCCCCGACATT-CTAATTAAAAA
* * * * * *
12655538 GATTGAAGTCGCAATGGCGAATCTTACTTCTTTGGTGGTGCAATGGAATAGATTGAAGCTACAAC
1 GATTGAAGCCGCAATGGCGAATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACAAT
** * *
12655603 AACGAATCTTGCTTCCCCAACATTCTAATTGAAAA
66 AGTGAATCTTGCTTCCCCGACATTCTAATTAAAAA
* * *
12655638 GATTGAAGCCACAATGGCGAATCTTACTTCCTTGGCGGTGTAGTGGAACAGATTGAACCTACAAT
1 GATTGAAGCCGCAATGGCGAATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACAAT
* *
12655703 AGTGAATCTTACTTCCTCGACATT
66 AGTGAATCTTGCTTCCCCGACATT
12655727 GTAGTTAATC
Statistics
Matches: 160, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
99 1 0.01
100 159 0.99
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (100 bp):
GATTGAAGCCGCAATGGCGAATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACAAT
AGTGAATCTTGCTTCCCCGACATTCTAATTAAAAA
Found at i:12656162 original size:26 final size:26
Alignment explanation
Indices: 12656133--12656187 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
12656123 ACCAGGCAAA
12656133 ATTGACCTTTCAAAGGTCTTTGCTCC
1 ATTGACCTTTCAAAGGTCTTTGCTCC
12656159 ATTGACCTTTCAAAGGTCTTTGCTCC
1 ATTGACCTTTCAAAGGTCTTTGCTCC
12656185 ATT
1 ATT
12656188 CTCGTTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (26 bp):
ATTGACCTTTCAAAGGTCTTTGCTCC
Found at i:12658298 original size:72 final size:72
Alignment explanation
Indices: 12658171--12658306 Score: 182
Period size: 72 Copynumber: 1.9 Consensus size: 72
12658161 TTTGAAAAAT
* * *
12658171 GGATCATGCCCAATAAGTTAGGACACAATCTTTTCTTAATTCCTGAGATCGTTTAAAACTTGAAA
1 GGATCATGCCCAATAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCATTTAAAACTTGAAA
12658236 ATAAAGG
66 ATAAAGG
* * ** * * *
12658243 GGATCATGCCTAGTAAGTTAGGACATGATCTCTTCTTGATTCCCGATATCATTTAATACTTGAA
1 GGATCATGCCCAATAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCATTTAAAACTTGAA
12658307 TTTGAAAAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 54 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (72 bp):
GGATCATGCCCAATAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCATTTAAAACTTGAAA
ATAAAGG
Found at i:12659418 original size:17 final size:17
Alignment explanation
Indices: 12659398--12659489 Score: 67
Period size: 17 Copynumber: 5.0 Consensus size: 17
12659388 AAGAATCTTA
*
12659398 GAAATACGAAAATTTTT
1 GAAACACGAAAATTTTT
*
12659415 GAAAACACGAAAATCTTT
1 G-AAACACGAAAATTTTT
* * *
12659433 AAAATATGAGAAAATTTCTTTT
1 GAAACA--CGAAAA--T-TTTT
12659455 GAAAACACGAAAATTTTT
1 G-AAACACGAAAATTTTT
*
12659473 GAAACACGAGAATTTTT
1 GAAACACGAAAATTTTT
12659490 AAGTTTTTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
17 20 0.34
18 19 0.33
19 6 0.10
21 6 0.10
22 3 0.05
23 4 0.07
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (17 bp):
GAAACACGAAAATTTTT
Found at i:12659715 original size:32 final size:33
Alignment explanation
Indices: 12659639--12659708 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
12659629 AATAAAATTA
* **
12659639 AATACGACTATAAAAAAATGCTTTAAAAAAACCT
1 AATACGA-AATAAAAAAATGCTTTAAAAAAACAG
12659673 AATACGAAATAAAAAAATGC-TT-AAAAAACAAG
1 AATACGAAATAAAAAAATGCTTTAAAAAAAC-AG
12659705 AATA
1 AATA
12659709 TTAAATATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 7 0.22
32 6 0.19
33 12 0.38
34 7 0.22
ACGTcount: A:0.61, C:0.11, G:0.07, T:0.20
Consensus pattern (33 bp):
AATACGAAATAAAAAAATGCTTTAAAAAAACAG
Found at i:12659844 original size:17 final size:16
Alignment explanation
Indices: 12659822--12659878 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 16
12659812 CGACTCGGGC
12659822 TTTTTCCTTATTTTCTT
1 TTTTTCCTT-TTTTCTT
12659839 TTTTTCCTTTTTTTTTCTT
1 TTTTTCC---TTTTTTCTT
12659858 TTTTT-CTTTTTTCTCT
1 TTTTTCCTTTTTTCT-T
12659874 TTTTT
1 TTTTT
12659879 TTTTGGCCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.22
16 6 0.17
17 7 0.19
18 1 0.03
19 12 0.33
20 2 0.06
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCCTTTTTTCTT
Found at i:12659848 original size:9 final size:9
Alignment explanation
Indices: 12659822--12659879 Score: 59
Period size: 10 Copynumber: 6.6 Consensus size: 9
12659812 CGACTCGGGC
12659822 TTTTTCCTT
1 TTTTTCCTT
*
12659831 ATTTT-CTT
1 TTTTTCCTT
12659839 TTTTTCCTTT
1 TTTTTCC-TT
*
12659849 TTTTTTCTT
1 TTTTTCCTT
12659858 TTTTT-C-T
1 TTTTTCCTT
12659865 TTTTTCTCTT
1 TTTTTC-CTT
12659875 TTTTT
1 TTTTT
12659880 TTTGGCCTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
7 6 0.15
8 8 0.20
9 13 0.32
10 14 0.34
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTCCTT
Found at i:12659862 original size:27 final size:28
Alignment explanation
Indices: 12659822--12659882 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
12659812 CGACTCGGGC
*
12659822 TTTTTCCTTATTTTCTTTTTT-TCCTTT
1 TTTTTTCTTATTTTCTTTTTTCTCCTTT
* *
12659849 TTTTTTCTTTTTTTCTTTTTTCTCTTTT
1 TTTTTTCTTATTTTCTTTTTTCTCCTTT
12659877 TTTTTT
1 TTTTTT
12659883 GGCCTGTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (28 bp):
TTTTTTCTTATTTTCTTTTTTCTCCTTT
Found at i:12659879 original size:17 final size:17
Alignment explanation
Indices: 12659822--12659878 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
12659812 CGACTCGGGC
12659822 TTTTTCCTTATTTTCT-T
1 TTTTTCCTT-TTTTCTCT
*
12659839 TTTTTCCTTTTTTTTTCT
1 TTTTTCC-TTTTTTCTCT
*
12659857 TTTTTTCTTTTTTCTCT
1 TTTTTCCTTTTTTCTCT
12659874 TTTTT
1 TTTTT
12659879 TTTTGGCCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 26 0.74
18 9 0.26
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCCTTTTTTCTCT
Found at i:12660203 original size:7 final size:7
Alignment explanation
Indices: 12660193--12660231 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
12660183 TTTTTTCTAT
12660193 TTTTTTC
1 TTTTTTC
12660200 TTTTTTTC
1 -TTTTTTC
12660208 TTTTTTC
1 TTTTTTC
12660215 TTTCTTTC
1 TTT-TTTC
*
12660223 TTTCTTC
1 TTTTTTC
12660230 TT
1 TT
12660232 CTTCTTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:12660203 original size:8 final size:8
Alignment explanation
Indices: 12660192--12660225 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
12660182 ATTTTTTCTA
12660192 TTTTTTTC
1 TTTTTTTC
12660200 TTTTTTTC
1 TTTTTTTC
12660208 -TTTTTTC
1 TTTTTTTC
*
12660215 TTTCTTTC
1 TTTTTTTC
12660223 TTT
1 TTT
12660226 CTTCTTCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTC
Found at i:12660211 original size:15 final size:15
Alignment explanation
Indices: 12660193--12660231 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
12660183 TTTTTTCTAT
*
12660193 TTTTTTCTTTTTTTC
1 TTTTTTCTTTCTTTC
12660208 TTTTTTCTTTCTTTC
1 TTTTTTCTTTCTTTC
*
12660223 TTTCTTCTT
1 TTTTTTCTT
12660232 CTTCTTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTCTTTC
Found at i:12660220 original size:4 final size:4
Alignment explanation
Indices: 12660196--12660228 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
12660186 TTTCTATTTT
*
12660196 TTTC TTTT TTTC TTT- TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
12660229 CTTCTTCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:12660975 original size:77 final size:77
Alignment explanation
Indices: 12660872--12661646 Score: 1001
Period size: 77 Copynumber: 10.0 Consensus size: 77
12660862 AAAAATTGAA
* * * * * * *
12660872 AATACCTTGGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCATTATGAGTTAATTTTTGAAAAAT
1 AATACCTCGGCATGT-GCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAC
* *
12660937 ATAAATTTCAAAG
65 AGAAATTTAAAAG
* * *
12660950 -ATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCATTATAAGTTGA-TTTTAAAAAAC
1 AATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAC
12661013 AGAAATTT-AAAG
65 AGAAATTTAAAAG
* *
12661025 AAATACCTCGGCATGTGTCC-AGGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTAAAAAAA
1 -AATACCTCGGCATGTGCCCGA-GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAA
12661088 CAGAAATTTAAAAG
64 CAGAAATTTAAAAG
* * *
12661102 AAATACCTCGGCATGCGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTAAAAAAA
1 -AATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAC
12661165 AGAAATTTAAAAG
65 AGAAATTTAAAAG
* *
12661178 AAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAA
1 -AATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTAAAAAA
* *
12661243 TAAAAATTTAAAAG
64 CAGAAATTTAAAAG
*
12661257 AAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAC
1 -AATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAC
*
12661322 AGAAATTTAATAG
65 AGAAATTTAAAAG
* *
12661335 AAATACCTCGGCATG-ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
1 -AATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAC
*
12661399 AGAAATATAAAAG
65 AGAAATTTAAAAG
* * * *
12661412 AAATACCTCGGCATGTGACTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAAC
1 -AATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAC
12661477 AGAAATTTAAAAG
65 AGAAATTTAAAAG
* * * * *
12661490 AAATACCTCAGCATG-ACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAAC
1 -AATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAC
12661554 AGAAATTTAAAAG
65 AGAAATTTAAAAG
* * * * * *
12661567 AAATACATTGGCATGTGTCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAAC
1 -AATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAC
*
12661632 AGAAATATAAAAG
65 AGAAATTTAAAAG
12661645 AA
1 AA
12661647 ATACAATATG
Statistics
Matches: 632, Mismatches: 54, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
75 5 0.01
76 139 0.22
77 252 0.40
78 163 0.26
79 73 0.12
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (77 bp):
AATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACA
GAAATTTAAAAG
Found at i:12661291 original size:232 final size:233
Alignment explanation
Indices: 12660890--12661650 Score: 1110
Period size: 232 Copynumber: 3.3 Consensus size: 233
12660880 GGCGTGTGGC
* * * * * * *
12660890 CCGAGGCTCAACTCACCTCTAGCATTATGAGTTAATTTTTGAAAAATATAAATTTCAAAG--ATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAACAGAAATATAAAAGAAATA
* * * *
12660953 CCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCATTATAAGTTGA-TTTTAAAAAACAGAA
65 CCTCGGCATGTGA-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAA
12661017 ATTT-AAAGAAATACCTCGGCATGTGTCC-AGGGCTCAACTCACCTCTCGCAATATGAGTTGA-T
129 ATTTAAAAGAAATACCTCGGCATGTGTCCGA-GGCTCAACTCACCTCTCGCAATATGAGTTGATT
12661079 TTAAAAAAACAGAAATTTAAAAGAAATACCTCGGCATGCGT
193 TTAAAAAAACAGAAATTTAAAAGAAATACCTCGGCATGCGT
* * *
12661120 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTAAAAAAAAGAAATTTAAAAGAAATAC
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATATAAAAGAAATAC
* * *
12661184 CTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAAAAA
66 CTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAA
12661249 TTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
130 TTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* *
12661314 TAAAAAACAGAAATTTAATAGAAATACCTCGGCATGAC--
195 AAAAAAACAGAAATTTAAAAGAAATACCTCGGCATG-CGT
12661352 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAGAAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAACAGAAATATAAAAGAAATA
* *
12661417 CCTCGGCATGTGACTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
65 CCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
* ** * *
12661482 TTTAAAAGAAATACCTCAGCATG-ACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTT
130 TTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* * *
12661546 AAAAAAACAGAAATTTAAAAGAAATACATTGGCATGTGT
195 AAAAAAACAGAAATTTAAAAGAAATACCTCGGCATGCGT
* *
12661585 CTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAGAAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAACAGAAATATAAAAGAAATA
12661650 C
65 C
12661651 AATATGAGTT
Statistics
Matches: 483, Mismatches: 36, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
228 19 0.04
229 33 0.07
230 46 0.10
231 16 0.03
232 159 0.33
233 139 0.29
234 71 0.15
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (233 bp):
CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATATAAAAGAAATAC
CTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT
TTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTA
AAAAAACAGAAATTTAAAAGAAATACCTCGGCATGCGT
Found at i:12661303 original size:155 final size:155
Alignment explanation
Indices: 12660871--12661650 Score: 1090
Period size: 155 Copynumber: 5.0 Consensus size: 155
12660861 CAAAAATTGA
* * * * *
12660871 AAATACCTTGGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCATTATGAGTTAATTTTTGAAAAA
1 AAATACCTCGGCATGT-GCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
* * * * * * *
12660936 TATAAATTTCAAAG--ATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGCATTATAAGT
65 CAGAAATTTAAAAGAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGT
12660999 TGATTTTAAAAAACAGAAATTT-AAAG
129 TGATTTTAAAAAACAGAAATTTAAAAG
* **
12661025 AAATACCTCGGCATGTGTCC-AGGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTAAAAAAA
1 AAATACCTCGGCATGTGCCCGA-GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
*
12661088 CAGAAATTTAAAAGAAATACCTCGGCATGCGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
65 CAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
12661153 GA-TTTAAAAAAAAGAAATTTAAAAG
130 GATTTTAAAAAACAGAAATTTAAAAG
*
12661178 AAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAA
1 AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAA
* *
12661243 TAAAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
65 CAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
12661308 GATTTTTAAAAAACAGAAATTTAATAG
130 GA-TTTTAAAAAACAGAAATTTAAAAG
*
12661335 AAATACCTCGGCATG-ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
1 AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
* * * *
12661399 AGAAATATAAAAGAAATACCTCGGCATGTGACTGAGGCTCAACTCACTTCTCGCAATATGAGTTG
66 AGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
12661464 ATTTTTGAAAAACAGAAATTTAAAAG
131 A-TTTTAAAAAACAGAAATTTAAAAG
* * * * **
12661490 AAATACCTCAGCATG-ACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAAC
1 AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
* * * *
12661554 AGAAATTTAAAAGAAATACATTGGCATGTGTCTGAGGCTCAACTCACCTCTCGTAATATGAGTTG
66 AGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* *
12661619 ATTTTTGAAAAACAGAAATATAAAAG
131 A-TTTTAAAAAACAGAAATTTAAAAG
12661645 AAATAC
1 AAATAC
12661651 AATATGAGTT
Statistics
Matches: 571, Mismatches: 46, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
152 37 0.06
153 119 0.21
154 28 0.05
155 316 0.55
156 35 0.06
157 36 0.06
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (155 bp):
AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
AGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTAAAAAACAGAAATTTAAAAG
Found at i:12661669 original size:43 final size:43
Alignment explanation
Indices: 12661608--12661693 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
12661598 CACCTCTCGT
*
12661608 AATATGAGTTGATTTTTGAAAAACAGAAATATAAAAGAAATAC
1 AATATGAGTTGATTTTTGAAAAACAAAAATATAAAAGAAATAC
*
12661651 AATATGAGTTGATTTTTGAAAAACAAAAATTTAAAAGAAATAC
1 AATATGAGTTGATTTTTGAAAAACAAAAATATAAAAGAAATAC
12661694 CTCGGCATGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.53, C:0.05, G:0.13, T:0.29
Consensus pattern (43 bp):
AATATGAGTTGATTTTTGAAAAACAAAAATATAAAAGAAATAC
Found at i:12661757 original size:120 final size:121
Alignment explanation
Indices: 12661532--12661757 Score: 328
Period size: 120 Copynumber: 1.9 Consensus size: 121
12661522 CCTCTCGTAT
* * * *
12661532 TATGAGTTGATTTTAAAAAAACAGAAATTTAAAAGAAATACATTGGCATGTGTCTGAGGCTCAAC
1 TATGAGTTGATTTTAAAAAAACAAAAATTTAAAAGAAATACATCGGCATGTGCCCGAGGCTCAAC
** ***
12661597 TCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAGAAATACAA
66 TCACCTCTCACAATATGAGTTGATTTAAAAAAAACAGAAATATAAAAGAAATACAA
** *
12661653 TATGAGTTGATTTTTGAAAAACAAAAATTTAAAAGAAATACCTCGGCATG-GCCCGAGGCTCAAC
1 TATGAGTTGATTTTAAAAAAACAAAAATTTAAAAGAAATACATCGGCATGTGCCCGAGGCTCAAC
*
12661717 TCACCTCTCACATTATGAGTTGATTTAAAAAAAACAGAAAT
66 TCACCTCTCACAATATGAGTTGATTTAAAAAAAACAGAAAT
12661758 TGAAAAATAT
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
120 47 0.51
121 45 0.49
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.28
Consensus pattern (121 bp):
TATGAGTTGATTTTAAAAAAACAAAAATTTAAAAGAAATACATCGGCATGTGCCCGAGGCTCAAC
TCACCTCTCACAATATGAGTTGATTTAAAAAAAACAGAAATATAAAAGAAATACAA
Found at i:12668641 original size:18 final size:18
Alignment explanation
Indices: 12668618--12668764 Score: 54
Period size: 18 Copynumber: 7.9 Consensus size: 18
12668608 CACAGGAATT
12668618 TTTTTTGAAAACACGAAA
1 TTTTTTGAAAACACGAAA
*
12668636 TTTTTTTTGGAAATACAAG-AA
1 --TTTTTT-GAAA-ACACGAAA
* * *
12668657 -TCTTAG-AAATACGAAA
1 TTTTTTGAAAACACGAAA
*
12668673 ATTTTTGAAAACACGATAA
1 TTTTTTGAAAACACGA-AA
* *
12668692 -TCTTT-AAAATACGAGAAA
1 TTTTTTGAAAACAC--GAAA
** *
12668710 TTTTTTTTAAACATGAAGA
1 TTTTTTGAAAACACGAA-A
12668729 TTGTTTTTTGAAAACACGAAA
1 ---TTTTTTGAAAACACGAAA
*
12668750 ATTTTTG-AAACACGA
1 TTTTTTGAAAACACGA
12668765 GAAAGAGAAG
Statistics
Matches: 95, Mismatches: 18, Indels: 31
0.66 0.12 0.22
Matches are distributed among these distances:
15 3 0.03
16 4 0.04
17 19 0.20
18 25 0.26
19 9 0.09
20 10 0.11
21 7 0.07
22 18 0.19
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (18 bp):
TTTTTTGAAAACACGAAA
Found at i:12668641 original size:19 final size:20
Alignment explanation
Indices: 12668602--12668642 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12668592 CGTGATCCGA
* *
12668602 TTGAAACACAGGAATTTTTT
1 TTGAAACACACGAAATTTTT
12668622 TTGAAA-ACACGAAATTTTT
1 TTGAAACACACGAAATTTTT
12668641 TT
1 TT
12668643 TGGAAATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (20 bp):
TTGAAACACACGAAATTTTT
Found at i:12668648 original size:21 final size:21
Alignment explanation
Indices: 12668605--12668644 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12668595 GATCCGATTG
*
12668605 AAACACAGGAATTTTTTTTGA
1 AAACACAGAAATTTTTTTTGA
12668626 AAACAC-GAAATTTTTTTTG
1 AAACACAGAAATTTTTTTTG
12668645 GAAATACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
AAACACAGAAATTTTTTTTGA
Found at i:12668682 original size:17 final size:17
Alignment explanation
Indices: 12668639--12668714 Score: 55
Period size: 18 Copynumber: 4.3 Consensus size: 17
12668629 CACGAAATTT
12668639 TTTTTGGAAATAC-AAGAA
1 TTTTT-GAAATACGAA-AA
* *
12668657 TCTTAGAAATACGAAAA
1 TTTTTGAAATACGAAAA
* *
12668674 TTTTTGAAAACACGATAA
1 TTTTTG-AAATACGAAAA
* *
12668692 TCTTTAAAATACGAGAAA
1 TTTTTGAAATACGA-AAA
12668710 TTTTT
1 TTTTT
12668715 TTTAAACATG
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
17 20 0.45
18 24 0.55
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (17 bp):
TTTTTGAAATACGAAAA
Found at i:12675129 original size:20 final size:20
Alignment explanation
Indices: 12675104--12675142 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12675094 TTTTCTGCTT
12675104 TGTTTT-TTTCCCTTTTTTGC
1 TGTTTTGTTT-CCTTTTTTGC
*
12675124 TGTTTTGTTTTCTTTTTTG
1 TGTTTTGTTTCCTTTTTTG
12675143 GGGGGGCCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.74
Consensus pattern (20 bp):
TGTTTTGTTTCCTTTTTTGC
Found at i:12675215 original size:19 final size:16
Alignment explanation
Indices: 12675176--12675226 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
12675166 ATGCTGTTGC
12675176 GGGTCGGGTCGGATCT
1 GGGTCGGGTCGGATCT
12675192 GGGTCGGGTCGCGATTCGT
1 GGGTCGGGTCG-GA-TC-T
12675211 GGGTCGGGTCGG-TCT
1 GGGTCGGGTCGGATCT
12675226 G
1 G
12675227 ACCCGACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.06
16 13 0.41
17 2 0.06
18 3 0.09
19 12 0.38
ACGTcount: A:0.04, C:0.20, G:0.51, T:0.25
Consensus pattern (16 bp):
GGGTCGGGTCGGATCT
Found at i:12675263 original size:4 final size:4
Alignment explanation
Indices: 12675254--12675309 Score: 78
Period size: 4 Copynumber: 13.8 Consensus size: 4
12675244 AATTTTTTCC
*
12675254 CTTT CTTT CTTT CTTT CTTT -TTT CTTTT CTTTT CTTT CTTT CTTT TTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT C-TTT C-TTT CTTT CTTT CTTT CTTT
12675303 CTTT CTT
1 CTTT CTT
12675310 CTTCTTCTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 3 0.06
4 36 0.75
5 9 0.19
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
CTTT
Found at i:12675274 original size:25 final size:24
Alignment explanation
Indices: 12675246--12675309 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 24
12675236 TTTTCAATAA
12675246 TTTTTTCCCTTTCTTTCTTTCTTTC
1 TTTTTT-CCTTTCTTTCTTTCTTTC
*
12675271 TTTTTTCTTTTCTTTTCTTTCTTTC
1 TTTTTTCCTTTC-TTTCTTTCTTTC
*
12675296 TTTTTTTCTTTCTT
1 TTTTTTCCTTTCTT
12675310 CTTCTTCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.20
25 28 0.80
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTTCCTTTCTTTCTTTCTTTC
Found at i:12675293 original size:9 final size:9
Alignment explanation
Indices: 12675255--12675351 Score: 73
Period size: 9 Copynumber: 10.7 Consensus size: 9
12675245 ATTTTTTCCC
12675255 TTTCTTTC-
1 TTTCTTTCT
12675263 TTTCTTTCTTT
1 TTTCTTTC--T
12675274 TTTCTTTTCT
1 TTTC-TTTCT
12675284 TTTCTTTC-
1 TTTCTTTCT
12675292 TTTCTTT-T
1 TTTCTTTCT
12675300 TTTCTTTCT
1 TTTCTTTCT
12675309 TCTTC-TTCT
1 T-TTCTTTCT
12675318 TCTTC-TTCT
1 T-TTCTTTCT
12675327 TCTTC-TTCT
1 T-TTCTTTCT
12675336 TCTTC-TTCT
1 T-TTCTTTCT
12675345 TCTTCTT
1 T-TTCTT
12675352 CTTCTTCAAG
Statistics
Matches: 81, Mismatches: 0, Indels: 14
0.85 0.00 0.15
Matches are distributed among these distances:
8 22 0.27
9 42 0.52
10 9 0.11
11 4 0.05
12 4 0.05
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:12675295 original size:37 final size:41
Alignment explanation
Indices: 12675254--12675358 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 41
12675244 AATTTTTTCC
12675254 CTTTCTTTCTTTCTTTCTT-TT-TTCTT-TTCTT-TTCTTT
1 CTTTCTTTCTTTCTTTCTTCTTCTTCTTCTTCTTCTTCTTT
*
12675291 CTTTCTTTTTTTCTTTCTTCTTCTTCTTCTTCTTCTTC-TT
1 CTTTCTTTCTTTCTTTCTTCTTCTTCTTCTTCTTCTTCTTT
12675331 C-TTC-TTC-TTC-TTCTTCTTCTTCTTCTTC
1 CTTTCTTTCTTTCTTTCTTCTTCTTCTTCTTC
12675359 AAGCCCTAGG
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
36 18 0.29
37 21 0.34
38 4 0.06
39 8 0.13
40 8 0.13
41 3 0.05
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (41 bp):
CTTTCTTTCTTTCTTTCTTCTTCTTCTTCTTCTTCTTCTTT
Found at i:12675311 original size:3 final size:3
Alignment explanation
Indices: 12675275--12675358 Score: 111
Period size: 3 Copynumber: 28.0 Consensus size: 3
12675265 TCTTTCTTTT
*
12675275 TTC TT- TTC TT- TTC TTTC TTTC TT- TTT TTC TTTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC -TTC TTC TTC TTC TTC
12675320 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12675359 AAGCCCTAGG
Statistics
Matches: 75, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
2 6 0.08
3 59 0.79
4 10 0.13
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:12675398 original size:15 final size:16
Alignment explanation
Indices: 12675369--12675412 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
12675359 AAGCCCTAGG
*
12675369 TGCTGCCGCCGTCGCT
1 TGCTACCGCCGTCGCT
*
12675385 TGC-ACCGTCGTCGCT
1 TGCTACCGCCGTCGCT
12675400 TGCTACCGCCGTC
1 TGCTACCGCCGTC
12675413 TTCTCCTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.05, C:0.43, G:0.27, T:0.25
Consensus pattern (16 bp):
TGCTACCGCCGTCGCT
Found at i:12675750 original size:30 final size:29
Alignment explanation
Indices: 12675707--12675850 Score: 189
Period size: 30 Copynumber: 4.9 Consensus size: 29
12675697 TAATTTTGAG
*
12675707 AAAATTTAAGGGTCATAATGTAATTTCAA
1 AAAATTTAAGGGTCAAAATGTAATTTCAA
*
12675736 AAAATTTTATGGGTCAAAATGTAATTTCAA
1 AAAA-TTTAAGGGTCAAAATGTAATTTCAA
* * * *
12675766 AAAATTTAGGGGTCAAAATATAATTTTAGG
1 AAAATTTAAGGGTCAAAATGTAATTTCA-A
*
12675796 AAAATTTAAGGGTCAAAATGCAATTTCAA
1 AAAATTTAAGGGTCAAAATGTAATTTCAA
* *
12675825 AAAGTTTAAGGGCCAAAATGTAATTT
1 AAAATTTAAGGGTCAAAATGTAATTT
12675851 TTTATTTTTT
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
29 48 0.48
30 51 0.52
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (29 bp):
AAAATTTAAGGGTCAAAATGTAATTTCAA
Found at i:12675779 original size:59 final size:59
Alignment explanation
Indices: 12675707--12675850 Score: 191
Period size: 59 Copynumber: 2.4 Consensus size: 59
12675697 TAATTTTGAG
* * *
12675707 AAAATTTAAGGGTCATAATGTAATTTCA-AAAAATTTTATGGGTCAAAATGTAATTTCAA
1 AAAATTTAAGGGTCAAAATGTAATTTCAGAAAAA-TTTAAGGGTCAAAATGCAATTTCAA
* * * *
12675766 AAAATTTAGGGGTCAAAATATAATTTTAGGAAAATTTAAGGGTCAAAATGCAATTTCAA
1 AAAATTTAAGGGTCAAAATGTAATTTCAGAAAAATTTAAGGGTCAAAATGCAATTTCAA
* *
12675825 AAAGTTTAAGGGCCAAAATGTAATTT
1 AAAATTTAAGGGTCAAAATGTAATTT
12675851 TTTATTTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 69 0.95
60 4 0.05
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (59 bp):
AAAATTTAAGGGTCAAAATGTAATTTCAGAAAAATTTAAGGGTCAAAATGCAATTTCAA
Found at i:12679697 original size:11 final size:11
Alignment explanation
Indices: 12679683--12679754 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 11
12679673 TAAAAAAATT
12679683 ATTTTAAAAAA
1 ATTTTAAAAAA
12679694 ATTTT---AAA
1 ATTTTAAAAAA
12679702 A--TTAAAAAA
1 ATTTTAAAAAA
**
12679711 ATTAAAAAAAA
1 ATTTTAAAAAA
*
12679722 GTATTTTAAAAAT
1 --ATTTTAAAAAA
*
12679735 ATTTTAAAAAT
1 ATTTTAAAAAA
12679746 ATTTTAAAA
1 ATTTTAAAA
12679755 TTTAAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
6 2 0.04
8 4 0.08
9 4 0.08
11 31 0.63
13 8 0.16
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:12679714 original size:40 final size:41
Alignment explanation
Indices: 12679667--12679743 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
12679657 AATTTATTTT
*
12679667 AAAAATT-AAAAAAATTATTTTAAAAAAATTTTAAAATTAA
1 AAAAATTAAAAAAAAGTATTTTAAAAAAATTTTAAAATTAA
*
12679707 AAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAA
1 AAAAATTAAAAAAAAGTATTTTAAAAAAATTTTAAAA
12679744 ATATTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 7 0.21
41 27 0.79
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (41 bp):
AAAAATTAAAAAAAAGTATTTTAAAAAAATTTTAAAATTAA
Found at i:12679719 original size:17 final size:17
Alignment explanation
Indices: 12679686--12679719 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12679676 AAAAATTATT
**
12679686 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTAAAAAA
12679703 TTAAAAAAATTAAAAAA
1 TTAAAAAAATTAAAAAA
12679720 AAGTATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAAAATTAAAAAA
Found at i:12679734 original size:31 final size:31
Alignment explanation
Indices: 12679661--12679734 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
12679651 ATCAAAAATT
****
12679661 TATTTTAAAAATTAAAAAAATTATTTTAAAA
1 TATTTTAAAAATTAAAAAAATTAAAAAAAAA
* * * *
12679692 AAATTTTAAAATTAAAAAAATTAAAAAAAAG
1 TATTTTAAAAATTAAAAAAATTAAAAAAAAA
12679723 TATTTTAAAAAT
1 TATTTTAAAAAT
12679735 ATTTTAAAAA
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (31 bp):
TATTTTAAAAATTAAAAAAATTAAAAAAAAA
Found at i:12679741 original size:52 final size:52
Alignment explanation
Indices: 12679676--12679795 Score: 186
Period size: 52 Copynumber: 2.3 Consensus size: 52
12679666 TAAAAATTAA
12679676 AAAAATTATTTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTT
1 AAAAA-TATTTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTT
* * *
12679729 AAAAATATTTTAAAAATATTTTAAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAAATATTTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTT
* *
12679781 AATAGTATTTTAAAA
1 AAAAATATTTTAAAA
12679796 TTAAAAAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
52 57 0.92
53 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (52 bp):
AAAAATATTTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTT
Found at i:12679765 original size:9 final size:9
Alignment explanation
Indices: 12679726--12679772 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
12679716 AAAAAAGTAT
12679726 TTTAAAAATA
1 TTTAAAAA-A
12679736 TTTTAAAAATA
1 -TTTAAAAA-A
*
12679747 TTT-TAAAA
1 TTTAAAAAA
12679755 TTTAAAAAA
1 TTTAAAAAA
12679764 TTTAAAAAA
1 TTTAAAAAA
12679773 AGTATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 4 0.12
9 16 0.48
10 3 0.09
11 10 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:12693732 original size:20 final size:22
Alignment explanation
Indices: 12693707--12693750 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
12693697 TTTTTTATTA
12693707 TTTAGAATTTTTA-A-CTTTTT
1 TTTAGAATTTTTATATCTTTTT
12693727 TTTAGAATTTTTATATCTTTTT
1 TTTAGAATTTTTATATCTTTTT
12693749 TT
1 TT
12693751 AATATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.59
21 1 0.05
22 8 0.36
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTAGAATTTTTATATCTTTTT
Found at i:12693747 original size:19 final size:18
Alignment explanation
Indices: 12693687--12693748 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 18
12693677 AAAATAATTA
*
12693687 TTTTAGAAATTTTTTTATT
1 TTTTAG-AATTTTTATATT
* *
12693706 ATTTAGAATTTTTAACTTTT
1 TTTTAGAATTTTT-A-TATT
12693726 TTTTAGAATTTTTATATCT
1 TTTTAGAATTTTTATAT-T
12693745 TTTT
1 TTTT
12693749 TTAATATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 9 0.26
19 11 0.31
20 15 0.43
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTAGAATTTTTATATT
Found at i:12694465 original size:11 final size:11
Alignment explanation
Indices: 12694443--12694500 Score: 71
Period size: 11 Copynumber: 5.2 Consensus size: 11
12694433 AACTAATCCT
12694443 CTCTCAAATTTC
1 CTCTC-AATTTC
12694455 CTCTCAATTTC
1 CTCTCAATTTC
* *
12694466 CTCTAAATTTT
1 CTCTCAATTTC
*
12694477 CTCTCAATTTG
1 CTCTCAATTTC
*
12694488 CTCTCAAATTC
1 CTCTCAATTTC
12694499 CT
1 CT
12694501 TCCAAATTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
11 35 0.88
12 5 0.12
ACGTcount: A:0.22, C:0.31, G:0.02, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:12694480 original size:22 final size:23
Alignment explanation
Indices: 12694443--12694497 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
12694433 AACTAATCCT
12694443 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
* *
12694466 CTCT-AAATTTTCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
12694488 CTCTCAAATT
1 CTCTCAAATT
12694498 CCTTCCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:12694492 original size:33 final size:34
Alignment explanation
Indices: 12694442--12694518 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
12694432 AAACTAATCC
* *
12694442 TCTCTCAAATTTCCTCTCAATTTCC-TCTAAATTT
1 TCTCTCAAATTTCCTCTCAAATTCCTTCCAAA-TT
*
12694476 TCTCTC-AATTTGCTCTCAAATTCCTTCCAAATT
1 TCTCTCAAATTTCCTCTCAAATTCCTTCCAAATT
*
12694509 TCTCTGAAAT
1 TCTCTCAAAT
12694519 CCATATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 23 0.62
34 14 0.38
ACGTcount: A:0.25, C:0.29, G:0.03, T:0.44
Consensus pattern (34 bp):
TCTCTCAAATTTCCTCTCAAATTCCTTCCAAATT
Found at i:12694536 original size:51 final size:51
Alignment explanation
Indices: 12694478--12694577 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
12694468 CTAAATTTTC
*
12694478 TCTCAATTTGCTCTCAAATTCCT-TCCAAATTTCTCTGAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTCT-CAAATTTATCTGAAATCCATATTTAA
* * * *
12694529 TCTCAATTTGCTCTCAATTTCCTCTTAAATTTATCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTCTCAAATTTATCTGAAATCCATATTT
12694578 TAAATAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTCTCAAATTTATCTGAAATCCATATTTAA
Found at i:12697173 original size:19 final size:21
Alignment explanation
Indices: 12697151--12697194 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 21
12697141 TTTTTTATTA
12697151 TTTAGAATTTTTA-A-CTTTT
1 TTTAGAATTTTTATATCTTTT
12697170 TTTAGAATTTTTATATCTTTT
1 TTTAGAATTTTTATATCTTTT
12697191 TTTA
1 TTTA
12697195 ATATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.57
20 1 0.04
21 9 0.39
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTAGAATTTTTATATCTTTT
Found at i:12697906 original size:11 final size:11
Alignment explanation
Indices: 12697884--12697941 Score: 71
Period size: 11 Copynumber: 5.2 Consensus size: 11
12697874 AACTAATCCT
12697884 CTCTCAAATTTC
1 CTCTC-AATTTC
12697896 CTCTCAATTTC
1 CTCTCAATTTC
* *
12697907 CTCTAAATTTT
1 CTCTCAATTTC
*
12697918 CTCTCAATTTG
1 CTCTCAATTTC
*
12697929 CTCTCAAATTC
1 CTCTCAATTTC
12697940 CT
1 CT
12697942 TCCAAATTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
11 35 0.88
12 5 0.12
ACGTcount: A:0.22, C:0.31, G:0.02, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:12697921 original size:22 final size:23
Alignment explanation
Indices: 12697884--12697938 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
12697874 AACTAATCCT
12697884 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
* *
12697907 CTCT-AAATTTTCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
12697929 CTCTCAAATT
1 CTCTCAAATT
12697939 CCTTCCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:12697933 original size:33 final size:34
Alignment explanation
Indices: 12697883--12697959 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
12697873 AAACTAATCC
* *
12697883 TCTCTCAAATTTCCTCTCAATTTCC-TCTAAATTT
1 TCTCTCAAATTTCCTCTCAAATTCCTTCCAAA-TT
*
12697917 TCTCTC-AATTTGCTCTCAAATTCCTTCCAAATT
1 TCTCTCAAATTTCCTCTCAAATTCCTTCCAAATT
*
12697950 TCTCTGAAAT
1 TCTCTCAAAT
12697960 CCATATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 23 0.62
34 14 0.38
ACGTcount: A:0.25, C:0.29, G:0.03, T:0.44
Consensus pattern (34 bp):
TCTCTCAAATTTCCTCTCAAATTCCTTCCAAATT
Found at i:12697977 original size:51 final size:51
Alignment explanation
Indices: 12697919--12698018 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
12697909 CTAAATTTTC
*
12697919 TCTCAATTTGCTCTCAAATTCCT-TCCAAATTTCTCTGAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTCT-CAAATTTATCTGAAATCCATATTTAA
* * * *
12697970 TCTCAATTTGCTCTCAATTTCCTCTTAAATTTATCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTCTCAAATTTATCTGAAATCCATATTT
12698019 TTAAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTCTCAAATTTATCTGAAATCCATATTTAA
Found at i:12700285 original size:22 final size:21
Alignment explanation
Indices: 12700269--12700612 Score: 413
Period size: 22 Copynumber: 16.0 Consensus size: 21
12700259 TTTAATTGAC
12700269 AAACCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
* *
12700291 AAAACCTAACCCTTAACCTAA
1 AAACCCTAACCCTTAACTTAA
* *
12700312 AAACTCTAAACCCTTAACCTAA
1 AAACCCT-AACCCTTAACTTAA
12700334 AAACCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
* * *
12700356 AAACCCTAACCCTGACCCCT--
1 AAACCCTAACCCTTA-ACTTAA
* * *
12700376 AAACACTAACCCTTAAATAAA
1 AAACCCTAACCCTTAACTTAA
*
12700397 AAACCCTAACCCTTAACTTTA
1 AAACCCTAACCCTTAACTTAA
*
12700418 AAACCCTAACCCTTAACTTTA
1 AAACCCTAACCCTTAACTTAA
* *
12700439 AAACTCTACACCTTTAACTTAA
1 AAACCCTA-ACCCTTAACTTAA
12700461 AAACCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
*
12700483 AAACCCTAACCTTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* *
12700504 AAACCATAAACCTTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
12700526 AAACCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
* * *
12700548 AAACACTAACCCTTGACTTTA
1 AAACCCTAACCCTTAACTTAA
12700569 AAACCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
12700591 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
12700612 A
1 A
12700613 TATAATTTGA
Statistics
Matches: 280, Mismatches: 34, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.05
21 122 0.44
22 144 0.51
23 1 0.00
ACGTcount: A:0.44, C:0.31, G:0.01, T:0.24
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTAA
Found at i:12700322 original size:43 final size:43
Alignment explanation
Indices: 12700269--12700612 Score: 387
Period size: 43 Copynumber: 8.0 Consensus size: 43
12700259 TTTAATTGAC
*
12700269 AAACCCTAAACCCTTAACTTAAAAAACCTAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAAACCTAACCCTTAACTTAA
* * *
12700312 AAACTCTAAACCCTTAACCTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAAACCT-AACCCTTAACTTAA
* * * * * *
12700356 AAACCCT-AACCCTGACCCCT-AAACA-CTAACCCTTAAATAAA
1 AAACCCTAAACCCTTA-ACTTAAAAAACCTAACCCTTAACTTAA
* * *
12700397 AAACCCT-AACCCTTAACTTTAAAACCCTAACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAAAAAACCTAACCCTTAACTTAA
* * * *
12700439 AAACTCTACACCTTTAACTTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAAACCT-AACCCTTAACTTAA
* *
12700483 AAACCCT-AACCTTTAACTT-AAAAACCATAAACCTTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAAACC-T-AACCCTTAACTTAA
* *
12700526 AAACCCTAAACCCTTAACTT-AAAAACACTAACCCTTGACTTTA
1 AAACCCTAAACCCTTAACTTAAAAAAC-CTAACCCTTAACTTAA
*
12700569 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAAACCTAACCCTTAACTTAA
12700612 A
1 A
12700613 TATAATTTGA
Statistics
Matches: 256, Mismatches: 35, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
40 2 0.01
41 29 0.11
42 27 0.11
43 133 0.52
44 64 0.25
45 1 0.00
ACGTcount: A:0.44, C:0.31, G:0.01, T:0.24
Consensus pattern (43 bp):
AAACCCTAAACCCTTAACTTAAAAAACCTAACCCTTAACTTAA
Found at i:12700348 original size:65 final size:65
Alignment explanation
Indices: 12700269--12700612 Score: 457
Period size: 65 Copynumber: 5.4 Consensus size: 65
12700259 TTTAATTGAC
* * *
12700269 AAACCCTAAACCCTTAACTTAAAAAACCTAACCCTTAACCTAAAAACTCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACTCTAAACCCTTAACTTAA
* * * * * *
12700334 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTGACCCCT--AAACACT-AACCCTTAAATAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTA-ACTTAAAAACTCTAAACCCTTAACTTA
12700396 A
65 A
* * * *
12700397 AAACCCT-AACCCTTAACTTTAAAACCCTAACCCTTAACTTTAAAACTCTACACCTTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACTCTAAACCCTTAACTTAA
* *
12700461 AAACCCTAAACCCTTAACTTAAAAACCCTAACCTTTAACTTAAAAAC-CATAAACCTTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACTC-TAAACCCTTAACTTA
12700525 A
65 A
* * * *
12700526 AAACCCTAAACCCTTAACTTAAAAACACTAACCCTTGACTTTAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACTCTAAACCCTTAACTTAA
12700591 AAACCCT-AACCCTTAACTTAAA
1 AAACCCTAAACCCTTAACTTAAA
12700613 TATAATTTGA
Statistics
Matches: 247, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
61 2 0.01
62 27 0.11
63 24 0.10
64 39 0.16
65 151 0.61
66 4 0.02
ACGTcount: A:0.44, C:0.31, G:0.01, T:0.24
Consensus pattern (65 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACTCTAAACCCTTAACTTAA
Found at i:12700746 original size:37 final size:38
Alignment explanation
Indices: 12700705--12700872 Score: 107
Period size: 37 Copynumber: 4.4 Consensus size: 38
12700695 TTTTGACTGG
12700705 TACTAACAATTAATA-ATTTGATATAATTTGATAATTT
1 TACTAACAATTAATACATTTGATATAATTTGATAATTT
* * * *
12700742 TACTAACCATTAATACA-AT--TATCATTTAATAATTT
1 TACTAACAATTAATACATTTGATATAATTTGATAATTT
* * ** * * * * **
12700777 TACATTCACATAATGTTAGATTTGGA-AAAATGTT-TTGACTGG
1 TAC--TAACA-ATTAATACATTT-GATATAAT-TTGAT-AATTT
12700819 TACTAACAATTAATA-ATTTGATATAATTTGATAATTT
1 TACTAACAATTAATACATTTGATATAATTTGATAATTT
12700856 TACTAACAATTAATACA
1 TACTAACAATTAATACA
12700873 ATTATCAATT
Statistics
Matches: 92, Mismatches: 26, Indels: 25
0.64 0.18 0.17
Matches are distributed among these distances:
35 17 0.18
37 39 0.42
38 16 0.17
39 5 0.05
40 4 0.04
41 4 0.04
42 7 0.08
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (38 bp):
TACTAACAATTAATACATTTGATATAATTTGATAATTT
Found at i:12700811 original size:114 final size:114
Alignment explanation
Indices: 12700612--12700889 Score: 513
Period size: 114 Copynumber: 2.4 Consensus size: 114
12700602 CTTAACTTAA
12700612 ATATAATTTGATAATTTTAC-AACCATTAATACAATTATCAATTAATAATTTTACATTCACATAA
1 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTACATTCACATAA
12700676 TGTTAGATTTAAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
66 TGTTAGATTTAAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
*
12700725 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCATTTAATAATTTTACATTCACATAA
1 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTACATTCACATAA
**
12700790 TGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
66 TGTTAGATTTAAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
*
12700839 ATATAATTTGATAATTTTACTAACAATTAATACAATTATCAATTAATAATT
1 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATT
12700890 GAAAAAAATA
Statistics
Matches: 159, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
113 20 0.13
114 139 0.87
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (114 bp):
ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTACATTCACATAA
TGTTAGATTTAAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
Found at i:12701703 original size:372 final size:372
Alignment explanation
Indices: 12701018--12701764 Score: 1395
Period size: 372 Copynumber: 2.0 Consensus size: 372
12701008 ATATCCATAT
*
12701018 TGTTACATATTCTAGTCGAGCAAGGTCGACTCTTTGGTTTGCGACGTAATTCTCTATCCGGTAAC
1 TGTTACATATTCTAGTCGAGCAAGGTCGACTATTTGGTTTGCGACGTAATTCTCTATCCGGTAAC
* * *
12701083 AGCTTAAAAGGAGCAATAGATACGGGCGACAACTTACGTTCATTTGGGACTGGTGGGAAAACGTG
66 AGCTTAAAAGGAACAAGAGATACGGGCGACAACTTACGTTCATCTGGGACTGGTGGGAAAACGTG
12701148 TCTCCAGATGCTGTACATGTTTTCGAATTTGTACACTTAGTCCACATAGCTCATCGGATCCAGAC
131 TCTCCAGATGCTGTACATGTTTTCGAATTTGTACACTTAGTCCACATAGCTCATCGGATCCAGAC
* *
12701213 GGAGATTTTGACAAGCTGCAATAACATGAGCGCATGGATAATGAAGTGCATCAAACATCCCACAG
196 GGAGATTCTGACAAGCTGCAATAACATGAGCGCATGGATAACGAAGTGCATCAAACATCCCACAG
12701278 TCGCAAGTCCTATTTCGCAAGTGTACACGATATTGCCAGCCAACAACACCTTGGTGCGGTCTGTC
261 TCGCAAGTCCTATTTCGCAAGTGTACACGATATTGCCAGCCAACAACACCTTGGTGCGGTCTGTC
*
12701343 AAACTCTGTCACGCGAAACCATAAGTTGTCTTAATCGTGACACACTA
326 AAACTCTGTCACGCGAAACCATAAGTTGTCTCAATCGTGACACACTA
12701390 TGTTACATATTCTAGTCGAGCAAGGTCGACTATTTGGTTTGCGACGTAATTCTCTATCCGGTAAC
1 TGTTACATATTCTAGTCGAGCAAGGTCGACTATTTGGTTTGCGACGTAATTCTCTATCCGGTAAC
12701455 AGCTTAAAAGGAACAAGAGATACGGGCGACAACTTACGTTCATCTGGGACTGGTGGGAAAACGTG
66 AGCTTAAAAGGAACAAGAGATACGGGCGACAACTTACGTTCATCTGGGACTGGTGGGAAAACGTG
* *
12701520 TCTCTAGATGCTGTACATGTTTTCTAATTTGTACACTTAGTCCACATAGCTCATCGGATCCAGAC
131 TCTCCAGATGCTGTACATGTTTTCGAATTTGTACACTTAGTCCACATAGCTCATCGGATCCAGAC
12701585 GGAGATTCTGACAAGCTGCAATAACATGAGCGCATGGATAACGAAGTGCATCAAACATCCCACAG
196 GGAGATTCTGACAAGCTGCAATAACATGAGCGCATGGATAACGAAGTGCATCAAACATCCCACAG
*
12701650 TCGCAAGTCTTATTTCGCAAGTGTACACGATATTGCCAGCCAACAACACCTTGGTGCGGTCTGTC
261 TCGCAAGTCCTATTTCGCAAGTGTACACGATATTGCCAGCCAACAACACCTTGGTGCGGTCTGTC
*
12701715 AAACTCTGTCACGCGAAACCATAAGTTGTCTCGATCGTGACACACTA
326 AAACTCTGTCACGCGAAACCATAAGTTGTCTCAATCGTGACACACTA
12701762 TGT
1 TGT
12701765 GCATGATGTT
Statistics
Matches: 364, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
372 364 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (372 bp):
TGTTACATATTCTAGTCGAGCAAGGTCGACTATTTGGTTTGCGACGTAATTCTCTATCCGGTAAC
AGCTTAAAAGGAACAAGAGATACGGGCGACAACTTACGTTCATCTGGGACTGGTGGGAAAACGTG
TCTCCAGATGCTGTACATGTTTTCGAATTTGTACACTTAGTCCACATAGCTCATCGGATCCAGAC
GGAGATTCTGACAAGCTGCAATAACATGAGCGCATGGATAACGAAGTGCATCAAACATCCCACAG
TCGCAAGTCCTATTTCGCAAGTGTACACGATATTGCCAGCCAACAACACCTTGGTGCGGTCTGTC
AAACTCTGTCACGCGAAACCATAAGTTGTCTCAATCGTGACACACTA
Found at i:12704548 original size:126 final size:125
Alignment explanation
Indices: 12704264--12704672 Score: 669
Period size: 126 Copynumber: 3.3 Consensus size: 125
12704254 CCCAAGTATG
*
12704264 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
12704329 TAGAAGCG-TTTTTATATTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGAC
*
12704388 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
12704453 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTT-TTCCAGGAC
* * *
12704514 CTACTGTAGCAAAAGCGCATCCACGAGGGTGCGATTTCACAAATTTTTCTCATAA-AGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
* * *
12704578 CTTGAAGCATTTTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTCCAGGAC
65 CTTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGAC
* *
12704639 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGA
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGA
12704673 CTTTAGAAAT
Statistics
Matches: 265, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
124 70 0.26
125 79 0.30
126 114 0.43
127 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGAC
Found at i:12705604 original size:28 final size:28
Alignment explanation
Indices: 12705559--12705612 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
12705549 ATAAAAAAAT
* *
12705559 ATTTTTAAAATTTAAATTTAAT-TATAAA
1 ATTTATAAAATATAAA-TTAATATATAAA
*
12705587 ATTTATAAAATATCAATTAATATATA
1 ATTTATAAAATATAAATTAATATATA
12705613 TATTATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTATAAAATATAAATTAATATATAAA
Found at i:12706754 original size:19 final size:19
Alignment explanation
Indices: 12706726--12706765 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12706716 TATCACATTA
*
12706726 AACATGTGCTTAATAGTCT
1 AACATATGCTTAATAGTCT
*
12706745 AACATATGCTTAATATTCT
1 AACATATGCTTAATAGTCT
12706764 AA
1 AA
12706766 TATTTTCCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
AACATATGCTTAATAGTCT
Found at i:12709693 original size:35 final size:35
Alignment explanation
Indices: 12709647--12709713 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
12709637 TGATCGGGTC
12709647 ACCTCGACAAGTGGTTGTTTTTAATAAAAATTAAA
1 ACCTCGACAAGTGGTTGTTTTTAATAAAAATTAAA
12709682 ACCTCGACAAGTGGTTGTTTTTAATAAAAATT
1 ACCTCGACAAGTGGTTGTTTTTAATAAAAATT
12709714 TTAATTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (35 bp):
ACCTCGACAAGTGGTTGTTTTTAATAAAAATTAAA
Found at i:12712295 original size:20 final size:21
Alignment explanation
Indices: 12712269--12712314 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
12712259 TTGGGTTTAA
12712269 ATTTTGGGTCAT-TTGTATTTT
1 ATTTTGGG-CATGTTGTATTTT
*
12712290 -TTTTGGGCCTGTTGTATTTT
1 ATTTTGGGCATGTTGTATTTT
12712310 ATTTT
1 ATTTT
12712315 CTTGGGTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 2 0.09
20 16 0.73
21 4 0.18
ACGTcount: A:0.11, C:0.07, G:0.20, T:0.63
Consensus pattern (21 bp):
ATTTTGGGCATGTTGTATTTT
Found at i:12712662 original size:15 final size:15
Alignment explanation
Indices: 12712642--12712672 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12712632 CAGCCAAAAG
12712642 TGCTTTTGAGGTTGA
1 TGCTTTTGAGGTTGA
12712657 TGCTTTTGAGGTTGA
1 TGCTTTTGAGGTTGA
12712672 T
1 T
12712673 TTTATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.06, G:0.32, T:0.48
Consensus pattern (15 bp):
TGCTTTTGAGGTTGA
Found at i:12713940 original size:16 final size:16
Alignment explanation
Indices: 12713919--12713952 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12713909 TTTTCAATTT
12713919 TTCCATGTGTAATGAA
1 TTCCATGTGTAATGAA
*
12713935 TTCCATGTGTAATTAA
1 TTCCATGTGTAATGAA
12713951 TT
1 TT
12713953 GAATATTTTT
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:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (16 bp):
TTCCATGTGTAATGAA
Found at i:12717006 original size:3 final size:3
Alignment explanation
Indices: 12716991--12717029 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
12716981 CCAACAGAGT
* * *
12716991 GAA GAA GAG GAA GAA GAA GAA TAA GAA AAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
12717030 ACCACTGCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:12717606 original size:25 final size:25
Alignment explanation
Indices: 12717556--12717608 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
12717546 AAACTGAAGT
*
12717556 TTTTTTCAATTAGTATCAAAGGAGG
1 TTTTTTCAATTAGTATCAAAGCAGG
* *
12717581 TTTTTTCATTTGGTATCAGAA-CAGG
1 TTTTTTCAATTAGTATCA-AAGCAGG
12717606 TTT
1 TTT
12717609 CAGACACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.45
Consensus pattern (25 bp):
TTTTTTCAATTAGTATCAAAGCAGG
Found at i:12720610 original size:14 final size:15
Alignment explanation
Indices: 12720584--12720613 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12720574 TTGAAGGCTG
12720584 GAGAGATAAAAAGGT
1 GAGAGATAAAAAGGT
12720599 GAGAGA-AAAAAGGT
1 GAGAGATAAAAAGGT
12720613 G
1 G
12720614 GAGTCGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.37, T:0.10
Consensus pattern (15 bp):
GAGAGATAAAAAGGT
Found at i:12722178 original size:14 final size:12
Alignment explanation
Indices: 12722131--12722173 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
12722121 TACACATACT
12722131 TATATATTTTATA
1 TATATATTTT-TA
*
12722144 TTTTATAATTTTTA
1 -TATAT-ATTTTTA
12722158 TATATATTTTTA
1 TATATATTTTTA
12722170 TATA
1 TATA
12722174 CATATACGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 11 0.42
13 4 0.15
14 6 0.23
15 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATATTTTTA
Found at i:12723349 original size:18 final size:19
Alignment explanation
Indices: 12723307--12723349 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
12723297 CCAAACTTGT
*
12723307 TGTTTTAATAAAATCAAAC
1 TGTTTTAATAAAAACAAAC
*
12723326 TG-TTTATTAAAAAC-AAC
1 TGTTTTAATAAAAACAAAC
12723343 TGTTTTA
1 TGTTTTA
12723350 CGAGGTGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 14 0.67
19 2 0.10
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (19 bp):
TGTTTTAATAAAAACAAAC
Found at i:12724533 original size:19 final size:20
Alignment explanation
Indices: 12724493--12724536 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
12724483 GTTTCTTTTG
* *
12724493 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
12724512 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
12724531 GCATTA
1 GCATTA
12724537 GACTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:12728804 original size:86 final size:86
Alignment explanation
Indices: 12728659--12728922 Score: 411
Period size: 86 Copynumber: 3.1 Consensus size: 86
12728649 AGTAAAAATT
* * * * * * *
12728659 GAAGATAAACCTTGCCTCTCTCGGTCGTAGCAGAGCTGGTTGAAGTTATCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
12728724 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
12728745 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
12728810 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* *
12728831 GAAGACAAACCTTACCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATTGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
* *
12728896 GTATTTGGCAGCGAAGCAGATC
66 GCA-TTGACAGCGAAGCAGATC
*
12728918 AAAGA
1 GAAGA
12728923 TGGCAGATTT
Statistics
Matches: 165, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
86 144 0.87
87 21 0.13
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (86 bp):
GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
GCATTGACAGCGAAGCAGATC
Found at i:12729111 original size:134 final size:134
Alignment explanation
Indices: 12728870--12729116 Score: 386
Period size: 134 Copynumber: 1.8 Consensus size: 134
12728860 GTAGAGCTGG
*
12728870 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCAAAGCAGATCAAAGATGGCAGATTTTA
*
12728935 CCTCTCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTCGGCAGTGGAA
66 CCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTCGGCAGTGGAA
12729000 TAGA
131 TAGA
* * ** *
12729004 TTGAATATTGCAGATCTTGCCTTCCTGTATTTGGCAGCAAAGCAGGTTGAAGATGGCGGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCAAAGCAGATCAAAGATGGCAGATTTTA
** * **
12729069 CCTCCCTGATTACAGTGGAGTACATTGAAGCTGATAGTTCTATCTCCC
66 CCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCC
12729117 GGGGCAAGAA
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
134 101 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (134 bp):
TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCAAAGCAGATCAAAGATGGCAGATTTTA
CCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTCGGCAGTGGAA
TAGA
Found at i:12729180 original size:44 final size:45
Alignment explanation
Indices: 12729124--12730379 Score: 1159
Period size: 44 Copynumber: 28.5 Consensus size: 45
12729114 CCCGGGGCAA
* * *
12729124 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * *
12729168 GAAATGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * * *
12729212 GAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * *
12729256 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * *
12729300 GAAATGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * * *
12729344 GAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * *
12729388 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * *
12729432 GAAATGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * *
12729476 GAAGTAGATCGAAGA-AGCAGATCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * *
12729519 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * * *
12729563 GAAATGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTTGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * * *
12729607 GAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * *
12729651 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * *
12729695 GAAATGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * * *
12729739 GAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * *
12729783 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * *
12729827 GAAATGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * * *
12729871 GAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * *
12729915 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * *
12729959 GAAATGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTTGC
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * * * *
12730003 GAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * *
12730047 GAAGTAGATCGAAGGTAGCAGATCCTGTCTTTCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * *
12730091 GAAGTGGATCGAAAATA-CAGATCTTGTCTTCCCATATTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * * * *
12730135 GAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * *
12730179 GAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG-
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * * * * *
12730223 GAAGTGGATCCAAGATA-CAAATCTTGTCTTCCCATACTGGTGGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
* * * ** *
12730267 GAAGTAGATCGAAGAAAGCAGATCTTATC--CCTGTATTTGACAGTG
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATA-TTGGTAG-C
* * * * * * *
12730312 GAA-TAGATTGAGGATTGCAGATCTTGCCTTCCTGTATTTGGCAAC
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATA-TTGGTAGC
* *
12730357 GAAGCAGATCGAAGATGGCAGAT
1 GAAGTAGATCGAAGATAGCAGAT
12730380 TTTACCTCCC
Statistics
Matches: 964, Mismatches: 216, Indels: 62
0.78 0.17 0.05
Matches are distributed among these distances:
43 213 0.22
44 556 0.58
45 168 0.17
46 27 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (45 bp):
GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
Found at i:12729361 original size:132 final size:132
Alignment explanation
Indices: 12729124--12730292 Score: 2124
Period size: 132 Copynumber: 8.9 Consensus size: 132
12729114 CCCGGGGCAA
12729124 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
12729189 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
12729254 GT
131 GT
12729256 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
12729321 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
12729386 GT
131 GT
12729388 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
12729453 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGA-AGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
12729517 GT
131 GT
12729519 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
*
12729584 TCTTGTCTTCCCATATTTGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
12729649 GT
131 GT
12729651 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
12729716 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
12729781 GT
131 GT
12729783 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
12729848 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
12729913 GT
131 GT
12729915 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
* * *
12729980 TCTTGTCTTCCCATATTGGTTGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
12730045 GT
131 GT
* * * * * * *
12730047 GAAGTAGATCGAAGGTAGCAGATCCTGTCTTTCTATATTGGTAGGAAGTGGATCGAAAATACAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
* *
12730112 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
12730177 GT
131 GT
* * * * * * *
12730179 GAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAAA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
* * *
12730244 TCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTT
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTT
12730293 ATCCCTGTAT
Statistics
Matches: 1012, Mismatches: 24, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
131 130 0.13
132 882 0.87
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (132 bp):
GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGAGCAGATCTTGTCTTCATGTATTGGC
GT
Found at i:12730498 original size:43 final size:40
Alignment explanation
Indices: 12730443--12730539 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
12730433 CTGTATTAAA
* *
12730443 TAGTGGAATAGATCGAAGATTACAATCTTATCTCCCTAAGTAG
1 TAGTGGAATAGATCG--CATTA-AATCTTATCTCCCTAAGCAG
* *
12730486 TAGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAG
1 TAGTGGAATAGATCGCATTAAATCTTATCTCCCTAAGCAG
12730526 TAG-GGAAATAGATC
1 TAGTGG-AATAGATC
12730540 AAAGACGAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
39 2 0.04
40 28 0.58
41 4 0.08
43 14 0.29
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (40 bp):
TAGTGGAATAGATCGCATTAAATCTTATCTCCCTAAGCAG
Found at i:12730743 original size:44 final size:44
Alignment explanation
Indices: 12730516--12730925 Score: 268
Period size: 44 Copynumber: 9.5 Consensus size: 44
12730506 AGTCTTATCT
* * * * *
12730516 CCCTAAGCAGTAGGGAAATAGATCAAAGACGAAGGGTCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGCCTTAACC
* * * * * * *
12730560 CCCTGAGCAGTAGGGTAACAGACCGAA-TTGCA-GACCTTATCC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGCCTTAACC
* * * ** * *
12730602 CCCTAAGTAGTGGGGAAACAGATCAAAGACAAAGGGTCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGCCTTAACC
* * * * * ** * *
12730646 CCTTAAGCAGTAGGGTAACAGGTTG-A-ATTACA-GATCTTATCT
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGA-AGGGCCTTAACC
* *
12730688 CCCTAAGCAGTAGGAAAACAGATCGAAGACGAAGGGCCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGCCTTAACC
* * * * **
12730732 CCTTAAGCAGTAGGGTAACAG-GC-AA-ATTTACA-GATCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGA-TGA-AGGGCCTTAACC
*
12730774 CCCTAAGCAGTAGGGAAACAGATCGAAGGTGAAGGGCCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGCCTTAACC
* * * * * **
12730818 CCTTAAGCAGTAGGGTAACAG-GCTAA-ATTTACA-GATCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGA-TGA-AGGGCCTTAACC
**
12730861 CCCTAAGCAGTAGGGAAACAGATCGAAGGCGAAGGGCCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGCCTTAACC
*
12730905 CCCTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGAAACAG
12730926 GCTGAATTTA
Statistics
Matches: 266, Mismatches: 83, Indels: 34
0.69 0.22 0.09
Matches are distributed among these distances:
41 1 0.00
42 85 0.32
43 44 0.17
44 136 0.51
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.18
Consensus pattern (44 bp):
CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGGCCTTAACC
Found at i:12730868 original size:87 final size:87
Alignment explanation
Indices: 12730516--12730967 Score: 624
Period size: 86 Copynumber: 5.2 Consensus size: 87
12730506 AGTCTTATCT
* * * *
12730516 CCCTAAGCAGTAGGGAAATAGATCAAAGACGAAGGGTCTTAAACCCC-TGAGCAGTAGGGTAACA
1 CCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTT-AACCCCTTAAGCAGTAGGGTAACA
* * * * *
12730580 GACCGAA-TTGCAGACCTTATCC
65 GGCTGAATTTACAGATCTTAACC
* * * * * *
12730602 CCCTAAGTAGTGGGGAAACAGATCAAAGACAAAGGGTCTTAAACCCTTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAACCCCTTAAGCAGTAGGGTAACAG
* * *
12730667 GTTGAA-TTACAGATCTTATCT
66 GCTGAATTTACAGATCTTAACC
*
12730688 CCCTAAGCAGTAGGAAAACAGATCGAAGACGAAGGGCCTTAACCCCTTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAACCCCTTAAGCAGTAGGGTAACAG
*
12730753 GC-AAATTTACAGATCTTAACC
66 GCTGAATTTACAGATCTTAACC
**
12730774 CCCTAAGCAGTAGGGAAACAGATCGAAGGTGAAGGGCCTTAACCCCTTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAACCCCTTAAGCAGTAGGGTAACAG
*
12730839 GCTAAATTTACAGATCTTAACC
66 GCTGAATTTACAGATCTTAACC
* *
12730861 CCCTAAGCAGTAGGGAAACAGATCGAAGGCGAAGGGCCTTAACCCCCTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAACCCCTTAAGCAGTAGGGTAACAG
12730926 GCTGAATTTACAGATCTTAACC
66 GCTGAATTTACAGATCTTAACC
* *
12730948 CCCTAAGTAGTAGGGTAACA
1 CCCTAAGCAGTAGGGAAACA
12730968 AGCTGGAAAT
Statistics
Matches: 332, Mismatches: 31, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
85 7 0.02
86 204 0.61
87 121 0.36
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (87 bp):
CCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAACCCCTTAAGCAGTAGGGTAACAG
GCTGAATTTACAGATCTTAACC
Found at i:12734795 original size:16 final size:16
Alignment explanation
Indices: 12734770--12734805 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
12734760 GATTGCAATG
12734770 AATTTCATGTTTAGTT
1 AATTTCATGTTTAGTT
*
12734786 AATTTTATGTTTAGTT
1 AATTTCATGTTTAGTT
12734802 AATT
1 AATT
12734806 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.58
Consensus pattern (16 bp):
AATTTCATGTTTAGTT
Found at i:12749734 original size:21 final size:22
Alignment explanation
Indices: 12749710--12749750 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12749700 GCTCTATACT
* *
12749710 TATAA-ACCATAACCGAATCTA
1 TATAATACCAAAACCAAATCTA
12749731 TATAATACCAAAACCAAATC
1 TATAATACCAAAACCAAATC
12749751 ACACCATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.22
Consensus pattern (22 bp):
TATAATACCAAAACCAAATCTA
Found at i:12758198 original size:32 final size:32
Alignment explanation
Indices: 12758155--12758231 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
12758145 CAAAATAAAT
** *
12758155 TATGAAAAGTTACGAATGTGAAGAGGCTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
* **
12758187 TATGAAGAGTTAATAATGCAAAGAGACTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
*
12758219 GATGAAAAGTTAC
1 TATGAAAAGTTAC
12758232 ACACATGCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (32 bp):
TATGAAAAGTTACGAATGCAAAGAGACTTGAA
Found at i:12762709 original size:32 final size:32
Alignment explanation
Indices: 12762666--12762742 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
12762656 CAAAATAAAT
** *
12762666 TATGAAAAGTTACGAATGTGAAGAGGCTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
* **
12762698 TATGAAGAGTTAATAATGCAAAGAGACTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
*
12762730 GATGAAAAGTTAC
1 TATGAAAAGTTAC
12762743 ACACATGCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (32 bp):
TATGAAAAGTTACGAATGCAAAGAGACTTGAA
Found at i:12764201 original size:18 final size:17
Alignment explanation
Indices: 12764168--12764206 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
12764158 TTGTATAAAT
12764168 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
12764186 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
12764203 TGTG
1 TGTG
12764207 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:12764458 original size:23 final size:23
Alignment explanation
Indices: 12764432--12764529 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
12764422 AGTGTTATTG
12764432 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
12764455 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
12764478 -CCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
12764500 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
12764523 ATCAGTG
1 ATCAGTG
12764530 TGGCACTTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 21 0.30
23 49 0.70
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:12764498 original size:45 final size:45
Alignment explanation
Indices: 12764434--12764522 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
12764424 TGTTATTGAT
*
12764434 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
*
12764479 CAGTGGTAGCTTTGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
12764523 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:12771384 original size:18 final size:17
Alignment explanation
Indices: 12771351--12771389 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
12771341 TTGTATAAAT
12771351 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
12771369 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
12771386 TGTG
1 TGTG
12771390 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:12771668 original size:22 final size:22
Alignment explanation
Indices: 12771617--12771704 Score: 131
Period size: 22 Copynumber: 4.0 Consensus size: 22
12771607 TGTTATTGAT
*
12771617 CAGTGGTAGCTTCGGCTACATTT
1 CAGTGGTAGCTTCGGCTACA-TC
*
12771640 CAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATC
*
12771662 CAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATC
*
12771684 CTGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACAT
12771705 ATCAGTGTGG
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 42 0.69
23 19 0.31
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (22 bp):
CAGTGGTAGCTTCGGCTACATC
Found at i:12771711 original size:45 final size:46
Alignment explanation
Indices: 12771615--12771711 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 46
12771605 AGTGTTATTG
* *
12771615 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTCCAGTGGTAGCTTCGGCTACAT
* * *
12771661 -CCAGTGGTAGCTTTGGCTACA-TCCTGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTCCAGTGGTAGCTTCGGCTACAT
12771705 ATCAGTG
1 ATCAGTG
12771712 TGGCACTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
44 20 0.45
45 24 0.55
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTCCAGTGGTAGCTTCGGCTACAT
Found at i:12777578 original size:21 final size:20
Alignment explanation
Indices: 12777554--12777602 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
12777544 AAATAAGAGG
* *
12777554 GAAAGAAAGAAAATAAGGGAA
1 GAAAGAAAGAAAAGAA-AGAA
12777575 GAAAGAAAGAAAAGAAAGAA
1 GAAAGAAAGAAAAGAAAGAA
12777595 GAAAGAAA
1 GAAAGAAA
12777603 AAGAAGAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (20 bp):
GAAAGAAAGAAAAGAAAGAA
Found at i:12777593 original size:17 final size:17
Alignment explanation
Indices: 12777554--12777603 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
12777544 AAATAAGAGG
*
12777554 GAAAGAAAGAAA-ATAAG
1 GAAAGAAAGAAAGA-AAA
*
12777571 GGAAGAAAGAAAGAAAA
1 GAAAGAAAGAAAGAAAA
12777588 GAAAG-AAGAAAGAAAA
1 GAAAGAAAGAAAGAAAA
12777604 AGAAGAGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 11 0.38
17 17 0.59
18 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (17 bp):
GAAAGAAAGAAAGAAAA
Found at i:12794714 original size:50 final size:48
Alignment explanation
Indices: 12794639--12795225 Score: 387
Period size: 50 Copynumber: 11.7 Consensus size: 48
12794629 TTGCAATTCA
* *
12794639 AAAGATTGAATCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCAG
1 AAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGC-ATGCAGCAG
* * * * * *
12794688 AACAGATTGAAGCTACGACGGTGAATCTCACTTCCCCGACATTGCAATTCA-
1 AA-AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCA-TGC-A-GCAG
* * *
12794739 AAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGCGG
1 AAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGGC-ATGCAGCAG
* * * * * *
12794789 AACAGATTGAAGCTACGACGGCGAATCTCACTTCCCCGACATTACAATTCA-
1 AA-AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCA-TGC-A-GCAG
* * * * *
12794840 AAATATTGAGGCTACAACGGTGAATCCTACTTTCCCAGGCGATGCAGCGG
1 AAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGGC-ATGCAGCAG
* * * * *
12794890 AACAGATTGAAGCTACGACGGTGAATCTCACTTCCCCGACATTGCAAGTCA-
1 AA-AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCA-TGC-AG-CAG
* * **
12794941 AAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCAGGCAATGCAGTGG
1 AAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGGC-ATGCAGCAG
* * * * *
12794991 AACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCTGACATTGTAATTCA-
1 AA-AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCA-TG-CA-GCAG
* * *
12795042 AAATATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCAATGCAGCGG
1 AAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGC-ATGCAGCAG
* * * * *
12795091 AACAGATTGAAGCTACAACGGCAAATCTTGCTTCCCTA-ACATTGTAATTCA-
1 AA-AGATTGAAGCTACAACGGCGAATCTTACTTCCC-AGGCA-TG-CA-GCAG
* * **
12795142 AAAGATTGAAGCTACAATGGCGAATCTTACTT-CCAGGCGATGTAGTGG
1 AAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGC-ATGCAGCAG
* * *
12795190 AATAGACTGAAGCTACGATGGCGAATCTTACTTCCC
1 AA-AGATTGAAGCTACAACGGCGAATCTTACTTCCC
12795226 TGACATTGCA
Statistics
Matches: 412, Mismatches: 89, Indels: 73
0.72 0.16 0.13
Matches are distributed among these distances:
48 5 0.01
49 45 0.11
50 235 0.57
51 119 0.29
52 8 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (48 bp):
AAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCATGCAGCAG
Found at i:12794815 original size:101 final size:100
Alignment explanation
Indices: 12794629--12795235 Score: 820
Period size: 101 Copynumber: 6.0 Consensus size: 100
12794619 AAACCATGGT
* *
12794629 TTGCAATTCAAAAGATTGAATCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCAGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
*
12794694 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
66 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
*
12794729 TTGCAATTCAAAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCAGGCGATGCAGCGGAACAG
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGATGCAGCGGAACAG
12794794 ATTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
65 ATTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
* * * * * *
12794830 TTACAATTCAAAATATTGAGGCTACAACGGTGAATCCTACTTTCCCAGGCGATGCAGCGGAACAG
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGATGCAGCGGAACAG
*
12794895 ATTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
65 ATTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
* * * *
12794931 TTGCAAGTCAAAAGATTGAGGCCACAACGGCGAATCTTACTTTCCCAGGCAATGCAGTGGAACAG
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGATGCAGCGGAACAG
* ** *
12794996 ATTGAAGCTACAACGGCGAATCTTGCTTCCCTGACA
65 ATTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
* * * * *
12795032 TTGTAATTCAAAATATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCAATGCAGCGGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * ** **
12795097 TTGAAGCTACAACGGCAAATCTTGCTTCCCTAACA
66 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
* * * * * *
12795132 TTGTAATTCAAAAGATTGAAGCTACAATGGCGAATCTTACTT-CCAGGCGATGTAGTGGAATAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * * *
12795196 CTGAAGCTACGATGGCGAATCTTACTTCCCTGACA
66 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
12795231 TTGCA
1 TTGCA
12795236 GTTATACAAA
Statistics
Matches: 460, Mismatches: 46, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
99 51 0.11
100 134 0.29
101 275 0.60
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (100 bp):
TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
Found at i:12816519 original size:28 final size:27
Alignment explanation
Indices: 12816488--12816561 Score: 112
Period size: 28 Copynumber: 2.7 Consensus size: 27
12816478 TAATAATCAC
* *
12816488 ACTCGCACACTTAGTGCTTTACCATTAT
1 ACTCGCACACTTAGTGCTTT-CAATTAA
12816516 ACTCGCACACTTAGTGCATTTCAATTAA
1 ACTCGCACACTTAGTGC-TTTCAATTAA
12816544 ACTCGCACACTTAGTGCT
1 ACTCGCACACTTAGTGCT
12816562 AATCTCATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 1 0.02
28 39 0.91
29 3 0.07
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.32
Consensus pattern (27 bp):
ACTCGCACACTTAGTGCTTTCAATTAA
Found at i:12828160 original size:19 final size:20
Alignment explanation
Indices: 12828123--12828163 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12828113 TACAACACAA
*
12828123 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
12828143 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
12828162 TT
1 TT
12828164 GCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:12829051 original size:16 final size:16
Alignment explanation
Indices: 12829027--12829059 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12829017 CAATTTCAAT
12829027 AAAACAAAAATTTTCA
1 AAAACAAAAATTTTCA
*
12829043 AAAATAAAAATTTTCA
1 AAAACAAAAATTTTCA
12829059 A
1 A
12829060 TAATTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAACAAAAATTTTCA
Found at i:12830797 original size:36 final size:36
Alignment explanation
Indices: 12830745--12830828 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
12830735 ATATATAATT
* * * * *
12830745 ATCACTTTTAAATATTACAACTATATCATTATGCCGA
1 ATCACTTAT-AATATTACAAATACATCAATAGGCCGA
12830782 ATCACTTATAATATTACAAATACATCAATAGGCCGA
1 ATCACTTATAATATTACAAATACATCAATAGGCCGA
*
12830818 ATTACTTATAA
1 ATCACTTATAA
12830829 GTTCAATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
36 33 0.80
37 8 0.20
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.35
Consensus pattern (36 bp):
ATCACTTATAATATTACAAATACATCAATAGGCCGA
Found at i:12831098 original size:43 final size:43
Alignment explanation
Indices: 12831032--12831152 Score: 149
Period size: 43 Copynumber: 2.8 Consensus size: 43
12831022 GGCTCGTACA
* * * *
12831032 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCATATA-TTG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-AGTCG
12831075 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGTCG
*
12831118 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAAC
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAAC
12831153 GCATATCGGA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
42 4 0.06
43 61 0.90
44 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAGTCG
Found at i:12836466 original size:36 final size:36
Alignment explanation
Indices: 12836387--12836468 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 36
12836377 GTAATATTGT
* *
12836387 TACTGGTATATTGTTGCTTATGTTGTTATACATAGC
1 TACTGGTATATTGTTGCTTATATTGTTACACATAGC
** *
12836423 TGTTGGTATATTGTTGCTTATATTGTTACACATGGC
1 TACTGGTATATTGTTGCTTATATTGTTACACATAGC
12836459 TACTGGTATA
1 TACTGGTATA
12836469 CATGGCTAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.22, C:0.11, G:0.21, T:0.46
Consensus pattern (36 bp):
TACTGGTATATTGTTGCTTATATTGTTACACATAGC
Found at i:12837188 original size:21 final size:21
Alignment explanation
Indices: 12837162--12837213 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12837152 ATCTTTATGG
*
12837162 TGAGTTGGGGCAACTTGTTGA-
1 TGAGTTGGGGCAACTTG-TAAT
*
12837183 TGAGTTGGGGCAATTTGTAAT
1 TGAGTTGGGGCAACTTGTAAT
12837204 TGAGTTGGGG
1 TGAGTTGGGG
12837214 TAACCTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.19, C:0.06, G:0.40, T:0.35
Consensus pattern (21 bp):
TGAGTTGGGGCAACTTGTAAT
Found at i:12838012 original size:26 final size:25
Alignment explanation
Indices: 12837940--12838025 Score: 109
Period size: 26 Copynumber: 3.3 Consensus size: 25
12837930 CACACCTACC
12837940 TAAAAAATAGTCACTACATGCATATTAT
1 TAAAAAATAGTCACTACATG--TA-TAT
* *
12837968 TAAAAAATACTCATTACATGTATAT
1 TAAAAAATAGTCACTACATGTATAT
*
12837993 TAAAAAATAGTCAACAACATGTATAT
1 TAAAAAATAGTC-ACTACATGTATAT
12838019 TAAAAAA
1 TAAAAAA
12838026 ACAGTCATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
25 14 0.27
26 20 0.38
28 18 0.35
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (25 bp):
TAAAAAATAGTCACTACATGTATAT
Found at i:12838066 original size:96 final size:95
Alignment explanation
Indices: 12837950--12838186 Score: 318
Period size: 96 Copynumber: 2.5 Consensus size: 95
12837940 TAAAAAATAG
* *
12837950 TCACTACATGCATATTATTAAAAAATACTCATTACATGTATATTAAAAAATAGTCAACAACATGT
1 TCACTACATGCATATTATTAAAAAATACTCACTACATGCATATTAAAAAATAGTCAACAACATGT
* *
12838015 ATATTAAAAAAACAGTCATGCACACCAACAA
66 ATATT-AAAAAACAGGCATACACACCAACAA
* * * **
12838046 TCACAACATTCATATTATTAAAAAATACTCACTGCATGCATATTAAAAAATAGTCAACAGTATGT
1 TCACTACATGCATATTATTAAAAAATACTCACTACATGCATATTAAAAAATAGTCAACAACATGT
* *
12838111 ATATTAAAAAATAGGCGTACACACCAACAA
66 ATATTAAAAAACAGGCATACACACCAACAA
* * *
12838141 TCACTGCATGC--A-TATTAAAAAATAGTCACTACATGCATGTTAAAAA
1 TCACTACATGCATATTATTAAAAAATACTCACTACATGCATATTAAAAA
12838187 CACTCACTAA
Statistics
Matches: 124, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
92 31 0.25
93 1 0.01
95 29 0.23
96 63 0.51
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (95 bp):
TCACTACATGCATATTATTAAAAAATACTCACTACATGCATATTAAAAAATAGTCAACAACATGT
ATATTAAAAAACAGGCATACACACCAACAA
Found at i:12838114 original size:26 final size:25
Alignment explanation
Indices: 12838061--12838124 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
12838051 ACATTCATAT
* *
12838061 TATTAAAAAATACTCACTGCATGCA
1 TATTAAAAAATAGTCACAGCATGCA
* *
12838086 TATTAAAAAATAGTCAACAGTATGTA
1 TATTAAAAAATAGTC-ACAGCATGCA
12838112 TATTAAAAAATAG
1 TATTAAAAAATAG
12838125 GCGTACACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (25 bp):
TATTAAAAAATAGTCACAGCATGCA
Found at i:12838193 original size:24 final size:25
Alignment explanation
Indices: 12838136--12838195 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
12838126 CGTACACACC
*
12838136 AACAATCACTGCATGCATATTAAAA
1 AACAATCACTACATGCATATTAAAA
* * *
12838161 AATAGTCACTACATGCATGTT-AAA
1 AACAATCACTACATGCATATTAAAA
*
12838185 AACACTCACTA
1 AACAATCACTA
12838196 AAATAGCATG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (25 bp):
AACAATCACTACATGCATATTAAAA
Found at i:12839114 original size:28 final size:28
Alignment explanation
Indices: 12839074--12839138 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
12839064 GCCCTATAGC
12839074 CATCTTTGCATGCCTGTAGACAGACATA
1 CATCTTTGCATGCCTGTAGACAGACATA
12839102 CATCTTTGCATGCCTGTAGACAGACATA
1 CATCTTTGCATGCCTGTAGACAGACATA
12839130 CATCCTTTG
1 CAT-CTTTG
12839139 AAACAACTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 31 0.86
29 5 0.14
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (28 bp):
CATCTTTGCATGCCTGTAGACAGACATA
Found at i:12839393 original size:62 final size:60
Alignment explanation
Indices: 12839309--12839436 Score: 186
Period size: 62 Copynumber: 2.1 Consensus size: 60
12839299 ATGCAACATA
*
12839309 AATAACCAATACAAAATAATTTAATACAAACACAACCA-TTTCTGTCATACACATGGCAGAC
1 AATAACCAATACAAAATAATTTAATACAAACACAAACATTTTC-GTCATACACATGGCA-AC
* * *
12839370 AATAACCAATAGGAAAATAATTTAATACAAACACAAACATTTTCGTCATGCACATGGCAAT
1 AATAACCAATA-CAAAATAATTTAATACAAACACAAACATTTTCGTCATACACATGGCAAC
12839431 AATAAC
1 AATAAC
12839437 AAACAATAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
61 18 0.30
62 39 0.64
63 4 0.07
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.23
Consensus pattern (60 bp):
AATAACCAATACAAAATAATTTAATACAAACACAAACATTTTCGTCATACACATGGCAAC
Found at i:12839656 original size:6 final size:6
Alignment explanation
Indices: 12839647--12839794 Score: 134
Period size: 6 Copynumber: 23.7 Consensus size: 6
12839637 AAATAACCCT
* * * * **
12839647 AAATCA AAATCG AAATCA AAATCG AAATCG AAATAA AAATTG AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* * **
12839695 AAATCA AAATTA GAATCA GTGAGTGTTTCA AAATCA AAATCA AAATCA
1 AAATCA AAATCA AAATCA ---A---AATCA AAATCA AAATCA AAATCA
* *
12839743 AAATCA AAATCA AAATCA GAATCA AAATCA GAATCA AAATCA AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
12839791 AAAT
1 AAAT
12839795 TGAAATTGAA
Statistics
Matches: 115, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
6 111 0.97
9 1 0.01
12 3 0.03
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.20
Consensus pattern (6 bp):
AAATCA
Found at i:12853248 original size:18 final size:19
Alignment explanation
Indices: 12853226--12853276 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
12853216 ATATAATTAT
12853226 TAAAAATTATTTAAAT-C-
1 TAAAAATTATTTAAATCCA
*
12853243 TAAAAATTTATTAAAATCCA
1 TAAAAA-TTATTTAAATCCA
12853263 TAAAAA-TATTTAAA
1 TAAAAATTATTTAAA
12853277 ATTACCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 16 0.55
19 1 0.03
20 6 0.21
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAATTATTTAAATCCA
Found at i:12853313 original size:18 final size:18
Alignment explanation
Indices: 12853265--12853312 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
12853255 AAAATCCATA
12853265 AAAATATT-TAAAATTAC
1 AAAATATTATAAAATTAC
* *
12853282 CAAATTTTATAAAATT-C
1 AAAATATTATAAAATTAC
12853299 AAAATATTATAAAA
1 AAAATATTATAAAA
12853313 ACTTATAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATATTATAAAATTAC
Found at i:12875235 original size:16 final size:16
Alignment explanation
Indices: 12875193--12875243 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
12875183 CTGATTTTAG
*
12875193 AAAAT-CATAAAATTA
1 AAAATACATAAAAATA
* *
12875208 TAATTACA-AAAAATA
1 AAAATACATAAAAATA
12875223 AAAATACATAAAAATA
1 AAAATACATAAAAATA
12875239 TAAAA
1 -AAAA
12875244 AAAATCAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 15 0.54
16 9 0.32
17 4 0.14
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATACATAAAAATA
Found at i:12875367 original size:14 final size:15
Alignment explanation
Indices: 12875331--12875369 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
12875321 ATGTTTTAAA
12875331 ATTTAAAAGAAATATT
1 ATTTAAAA-AAATATT
*
12875347 TTTTAAAAAAA-ATT
1 ATTTAAAAAAATATT
12875361 ATTTAAAAA
1 ATTTAAAAA
12875370 GGATATGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 11 0.52
15 3 0.14
16 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
ATTTAAAAAAATATT
Found at i:12877506 original size:23 final size:24
Alignment explanation
Indices: 12877455--12877506 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
12877445 TCTTAAAAAA
*
12877455 AAAAAAACTCCACCATGAATCTAC
1 AAAAAAACTCCACCATGAATATAC
12877479 AAAAAAACTCCACCATGAATATAC
1 AAAAAAACTCCACCATGAATATAC
12877503 AAAA
1 AAAA
12877507 TCAACATTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.56, C:0.25, G:0.04, T:0.15
Consensus pattern (24 bp):
AAAAAAACTCCACCATGAATATAC
Found at i:12878034 original size:13 final size:13
Alignment explanation
Indices: 12878015--12878061 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
12878005 TTAAAATAAA
12878015 CAATTAATAAAAT
1 CAATTAATAAAAT
* *
12878028 CAGTTAATCAAAT
1 CAATTAATAAAAT
*
12878041 TAATTAATAAAAT
1 CAATTAATAAAAT
*
12878054 AAATTAAT
1 CAATTAAT
12878062 CAAACCAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.34
Consensus pattern (13 bp):
CAATTAATAAAAT
Found at i:12878045 original size:26 final size:26
Alignment explanation
Indices: 12878016--12878065 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
12878006 TAAAATAAAC
* *
12878016 AATTAATAAAATCAGTTAATCAAATT
1 AATTAATAAAATAAATTAATCAAATT
12878042 AATTAATAAAATAAATTAATCAAA
1 AATTAATAAAATAAATTAATCAAA
12878066 CCAATCACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (26 bp):
AATTAATAAAATAAATTAATCAAATT
Done.