Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 144 of 193
Found at i:44932721 original size:90 final size:89
Alignment explanation
Indices: 44932629--44932790 Score: 247
Period size: 89 Copynumber: 1.8 Consensus size: 89
44932619 AATTTGAATT
* * *
44932629 TTTTTTATCTG-AAAAAAGGGAGTGTCGGCCATTGTATGGCCAACACCCAAAAATTTGA-TTTTT
1 TTTTTTATCTGAAAAAAAAGAAGTGTCGGCCATTGCATGGCCAACACCCAAAAATTTGATTTTTT
44932692 TTATCAGATAAATAGAAAATTAAA
66 TTATCAGATAAATAGAAAATTAAA
* **
44932716 TTTTTTATCTGACAAAAAAAGAAGTGTCGGCTATTGCATGGCCAACATTCAAAAATTTGATTTTT
1 TTTTTTATCTGA-AAAAAAAGAAGTGTCGGCCATTGCATGGCCAACACCCAAAAATTTGATTTTT
44932781 TTTATCAGAT
65 TTTATCAGAT
44932791 TAAAAAGGGG
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
87 11 0.17
89 41 0.62
90 14 0.21
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (89 bp):
TTTTTTATCTGAAAAAAAAGAAGTGTCGGCCATTGCATGGCCAACACCCAAAAATTTGATTTTTT
TTATCAGATAAATAGAAAATTAAA
Found at i:44933305 original size:22 final size:22
Alignment explanation
Indices: 44933274--44933316 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
44933264 GCTAAAAAAA
*
44933274 TTGTTATTTTCTTACTGTTTTG
1 TTGTTATTTTCTCACTGTTTTG
* *
44933296 TTGTTGTTTTCTCATTGTTTT
1 TTGTTATTTTCTCACTGTTTT
44933317 TCCATCATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.09, G:0.14, T:0.70
Consensus pattern (22 bp):
TTGTTATTTTCTCACTGTTTTG
Found at i:44938269 original size:12 final size:12
Alignment explanation
Indices: 44938254--44938296 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
44938244 TTATTCAAGA
44938254 AAAATTTATTAG
1 AAAATTTATTAG
* *
44938266 AAAATGTAACTA-
1 AAAAT-TTATTAG
44938278 AAAATTTATTAG
1 AAAATTTATTAG
44938290 AAAATTT
1 AAAATTT
44938297 TTACATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 4 0.16
12 17 0.68
13 4 0.16
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (12 bp):
AAAATTTATTAG
Found at i:44939492 original size:17 final size:16
Alignment explanation
Indices: 44939472--44939530 Score: 73
Period size: 17 Copynumber: 3.6 Consensus size: 16
44939462 CATTTGGAAA
44939472 TTAAATTTATTTTAATT
1 TTAAATTTATTTTAA-T
*
44939489 TTAAATTTATTTTAAA
1 TTAAATTTATTTTAAT
* *
44939505 TTCAATTTGAATTTAAT
1 TTAAATTT-ATTTTAAT
44939522 TTAAATTTA
1 TTAAATTTA
44939531 ATATTATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 8 0.22
17 28 0.78
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
TTAAATTTATTTTAAT
Found at i:44939500 original size:11 final size:11
Alignment explanation
Indices: 44939469--44939532 Score: 67
Period size: 11 Copynumber: 5.8 Consensus size: 11
44939459 AACCATTTGG
*
44939469 AAATTAAATTT
1 AAATTTAATTT
*
44939480 -ATTTTAATTTT
1 AAATTTAA-TTT
*
44939491 AAATTTATTTT
1 AAATTTAATTT
*
44939502 AAATTCAATTT
1 AAATTTAATTT
*
44939513 GAATTTAATTT
1 AAATTTAATTT
44939524 AAATTTAAT
1 AAATTTAAT
44939533 ATTATTATAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
10 5 0.12
11 32 0.76
12 5 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:44941906 original size:59 final size:59
Alignment explanation
Indices: 44941488--44941925 Score: 598
Period size: 59 Copynumber: 7.4 Consensus size: 59
44941478 TGAACTGTCT
* *
44941488 AAAAATTACCATTTTAGCCC-CGAACTTTACAAAATTCCATTTTTAACCTCGATTTCACC
1 AAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
44941547 AAAAATTACCATTTTAGCCCT-GAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACC
1 AAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
44941606 AAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCAAC
1 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
44941665 AAAAATTACCATTTTACCC-CTAAACTTTCCAAAA-TCCTATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCTC-GAACTTTCCAAAATTCC-ATTTTTAACCCCGATTTCACC
* * * * * *
44941724 AAAAATTACCGTTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCTGATTTTACC
1 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
44941783 AAAAATTACCGTTTTAGCCC-CGAACTTTCCAAAATTCCATTTTAAACCTCGATTTCACC
1 AAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* *
44941842 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACT
1 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* ** *
44941901 GAAAATTTTCGTTTTACCCTCGAAC
1 AAAAATTACCATTTTACCCTCGAAC
44941926 CTTCTTAAAT
Statistics
Matches: 343, Mismatches: 28, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
58 10 0.03
59 327 0.95
60 6 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:44952170 original size:49 final size:49
Alignment explanation
Indices: 44952110--44952210 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
44952100 TGTATAAGAG
*
44952110 AAGAAAGGATCAGGTGTTATTGAGATGTGTGGACTCAATCGAGGCTAAA
1 AAGAAAAGATCAGGTGTTATTGAGATGTGTGGACTCAATCGAGGCTAAA
44952159 AAGAAAAGATCAGGTGTTATTGAGATGTGTGGACTCAATCGAGGCTAAA
1 AAGAAAAGATCAGGTGTTATTGAGATGTGTGGACTCAATCGAGGCTAAA
44952208 AAG
1 AAG
44952211 TTCTTAGAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.37, C:0.10, G:0.30, T:0.24
Consensus pattern (49 bp):
AAGAAAAGATCAGGTGTTATTGAGATGTGTGGACTCAATCGAGGCTAAA
Found at i:44954229 original size:38 final size:37
Alignment explanation
Indices: 44954178--44954606 Score: 178
Period size: 38 Copynumber: 11.4 Consensus size: 37
44954168 CCTATCCGCT
44954178 TGAAATTGAAGTAGAGTTGGACAACACGTCTTTATCTC
1 TGAAATTGAAGTAGAG-TGGACAACACGTCTTTATCTC
* * * * *
44954216 TGAAATTGAAGTAG-G-AG-CAAGATC-TTTTCCTGTCCGC
1 TGAAATTGAAGTAGAGTGGACAACA-CGTCTT--TAT-CTC
* *
44954253 TTGAAATTGAAGTAAAGTGGATAACACGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTGGACAACACGTCTTTATCTC
* * * * *
44954291 TGAAATTGAAGTAG-G-AG-CAAGATC-TTTTCCTGTCCGC
1 TGAAATTGAAGTAGAGTGGACAACA-CGTCTT--TAT-CTC
* *
44954328 TTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTGGACAACACGTCTTTATCTC
* * * *
44954366 TGAAATTGAAGTA-A--GAACAAGATCAT-TTCCTGTCCTC
1 TGAAATTGAAGTAGAGTGGACAACA-CGTCTT--TAT-CTC
* *
44954403 TTGAAATTGAAGTAGAGATGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAG-TGGACAACACGTCTTTATCTC
* *
44954442 TGAAATTGAAGTA-AG-AG-CAACATTGT-TTCCTATCCTC
1 TGAAATTGAAGTAGAGTGGACAACA-CGTCTT--TAT-CTC
* *
44954479 TTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAG-TGGACAACACGTCTTTATCTC
* * *
44954518 TGAAATTGAAGTA-AG-AG-CAAGATC-TTTTCCTATCCTC
1 TGAAATTGAAGTAGAGTGGACAACA-CGTCTT--TAT-CTC
* * * *
44954555 TTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAG-TGGACAACACGTCTTTATCTC
44954594 TGAAATTGAAGTA
1 TGAAATTGAAGTA
44954607 AGAGCAAGAT
Statistics
Matches: 288, Mismatches: 55, Indels: 96
0.66 0.13 0.22
Matches are distributed among these distances:
34 32 0.11
35 9 0.03
36 14 0.05
37 44 0.15
38 123 0.43
39 20 0.07
40 11 0.04
41 17 0.06
42 18 0.06
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (37 bp):
TGAAATTGAAGTAGAGTGGACAACACGTCTTTATCTC
Found at i:44954307 original size:75 final size:76
Alignment explanation
Indices: 44954157--44954695 Score: 769
Period size: 76 Copynumber: 7.1 Consensus size: 76
44954147 GAGACCGCAC
* * * *
44954157 CAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGACAACACGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAAT
*
44954222 TGAAGTAGGAG
66 TGAAGTAAGAG
* * * *
44954233 CAAGATCTTTTCCTGTCCGCTTGAAATTGAAGTAAAG-TGGATAACACGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAAT
*
44954297 TGAAGTAGGAG
66 TGAAGTAAGAG
* *
44954308 CAAGATCTTTTCCTGTCCGCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAAT
*
44954372 TGAAGTAAGAA
66 TGAAGTAAGAG
* * *
44954383 CAAGATCATTTCCTGTCCTCTTGAAATTGAAGTAGAGATGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAAT
44954448 TGAAGTAAGAG
66 TGAAGTAAGAG
* *
44954459 CAACAT-TGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
1 CAAGATCT-TTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAA
44954523 TTGAAGTAAGAG
65 TTGAAGTAAGAG
* *
44954535 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAAT
44954600 TGAAGTAAGAG
66 TGAAGTAAGAG
* * * * * **
44954611 CAAGATCATTTCATATCCTCTTGAAATTGAAGTAAAAGCTGGATATCAAGCCTTCGTCCCTCTGA
1 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTT--TATCTCTGA
44954676 AATTGAAGTAAGAG
63 AATTGAAGTAAGAG
*
44954690 TAAGAT
1 CAAGAT
44954696 GAAGCACCAA
Statistics
Matches: 433, Mismatches: 24, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
75 143 0.33
76 244 0.56
77 20 0.05
79 26 0.06
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (76 bp):
CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAAT
TGAAGTAAGAG
Found at i:44954607 original size:38 final size:38
Alignment explanation
Indices: 44954556--44954686 Score: 115
Period size: 38 Copynumber: 3.4 Consensus size: 38
44954546 CCTATCCTCT
44954556 TGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
1 TGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
* * ** *
44954594 TGAAATTGAAGTAAGAGC--AAGATCATTTC-ATATCCTC
1 TGAAATTGAAGTAA-AGCTGGATATCAAGTCTTTAT-CTC
* **
44954631 TTGAAATTGAAGTAAAAGCTGGATATCAAGCCTTCGTCCCTC
1 -TGAAATTGAAGT-AAAGCTGGATATCAAGTCTT--TATCTC
44954673 TGAAATTGAAGTAA
1 TGAAATTGAAGTAA
44954687 GAGTAAGATG
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
36 3 0.04
37 10 0.14
38 29 0.41
39 5 0.07
40 8 0.11
41 12 0.17
42 3 0.04
43 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (38 bp):
TGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
Found at i:44954777 original size:92 final size:92
Alignment explanation
Indices: 44954615--44954828 Score: 344
Period size: 92 Copynumber: 2.3 Consensus size: 92
44954605 TAAGAGCAAG
*
44954615 ATCA-TTTCATATCCTCTTGAAATTGAAGTAAAAGCTGGATATCAAGCCTTCGTCCCTCTGAAAT
1 ATCATTTTCATATCCTCTTGAAATTGAAGT-AAAGCTGGATAACAAGCCTTCGTCCCTCTGAAAT
*
44954679 TGAAGTAAGAGTAAGATGAAGCACCAAC
65 TCAAGTAAGAGTAAGATGAAGCACCAAC
* *
44954707 ATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGCCTTCGTCCCTCTGAAATT
1 ATCATTTTCATATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATT
*
44954772 CAAGTAAGAGTAAGATGAGGCACCAAC
66 CAAGTAAGAGTAAGATGAAGCACCAAC
*
44954799 ATCATTTTCGT-TCCT-TTGAAATTGAAGTAA
1 ATCATTTTCATATCCTCTTGAAATTGAAGTAA
44954829 GAGTAAGACA
Statistics
Matches: 115, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
90 15 0.13
91 4 0.03
92 72 0.63
93 24 0.21
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (92 bp):
ATCATTTTCATATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATT
CAAGTAAGAGTAAGATGAAGCACCAAC
Found at i:44954850 original size:50 final size:50
Alignment explanation
Indices: 44954755--44954852 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 50
44954745 ATAACAAGCC
** * *
44954755 TTCGTCCCTCTGAAATTCAAGTAAGAGTAAGATGAGGCACCAACATCATT
1 TTCGTCCCTCTGAAATTCAAGTAAGAGTAAGACAAAGCACAAACATCATT
* * *
44954805 TTCGTTCCTTTGAAATTGAAGTAAGAGTAAGACAAAGC-CTAAACATCA
1 TTCGTCCCTCTGAAATTCAAGTAAGAGTAAGACAAAGCAC-AAACATCA
44954853 AACCCTACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.03
50 39 0.98
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (50 bp):
TTCGTCCCTCTGAAATTCAAGTAAGAGTAAGACAAAGCACAAACATCATT
Found at i:44955129 original size:11 final size:11
Alignment explanation
Indices: 44955111--44955161 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
44955101 TTAAATTGAT
44955111 TTTAATTTTAAA
1 TTTAA-TTTAAA
*
44955123 TTTATTTTAAA
1 TTTAATTTAAA
* *
44955134 TTCAATTTGAA
1 TTTAATTTAAA
44955145 TTTAATTTAAA
1 TTTAATTTAAA
44955156 TTTAAT
1 TTTAAT
44955162 ATTATTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 29 0.88
12 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:44955158 original size:17 final size:17
Alignment explanation
Indices: 44955101--44955158 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
44955091 CATTTGGAAA
44955101 TTAAA-TTGATTTTAATT
1 TTAAATTTGATTTTAA-T
*
44955118 TTAAATTT-ATTTTAAA
1 TTAAATTTGATTTTAAT
* *
44955134 TTCAATTTGAATTTAAT
1 TTAAATTTGATTTTAAT
44955151 TTAAATTT
1 TTAAATTT
44955159 AATATTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 7 0.21
17 25 0.74
18 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (17 bp):
TTAAATTTGATTTTAAT
Found at i:44957182 original size:59 final size:59
Alignment explanation
Indices: 44957114--44957401 Score: 400
Period size: 59 Copynumber: 4.9 Consensus size: 59
44957104 CCTAGACTGT
44957114 CCAAAAATTACCATTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * * * *
44957173 TCAAAAATTACCATTTTATCCTCGAACTTTCCAAAATTCTATTTTAAACCCCAATTTCA
1 CCAAAAATTACCATTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
44957232 CCGAAAATTACCGTTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
44957291 TCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
44957350 CCAAAAATTATCGTTTTA-CCCTCAAACCTTCCAAAA-TCTCATTTTTGACCCC
1 CCAAAAATTACCATTTTAGCCC-CAAACTTTCCAAAATTC-CATTTTTAACCCC
44957402 AAATTTTCCC
Statistics
Matches: 200, Mismatches: 27, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
58 5 0.03
59 195 0.98
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:44957325 original size:118 final size:118
Alignment explanation
Indices: 44957114--44957401 Score: 454
Period size: 118 Copynumber: 2.4 Consensus size: 118
44957104 CCTAGACTGT
*
44957114 CCAAAAATTACCATTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAA
1 CCAAAAATTACCGTTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAA
* * *
44957179 ATTACCATTTTATCCTCGAACTTTCCAAAATTCTATTTTAAACCCCAATTTCA
66 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAAACCCCAATTTCA
*
44957232 CCGAAAATTACCGTTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAA
1 CCAAAAATTACCGTTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAA
* *
44957297 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
66 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAAACCCCAATTTCA
* * *
44957350 CCAAAAATTATCGTTTTA-CCCTCAAACCTTCCAAAA-TCTCATTTTTGACCCC
1 CCAAAAATTACCGTTTTAGCCC-CAAACTTTCCAAAATTC-CATTTTTAACCCC
44957402 AAATTTTCCC
Statistics
Matches: 157, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
117 5 0.03
118 152 0.97
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.34
Consensus pattern (118 bp):
CCAAAAATTACCGTTTTAGCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAA
ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAAACCCCAATTTCA
Found at i:44957470 original size:28 final size:29
Alignment explanation
Indices: 44957410--44957471 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
44957400 CCAAATTTTC
*
44957410 CCAAAATTACATTTTTGTCCCCCGAGAGT
1 CCAAAATTACATTTTTGTCCCCCGAGAAT
44957439 -CAAAATTACCA-TTTTG-CCCCCGA-ATAT
1 CCAAAATTA-CATTTTTGTCCCCCGAGA-AT
44957466 CCAAAA
1 CCAAAA
44957472 GTCTCGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
26 1 0.03
27 8 0.28
28 18 0.62
29 2 0.07
ACGTcount: A:0.34, C:0.29, G:0.10, T:0.27
Consensus pattern (29 bp):
CCAAAATTACATTTTTGTCCCCCGAGAAT
Found at i:44958771 original size:3 final size:3
Alignment explanation
Indices: 44958763--44958800 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
44958753 TTGTTAAAAA
*
44958763 ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
44958801 ATCACTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:44971122 original size:15 final size:15
Alignment explanation
Indices: 44971094--44971137 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
44971084 ACACATGTCA
44971094 TAAAACAAAGAAAGG
1 TAAAACAAAGAAAGG
* *
44971109 TAAAATAAATAAAGG
1 TAAAACAAAGAAAGG
* *
44971124 TCAAACATAGAAAG
1 TAAAACAAAGAAAG
44971138 ACCCAGACAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.64, C:0.07, G:0.16, T:0.14
Consensus pattern (15 bp):
TAAAACAAAGAAAGG
Found at i:44973099 original size:23 final size:25
Alignment explanation
Indices: 44973073--44973118 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
44973063 CCAATTAGGG
44973073 AATTA-TTGTTTAGA-TTTAATTCT
1 AATTATTTGTTTAGAGTTTAATTCT
*
44973096 AATTATTTTTTTAGAGTTTAATT
1 AATTATTTGTTTAGAGTTTAATT
44973119 TGGATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 8 0.40
25 7 0.35
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (25 bp):
AATTATTTGTTTAGAGTTTAATTCT
Found at i:44977980 original size:12 final size:12
Alignment explanation
Indices: 44977963--44977987 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44977953 GAAGTGAGTT
44977963 CTCCTCCTCTTC
1 CTCCTCCTCTTC
44977975 CTCCTCCTCTTC
1 CTCCTCCTCTTC
44977987 C
1 C
44977988 AAAGATAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTCCTCTTC
Found at i:44979373 original size:17 final size:17
Alignment explanation
Indices: 44979351--44979416 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
44979341 CCCAATAAAA
*
44979351 TAAATTTAGATTTATTT
1 TAAATTTAAATTTATTT
***
44979368 TAAATTTAAATTTGCAT
1 TAAATTTAAATTTATTT
* *
44979385 AAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
44979402 TAAATTTTAAATTTA
1 TAAA-TTTAAATTTA
44979417 AAATTAAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 28 0.74
18 10 0.26
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:44979375 original size:6 final size:6
Alignment explanation
Indices: 44979351--44979430 Score: 53
Period size: 6 Copynumber: 13.8 Consensus size: 6
44979341 CCCAATAAAA
* * ** *
44979351 TAAATT TAGATT T-ATTT TAAATT TAAATT TGCA-T AAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
44979397 T--ATT ATAAATTT TAAATT TAAAAT TAAA-T TAAAT
1 TAAATT -TAAA-TT TAAATT TAAATT TAAATT TAAAT
44979431 GTCCATTTAC
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
4 3 0.05
5 11 0.20
6 35 0.62
7 5 0.09
8 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:44980957 original size:29 final size:28
Alignment explanation
Indices: 44980925--44981017 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 28
44980915 CCGAACTTTT
44980925 CAAAATCCTATTTTTAACCCCGATTTCAC
1 CAAAATCC-ATTTTTAACCCCGATTTCAC
44980954 CAAAAATTACCA-TTTT-ACCCTCGAACTTT--C
1 C-AAAA-T-CCATTTTTAACCC-CG-A-TTTCAC
*
44980984 CAAAATCCCATTTTTAACCTCGATTTCAC
1 CAAAAT-CCATTTTTAACCCCGATTTCAC
44981013 CAAAA
1 CAAAA
44981018 ATTACCATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
27 3 0.06
28 5 0.10
29 21 0.40
30 15 0.29
31 3 0.06
32 5 0.10
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.32
Consensus pattern (28 bp):
CAAAATCCATTTTTAACCCCGATTTCAC
Found at i:44980960 original size:30 final size:29
Alignment explanation
Indices: 44980926--44981322 Score: 85
Period size: 30 Copynumber: 13.4 Consensus size: 29
44980916 CGAACTTTTC
44980926 AAAATCCTATTTTTAACCCCGATTTCACCA
1 AAAATCC-ATTTTTAACCCCGATTTCACCA
44980956 AAAATTACCA-TTTT-ACCCTCGAACTTT--CC-
1 AAAA-T-CCATTTTTAACCC-CG-A-TTTCACCA
*
44980985 AAAATCCCATTTTTAACCTCGATTTCACCA
1 AAAAT-CCATTTTTAACCCCGATTTCACCA
**
44981015 AAAATTACCA--TTT-ACCCTTAAACTTT--CC-
1 AAAA-T-CCATTTTTAACCC--CGA-TTTCACCA
* *
44981043 AAAATCCCATTTTTAACCTCGATTTCACTA
1 AAAAT-CCATTTTTAACCCCGATTTCACCA
* *
44981073 AAAATTACCA-TTTTATCCCTGAACTTT--CC-
1 AAAA-T-CCATTTTTAACCCCG-A-TTTCACCA
* *
44981102 AAAATCCCATTTTTAACCCCGCTTTCACTA
1 AAAAT-CCATTTTTAACCCCGATTTCACCA
* * *
44981132 AAAATTACCA-TCTTACCCCCGAACTTT---CT
1 AAAA-T-CCATTTTTAACCCCG-A-TTTCACCA
* *
44981161 AAAATCCCATTTTTAATCCCGATTTTACCA
1 AAAAT-CCATTTTTAACCCCGATTTCACCA
* * *
44981191 AAAAT-TATCATTTT-ACCCCTAAACTTT---CT
1 AAAATCCAT--TTTTAACCCC--GA-TTTCACCA
*
44981220 AAAATCCCATTTTTAACCCTGATTTCACCA
1 AAAAT-CCATTTTTAACCCCGATTTCACCA
* *
44981250 AAAATTGCC-GTTTTACCCCCGAACTTT--CC-
1 AAAA-T-CCATTTTTAACCCCG-A-TTTCACCA
*
44981279 AAAATCCTATTTTTAACCCCGATTTCACTA
1 AAAATCC-ATTTTTAACCCCGATTTCACCA
44981309 AAAATTACCATTTT
1 AAAA-T-CCATTTT
44981323 ACCCTCGAAA
Statistics
Matches: 265, Mismatches: 47, Indels: 109
0.63 0.11 0.26
Matches are distributed among these distances:
27 24 0.09
28 27 0.10
29 80 0.30
30 83 0.31
31 32 0.12
32 19 0.07
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATCCATTTTTAACCCCGATTTCACCA
Found at i:44980970 original size:59 final size:59
Alignment explanation
Indices: 44980907--44981331 Score: 600
Period size: 59 Copynumber: 7.2 Consensus size: 59
44980897 GAAATTATAT
* *
44980907 TTTTACCCCCGAACTTTTCAAAATCCTATTTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* *
44980966 TTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCA
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
*** * *
44981025 -TTTACCCTTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACTAAAAATTACCA
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* * * *
44981083 TTTTATCCCTGAACTTTCCAAAATCCCATTTTTAACCCCGCTTTCACTAAAAATTACCA
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* * * * *
44981142 TCTTACCCCCGAACTTTCTAAAATCCCATTTTTAATCCCGATTTTACCAAAAATTATCA
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
** * * * *
44981201 TTTTACCCCTAAACTTTCTAAAATCCCATTTTTAACCCTGATTTCACCAAAAATTGCCG
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* *
44981260 TTTTACCCCCGAACTTTCCAAAATCCTATTTTTAACCCCGATTTCACTAAAAATTACCA
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
*
44981319 TTTTACCCTCGAA
1 TTTTACCCCCGAA
44981332 AGTCAAAAAT
Statistics
Matches: 326, Mismatches: 39, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
58 55 0.17
59 271 0.83
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.35
Consensus pattern (59 bp):
TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
Found at i:44981028 original size:29 final size:30
Alignment explanation
Indices: 44980936--44981087 Score: 115
Period size: 29 Copynumber: 5.2 Consensus size: 30
44980926 AAAATCCTAT
*
44980936 TTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTAACCTCGATTTCACCAAAAATTACCA
* *
44980966 TTTTACCCTCGAACTTT--CC-AAAA-TCCCA
1 TTTTAACCTCG-A-TTTCACCAAAAATTACCA
44980994 TTTTTAACCTCGATTTCACCAAAAATTACCA
1 -TTTTAACCTCGATTTCACCAAAAATTACCA
* ** *
44981025 -TTTACCCTTAAACTTT--CC-AAAA-TCCCA
1 TTTTAACC-TCGA-TTTCACCAAAAATTACCA
*
44981052 TTTTTAACCTCGATTTCACTAAAAATTACCA
1 -TTTTAACCTCGATTTCACCAAAAATTACCA
44981083 TTTTA
1 TTTTA
44981088 TCCCTGAACT
Statistics
Matches: 93, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
27 10 0.11
28 11 0.12
29 31 0.33
30 26 0.28
31 12 0.13
32 3 0.03
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (30 bp):
TTTTAACCTCGATTTCACCAAAAATTACCA
Found at i:44983540 original size:31 final size:31
Alignment explanation
Indices: 44983505--44983575 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
44983495 TTTGATTAAC
*
44983505 TTTAGTCATTATA-TTTTTCTAATTAGTCAAT
1 TTTAGTCATTATACTTTTT-AAATTAGTCAAT
* * *
44983536 TTTAGTTC-CTATACTTTTTAAATTTGTTAAT
1 TTTAG-TCATTATACTTTTTAAATTAGTCAAT
44983567 TTTAGTCAT
1 TTTAGTCAT
44983576 GACCAGATGG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
30 2 0.06
31 23 0.72
32 7 0.22
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.56
Consensus pattern (31 bp):
TTTAGTCATTATACTTTTTAAATTAGTCAAT
Found at i:44985534 original size:20 final size:20
Alignment explanation
Indices: 44985493--44985534 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
44985483 GGAACCTACT
*
44985493 TAGTATATCATATCAATGAA
1 TAGTATATCATATCAATAAA
44985513 TAGTAT-TCATATCATATAAA
1 TAGTATATCATATCA-ATAAA
44985533 TA
1 TA
44985535 TACAAACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (20 bp):
TAGTATATCATATCAATAAA
Found at i:44991493 original size:2 final size:2
Alignment explanation
Indices: 44991486--44991516 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44991476 CATCACCTTT
44991486 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
44991517 GGATTCATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:45005389 original size:15 final size:16
Alignment explanation
Indices: 45005360--45005392 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45005350 ATTTGATATT
*
45005360 TAAAAAGATAGAAAAA
1 TAAAAAGATACAAAAA
45005376 TAAAAAGAT-CAAAAA
1 TAAAAAGATACAAAAA
45005391 TA
1 TA
45005393 TATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.73, C:0.03, G:0.09, T:0.15
Consensus pattern (16 bp):
TAAAAAGATACAAAAA
Found at i:45016955 original size:23 final size:22
Alignment explanation
Indices: 45016929--45016985 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
45016919 AGAGGTTTTC
*
45016929 AAAATTTTAAAAATTATAT-ATT
1 AAAATTTTAAAAATT-TATGAGT
*
45016951 GAAAATTTTTAAAATTTATGAGT
1 -AAAATTTTAAAAATTTATGAGT
45016974 AAAATTTTAAAA
1 AAAATTTTAAAA
45016986 GGAGATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
AAAATTTTAAAAATTTATGAGT
Found at i:45024567 original size:42 final size:42
Alignment explanation
Indices: 45024501--45024590 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
45024491 GGAAAATTGT
*
45024501 GCTTTCTTATCAACTGTGTAGAAAGCTCGTCTAGCTGGACAA
1 GCTTTCTTATCAACTGTGCAGAAAGCTCGTCTAGCTGGACAA
* * * * * *
45024543 GCTTTCTTGTCAATTGTGCCGAAAGCTCGTTTAGTTGGACGA
1 GCTTTCTTATCAACTGTGCAGAAAGCTCGTCTAGCTGGACAA
45024585 GCTTTC
1 GCTTTC
45024591 CTGACATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (42 bp):
GCTTTCTTATCAACTGTGCAGAAAGCTCGTCTAGCTGGACAA
Found at i:45024667 original size:42 final size:42
Alignment explanation
Indices: 45024608--45024707 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
45024598 ATTTTCCTAA
* * *
45024608 CAATTGTGTAAAAAGCTCGCCCAGTTGGACGAGC-TTTCTTGC
1 CAATTGTGCAAAAAGCTCGCCCAATTGGACAAGCTTTTC-TGC
* *
45024650 CAATTGTGCGAAAAGCTCGCTCAATTGGACAAGCTTTTCTGC
1 CAATTGTGCAAAAAGCTCGCCCAATTGGACAAGCTTTTCTGC
*
45024692 CAACTGTGCAAAAAGC
1 CAATTGTGCAAAAAGC
45024708 GCTCAGCTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 46 0.92
43 4 0.08
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (42 bp):
CAATTGTGCAAAAAGCTCGCCCAATTGGACAAGCTTTTCTGC
Found at i:45025104 original size:17 final size:17
Alignment explanation
Indices: 45025084--45025122 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
45025074 TCACTAAGTA
* *
45025084 TAATTATAATATTTATT
1 TAATTAGAATATGTATT
*
45025101 TAATGAGAATATGTATT
1 TAATTAGAATATGTATT
45025118 TAATT
1 TAATT
45025123 TAGTGAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (17 bp):
TAATTAGAATATGTATT
Found at i:45028784 original size:28 final size:28
Alignment explanation
Indices: 45028749--45028842 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 28
45028739 ATTTTACAAA
45028749 ATAA-ATAGTCATTGGCGGACATTACAC
1 ATAAGATAGTCATTGGCGGACATTACAC
* * * * *
45028776 TTAAGATAGTCCA-TGACGGACTTTTCGC
1 ATAAGATAGT-CATTGGCGGACATTACAC
* * * *
45028804 ATAAGACAATTATTGGCGGACATTCCAC
1 ATAAGATAGTCATTGGCGGACATTACAC
45028832 ATAAGATAGTC
1 ATAAGATAGTC
45028843 CCTGACGGAA
Statistics
Matches: 48, Mismatches: 16, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
27 4 0.08
28 42 0.88
29 2 0.04
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (28 bp):
ATAAGATAGTCATTGGCGGACATTACAC
Found at i:45028825 original size:56 final size:56
Alignment explanation
Indices: 45028759--45028866 Score: 171
Period size: 56 Copynumber: 1.9 Consensus size: 56
45028749 ATAAATAGTC
* * *
45028759 ATTGGCGGACATTACACTTAAGATAGTCCATGACGGACTTTTCGCATAAGACAATT
1 ATTGGCGGACATTACACATAAGATAGTCCATGACGGAATTTACGCATAAGACAATT
* *
45028815 ATTGGCGGACATTCCACATAAGATAGTCCCTGACGGAATTTACGCATAAGAC
1 ATTGGCGGACATTACACATAAGATAGTCCATGACGGAATTTACGCATAAGAC
45028867 GGTCCTTGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (56 bp):
ATTGGCGGACATTACACATAAGATAGTCCATGACGGAATTTACGCATAAGACAATT
Found at i:45028851 original size:28 final size:28
Alignment explanation
Indices: 45028764--45028865 Score: 73
Period size: 28 Copynumber: 3.6 Consensus size: 28
45028754 TAGTCATTGG
*
45028764 CGGACATTACACTTAAGATAGTCCATGA
1 CGGACATTACACATAAGATAGTCCATGA
* * * * * * *
45028792 CGGACTTTTCGCATAAGACAAT-TATTGG
1 CGGACATTACACATAAGATAGTCCA-TGA
* *
45028820 CGGACATTCCACATAAGATAGTCCCTGA
1 CGGACATTACACATAAGATAGTCCATGA
*
45028848 CGGA-ATTTACGCATAAGA
1 CGGACA-TTACACATAAGA
45028866 CGGTCCTTGG
Statistics
Matches: 53, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
27 2 0.04
28 51 0.96
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (28 bp):
CGGACATTACACATAAGATAGTCCATGA
Found at i:45028871 original size:28 final size:28
Alignment explanation
Indices: 45028831--45028895 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
45028821 GGACATTCCA
*
45028831 CATAAGATAGTCCCTGACGGAATTTACG
1 CATAAGACAGTCCCTGACGGAATTTACG
* * ** * *
45028859 CATAAGACGGTCCTTGGTGGACTTTCCG
1 CATAAGACAGTCCCTGACGGAATTTACG
45028887 CATAAGACA
1 CATAAGACA
45028896 ACCCTTCGCG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (28 bp):
CATAAGACAGTCCCTGACGGAATTTACG
Found at i:45028891 original size:56 final size:56
Alignment explanation
Indices: 45028757--45028893 Score: 166
Period size: 56 Copynumber: 2.4 Consensus size: 56
45028747 AAATAAATAG
* * * *
45028757 TCATTGGCGGACATTACACTTAAGATAGTCCATGACGGACTTTTCGCATAAGACAA
1 TCATTGGCGGACATTCCACATAAGATAGTCCATGACGGAATTTACGCATAAGACAA
* * **
45028813 TTATTGGCGGACATTCCACATAAGATAGTCCCTGACGGAATTTACGCATAAGACGG
1 TCATTGGCGGACATTCCACATAAGATAGTCCATGACGGAATTTACGCATAAGACAA
* * * *
45028869 TCCTTGGTGGACTTTCCGCATAAGA
1 TCATTGGCGGACATTCCACATAAGA
45028894 CAACCCTTCG
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (56 bp):
TCATTGGCGGACATTCCACATAAGATAGTCCATGACGGAATTTACGCATAAGACAA
Found at i:45028945 original size:84 final size:84
Alignment explanation
Indices: 45028793--45028959 Score: 208
Period size: 84 Copynumber: 2.0 Consensus size: 84
45028783 AGTCCATGAC
* ** * * *
45028793 GGACTTTTCGCATAAGACAATTATTGGCGGACATTCCACATAAGATAGTCCCTGACGGAATTTAC
1 GGACTTTCCGCATAAGACAACCATTCGCGGACATTCCACATAAAATAGTCCCTGACAGAATTTAC
*
45028858 GCATAAGACGGTCCTTGGT
66 GCATAAGACGATCCTTGGT
* ** * * *
45028877 GGACTTTCCGCATAAGACAACCCTTCGCGGACATTCCACATAAAATAGTCTGTGGCAGACTTTTC
1 GGACTTTCCGCATAAGACAACCATTCGCGGACATTCCACATAAAATAGTCCCTGACAGAATTTAC
*
45028942 GCATAAGATGATCCTTGG
66 GCATAAGACGATCCTTGG
45028960 CGGGCTTCCC
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (84 bp):
GGACTTTCCGCATAAGACAACCATTCGCGGACATTCCACATAAAATAGTCCCTGACAGAATTTAC
GCATAAGACGATCCTTGGT
Found at i:45029450 original size:35 final size:35
Alignment explanation
Indices: 45029397--45029507 Score: 98
Period size: 35 Copynumber: 3.2 Consensus size: 35
45029387 GTCCATAAAC
* * * *
45029397 CATTTACATGGTGTCGCTCTATAGAGCCAGTAGAA
1 CATTTCCATGATGCCGCTCTGTAGAGCCAGTAGAA
* * * *
45029432 CATTTCCATGATGCCGCTCCGTAGAGCTAATAGAC
1 CATTTCCATGATGCCGCTCTGTAGAGCCAGTAGAA
* ** *
45029467 CATTTCCATAATGCCAAT-TCGTAGAGCGAGTAGAA
1 CATTTCCATGATGCCGCTCT-GTAGAGCCAGTAGAA
45029502 CATTTC
1 CATTTC
45029508 TCCAACCAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (35 bp):
CATTTCCATGATGCCGCTCTGTAGAGCCAGTAGAA
Found at i:45044195 original size:37 final size:37
Alignment explanation
Indices: 45044129--45044200 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
45044119 CTTATTTGCA
*
45044129 TTGCTTTTTTGAGACTTTTTTGTCCGATTCGAGTTTT
1 TTGCTTTTTTGAGACTTTTTTGTCCGATTCAAGTTTT
* **
45044166 TTGCTTTTTTTAG-CTTTTTTTGTTTGATTCAAGTT
1 TTGCTTTTTTGAGAC-TTTTTTGTCCGATTCAAGTT
45044201 ACTTTACCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.03
37 29 0.97
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.61
Consensus pattern (37 bp):
TTGCTTTTTTGAGACTTTTTTGTCCGATTCAAGTTTT
Found at i:45051862 original size:22 final size:22
Alignment explanation
Indices: 45051837--45051882 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
45051827 TTGGAAATAG
45051837 TAAGAAAATAGGAGAAGGAAGA
1 TAAGAAAATAGGAGAAGGAAGA
45051859 TAAGAAAATAGGAGAAGGAAGA
1 TAAGAAAATAGGAGAAGGAAGA
45051881 TA
1 TA
45051883 GATCCCTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (22 bp):
TAAGAAAATAGGAGAAGGAAGA
Found at i:45052187 original size:16 final size:16
Alignment explanation
Indices: 45052166--45052198 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
45052156 CTGTAGGCTT
45052166 ATTGTTAGATTCGAAC
1 ATTGTTAGATTCGAAC
45052182 ATTGTTAGATTCGAAC
1 ATTGTTAGATTCGAAC
45052198 A
1 A
45052199 GTTAAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (16 bp):
ATTGTTAGATTCGAAC
Found at i:45060641 original size:31 final size:30
Alignment explanation
Indices: 45060593--45060650 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
45060583 GGGCTCAAAA
*
45060593 TTTTTTTATCAA-TTTTTAAGAGATCTAGTT
1 TTTTTTTATCAACTTTTAAAGA-ATCTAGTT
*
45060623 TTTTTTTCTTCAACTTTTAAAGAATCTA
1 TTTTTTT-ATCAACTTTTAAAGAATCTA
45060651 AAACTCCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.29
31 9 0.38
32 8 0.33
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (30 bp):
TTTTTTTATCAACTTTTAAAGAATCTAGTT
Found at i:45063233 original size:24 final size:22
Alignment explanation
Indices: 45063186--45063227 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
45063176 AAGGAAACTC
45063186 TGTCATTTTCATCTCTCTCTTT
1 TGTCATTTTCATCTCTCTCTTT
45063208 TGTCATTTTCATCTCTCTCT
1 TGTCATTTTCATCTCTCTCT
45063228 CTTTTGCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.10, C:0.29, G:0.05, T:0.57
Consensus pattern (22 bp):
TGTCATTTTCATCTCTCTCTTT
Found at i:45066452 original size:17 final size:17
Alignment explanation
Indices: 45066418--45066450 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
45066408 TAATTAAATT
*
45066418 TTTTAAAATTTGTAAAA
1 TTTTAAAATTAGTAAAA
45066435 TTTT-AAATTAGTAAAA
1 TTTTAAAATTAGTAAAA
45066451 ATAGAATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TTTTAAAATTAGTAAAA
Found at i:45084247 original size:27 final size:29
Alignment explanation
Indices: 45084215--45084283 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
45084205 AAAAATTGGT
*
45084215 AAAAATTATAAAA-TATATAGAAT-ATAA
1 AAAAATTATAAAATTATATAAAATCATAA
* *
45084242 AAAAATTATAAAATTTTATAAAATCGTAA
1 AAAAATTATAAAATTATATAAAATCATAA
*
45084271 GAAAATTATAAAA
1 AAAAATTATAAAA
45084284 AGTAAACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 13 0.36
28 8 0.22
29 15 0.42
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAAATTATAAAATTATATAAAATCATAA
Found at i:45084264 original size:18 final size:19
Alignment explanation
Indices: 45084214--45084265 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
45084204 AAAAAATTGG
45084214 TAAAA-ATTATAAAATATA
1 TAAAATATTATAAAATATA
* * *
45084232 TAGAATATAAAAAAAT-TA
1 TAAAATATTATAAAATATA
*
45084250 TAAAATTTTATAAAAT
1 TAAAATATTATAAAAT
45084266 CGTAAGAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAAATATTATAAAATATA
Found at i:45084279 original size:19 final size:18
Alignment explanation
Indices: 45084257--45084321 Score: 53
Period size: 21 Copynumber: 3.4 Consensus size: 18
45084247 TTATAAAATT
45084257 TTATAAAATCGTAAGAAAA
1 TTATAAAATCGTAA-AAAA
*
45084276 TTATAAAA-AGTAAACAAA
1 TTATAAAATCGTAAA-AAA
*
45084294 -TATAAAATTCATAAAAAAAA
1 TTATAAAA-TCGT--AAAAAA
45084314 TTATAAAA
1 TTATAAAA
45084322 ATTATTATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
17 8 0.22
18 7 0.19
19 9 0.24
20 3 0.08
21 10 0.27
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
TTATAAAATCGTAAAAAA
Found at i:45084619 original size:15 final size:16
Alignment explanation
Indices: 45084590--45084621 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45084580 AAATTTTATA
45084590 ATTTTTATAATTTTTT
1 ATTTTTATAATTTTTT
45084606 ATTTTTATAATTTTTT
1 ATTTTTATAATTTTTT
45084622 TTGTTATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTATAATTTTTT
Found at i:45084621 original size:10 final size:9
Alignment explanation
Indices: 45084583--45084620 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
45084573 CTATATTAAA
45084583 TTTTATAAT
1 TTTTATAAT
45084592 TTTTATAAT
1 TTTTATAAT
45084601 TTTT-T-AT
1 TTTTATAAT
45084608 TTTTATAAT
1 TTTTATAAT
45084617 TTTT
1 TTTT
45084621 TTTGTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 6 0.22
8 2 0.07
9 19 0.70
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATAAT
Found at i:45084628 original size:15 final size:16
Alignment explanation
Indices: 45084594--45084629 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
45084584 TTTATAATTT
*
45084594 TTATAATTTTTTATTT
1 TTATAATTTTTTATTG
45084610 TTATAATTTTTT-TTG
1 TTATAATTTTTTATTG
45084625 TTATA
1 TTATA
45084630 TGTCATGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTATAATTTTTTATTG
Found at i:45085421 original size:14 final size:16
Alignment explanation
Indices: 45085387--45085427 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
45085377 TATATTTGTA
45085387 AAAAAATATAAATTTT
1 AAAAAATATAAATTTT
*
45085403 AAAAAATA-AAATTTC
1 AAAAAATATAAATTTT
45085418 AAAAAATATA
1 AAAAAATATA
45085428 TTATAAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAATATAAATTTT
Found at i:45087787 original size:113 final size:113
Alignment explanation
Indices: 45087639--45087872 Score: 380
Period size: 113 Copynumber: 2.1 Consensus size: 113
45087629 TCCATTAACC
* * *
45087639 CAAAA-AAACTTAGCGGGAAGAAGATATTGAAACCAAAGATATTGAATCTTTTGGTTAATGAGTT
1 CAAAAGAAACTTAACGGGAAAAAGATATTGAAACCAAAGATATTGAATCTTTTGGTTAATGAGGT
* *
45087703 TTAAAAATTCAAGCTTTGAGACAGATTTGTAACTAAAGATCTTGAAAT
66 TTAAAAATTCAAGCTTTCAGACAGATTTGTAACTAAAGATATTGAAAT
* *
45087751 CAAAAGAAACTTAACGGGAAAAAGATATTGAAACCAAATATATTGAATCTTTTGGTTAATGGGGT
1 CAAAAGAAACTTAACGGGAAAAAGATATTGAAACCAAAGATATTGAATCTTTTGGTTAATGAGGT
* *
45087816 TTAAAGATTCAAGCTTTCAGATAGATTTGTAACTAAAGATATTGAAAT
66 TTAAAAATTCAAGCTTTCAGACAGATTTGTAACTAAAGATATTGAAAT
45087864 CAAAAGAAA
1 CAAAAGAAA
45087873 AGAAGATGAA
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
112 5 0.04
113 107 0.96
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (113 bp):
CAAAAGAAACTTAACGGGAAAAAGATATTGAAACCAAAGATATTGAATCTTTTGGTTAATGAGGT
TTAAAAATTCAAGCTTTCAGACAGATTTGTAACTAAAGATATTGAAAT
Found at i:45098397 original size:8 final size:8
Alignment explanation
Indices: 45098384--45098413 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
45098374 ACCCAATTAT
45098384 TTTTTTTA
1 TTTTTTTA
45098392 TTTTTTTTA
1 -TTTTTTTA
45098401 TTTTTTTA
1 TTTTTTTA
45098409 TTTTT
1 TTTTT
45098414 ATAATTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:45098398 original size:10 final size:9
Alignment explanation
Indices: 45098380--45098413 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
45098370 GGCAACCCAA
45098380 TTATTTTTT
1 TTATTTTTT
45098389 TTATTTTTT
1 TTATTTTTT
45098398 TTA-TTTTT
1 TTATTTTTT
45098406 TTATTTTT
1 TTATTTTT
45098414 ATAATTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTATTTTTT
Found at i:45098678 original size:13 final size:13
Alignment explanation
Indices: 45098662--45098697 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
45098652 ACCCTAATTT
45098662 CTTTTCCTTATAA
1 CTTTTCCTTATAA
*
45098675 CTTTTCTTTATAA
1 CTTTTCCTTATAA
*
45098688 TTTTTCCTTA
1 CTTTTCCTTA
45098698 ATCGCCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (13 bp):
CTTTTCCTTATAA
Found at i:45100272 original size:24 final size:24
Alignment explanation
Indices: 45100253--45100333 Score: 153
Period size: 24 Copynumber: 3.4 Consensus size: 24
45100243 TTTAGCTAAC
*
45100253 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
45100277 ACGAGCCCAAAATGATTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
45100301 ACGAGCCCAAAATGATTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
45100325 ACGAGCCCA
1 ACGAGCCCA
45100334 GATAGAGTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (24 bp):
ACGAGCCCAAAATGATTAGCTCTT
Found at i:45102248 original size:38 final size:38
Alignment explanation
Indices: 45102206--45102282 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
45102196 CCGATTATCC
45102206 GGTAACTTGCATTTTCCCAACCGAAACAACTGAGACAA
1 GGTAACTTGCATTTTCCCAACCGAAACAACTGAGACAA
45102244 GGTAACTTGCATTTTCCCAACCGAAACAACTGAGACAA
1 GGTAACTTGCATTTTCCCAACCGAAACAACTGAGACAA
45102282 G
1 G
45102283 TATGATCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (38 bp):
GGTAACTTGCATTTTCCCAACCGAAACAACTGAGACAA
Found at i:45104227 original size:25 final size:24
Alignment explanation
Indices: 45104190--45104237 Score: 62
Period size: 27 Copynumber: 1.9 Consensus size: 24
45104180 AATGAATTTT
45104190 AAATTTTATTA-TTATATTTTTAA
1 AAATTTTATTATTTATATTTTTAA
45104213 AAATATTTATGTATTTTATATTTTT
1 AAAT-TTTAT-TA-TTTATATTTTT
45104238 TTTTTGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
25 2 0.10
27 10 0.48
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AAATTTTATTATTTATATTTTTAA
Found at i:45114335 original size:12 final size:13
Alignment explanation
Indices: 45114318--45114354 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
45114308 GGCAATCCAA
45114318 TTATTTTTATTT-
1 TTATTTTTATTTC
45114330 TTATTTTTATTTC
1 TTATTTTTATTTC
45114343 TCTA-TTTTATTT
1 T-TATTTTTATTT
45114355 ATTTATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.52
13 9 0.39
14 2 0.09
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (13 bp):
TTATTTTTATTTC
Found at i:45131810 original size:18 final size:19
Alignment explanation
Indices: 45131777--45131812 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
45131767 TTGTGATTTT
45131777 TAAAAATTATAATAAATTA
1 TAAAAATTATAATAAATTA
*
45131796 TAAAAATT-TATTAAATT
1 TAAAAATTATAATAAATT
45131813 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAAATTATAATAAATTA
Found at i:45131815 original size:19 final size:20
Alignment explanation
Indices: 45131772--45131815 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
45131762 CCTAGTTGTG
*
45131772 ATTTTTAAAAATTATAATAA
1 ATTTATAAAAATTATAATAA
*
45131792 A-TTATAAAAATT-TATTAA
1 ATTTATAAAAATTATAATAA
45131810 ATTTAT
1 ATTTAT
45131816 TTTAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 14 0.67
20 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTATAAAAATTATAATAA
Found at i:45132187 original size:16 final size:16
Alignment explanation
Indices: 45132141--45132189 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
45132131 TCCTAGAAGT
45132141 ATTTTT-AAAATAATTA
1 ATTTTTAAAAAT-ATTA
*
45132157 TTTTTTGAGAAAATATTA
1 ATTTTT-A-AAAATATTA
45132175 ATTTTTAAAAATATT
1 ATTTTTAAAAATATT
45132190 TGCTGAAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 13 0.46
17 1 0.04
18 9 0.32
19 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (16 bp):
ATTTTTAAAAATATTA
Found at i:45137647 original size:19 final size:19
Alignment explanation
Indices: 45137596--45137650 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
45137586 TAAAGTCTTT
*
45137596 AATAATATAGTGTTAAAATA
1 AATAATATAATGTTAAAA-A
*
45137616 AA-AAAAT-AT-TTAAAAA
1 AATAATATAATGTTAAAAA
45137632 AATAATATAATGTTAAAAA
1 AATAATATAATGTTAAAAA
45137651 CTATACATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 3 0.10
17 10 0.34
18 3 0.10
19 11 0.38
20 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AATAATATAATGTTAAAAA
Found at i:45137650 original size:20 final size:20
Alignment explanation
Indices: 45137596--45137650 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
45137586 TAAAGTCTTT
*
45137596 AATAATATAGTGTTAAAATAA
1 AATAATATAATGTTAAAA-AA
45137617 AA-AA-AT-AT-TT-AAAAA
1 AATAATATAATGTTAAAAAA
45137632 AATAATATAATGTTAAAAA
1 AATAATATAATGTTAAAAA
45137651 CTATACATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 11
0.70 0.03 0.28
Matches are distributed among these distances:
15 4 0.14
16 5 0.18
17 4 0.14
18 3 0.11
19 4 0.14
20 6 0.21
21 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
AATAATATAATGTTAAAAAA
Found at i:45146121 original size:10 final size:11
Alignment explanation
Indices: 45146104--45146132 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
45146094 TCAAGAGAAG
45146104 TAAATAAATAA
1 TAAATAAATAA
45146115 T-AATAAATAA
1 TAAATAAATAA
45146125 TAAATAAA
1 TAAATAAA
45146133 AATCAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:45146321 original size:13 final size:13
Alignment explanation
Indices: 45146287--45146321 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
45146277 TCATTTTCTG
45146287 TTTCCTTTTTTTT
1 TTTCCTTTTTTTT
*
45146300 TTCCCTTTTTTTT
1 TTTCCTTTTTTTT
*
45146313 TTTCGTTTT
1 TTTCCTTTT
45146322 CATTGTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTCCTTTTTTTT
Found at i:45147425 original size:134 final size:133
Alignment explanation
Indices: 45147184--45147432 Score: 374
Period size: 134 Copynumber: 1.9 Consensus size: 133
45147174 AGTGACTAAT
* * *
45147184 TGTTCCACAACCAAACAACTGGCCACCCTAACAAACCATTGAACTAGACTAAATTAACAAAACCT
1 TGTTCCACAACCAAACAACTGGCCACCCTAACAAACCACTAAACTAGACTAAATCAACAAAACCT
* * * *
45147249 ACTCGAGATCTCCTACTAAAGATTCGAGTAGGCCATCAAAGATGTAGAAATAACTAATGGCAGCT
66 ACTCGAGATCTCCTACCAAAGATTCGAGTAGACCACCAAAGATATAGAAATAACTAATGGCAGCT
45147314 TAC
131 TAC
** *
45147317 TGTTCCACAACCAAACAACTGGTTACCCTAACAAACTACTAAACTAAAGACTAAATCAACAAAAC
1 TGTTCCACAACCAAACAACTGGCCACCCTAACAAACCACTAAACT--AGACTAAATCAACAAAAC
*
45147382 CTAC-CGAGATCTCCTACCGAAGATTCGAGTAGACCACCAAAGATATAGAAA
64 CTACTCGAGATCTCCTACCAAAGATTCGAGTAGACCACCAAAGATATAGAAA
45147433 CGGCTAAGGA
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
133 40 0.39
134 42 0.41
135 21 0.20
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (133 bp):
TGTTCCACAACCAAACAACTGGCCACCCTAACAAACCACTAAACTAGACTAAATCAACAAAACCT
ACTCGAGATCTCCTACCAAAGATTCGAGTAGACCACCAAAGATATAGAAATAACTAATGGCAGCT
TAC
Found at i:45149694 original size:22 final size:22
Alignment explanation
Indices: 45149666--45149711 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
45149656 CAAAAGCATG
45149666 TCTAAACATT-CATT-TAACTATT
1 TCTAAAC-TTCCATTCTAAC-ATT
45149688 TCTAAACTTCCATTCTAACATT
1 TCTAAACTTCCATTCTAACATT
45149710 TC
1 TC
45149712 CATAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 16 0.73
23 4 0.18
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (22 bp):
TCTAAACTTCCATTCTAACATT
Found at i:45150572 original size:20 final size:21
Alignment explanation
Indices: 45150535--45150575 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
45150525 ATACCACACT
* *
45150535 AGAGAGCACTGAAGTGCAAAC
1 AGAGAGCACTAAAATGCAAAC
45150556 AGAG-GCACTAAAATGCAAAC
1 AGAGAGCACTAAAATGCAAAC
45150576 CTATACAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (21 bp):
AGAGAGCACTAAAATGCAAAC
Found at i:45153272 original size:24 final size:24
Alignment explanation
Indices: 45153240--45153286 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
45153230 AGTTTGACTC
* *
45153240 AAACAAATAAATAGATTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
45153264 AAACAAATAAACAGAGTTTAATT
1 AAACAAATAAACAGAGTTTAATT
45153287 AAAAGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:45160992 original size:15 final size:15
Alignment explanation
Indices: 45160972--45161003 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
45160962 CTTCTTATTA
*
45160972 GGGGTGGGTAAATTT
1 GGGGTGGGTAAAATT
45160987 GGGGTGGGTAAAATT
1 GGGGTGGGTAAAATT
45161002 GG
1 GG
45161004 ATTAGATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.50, T:0.28
Consensus pattern (15 bp):
GGGGTGGGTAAAATT
Found at i:45161266 original size:20 final size:19
Alignment explanation
Indices: 45161237--45161308 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
45161227 TTACAAAAAA
*
45161237 AAAAAATCAAAATCATTTTT
1 AAAAATTCAAAAT-ATTTTT
*
45161257 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATATTTTT
* * *
45161276 AAAATTTTAAAATATTTAT
1 AAAAATTCAAAATATTTTT
45161295 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
45161309 TTATATTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 24 0.56
20 19 0.44
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATATTTTT
Found at i:45161283 original size:28 final size:29
Alignment explanation
Indices: 45161251--45161310 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
45161241 AATCAAAATC
*
45161251 ATTTTTAAAA-ATTCA-AAATAATTTTAAA
1 ATTTTTAAAATATTCATAAA-AATTTCAAA
*
45161279 A-TTTTAAAATATTTATAAAAATTTCAAA
1 ATTTTTAAAATATTCATAAAAATTTCAAA
45161307 ATTT
1 ATTT
45161311 ATATTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
27 8 0.30
28 14 0.52
29 5 0.19
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTTTAAAATATTCATAAAAATTTCAAA
Found at i:45162930 original size:11 final size:11
Alignment explanation
Indices: 45162857--45162932 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
45162847 ATTCCAAAAA
*
45162857 TAATATTATTT
1 TAATATTAATT
45162868 TAATAGTTTAATAT
1 TAATA--TTAAT-T
45162882 TAA-ATTAAATT
1 TAATATT-AATT
*
45162893 TAATACTTATTT
1 TAATA-TTAATT
*
45162905 TAATAGT-ATT
1 TAATATTAATT
45162915 T--TATTAATT
1 TAATATTAATT
45162924 TAATATTAA
1 TAATATTAA
45162933 AGTGATTATC
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 3 0.06
11 18 0.35
12 12 0.24
13 7 0.14
14 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (11 bp):
TAATATTAATT
Found at i:45170068 original size:16 final size:16
Alignment explanation
Indices: 45170049--45170095 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
45170039 AATTTTCAAT
45170049 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
45170065 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
45170081 AAATAAAACAATATA
1 AAATAAAA-AATATA
45170096 AATATTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:45171348 original size:14 final size:14
Alignment explanation
Indices: 45171329--45171377 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
45171319 TATTATTACT
* *
45171329 TTTACAAAAGTCTA
1 TTTACAAAAATCCA
45171343 TTTACAAAAATCCA
1 TTTACAAAAATCCA
45171357 TTTACAAAAA-CCA
1 TTTACAAAAATCCA
*
45171370 ATTACAAA
1 TTTACAAA
45171378 CCCAATGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (14 bp):
TTTACAAAAATCCA
Found at i:45171496 original size:22 final size:22
Alignment explanation
Indices: 45171468--45171548 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
45171458 CATTGCCAGT
45171468 CATCATCGCCACGTCAGTGCCA
1 CATCATCGCCACGTCAGTGCCA
* *
45171490 CATCATCGCCACATCAGCGCCATA
1 CATCATCGCCACGTCAGTGCC--A
* *
45171514 TCAACATCGCCACGTCAATGCCA
1 -CATCATCGCCACGTCAGTGCCA
*
45171537 CATCAGCGCCAC
1 CATCATCGCCAC
45171549 ATCAACATCA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 29 0.60
23 1 0.02
24 1 0.02
25 17 0.35
ACGTcount: A:0.27, C:0.42, G:0.15, T:0.16
Consensus pattern (22 bp):
CATCATCGCCACGTCAGTGCCA
Found at i:45171500 original size:11 final size:11
Alignment explanation
Indices: 45171468--45171552 Score: 66
Period size: 11 Copynumber: 7.5 Consensus size: 11
45171458 CATTGCCAGT
45171468 CATCATCGCCA
1 CATCATCGCCA
*
45171479 CGTCAGT-GCCA
1 CATCA-TCGCCA
45171490 CATCATCGCCA
1 CATCATCGCCA
*
45171501 CATCAGCGCCATA
1 CATCATCGCC--A
*
45171514 TCAACATCGCCA
1 -CATCATCGCCA
*
45171526 CGTCAAT-GCCA
1 CATC-ATCGCCA
*
45171537 CATCAGCGCCA
1 CATCATCGCCA
45171548 CATCA
1 CATCA
45171553 ACATCACCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
10 2 0.03
11 43 0.74
12 4 0.07
13 1 0.02
14 8 0.14
ACGTcount: A:0.28, C:0.41, G:0.14, T:0.16
Consensus pattern (11 bp):
CATCATCGCCA
Found at i:45171537 original size:36 final size:36
Alignment explanation
Indices: 45171497--45171577 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
45171487 CCACATCATC
* *
45171497 GCCACATCAGCGCCATATCAACATCGCCACGTCAAT
1 GCCACATCAGCGCCACATCAACATCACCACGTCAAT
45171533 GCCACATCAGCGCCACATCAACATCACCACGTCAAT
1 GCCACATCAGCGCCACATCAACATCACCACGTCAAT
45171569 GCCACATCA
1 GCCACATCA
45171578 ACACCTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.32, C:0.41, G:0.12, T:0.15
Consensus pattern (36 bp):
GCCACATCAGCGCCACATCAACATCACCACGTCAAT
Found at i:45173283 original size:3 final size:3
Alignment explanation
Indices: 45173277--45173309 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
45173267 AAAAAAAACG
45173277 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
45173310 TTAGTCAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:45184854 original size:49 final size:50
Alignment explanation
Indices: 45184814--45185098 Score: 268
Period size: 49 Copynumber: 5.8 Consensus size: 50
45184804 GGTGAACCTT
* * *
45184814 GTACCTTAGAAG-TGTCAAGGGAAAGATTTAAGCCACAACGGTGAATCCA
1 GTACCTCAGAAGATGTCAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
* * * * *
45184863 GTACCAC-GAAGATGTCAAAGGAAAGGTTTAAGCCGCAATGGCGAA-CCTT
1 GTACCTCAGAAGATGTCAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-A
* *
45184912 GTACCTCAGAAAAATG--AAGGGAAGGATTTAAGCCGCAACGGCGAATCCA
1 GTACCTCAG-AAGATGTCAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
* * * * *
45184961 GTACCACA-AAGATGTCAAGGGAAAGGTTTAAGCCGCAATGACGAA-CCTT
1 GTACCTCAGAAGATGTCAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-A
* * * * *
45185010 GTACCTCAGAAAATG--AAGAGAAGGATTTAAGACGCAATGGCGAATCCA
1 GTACCTCAGAAGATGTCAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
*
45185058 GTACCAT-A-AAGATGTCAAGGGAAAGATTTAAGCTGCAACGG
1 GTACC-TCAGAAGATGTCAAGGGAAAGATTTAAGCCGCAACGG
45185099 TGAAATTTAT
Statistics
Matches: 187, Mismatches: 36, Indels: 26
0.75 0.14 0.10
Matches are distributed among these distances:
47 10 0.05
48 38 0.20
49 126 0.67
50 8 0.04
51 5 0.03
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.18
Consensus pattern (50 bp):
GTACCTCAGAAGATGTCAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
Found at i:45185074 original size:97 final size:97
Alignment explanation
Indices: 45184807--45185095 Score: 418
Period size: 98 Copynumber: 3.0 Consensus size: 97
45184797 TAATAACGGT
* * * * * *
45184807 GAACCTTGTACCTTAG-AAGTGTCAAGGGAAAGATTTAAGCCACAACGGTGAATCCAGTACCACG
1 GAACCTTGTACCTCAGAAAATG--AAGGGAAGGATTTAAGCCGCAACGGCGAATCCAGTACCACA
* *
45184871 AAGATGTCAAAGGAAAGGTTTAAGCCGCAATGGC
64 AAGATGTCAAGGGAAAGGTTTAAGCCGCAATGAC
45184905 GAACCTTGTACCTCAGAAAAATGAAGGGAAGGATTTAAGCCGCAACGGCGAATCCAGTACCACAA
1 GAACCTTGTACCTCAG-AAAATGAAGGGAAGGATTTAAGCCGCAACGGCGAATCCAGTACCACAA
45184970 AGATGTCAAGGGAAAGGTTTAAGCCGCAATGAC
65 AGATGTCAAGGGAAAGGTTTAAGCCGCAATGAC
* * * *
45185003 GAACCTTGTACCTCAGAAAATGAAGAGAAGGATTTAAGACGCAATGGCGAATCCAGTACCATAAA
1 GAACCTTGTACCTCAGAAAATGAAGGGAAGGATTTAAGCCGCAACGGCGAATCCAGTACCACAAA
* *
45185068 GATGTCAAGGGAAAGATTTAAGCTGCAA
66 GATGTCAAGGGAAAGGTTTAAGCCGCAA
45185096 CGGTGAAATT
Statistics
Matches: 175, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
97 71 0.41
98 100 0.57
100 4 0.02
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (97 bp):
GAACCTTGTACCTCAGAAAATGAAGGGAAGGATTTAAGCCGCAACGGCGAATCCAGTACCACAAA
GATGTCAAGGGAAAGGTTTAAGCCGCAATGAC
Found at i:45185491 original size:15 final size:14
Alignment explanation
Indices: 45185454--45185501 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
45185444 TATTATTACT
* *
45185454 TTTATAAAAGTCCA
1 TTTACAAAAATCCA
45185468 TTTACAAAAATCCA
1 TTTACAAAAATCCA
45185482 TTTACAAAAA-CCA
1 TTTACAAAAATCCA
*
45185495 ATTACAA
1 TTTACAA
45185502 TCCCAATGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (14 bp):
TTTACAAAAATCCA
Found at i:45186259 original size:19 final size:19
Alignment explanation
Indices: 45186217--45186259 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
45186207 ACGAATCCCT
*
45186217 TTTTTAAAAAAGGGGGAAC
1 TTTTCAAAAAAGGGGGAAC
* * *
45186236 CTTTCAAAAAGGGGGGATC
1 TTTTCAAAAAAGGGGGAAC
45186255 TTTTC
1 TTTTC
45186260 TGTTTTTAAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (19 bp):
TTTTCAAAAAAGGGGGAAC
Found at i:45187363 original size:3 final size:3
Alignment explanation
Indices: 45187357--45187393 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
45187347 AAAAAAAACG
45187357 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45187394 GTTTAGTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:45192851 original size:29 final size:30
Alignment explanation
Indices: 45192803--45192871 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
45192793 TTAAATTAAG
*
45192803 AATGATAAAATTGCACTTTAGTCC-TAAAA
1 AATGATAAAATTGCACTTTAATCCTTAAAA
*
45192832 AATGATAAAATTTTG-A-TTTAATCCTTTAAA
1 AATGATAAAA--TTGCACTTTAATCCTTAAAA
*
45192862 AATTATAAAA
1 AATGATAAAA
45192872 ATATAGATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 17 0.50
30 14 0.41
31 3 0.09
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (30 bp):
AATGATAAAATTGCACTTTAATCCTTAAAA
Found at i:45198564 original size:2 final size:2
Alignment explanation
Indices: 45198559--45198611 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
45198549 GTTAAATAAT
45198559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45198601 TA TA T- TA TA TA
1 TA TA TA TA TA TA
45198612 ATTACTAACC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45198615 original size:8 final size:9
Alignment explanation
Indices: 45198529--45198615 Score: 92
Period size: 10 Copynumber: 9.7 Consensus size: 9
45198519 TGTTAAAAAG
45198529 ATATTATAT
1 ATATTATAT
45198538 -TAGTTATAT
1 ATA-TTATAT
* *
45198547 ATGTTAAAT
1 ATATTATAT
45198556 A-ATTATAT
1 ATATTATAT
45198564 ATA-TATAT
1 ATATTATAT
45198572 ATATATATAT
1 ATAT-TATAT
45198582 ATATATATAT
1 ATAT-TATAT
45198592 ATATATATAT
1 ATAT-TATAT
45198602 ATATTATAT
1 ATATTATAT
45198611 A-ATTA
1 ATATTA
45198616 CTAACCCAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
8 20 0.29
9 19 0.28
10 30 0.43
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (9 bp):
ATATTATAT
Found at i:45205786 original size:21 final size:21
Alignment explanation
Indices: 45205756--45205795 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45205746 GAGAACAAGG
45205756 TGTACAGATTAAAAAAAGCAT
1 TGTACAGATTAAAAAAAGCAT
* * *
45205777 TGTACGGATTGAAATAAGC
1 TGTACAGATTAAAAAAAGC
45205796 TCCGAGGGCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (21 bp):
TGTACAGATTAAAAAAAGCAT
Found at i:45206746 original size:16 final size:17
Alignment explanation
Indices: 45206720--45206752 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
45206710 TAGAATCATT
45206720 GATCTAATTTTCTGCAA
1 GATCTAATTTTCTGCAA
45206737 GATC-AATTTTCTGCAA
1 GATCTAATTTTCTGCAA
45206753 AAGTGAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (17 bp):
GATCTAATTTTCTGCAA
Found at i:45208179 original size:288 final size:286
Alignment explanation
Indices: 45207540--45208529 Score: 1589
Period size: 287 Copynumber: 3.5 Consensus size: 286
45207530 TTTATAATGA
* *
45207540 AAATAATAAAAGGTCTCAGACATCCAAGGAAGG-ATAAAAGCAGCACAAGCTCTCAAGCCCGGCG
1 AAATCATAAAAGGTCTCAGACATCCAAGGAAGGAAT-GAAGCAGCACAAGCTCTCAAGCCCGGCG
* *
45207604 AAAGGCGAAAGCTCTTAGGCAGCCACTGCGAATGTTTTGAGAAACAAGCCTTTGGA-TTATCATC
65 AAAGGCGAAAGCTCTTAGGCGGCCACTGCGAATGTTTTGAGAAACAAGCCTTCGGACTTATCATC
* *
45207668 ATAAACCCATTCATAA-AAATATATTTCCCTTTGACTGAATTTTAAGAATATCGTTTATCAATGG
130 ATAAACCCATACACAAGAAATATATTTCCCTTTGACTGAATTTTAAGAATATCGTTTATCAATGG
* * *
45207732 AACTGATTAACAAGGAAAACATAGACAACCAGATATCTGAGAAAGTAATTGAATTTTCAAGCACA
195 AACTGATAAACAAGGAAAAAATATACAACCAGAT-TCTGAGAAAGTAATTGAATTTTCAAGCACA
45207797 AATAATAAAAAATAACAATCATATATATAC
259 AATAATAAAAAATAACAAT--TATATATAC
45207827 AAATCATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGA
1 AAATCATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGA
45207892 AAGGCGAAAGCTCTTAGGCGGCCACTGCGAATGTTTTGAGAAACAAGCCTTCGGACTTATCATCA
66 AAGGCGAAAGCTCTTAGGCGGCCACTGCGAATGTTTTGAGAAACAAGCCTTCGGACTTATCATCA
* * *
45207957 TAAACCCATACGCAAGAAATATATTTTCCTTTTGACTGAATTTTAAGAATATCGTTTATCAATTG
131 TAAACCCATACACAAGAAATATA-TTTCCCTTTGACTGAATTTTAAGAATATCGTTTATCAATGG
*
45208022 AACTGGTAAACAAGGAAAAAATATACAACCAGACTTCTGAGAAAGTAATTGAATTTTCAAGCACA
195 AACTGATAAACAAGGAAAAAATATACAACCAGA-TTCTGAGAAAGTAATTGAATTTTCAAGCACA
45208087 AATAATAAAAAATAACAATTATATATAC
259 AATAATAAAAAATAACAATTATATATAC
45208115 AAATCATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGA
1 AAATCATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGA
*
45208180 AAGGCGAAAGCTCTTAGGCGGCCACTGCGAATGTTTTGAGAAACAAGCCTTTGGACTTATCATCA
66 AAGGCGAAAGCTCTTAGGCGGCCACTGCGAATGTTTTGAGAAACAAGCCTTCGGACTTATCATCA
* *
45208245 TAAACCTATACACAAGAAATACATTTCCCTTTGACTGAATTTTAAGAATATCGTTTATCAATGGA
131 TAAACCCATACACAAGAAATATATTTCCCTTTGACTGAATTTTAAGAATATCGTTTATCAATGGA
* * * * * *
45208310 ACTGTTAAAAAAGGAAAAAAAATACAAACAGATTTCTGAGAAAGTAACTGGATTTTCAAGCACAA
196 ACTGATAAACAAGGAAAAAATATACAACCAGA-TTCTGAGAAAGTAATTGAATTTTCAAGCACAA
* * ** *
45208375 ATAAT-GAAAACAACAA-T-CGTATAG
260 ATAATAAAAAATAACAATTATATATAC
*
45208399 AAGTCATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGA
1 AAATCATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGA
* *
45208464 AAGGCGAAAGCTCTTAGACGGCCACTGCGAATGTTTTGAGAAACAAGCCTTAC-AACTTATCATC
66 AAGGCGAAAGCTCTTAGGCGGCCACTGCGAATGTTTTGAGAAACAAGCCTT-CGGACTTATCATC
45208528 AT
130 AT
45208530 CGACTTTATA
Statistics
Matches: 662, Mismatches: 35, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
284 130 0.20
285 1 0.00
286 9 0.01
287 216 0.33
288 181 0.27
289 7 0.01
290 117 0.18
291 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (286 bp):
AAATCATAAAAGGTCTCAGACATCCAAGGAAGGAATGAAGCAGCACAAGCTCTCAAGCCCGGCGA
AAGGCGAAAGCTCTTAGGCGGCCACTGCGAATGTTTTGAGAAACAAGCCTTCGGACTTATCATCA
TAAACCCATACACAAGAAATATATTTCCCTTTGACTGAATTTTAAGAATATCGTTTATCAATGGA
ACTGATAAACAAGGAAAAAATATACAACCAGATTCTGAGAAAGTAATTGAATTTTCAAGCACAAA
TAATAAAAAATAACAATTATATATAC
Found at i:45209623 original size:18 final size:18
Alignment explanation
Indices: 45209604--45209638 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45209594 CTTTATATAT
45209604 TTTTTA-GATTTTTTAAA
1 TTTTTATGATTTTTTAAA
*
45209621 TTTTTATTATTTTTTAAA
1 TTTTTATGATTTTTTAAA
45209639 AATATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTATGATTTTTTAAA
Found at i:45209650 original size:25 final size:26
Alignment explanation
Indices: 45209617--45209668 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
45209607 TTAGATTTTT
*
45209617 TAAATTTTTA-TTATTTTTTAAAAATA
1 TAAATTTTTAGAT-TTTTTTAAAAATA
*
45209643 TAAA-TTTTAGATTTTTTTATAAATA
1 TAAATTTTTAGATTTTTTTAAAAATA
45209668 T
1 T
45209669 TTTAGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TAAATTTTTAGATTTTTTTAAAAATA
Found at i:45209684 original size:18 final size:19
Alignment explanation
Indices: 45209657--45209697 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
45209647 TTTTAGATTT
* *
45209657 TTTTATAAA-TATTTTAGA
1 TTTTAAAAATTATTTTAAA
45209675 TTTTAAAAATTATTTTAAA
1 TTTTAAAAATTATTTTAAA
45209694 TTTT
1 TTTT
45209698 TTTTGTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:45212828 original size:21 final size:21
Alignment explanation
Indices: 45212783--45212839 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
45212773 AGTACATACT
* **
45212783 TCTATCGATACAAGTGACAGT
1 TCTACCGATACAAGTGACACA
* *
45212804 TCTACTGATACAAGTGACTCA
1 TCTACCGATACAAGTGACACA
*
45212825 TCTACCGAAACAAGT
1 TCTACCGATACAAGT
45212840 CTTACTTCTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (21 bp):
TCTACCGATACAAGTGACACA
Found at i:45212934 original size:21 final size:22
Alignment explanation
Indices: 45212897--45212972 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 22
45212887 TTTGTTACTT
**
45212897 CTACCGATACAAG-TAAACAAA
1 CTACCGATACTTGCTAAACAAA
45212918 CTACCGATACTT-CTAAACACATAA
1 CTACCGATACTTGCT-AA-ACA-AA
* **
45212942 CTACTGATACTTGCTATTCAAA
1 CTACCGATACTTGCTAAACAAA
45212964 -TACCGATAC
1 CTACCGATAC
45212973 AACCTAAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 19 0.43
22 4 0.09
23 5 0.11
24 14 0.32
25 2 0.05
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (22 bp):
CTACCGATACTTGCTAAACAAA
Found at i:45222844 original size:15 final size:17
Alignment explanation
Indices: 45222824--45222864 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
45222814 ATAAGAGTAG
45222824 ATAAAAATT-TTAAA-A
1 ATAAAAATTATTAAACA
45222839 ATAAAAATTATTAAACA
1 ATAAAAATTATTAAACA
45222856 ATAGAAAAT
1 ATA-AAAAT
45222865 AAACAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.39
16 5 0.22
17 4 0.17
18 5 0.22
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAAATTATTAAACA
Found at i:45223109 original size:3 final size:3
Alignment explanation
Indices: 45223101--45223128 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
45223091 TTTGTAAATA
45223101 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45223129 CACTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:45226872 original size:32 final size:32
Alignment explanation
Indices: 45226832--45226935 Score: 99
Period size: 32 Copynumber: 3.4 Consensus size: 32
45226822 TTTGTGACCC
*
45226832 AATTTGATACTTGAACTTGATATTTTTTTTCT
1 AATTTGATACCTGAACTTGATATTTTTTTTCT
* * * *
45226864 AATTTGATACCTAAAC-T--TA-TTTGTATCC
1 AATTTGATACCTGAACTTGATATTTTTTTTCT
* * *
45226892 AATTTGGTACCTGAACTTGACATTTTTTTCCT
1 AATTTGATACCTGAACTTGATATTTTTTTTCT
*
45226924 AATTTGGTACCT
1 AATTTGATACCT
45226936 AAAGTTTTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
28 20 0.36
29 3 0.05
31 2 0.04
32 31 0.55
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (32 bp):
AATTTGATACCTGAACTTGATATTTTTTTTCT
Found at i:45226881 original size:61 final size:60
Alignment explanation
Indices: 45226773--45226945 Score: 231
Period size: 60 Copynumber: 2.9 Consensus size: 60
45226763 TTAATATAAT
* * *
45226773 ATTTGGTACCTGAACTTGACA-CTTTTTTCTTATTTGGTACTTAAACTTTTTTGTGACCCA
1 ATTTGGTACCTGAACTTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTGT-ACCCA
* * * * * *
45226833 ATTTGATACTTGAACTTGATATTTTTTTTCTAATTTGATACCTAAACTTATTTGTATCCA
1 ATTTGGTACCTGAACTTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTGTACCCA
* *
45226893 ATTTGGTACCTGAACTTGACATTTTTTTCCTAATTTGGTACCTAAAGTTTTTT
1 ATTTGGTACCTGAACTTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTT
45226946 TAGATTCAAT
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 68 0.71
61 28 0.29
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.49
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTGTACCCA
Found at i:45227212 original size:28 final size:27
Alignment explanation
Indices: 45227171--45227230 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
45227161 AAATATCAAA
*
45227171 TTTAAGTATCAAATTGAATAAAAAAAAT
1 TTTAAGTATCAAATT-AAGAAAAAAAAT
* *
45227199 TTTAAGTTTTAAATTAAGAAAAAAAAT
1 TTTAAGTATCAAATTAAGAAAAAAAAT
*
45227226 GTTAA
1 TTTAA
45227231 ATTTAGATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (27 bp):
TTTAAGTATCAAATTAAGAAAAAAAAT
Found at i:45230419 original size:24 final size:22
Alignment explanation
Indices: 45230382--45230425 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
45230372 AATAGTGATG
*
45230382 AATTAAATTTAAAATCAAATCA
1 AATTAAATTTAAAATAAAATCA
45230404 AATTAAACCTTTAAAATAAAAT
1 AATTAAA--TTTAAAATAAAAT
45230426 AAAAAACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTAAATTTAAAATAAAATCA
Found at i:45238046 original size:60 final size:60
Alignment explanation
Indices: 45237934--45238046 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
45237924 CAGCCGCGAT
* * *** *
45237934 AGAGAAAGGGAAAAGGAAAAGGAGAGAGATAGGGATAGAGATTTAGAGAGGAGGAGCAGC
1 AGAGAAAGGGAAAAGGAAAAAGAGAGAGAAAGGGATAGAGAAAGAGAAAGGAGGAGCAGC
* * *
45237994 AGAGGAAGGGAAAAGGAAAAAGATAGAGAAAGGGATAGGGAAAGAGAAAGGAG
1 AGAGAAAGGGAAAAGGAAAAAGAGAGAGAAAGGGATAGAGAAAGAGAAAGGAG
45238047 AGATAAGGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.42, T:0.06
Consensus pattern (60 bp):
AGAGAAAGGGAAAAGGAAAAAGAGAGAGAAAGGGATAGAGAAAGAGAAAGGAGGAGCAGC
Found at i:45238110 original size:24 final size:24
Alignment explanation
Indices: 45238083--45238146 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 24
45238073 AGAGAGATAA
45238083 GGAGAGGAGAGA-GAGGAAGGAAAG
1 GGAGAGGAGAGAGGA-GAAGGAAAG
45238107 GGAGAAGGAGA-AGGAGAAGGAAAG
1 GGAG-AGGAGAGAGGAGAAGGAAAG
45238131 GGAGA-GAGAGAGGAGA
1 GGAGAGGAGAGAGGAGA
45238147 GAGAGAAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.11
23 7 0.19
24 18 0.49
25 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (24 bp):
GGAGAGGAGAGAGGAGAAGGAAAG
Found at i:45238115 original size:12 final size:12
Alignment explanation
Indices: 45238098--45238135 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
45238088 GGAGAGAGAG
45238098 GAAGGAAAGGGA
1 GAAGGAAAGGGA
45238110 GAAGGAGAA-GGA
1 GAAGGA-AAGGGA
45238122 GAAGGAAAGGGA
1 GAAGGAAAGGGA
45238134 GA
1 GA
45238136 GAGAGAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (12 bp):
GAAGGAAAGGGA
Found at i:45238118 original size:6 final size:6
Alignment explanation
Indices: 45238051--45238131 Score: 55
Period size: 6 Copynumber: 13.7 Consensus size: 6
45238041 AAGGAGAGAT
* * * *
45238051 AAGGAT AAGGAG AAAGAG AAAGAG -AGAGAT AAGGAG -AGGAG -AGAGAGG
1 AAGGAG AAGGAG AAGGAG AAGGAG AAG-GAG AAGGAG AAGGAG AAG-GA-G
45238099 AAGGA- AAGGGAG AAGGAG AAGGAG AAGGA- AAGG
1 AAGGAG AA-GGAG AAGGAG AAGGAG AAGGAG AAGG
45238132 GAGAGAGAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
5 14 0.22
6 40 0.63
7 7 0.11
8 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (6 bp):
AAGGAG
Found at i:45247484 original size:2 final size:2
Alignment explanation
Indices: 45247477--45247547 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
45247467 TATCATACTA
45247477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45247519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45247548 GTTTCAAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45249231 original size:21 final size:20
Alignment explanation
Indices: 45249207--45249258 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
45249197 TTTTTTACTA
*
45249207 TTTTTATTGTTGTTTTTGTAT
1 TTTTTATTGTTGTTTTGGT-T
* **
45249228 TTTTTTTTACTGTTTTGGTT
1 TTTTTATTGTTGTTTTGGTT
*
45249248 TTTTTACTGTT
1 TTTTTATTGTT
45249259 TTGGTTGTTA
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.08, C:0.04, G:0.13, T:0.75
Consensus pattern (20 bp):
TTTTTATTGTTGTTTTGGTT
Found at i:45249278 original size:20 final size:17
Alignment explanation
Indices: 45249229--45249264 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
45249219 TTTTTGTATT
45249229 TTTTTTTACTGTTTTGG
1 TTTTTTTACTGTTTTGG
45249246 TTTTTTTACTGTTTTGG
1 TTTTTTTACTGTTTTGG
45249263 TT
1 TT
45249265 GTTATTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.06, C:0.06, G:0.17, T:0.72
Consensus pattern (17 bp):
TTTTTTTACTGTTTTGG
Found at i:45249283 original size:23 final size:24
Alignment explanation
Indices: 45249257--45249314 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
45249247 TTTTTTACTG
* *
45249257 TTTTGGTTGTTATTTTCG-TGTTA
1 TTTTTGTTGTTATTTTCGTTGCTA
* *
45249280 TTTTTGCTGTTATTTTTGTTGCTA
1 TTTTTGTTGTTATTTTCGTTGCTA
45249304 TTTTTGTTGTT
1 TTTTTGTTGTT
45249315 TTTAATGTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.69
Consensus pattern (24 bp):
TTTTTGTTGTTATTTTCGTTGCTA
Found at i:45249284 original size:12 final size:12
Alignment explanation
Indices: 45249264--45249314 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
45249254 CTGTTTTGGT
*
45249264 TGTTATTTTCG-
1 TGTTATTTTTGC
45249275 TGTTATTTTTGC
1 TGTTATTTTTGC
*
45249287 TGTTATTTTTGT
1 TGTTATTTTTGC
* *
45249299 TGCTATTTTTGT
1 TGTTATTTTTGC
45249311 TGTT
1 TGTT
45249315 TTTAATGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
11 10 0.29
12 25 0.71
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.69
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:45249284 original size:50 final size:51
Alignment explanation
Indices: 45249186--45249284 Score: 119
Period size: 50 Copynumber: 1.9 Consensus size: 51
45249176 ATTATATTGT
* * * *
45249186 TGTTTTGGTGGTTTTTTACTATTTTTATTGTTGTTTTTGTATTTTTTTTTAC
1 TGTTTTGGT-GTTTTTTACTATTTTGATTGTTATTTTCGTATTATTTTTTAC
* * *
45249238 TGTTTTGGT-TTTTTTACTGTTTTGGTTGTTATTTTCGTGTTATTTTT
1 TGTTTTGGTGTTTTTTACTATTTTGATTGTTATTTTCGTATTATTTTT
45249285 GCTGTTATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 31 0.77
52 9 0.22
ACGTcount: A:0.08, C:0.04, G:0.17, T:0.71
Consensus pattern (51 bp):
TGTTTTGGTGTTTTTTACTATTTTGATTGTTATTTTCGTATTATTTTTTAC
Found at i:45249323 original size:24 final size:24
Alignment explanation
Indices: 45249278--45249324 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
45249268 ATTTTCGTGT
*
45249278 TATTTTTGCTGTTATTTTTGTTGC
1 TATTTTTGCTGTTATTTATGTTGC
*
45249302 TATTTTTGTTGTT-TTTAATGTTG
1 TATTTTTGCTGTTATTT-ATGTTG
45249325 TTTGCTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.11, C:0.04, G:0.17, T:0.68
Consensus pattern (24 bp):
TATTTTTGCTGTTATTTATGTTGC
Found at i:45249336 original size:43 final size:43
Alignment explanation
Indices: 45249282--45249371 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
45249272 TCGTGTTATT
* * *
45249282 TTTGCTGTTATTTTTGTTGCTATTTTTG-TTGTT-TTTAATGTTG
1 TTTGCTATTATTTTTGCTGCT-GTTTTGATTGTTATTT-ATGTTG
*
45249325 TTTGCTATTATTTTTGCTGCTGTTTTGATTGTTATTTTTGTTG
1 TTTGCTATTATTTTTGCTGCTGTTTTGATTGTTATTTATGTTG
45249368 TTTG
1 TTTG
45249372 GATGTTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 5 0.12
43 33 0.80
44 3 0.07
ACGTcount: A:0.09, C:0.06, G:0.19, T:0.67
Consensus pattern (43 bp):
TTTGCTATTATTTTTGCTGCTGTTTTGATTGTTATTTATGTTG
Found at i:45249384 original size:21 final size:21
Alignment explanation
Indices: 45249345--45249383 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
45249335 TTTTTGCTGC
*
45249345 TGTTTTGATTGTTATTTTTGT
1 TGTTTGGATTGTTATTTTTGT
45249366 TGTTTGGA-TGTTATTTTT
1 TGTTTGGATTGTTATTTTT
45249384 TTATGCGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (21 bp):
TGTTTGGATTGTTATTTTTGT
Found at i:45253861 original size:39 final size:39
Alignment explanation
Indices: 45253800--45253882 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
45253790 TCCCACAAGC
45253800 TTGCTTTTACCATCACAATAGTGACTTGATGTACAAACT
1 TTGCTTTTACCATCACAATAGTGACTTGATGTACAAACT
* * * * * *
45253839 TTGCTTTTACCTTTACATTAGTGATTTGGTGTACAAATT
1 TTGCTTTTACCATCACAATAGTGACTTGATGTACAAACT
45253878 TTGCT
1 TTGCT
45253883 CAATTCAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.43
Consensus pattern (39 bp):
TTGCTTTTACCATCACAATAGTGACTTGATGTACAAACT
Done.