Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 43 of 126
Found at i:12713982 original size:27 final size:28
Alignment explanation
Indices: 12713920--12713982 Score: 112
Period size: 27 Copynumber: 2.3 Consensus size: 28
12713910 GTTATGCACA
12713920 ATATATTACCTACATAAATTATAAATCT
1 ATATATTACCTACATAAATTATAAATCT
12713948 A-ATATTACCTACATAAATTATAAATCT
1 ATATATTACCTACATAAATTATAAATCT
12713975 ATAT-TTAC
1 ATATATTAC
12713983 TATTATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 31 0.91
28 3 0.09
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATATTACCTACATAAATTATAAATCT
Found at i:12715842 original size:6 final size:6
Alignment explanation
Indices: 12715831--12715855 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12715821 TTTTGAATTT
12715831 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
12715856 ACTTTGGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:12728177 original size:17 final size:18
Alignment explanation
Indices: 12728155--12728190 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12728145 TAGGTTTAGC
*
12728155 AATGC-TTTTATCTCAAA
1 AATGCTTTTTATCCCAAA
12728172 AATGCTTTTTATCCCAAA
1 AATGCTTTTTATCCCAAA
12728190 A
1 A
12728191 GTGCATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (18 bp):
AATGCTTTTTATCCCAAA
Found at i:12738264 original size:29 final size:30
Alignment explanation
Indices: 12738231--12738291 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
12738221 TTCTTTTCTA
*
12738231 TTATATAGTGGCTTT-TTTTCCTTCTCCTT
1 TTATATAGCGGCTTTCTTTTCCTTCTCCTT
* * *
12738260 TTATATCGCGGCTTTCTTTTTCTTCTCTTT
1 TTATATAGCGGCTTTCTTTTCCTTCTCCTT
12738290 TT
1 TT
12738292 TTATCACAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.08, C:0.21, G:0.10, T:0.61
Consensus pattern (30 bp):
TTATATAGCGGCTTTCTTTTCCTTCTCCTT
Found at i:12742942 original size:20 final size:20
Alignment explanation
Indices: 12742919--12742956 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12742909 TGATACCCTC
* *
12742919 AGAGTTCTACTGATACAAGG
1 AGAGATCTACTGAAACAAGG
12742939 AGAGATCTACTGAAACAA
1 AGAGATCTACTGAAACAA
12742957 CGACTCCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (20 bp):
AGAGATCTACTGAAACAAGG
Found at i:12745887 original size:51 final size:50
Alignment explanation
Indices: 12745820--12746004 Score: 271
Period size: 51 Copynumber: 3.6 Consensus size: 50
12745810 CCGAATAGAA
* * * *
12745820 ATTCATATACTCACGATGACACTGAGTCATCGGACCTTTAATTCGTCATGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGT-AAGG
* *
12745871 ATTCATTTACTCACGATGATACTTAGTCATCGGACCTTTAATCCATAGAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTA-AGG
* *
12745922 ATTCGTTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGAAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCG-TAAGG
12745973 ATTCATTTACTCACGATGACACTTAGTCATCG
1 ATTCATTTACTCACGATGACACTTAGTCATCG
12746005 AACTCTTTCG
Statistics
Matches: 121, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.01
51 119 0.98
52 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (50 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAGG
Found at i:12753150 original size:51 final size:51
Alignment explanation
Indices: 12753084--12753266 Score: 212
Period size: 51 Copynumber: 3.6 Consensus size: 51
12753074 CGTATAGAAG
*
12753084 TTCATATACTCACGATGACA-TTGAGTCATCGGACCTTTAATTCGTCATGAA
1 TTCATTTACTCACGATGACACTT-AGTCATCGGACCTTTAATTCGTCATGAA
* *
12753135 TTCATTTACTCACGATGATACTTAGTCATCAGACCTTTAA-TC--CATAGAGGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTCAT-GA--A
* * * * * *
12753186 TTCGTTTACTCACGATGACACTTGGTCATCGGACCTTTAATCCGTAAAGGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTCATGAA
*
12753237 TTCATTTACTCACGATAACACTTAGTCATC
1 TTCATTTACTCACGATGACACTTAGTCATC
12753267 AAACTCTTTC
Statistics
Matches: 111, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
48 3 0.03
49 2 0.02
50 2 0.02
51 99 0.89
52 3 0.03
53 1 0.01
54 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTCATGAA
Found at i:12755467 original size:2 final size:2
Alignment explanation
Indices: 12755460--12755484 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12755450 CTTCATTTCT
12755460 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12755485 TGGCATTCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12757165 original size:50 final size:49
Alignment explanation
Indices: 12757085--12757196 Score: 188
Period size: 50 Copynumber: 2.3 Consensus size: 49
12757075 ACAAGTCATG
* *
12757085 CTTCTATCGATACTAAAACTCCAGAGAGCTAAGCAGTCTCACCCTACAA
1 CTTCTACCGATACTAAAACTCCAGAGAGCTAAGAAGTCTCACCCTACAA
*
12757134 CTTCTACCGATACTAAAAACTCCAGAGAGCTAAGAAGTCTCACCCTGCAA
1 CTTCTACCGATACT-AAAACTCCAGAGAGCTAAGAAGTCTCACCCTACAA
12757184 CTTCTACCGATAC
1 CTTCTACCGATAC
12757197 AAGCATATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
49 13 0.22
50 46 0.78
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.22
Consensus pattern (49 bp):
CTTCTACCGATACTAAAACTCCAGAGAGCTAAGAAGTCTCACCCTACAA
Found at i:12760399 original size:27 final size:27
Alignment explanation
Indices: 12760369--12760432 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
12760359 CAATATATCT
* * *
12760369 AAATAATTGACATGATGTGTTTTGAAA
1 AAATAATTGACAAGATGGGTTCTGAAA
*
12760396 AAATAATTTTGAGAAGATGGGTTCTGAAA
1 AAATAA--TTGACAAGATGGGTTCTGAAA
12760425 AAATAATT
1 AAATAATT
12760433 TTGAGATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 8 0.26
29 23 0.74
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (27 bp):
AAATAATTGACAAGATGGGTTCTGAAA
Found at i:12760414 original size:29 final size:29
Alignment explanation
Indices: 12760382--12760438 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
12760372 TAATTGACAT
* *
12760382 GATGTGTTTTGAAAAAATAATTTTGAGAA
1 GATGGGTTCTGAAAAAATAATTTTGAGAA
12760411 GATGGGTTCTGAAAAAATAATTTTGAGA
1 GATGGGTTCTGAAAAAATAATTTTGAGA
12760439 TTTGAGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (29 bp):
GATGGGTTCTGAAAAAATAATTTTGAGAA
Found at i:12760450 original size:36 final size:36
Alignment explanation
Indices: 12760403--12760472 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
12760393 AAAAAATAAT
*
12760403 TTTGAGAAGATGGGTTCTGAAAAAATAATTTTGAGA
1 TTTGAGAAGATGAGTTCTGAAAAAATAATTTTGAGA
*
12760439 TTTGAGAAGATGAGTTCTGAAAAAATTATTTTGA
1 TTTGAGAAGATGAGTTCTGAAAAAATAATTTTGA
12760473 CGAGATGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.36
Consensus pattern (36 bp):
TTTGAGAAGATGAGTTCTGAAAAAATAATTTTGAGA
Found at i:12761096 original size:21 final size:20
Alignment explanation
Indices: 12761070--12761120 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
12761060 ATCGACAAAT
*
12761070 TAATTAATATATTATTAAAAA
1 TAATTAA-ATATTATAAAAAA
12761091 TAATT-AA-ATTATAAAAAA
1 TAATTAAATATTATAAAAAA
*
12761109 AAATTAAATATT
1 TAATTAAATATT
12761121 TTTTATAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 14 0.54
19 3 0.12
20 4 0.15
21 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATTAAATATTATAAAAAA
Found at i:12761185 original size:22 final size:21
Alignment explanation
Indices: 12761133--12761184 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
12761123 TTATAGCCAT
* *
12761133 TAATTTAAATTATCTAAACCC
1 TAATTTAAAATATCAAAACCC
*
12761154 TTATTTAAAATATCAAAACCC
1 TAATTTAAAATATCAAAACCC
12761175 TAATTTAAAA
1 TAATTTAAAA
12761185 AACCCTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATTTAAAATATCAAAACCC
Found at i:12761887 original size:2 final size:2
Alignment explanation
Indices: 12761880--12761904 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12761870 TCACACGTGT
12761880 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12761905 CTAAAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12762201 original size:17 final size:17
Alignment explanation
Indices: 12762170--12762237 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
12762160 ATAATTTAAT
*
12762170 TTTTAAA-TTAGATTTA
1 TTTTAAATTTAAATTTA
12762186 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
** * *
12762203 CATAAAATTTAAGTTTA
1 TTTTAAATTTAAATTTA
*
12762220 TTATAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
12762237 T
1 T
12762238 AAATTAAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 7 0.17
17 34 0.83
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:12764097 original size:162 final size:162
Alignment explanation
Indices: 12763825--12764163 Score: 534
Period size: 162 Copynumber: 2.1 Consensus size: 162
12763815 GATTTTCGAT
* *
12763825 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACCTTTTGGCTTATTTATGCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCCGCCACGTGCCACCTTTTGGCTTATTTATGCA
12763890 TTTAGTCCCCGTCATTTTTAATTTGTATTAATTTAATCCTCAAATCAACTTCAACTTAATTACAA
66 TTTAGTCCCCGTCATTTTTAATTTGTATTAATTTAATCCTCAAATCAACTTCAACTTAATTACAA
*
12763955 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
* * *
12763987 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCCGTCACGTGCCACTTTTTGGTTTATTTATGCA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCCGCCACGTGCCACCTTTTGGCTTATTTATGCA
* * * * **
12764052 TTTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCTTCAAATCAGCTTCTGCTTAATTACAA
66 TTTAGTCCCCGTCATTTTTAATTTGTATTAATTTAATCCTCAAATCAACTTCAACTTAATTACAA
* * *
12764117 AATTGGCTCAAGAATTTTTTAAGATTTACAAT
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
*
12764149 TTAGTCCTTTGACTG
1 TTAATCCTTTGACTG
12764164 CTGGATGCCT
Statistics
Matches: 161, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
162 161 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (162 bp):
TTAATCCTTTGACTGTTTGACTGCACCAGAGGCCGCCACGTGCCACCTTTTGGCTTATTTATGCA
TTTAGTCCCCGTCATTTTTAATTTGTATTAATTTAATCCTCAAATCAACTTCAACTTAATTACAA
AATTGGCCCAAGAATTTTTCAAGATTTACAAA
Found at i:12764310 original size:30 final size:30
Alignment explanation
Indices: 12764266--12764490 Score: 148
Period size: 29 Copynumber: 7.7 Consensus size: 30
12764256 AAAACTTTCC
12764266 AAAATT-CCATTTTTAA-CCTCGATTTCATCA
1 AAAATTACCA-TTTTAACCCT-GATTTCATCA
* * * ** *
12764296 AAAATTAACATTTTACCCCTAAACTC-TCT
1 AAAATTACCATTTTAACCCTGATTTCATCA
12764325 AAAATT-CCATTTTAACCCTGATTTCATCA
1 AAAATTACCATTTTAACCCTGATTTCATCA
* * ** *
12764354 AAAATTACCATTTTACCCCTAAACTC-TCC
1 AAAATTACCATTTTAACCCTGATTTCATCA
* *
12764383 AAAATT-CTATTTTTAACCCTAATTTCA-CAA
1 AAAATTACCA-TTTTAACCCTGATTTCATC-A
* ** *
12764413 AAAATTACCATTTTACCCCCAAACTT--TCA
1 AAAATTACCATTTTA-ACCCTGATTTCATCA
**
12764442 AAAATT-CCATTTTTAACCCCAATTTCATCA
1 AAAATTACCA-TTTTAACCCTGATTTCATCA
12764472 AAAATTACCATTTT-ACCCT
1 AAAATTACCATTTTAACCCT
12764491 TAAACTCTCC
Statistics
Matches: 151, Mismatches: 30, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
28 26 0.17
29 54 0.36
30 54 0.36
31 17 0.11
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCTGATTTCATCA
Found at i:12764314 original size:59 final size:58
Alignment explanation
Indices: 12764234--12764548 Score: 404
Period size: 59 Copynumber: 5.4 Consensus size: 58
12764224 CCTAAACTGT
* * *
12764234 TCAAAAATTA-TATTTTGACCCCAAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 TCAAAAATTACCATTTT-ACCCCTAAACTCTCCAAAATTCCATTTTTAACC-CGATTTCA
* *
12764293 TCAAAAATTAACATTTTACCCCTAAACTCTCTAAAATTCCA-TTTTAACCCTGATTTCA
1 TCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCC-GATTTCA
* *
12764351 TCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCTATTTTTAACCCTAATTTCA
1 TCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCC-GATTTCA
* * * *
12764410 -CAAAAAATTACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCAATTTCA
1 TC-AAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAA-CCCGATTTCA
* *
12764469 TCAAAAATTACCATTTTACCCTTAAACTCTCCAAAACTCCATTTTTAACCTCGATTTCA
1 TCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACC-CGATTTCA
* *
12764528 -CCAAAATTACCATTTCACCCC
1 TCAAAAATTACCATTTTACCCC
12764549 CGAGTATCCA
Statistics
Matches: 228, Mismatches: 21, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
57 1 0.00
58 74 0.32
59 144 0.63
60 9 0.04
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.35
Consensus pattern (58 bp):
TCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCCGATTTCA
Found at i:12764446 original size:117 final size:117
Alignment explanation
Indices: 12764234--12764549 Score: 440
Period size: 117 Copynumber: 2.7 Consensus size: 117
12764224 CCTAAACTGT
* * *
12764234 TCAAAAATTA-TATTTTGACCCCAAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCATCAAA
1 TCAAAAATTACCATTTT-ACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCA-CAAA
* * * **
12764298 AATTAACATTTTACCCCTAAACTCTCTAAAATTCCA-TTTTAACCCTGATTTCA
64 AATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCAATTTCA
* *
12764351 TCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCTATTTTTAACC-CTAATTTCACAAAA
1 TCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTC-GATTTCAC-AAA
*
12764415 AATTACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCAATTTCA
64 AATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCAATTTCA
* * *
12764469 TCAAAAATTACCATTTTACCCTTAAACTCTCCAAAACTCCATTTTTAACCTCGATTTCACCAAAA
1 TCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCACAAAAA
*
12764534 TTACCATTTCACCCCC
66 TTACCATTTTACCCCC
12764550 GAGTATCCAA
Statistics
Matches: 177, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
116 2 0.01
117 100 0.56
118 74 0.42
119 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.35
Consensus pattern (117 bp):
TCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCACAAAAA
TTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCAATTTCA
Found at i:12764585 original size:176 final size:176
Alignment explanation
Indices: 12764236--12764585 Score: 449
Period size: 176 Copynumber: 2.0 Consensus size: 176
12764226 TAAACTGTTC
* * * *
12764236 AAAAATTATATTTTGACCCCAAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCATCAAAAAT
1 AAAAATTACATTTTGACCCCAAAACTTTCAAAAATTCCATTTTTAACCCCAATTTCATCAAAAAT
* *
12764301 TAACATTTTACCCCTAAACTCTCTAAAATTCCATTTTAACCCTGATTTCATCAAAAATTACCATT
66 TAACATTTTACCCCTAAACTCTCCAAAACTCCATTTTAACCCTGATTTCATCAAAAATTACCATT
* * * * * *
12764366 TTACCCCTAAACTCTCCAAAATTCTATTTTTAACCCTAATTTCACA
131 TCACCCCTAAACTATCCAAAATCCGATTTTCAACCCCAATTTCACA
*
12764412 AAAAATTACCATTTT-ACCCCCAAACTTTCAAAAATTCCATTTTTAACCCCAATTTCATCAAAAA
1 AAAAATTA-CATTTTGACCCCAAAACTTTCAAAAATTCCATTTTTAACCCCAATTTCATCAAAAA
* * *
12764476 TTACCATTTTACCCTTAAACTCTCCAAAACTCCATTTTTAA-CCTCGATTTCA-CCAAAATTACC
65 TTAACATTTTACCCCTAAACTCTCCAAAACTCCA-TTTTAACCCT-GATTTCATCAAAAATTACC
** *
12764539 ATTTCACCCC-CGAGTATCCAAAAGTCCCGA-TTTCAACCCCAATTTCA
128 ATTTCACCCCTAAACTATCCAAAA-T-CCGATTTTCAACCCCAATTTCA
12764586 TCGTTTCTTC
Statistics
Matches: 150, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
175 9 0.06
176 121 0.81
177 20 0.13
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (176 bp):
AAAAATTACATTTTGACCCCAAAACTTTCAAAAATTCCATTTTTAACCCCAATTTCATCAAAAAT
TAACATTTTACCCCTAAACTCTCCAAAACTCCATTTTAACCCTGATTTCATCAAAAATTACCATT
TCACCCCTAAACTATCCAAAATCCGATTTTCAACCCCAATTTCACA
Found at i:12776773 original size:149 final size:148
Alignment explanation
Indices: 12776558--12777026 Score: 701
Period size: 149 Copynumber: 3.1 Consensus size: 148
12776548 ACCAAGATCT
*
12776558 TTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTAAAGTAAG
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGTGGAT-A-ACGTCTTTATCTCTGAAATTGAAGTAAG
12776623 GGCAACGTCATTTCCTATCCGCTTGAAATTGAAGTAGAGTGGATAACGCGTCTTTATCTCTGAAA
64 GGCAACGTCATTTCCTATCCGCTTGAAATTGAAGTAGAGTGGATAACGCGTCTTTATCTCTGAAA
12776688 TTGAAGTAAGAGCAACATCA
129 TTGAAGTAAGAGCAACATCA
*
12776708 TTTCCTATCCACTTGAAATTGAAGTAGAGTTGGATAACGTCTTTATCTCTGAAATTGAAGTAAGG
1 TTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACGTCTTTATCTCTGAAATTGAAGTAAGG
* *
12776773 GCAACATCATTTCCTATCCGCTTGAAATTGAAGTAGAGTGGATAATGCGTCTTTATCTCTGAAAT
65 GCAACGTCATTTCCTATCCGCTTGAAATTGAAGTAGAGTGGATAACGCGTCTTTATCTCTGAAAT
12776838 TGAAGTAAGAGCAACAT-A
130 TGAAGTAAGAGCAACATCA
*
12776856 TTTTCCTGTCCTCTTGAAATTGAAGTAGAGATGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
1 -TTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAAC--GTCTTTATCTCTGAAATTGAAGTA
* * * * **
12776921 AGAGCAA-GATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGGTAACAAGT-TTTCATCTC
62 AGGGCAACG-TCATTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGATAACGCGTCTTT-ATCTC
** *
12776984 TGAAATTGAAGTAAGAATAAGATCA
124 TGAAATTGAAGTAAGAGCAACATCA
12777009 TTTCCTATCCTCTTGAAA
1 TTTCCTATCCTCTTGAAA
12777027 CAAGCGAGGC
Statistics
Matches: 292, Mismatches: 19, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
148 1 0.00
149 143 0.49
150 29 0.10
151 68 0.23
152 50 0.17
153 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (148 bp):
TTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACGTCTTTATCTCTGAAATTGAAGTAAGGG
CAACGTCATTTCCTATCCGCTTGAAATTGAAGTAGAGTGGATAACGCGTCTTTATCTCTGAAATT
GAAGTAAGAGCAACATCA
Found at i:12776921 original size:76 final size:75
Alignment explanation
Indices: 12776558--12777026 Score: 694
Period size: 75 Copynumber: 6.2 Consensus size: 75
12776548 ACCAAGATCT
*
12776558 TTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTAAAGTAAG
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAG
* *
12776623 GGCAACGTCA
66 AGCAACATCA
* *
12776633 TTTCCTATCCGCTTGAAATTGAAGTAGAGTGGATAACGCGTCTTTATCTCTGAAATTGAAGTAAG
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAG
12776698 AGCAACATCA
66 AGCAACATCA
*
12776708 TTTCCTATCCACTTGAAATTGAAGTAGAGTTGGAT-A-ACGTCTTTATCTCTGAAATTGAAGTAA
1 TTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAA
*
12776771 GGGCAACATCA
65 GAGCAACATCA
* **
12776782 TTTCCTATCCGCTTGAAATTGAAGTAGAGTGGATAATGCGTCTTTATCTCTGAAATTGAAGTAAG
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAG
12776847 AGCAACAT-A
66 AGCAACATCA
* *
12776856 TTTTCCTGTCCTCTTGAAATTGAAGTAGAGATGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
1 -TTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTA
* *
12776921 AGAGCAAGATCT
64 AGAGCAACATCA
* *
12776933 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGGTAACAAGT-TTTCATCTCTGAAATTGAAGTA
1 TTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTT-ATCTCTGAAATTGAAGTA
** *
12776997 AGAATAAGATCA
64 AGAGCAACATCA
12777009 TTTCCTATCCTCTTGAAA
1 TTTCCTATCCTCTTGAAA
12777027 CAAGCGAGGC
Statistics
Matches: 363, Mismatches: 24, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
73 5 0.01
74 66 0.18
75 163 0.45
76 129 0.36
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (75 bp):
TTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAG
AGCAACATCA
Found at i:12777026 original size:38 final size:38
Alignment explanation
Indices: 12776551--12777026 Score: 192
Period size: 38 Copynumber: 12.7 Consensus size: 38
12776541 AGACCGCACC
*
12776551 AAGATCTTTTCCTATCCTCTTGAAATTGAAGT-AGAGT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGT
* ** * * * *
12776588 -GGATAACACGTCTTTAT-CTC-TGAAATTAAAGTAAGGGC
1 AAGAT--CATTTC-CTATCCTCTTGAAATTGAAGTAAGAGT
*
12776626 AACG-TCATTTCCTATCCGCTTGAAATTGAAGT-AGAGT
1 AA-GATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGT
* *** * *
12776663 -GGATAACGCGTCTTTAT-CTC-TGAAATTGAAGTAAGAGC
1 AAGAT--CATTTC-CTATCCTCTTGAAATTGAAGTAAGAGT
* *
12776701 AACATCATTTCCTATCCACTTGAAATTGAAGT-AGAGT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGT
** * ** * * *
12776738 TGGATAACGTCTTTAT-CTC-TGAAATTGAAGTAAGGGC
1 AAGATCATTTC-CTATCCTCTTGAAATTGAAGTAAGAGT
* *
12776775 AACATCATTTCCTATCCGCTTGAAATTGAAGT-AGAGT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGT
* * * * *
12776812 -GGATAATGCGTCTTTAT-CTC-TGAAATTGAAGTAAGAGC
1 AAGATCAT--TTC-CTATCCTCTTGAAATTGAAGTAAGAGT
* *
12776850 AACAT-ATTTTCCTGTCCTCTTGAAATTGAAGT-AGAG-
1 AAGATCA-TTTCCTATCCTCTTGAAATTGAAGTAAGAGT
* ** * *
12776886 ATGGATAACAAGTCTTTAT-CTC-TGAAATTGAAGTAAGAGC
1 A-AGAT--CATTTC-CTATCCTCTTGAAATTGAAGTAAGAGT
*
12776926 AAGATCTTTTCCTATCCTCTTGAAATTGAAGT-AGAGTT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAAGAG-T
** * * *
12776964 GGGTAACAAGTTTTC-AT-CTC-TGAAATTGAAGTAAGAAT
1 AAG-ATC-A-TTTCCTATCCTCTTGAAATTGAAGTAAGAGT
12777002 AAGATCATTTCCTATCCTCTTGAAA
1 AAGATCATTTCCTATCCTCTTGAAA
12777027 CAAGCGAGGC
Statistics
Matches: 309, Mismatches: 85, Indels: 89
0.64 0.18 0.18
Matches are distributed among these distances:
35 5 0.02
36 38 0.12
37 99 0.32
38 121 0.39
39 35 0.11
40 7 0.02
41 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (38 bp):
AAGATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGT
Found at i:12777558 original size:17 final size:17
Alignment explanation
Indices: 12777527--12777594 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
12777517 ATAATTTAAT
*
12777527 TTTTAAA-TTAGATTTA
1 TTTTAAATTTAAATTTA
12777543 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
** * *
12777560 CATAAAATTTAAGTTTA
1 TTTTAAATTTAAATTTA
*
12777577 TTATAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
12777594 T
1 T
12777595 AAATTAAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 7 0.17
17 34 0.83
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:12779421 original size:162 final size:162
Alignment explanation
Indices: 12779149--12779484 Score: 539
Period size: 162 Copynumber: 2.1 Consensus size: 162
12779139 GATTTTCGAT
* *
12779149 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACCTTTTGGCTTATTTATACA
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGCCACCTTTTGACTTATTTATACA
12779214 TTGAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCAGCTTAATTACAA
66 TTGAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCAGCTTAATTACAA
*
12779279 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
* * * *
12779311 TTAATCCTTTGACTGTTTGACTGCACCAGAGG-TCGCCACGTGCCACTTTTTTATTTATTTATGC
1 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCT-GCCACGTGCCACCTTTTGACTTATTTATAC
* * ** *
12779375 ATTTAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCTTCAAATCAGTTTCTGCTTAATTACA
65 ATTGAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCAGCTTAATTACA
*
12779440 AAATTGGCCCAAGAATTTTTCAAGATTTACAAT
130 AAATTGGCCCAAGAATTTTTCAAGATTTACAAA
12779473 TTAATCCTTTGA
1 TTAATCCTTTGA
12779485 TTGCTGGATG
Statistics
Matches: 160, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
161 1 0.01
162 159 0.99
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (162 bp):
TTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGCCACCTTTTGACTTATTTATACA
TTGAGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCAGCTTAATTACAA
AATTGGCCCAAGAATTTTTCAAGATTTACAAA
Found at i:12779708 original size:58 final size:59
Alignment explanation
Indices: 12779559--12779919 Score: 447
Period size: 59 Copynumber: 6.3 Consensus size: 59
12779549 CTAAACTGTT
* * * * *
12779559 CAAAAATTA-TATTTTGACCCCAAAACTTTCCAAAATTCTATTTTTAACCTCGATTTCAT
1 CAAAAATTACCATTTT-ACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCAC
*
12779618 CAAAAATTACCGTTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACC-CGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCAC
** * * *
12779676 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACC-CTAATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTC-GATTTCAC
*
12779735 CAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCA-TTTTAACCTCGATTTTAC
1 CAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCAC
* * * * *
12779793 CAAAAATTACCATTTTACCCCTAAACTCTCTAAAACTCTATTTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCAC
* *
12779852 CAAAAATTACCATTTTATCCCC-GAACT-T----AATTCCATTTTTAACCTTGATTTCAC
1 CAAAAATTACCATTTTA-CCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCAC
12779906 C-AAAATTACCATTT
1 CAAAAATTACCATTT
12779920 CGCCCCCGGG
Statistics
Matches: 267, Mismatches: 30, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
53 13 0.05
54 22 0.08
58 105 0.39
59 119 0.45
60 8 0.03
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.36
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCAC
Found at i:12779765 original size:117 final size:118
Alignment explanation
Indices: 12779559--12779919 Score: 492
Period size: 117 Copynumber: 3.1 Consensus size: 118
12779549 CTAAACTGTT
*
12779559 CAAAAATTA-TATTTTGACCCCAAAACTTTCCAAAATTCTATTTTTAA-CCTCGATTTCATCAAA
1 CAAAAATTACCATTTT-ACCCCAAAACTTTCCAAAATTCTATTTTTAACCCT-GATTTCATCAAA
*
12779622 AATTACCGTTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACC-CGATTTCAC
64 AATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCAC
** * *
12779676 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTAATTTCATCAAAAA
1 CAAAAATTACCATTTTACCCCAAAACTTTCCAAAATTCTATTTTTAACCCTGATTTCATCAAAAA
*
12779741 TTACCATTTTACCCCTAAACTCTCCAAAATTCCA-TTTTAACCTCGATTTTAC
66 TTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCAC
* * * * *
12779793 CAAAAATTACCATTTTACCCCTAAACTCTCTAAAACTCTATTTTTAACCCCGATTTCATCAAAAA
1 CAAAAATTACCATTTTACCCCAAAACTTTCCAAAATTCTATTTTTAACCCTGATTTCATCAAAAA
* *
12779858 TTACCATTTTATCCCC-GAACT-T----AATTCCATTTTTAACCTTGATTTCAC
66 TTACCATTTTA-CCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCAC
12779906 C-AAAATTACCATTT
1 CAAAAATTACCATTT
12779920 CGCCCCCGGG
Statistics
Matches: 221, Mismatches: 18, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
112 20 0.09
113 17 0.08
116 9 0.04
117 163 0.74
118 12 0.05
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.36
Consensus pattern (118 bp):
CAAAAATTACCATTTTACCCCAAAACTTTCCAAAATTCTATTTTTAACCCTGATTTCATCAAAAA
TTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCAC
Found at i:12783283 original size:51 final size:51
Alignment explanation
Indices: 12783200--12783392 Score: 278
Period size: 51 Copynumber: 3.8 Consensus size: 51
12783190 GTTATAAACA
12783200 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
12783252 AAAGGCCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * *
12783303 AAAGGTCTGATGACTAAGTATCATCATGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
12783354 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAAT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT
12783393 TTCTATACGG
Statistics
Matches: 124, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 120 0.97
52 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:12792507 original size:36 final size:32
Alignment explanation
Indices: 12792439--12792503 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
12792429 CCTCGGCCTC
12792439 ACACGAAAACATGACACTGACTGAATTGATAG
1 ACACGAAAACATGACACTGACTGAATTGATAG
12792471 ACACGAAAACATGACACTGACTGAATTGATAG
1 ACACGAAAACATGACACTGACTGAATTGATAG
12792503 A
1 A
12792504 TAGAACCATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (32 bp):
ACACGAAAACATGACACTGACTGAATTGATAG
Found at i:12794977 original size:45 final size:45
Alignment explanation
Indices: 12794927--12795016 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
12794917 ATATGAATTG
*
12794927 CATTTACGTTAAAAGCATTCAGAGCAGGTGATATCTGAGTACATA
1 CATTTACATTAAAAGCATTCAGAGCAGGTGATATCTGAGTACATA
*
12794972 CATTTACATTAAAAGCATTCAGAGCAGGTGATATTTGAGTACATA
1 CATTTACATTAAAAGCATTCAGAGCAGGTGATATCTGAGTACATA
12795017 TGAATTGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (45 bp):
CATTTACATTAAAAGCATTCAGAGCAGGTGATATCTGAGTACATA
Found at i:12795669 original size:2 final size:2
Alignment explanation
Indices: 12795662--12795711 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
12795652 TACACATTTT
12795662 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
12795704 TA TA TA TA
1 TA TA TA TA
12795712 ATCTTTAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12796232 original size:6 final size:6
Alignment explanation
Indices: 12796211--12796245 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
12796201 TTATTTAATT
*
12796211 ATCTCA AT-TAA ATCTCA ATCTCA ATCTCA ATCTCA
1 ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA
12796246 TAATATTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (6 bp):
ATCTCA
Found at i:12797189 original size:17 final size:17
Alignment explanation
Indices: 12797167--12797257 Score: 137
Period size: 17 Copynumber: 5.4 Consensus size: 17
12797157 CCCATTTTTA
*
12797167 AAATTTATTTTAAGGTT
1 AAATTTATTTTAAGTTT
*
12797184 AAATTTATTTTAAATTT
1 AAATTTATTTTAAGTTT
12797201 AAATTTATTTTAAGTTT
1 AAATTTATTTTAAGTTT
* *
12797218 AAATTTGTTTTAAATTT
1 AAATTTATTTTAAGTTT
*
12797235 AAATTTAATTTAAGTTT
1 AAATTTATTTTAAGTTT
12797252 AAATTT
1 AAATTT
12797258 GAAATTGTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 66 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
AAATTTATTTTAAGTTT
Found at i:12797198 original size:11 final size:12
Alignment explanation
Indices: 12797182--12797263 Score: 73
Period size: 11 Copynumber: 7.1 Consensus size: 12
12797172 TATTTTAAGG
*
12797182 TTAAATTT-ATT
1 TTAAATTTAAAT
12797193 TTAAATTTAAAT
1 TTAAATTTAAAT
* *
12797205 TT-ATTTTAAGT
1 TTAAATTTAAAT
**
12797216 TTAAATTT-GTT
1 TTAAATTTAAAT
12797227 TTAAATTTAAAT
1 TTAAATTTAAAT
*
12797239 TT-AATTTAAGT
1 TTAAATTTAAAT
12797250 TTAAATTTGAAAT
1 TTAAATTT-AAAT
12797263 T
1 T
12797264 GTTCTAAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
11 36 0.64
12 16 0.29
13 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:12797258 original size:34 final size:34
Alignment explanation
Indices: 12797167--12797258 Score: 157
Period size: 34 Copynumber: 2.7 Consensus size: 34
12797157 CCCATTTTTA
* *
12797167 AAATTTATTTTAAGGTTAAATTTATTTTAAATTT
1 AAATTTATTTTAAGTTTAAATTTGTTTTAAATTT
12797201 AAATTTATTTTAAGTTTAAATTTGTTTTAAATTT
1 AAATTTATTTTAAGTTTAAATTTGTTTTAAATTT
*
12797235 AAATTTAATTTAAGTTTAAATTTG
1 AAATTTATTTTAAGTTTAAATTTG
12797259 AAATTGTTCT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (34 bp):
AAATTTATTTTAAGTTTAAATTTGTTTTAAATTT
Found at i:12797272 original size:51 final size:50
Alignment explanation
Indices: 12797167--12797275 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 50
12797157 CCCATTTTTA
* * **
12797167 AAATTTATTTTAAGGTTAAATTTATTTTAAATTTAAATTTATTTTAAGTTT
1 AAATTTATTTTAAAGTTAAATTTAATTTAAATTTAAATTTAAATT-AGTTT
* * *
12797218 AAATTTGTTTTAAATTTAAATTTAATTTAAGTTTAAATTTGAAATT-GTTCT
1 AAATTTATTTTAAAGTTAAATTTAATTTAAATTTAAATTT-AAATTAGTT-T
12797269 AAATTTA
1 AAATTTA
12797276 AATTGATAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
50 3 0.06
51 42 0.88
52 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (50 bp):
AAATTTATTTTAAAGTTAAATTTAATTTAAATTTAAATTTAAATTAGTTT
Found at i:12797279 original size:6 final size:6
Alignment explanation
Indices: 12797182--12797263 Score: 73
Period size: 6 Copynumber: 14.2 Consensus size: 6
12797172 TATTTTAAGG
* * * **
12797182 TTAAAT TT-ATT TTAAAT TTAAAT TT-ATT TTAAGT TTAAAT TT-GTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
12797227 TTAAAT TTAAAT TT-AAT TTAAGT TTAAAT TTGAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT T
12797264 GTTCTAAATT
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
5 16 0.27
6 39 0.65
7 5 0.08
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:12798967 original size:30 final size:30
Alignment explanation
Indices: 12798922--12799292 Score: 187
Period size: 29 Copynumber: 12.5 Consensus size: 30
12798912 CTTGAACTGT
* * * *
12798922 TCAAAAATCATATTTTAACCCTTAAACTTC
1 TCAAAAATTACATTTTTACCCTCAAACTTC
* * * *
12798952 TCAAGAATTATATTTTTACCCTTAAAATTC
1 TCAAAAATTACATTTTTACCCTCAAACTTC
* * * *
12798982 TAAAAAATTACATATTTGCCCAT-GAACTTC
1 TCAAAAATTACATTTTTACCC-TCAAACTTC
* * *
12799012 T--AAAATTACATTTTTGCCCCCAAACATC
1 TCAAAAATTACATTTTTACCCTCAAACTTC
*
12799040 -CAAAAATTACATTTTTGCCC-CAAACTTC
1 TCAAAAATTACATTTTTACCCTCAAACTTC
* *
12799068 TCAAAAATTATATTTTTACCCTCGAACTTC
1 TCAAAAATTACATTTTTACCCTCAAACTTC
**
12799098 -CAAAAATTACATTTTGCCCTCGAATTTCTAAACTTC
1 TCAAAAATTACATTTTTACC-C-----TC-AAACTTC
* * *
12799134 -CAAAACTTACATTTTT-CCCCCGAACTTC
1 TCAAAAATTACATTTTTACCCTCAAACTTC
* * * * *
12799162 -CAAAAATCATATTTTTGCCCCCAAACCTC
1 TCAAAAATTACATTTTTACCCTCAAACTTC
* * * **
12799191 -CAAAAATCACGTTTTTACCCTGAATTTTC
1 TCAAAAATTACATTTTTACCCTCAAACTTC
* * *
12799220 -CTAAAATGACATTTTTACCCCTAAAACTT-
1 TCAAAAATTACATTTTTA-CCCTCAAACTTC
* * *
12799249 TCCAAAATTGCATTTTAACCCT-AAAC-TC
1 TCAAAAATTACATTTTTACCCTCAAACTTC
*
12799277 TCTAAAACTT-CATTTT
1 TC-AAAAATTACATTTT
12799293 GACATTTTTT
Statistics
Matches: 271, Mismatches: 52, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
27 1 0.00
28 60 0.22
29 107 0.39
30 77 0.28
31 1 0.00
34 1 0.00
35 4 0.01
36 20 0.07
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (30 bp):
TCAAAAATTACATTTTTACCCTCAAACTTC
Found at i:12799195 original size:122 final size:122
Alignment explanation
Indices: 12799006--12799234 Score: 302
Period size: 122 Copynumber: 1.9 Consensus size: 122
12798996 TTTGCCCATG
* * *
12799006 AACTTCTAAAATTACATTTTTGCCCCCAAACATCCAAAAATTACATTTTTGCCCCAAACTTCTCA
1 AACTTCCAAAATTACATTTTTGCCCCCAAACATCCAAAAATCACATTTTTGCCCCAAACCTCTCA
* * *
12799071 AAAATTATATTTTTACCCTCGAA-CTTCCAAAAATTACATTTTGCCCTCGAATTTCTA
66 AAAATCACATTTTTACCCT-GAATCTTCCAAAAATGACATTTTGCCCTCGAATTTCTA
* * *
12799128 AACTTCCAAAACTTACATTTTT-CCCCCGAACTTCCAAAAATCATATTTTTGCCCCCAAACCTC-
1 AACTTCCAAAA-TTACATTTTTGCCCCCAAACATCCAAAAATCACATTTTTG-CCCCAAACCTCT
* * *
12799191 CAAAAATCACGTTTTTACCCTGAATTTTCCTAAAATGACATTTT
64 CAAAAATCACATTTTTACCCTGAATCTTCCAAAAATGACATTTT
12799235 TACCCCTAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
121 3 0.03
122 69 0.75
123 20 0.22
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (122 bp):
AACTTCCAAAATTACATTTTTGCCCCCAAACATCCAAAAATCACATTTTTGCCCCAAACCTCTCA
AAAATCACATTTTTACCCTGAATCTTCCAAAAATGACATTTTGCCCTCGAATTTCTA
Found at i:12799283 original size:28 final size:29
Alignment explanation
Indices: 12799232--12799292 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
12799222 AAAATGACAT
* *
12799232 TTTTACCCCTAAAACTTTCCAAAA-TTGCA
1 TTTTAACCCTAAAACTCTCCAAAACTT-CA
*
12799261 TTTTAACCCT-AAACTCTCTAAAACTTCA
1 TTTTAACCCTAAAACTCTCCAAAACTTCA
12799289 TTTT
1 TTTT
12799293 GACATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (29 bp):
TTTTAACCCTAAAACTCTCCAAAACTTCA
Found at i:12799711 original size:97 final size:97
Alignment explanation
Indices: 12799559--12799738 Score: 288
Period size: 97 Copynumber: 1.9 Consensus size: 97
12799549 CAAGGCAATA
* * * * *
12799559 TTCCTTTATTTTGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGATTTTTCTTCAAACCG
1 TTCCTTTATCTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCAACTTTTCTTCAAACCG
12799624 GGATAATCGAATACCCTTAAATCGAGATAATG
66 GGATAATCGAATACCCTTAAATCGAGATAATG
* *
12799656 TTCCTTTATCTCGAGTTTTGAAAATTTGTGCCTTAACTTATTAGGCGCAACTTTTCTTTAAACCG
1 TTCCTTTATCTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCAACTTTTCTTCAAACCG
*
12799721 GGATAATCGAATATCCTT
66 GGATAATCGAATACCCTT
12799739 TTTCAAGGTT
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 75 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (97 bp):
TTCCTTTATCTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCAACTTTTCTTCAAACCG
GGATAATCGAATACCCTTAAATCGAGATAATG
Found at i:12811772 original size:117 final size:117
Alignment explanation
Indices: 12811316--12811840 Score: 393
Period size: 117 Copynumber: 4.5 Consensus size: 117
12811306 CAGCCATTCG
* * * * * * * * *
12811316 ATCTTTTACCACGAGCCTGGGGCAGATCACCATCATTTAATATCTTACCTCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGAGGCAGA
* * ** * * * * *
12811381 -T-CATTATCAACAAATCTCTTACCCCGAGCCTAGGGCAGATT-GCAGCCATCCG
66 TTGCA--ACCATCCGATCTTTTACCCCGAGCCTAGGGCAGATTATCA-TCAGCCA
* *
12811433 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGTAAATCTCTTACCCCGAGCCTAGGGCAGG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCT---G-A-G
* * * * * *
12811498 GCAGATTGCAGCCATCCGATCTCTTACCCCGAGCCTAGGGTAGATAATCATTAGCAA
61 GCAGATTGCAACCATCCGATCTTTTACCCCGAGCCTAGGGCAGATTATCATCAGCCA
* * * * * * * *
12811555 ATCTCTTACCCCGAGCTT-GGGAAGATTA-TAGCCATTCGATCTCTTACCCCAAGCTTGAGGCAG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGTCAATCTCTTACCCCGAGCCTGAGGCAG
* * * * ****
12811618 A-T-C-ACCATCAGCGTATCTTTTACCCCGATCATGGGGCAGATTA-CAGTTATTTG
65 ATTGCAACCATC--CG-ATCTTTTACCCCGAGCCTAGGGCAGATTATCA-TCAGCCA
* *
12811671 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGAGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGAGGCAGA
* ** * *
12811736 TTGCAACCATTCGATCTTTTACCTTGAGCCTAGGGCAGATCATCATCAGTCA
66 TTGCAACCATCCGATCTTTTACCCCGAGCCTAGGGCAGATTATCATCAGCCA
* * * *
12811788 ATCTCTTACCCCGAGCTTGGGGTAGATCACCATCAGCCAGTCTCTTACTCCGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGA
12811841 TCATGGGGCA
Statistics
Matches: 320, Mismatches: 69, Indels: 38
0.75 0.16 0.09
Matches are distributed among these distances:
113 5 0.02
114 1 0.00
115 5 0.02
116 50 0.16
117 157 0.49
118 7 0.02
119 1 0.00
120 7 0.02
121 27 0.08
122 55 0.17
123 3 0.01
124 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (117 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGAGGCAGA
TTGCAACCATCCGATCTTTTACCCCGAGCCTAGGGCAGATTATCATCAGCCA
Found at i:12811812 original size:78 final size:79
Alignment explanation
Indices: 12811358--12811814 Score: 428
Period size: 78 Copynumber: 5.8 Consensus size: 79
12811348 TCATTTAATA
* * * * * * *
12811358 TCTTACCTCGAGCTTGGGGCAGATCATTATCA-ACAAATCTCTTACCCCGAGCCTAGGGCAGATT
1 TCTTACCCCGAGCCTAGGGCAGATCATCATCAGTCAAATCTCTTACCCCGAGCTTGGGGCAGATT
*
12811422 GCAGCCATCCGATC
66 GCAGCCATTCGATC
* * *
12811436 TCTTACCCCGAGCTTGGGGCAGATCATCATCAGT-AAATCTCTTACCCCGAGCCTAGGGCAGGGC
1 TCTTACCCCGAGCCTAGGGCAGATCATCATCAGTCAAATCTCTTACCCCGAG-CT--TG--GGGC
*
12811500 AGATTGCAGCCATCCGATC
61 AGATTGCAGCCATTCGATC
* * * *
12811519 TCTTACCCCGAGCCTAGGGTAGATAATCATTAG-CAAATCTCTTACCCCGAGCTT-GGGAAGATT
1 TCTTACCCCGAGCCTAGGGCAGATCATCATCAGTCAAATCTCTTACCCCGAGCTTGGGGCAGATT
**
12811582 ATAGCCATTCGATC
66 GCAGCCATTCGATC
* * * ** * * *
12811596 TCTTACCCCAAG-CTTGAGGCAGATCACCATCAG-CGTATCTTTTACCCCGATCATGGGGCAGAT
1 TCTTACCCCGAGCCTAG-GGCAGATCATCATCAGTCAAATCTCTTACCCCGAGCTTGGGGCAGAT
* ** *
12811659 TACAGTTATTTGATC
65 TGCAGCCATTCGATC
* * * * *
12811674 TCTTACCCCGAG-CTTGAGGCAGATCACCATCAGTC-AATCTCTTACCCCGAGCCTGAGGTAGAT
1 TCTTACCCCGAGCCTAG-GGCAGATCATCATCAGTCAAATCTCTTACCCCGAGCTTGGGGCAGAT
*
12811737 TGCAACCATTCGATC
65 TGCAGCCATTCGATC
* ** *
12811752 TTTTACCTTGAGCCTAGGGCAGATCATCATCAGTC-AATCTCTTACCCCGAGCTTGGGGTAGAT
1 TCTTACCCCGAGCCTAGGGCAGATCATCATCAGTCAAATCTCTTACCCCGAGCTTGGGGCAGAT
12811815 CACCATCAGC
Statistics
Matches: 317, Mismatches: 51, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
76 3 0.01
77 58 0.18
78 181 0.57
79 5 0.02
82 2 0.01
83 68 0.21
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (79 bp):
TCTTACCCCGAGCCTAGGGCAGATCATCATCAGTCAAATCTCTTACCCCGAGCTTGGGGCAGATT
GCAGCCATTCGATC
Found at i:12811822 original size:39 final size:39
Alignment explanation
Indices: 12811238--12811853 Score: 337
Period size: 39 Copynumber: 15.7 Consensus size: 39
12811228 TTGAAGATTA
* * * *
12811238 AATCTCTTACCTCGATCTTGGGGCAGATCACCATTAGTT
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
*
12811277 AATCTCTTA-CCCGAGCTTGAGGCAGATTGCAGCCAT---TC
1 AATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGTC
* * * * * *
12811315 GATCTTTTACCACGAGCCTGGGGCAGATCACCATCATTT
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
* * ** *
12811354 AATATCTTACCTCGAGCTTGGGGCAGATCATTATCA-AC
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
* *
12811392 AAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATC---C
1 -AATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGTC
* * *
12811432 GATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGTA
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
*
12811471 AATCTCTTACCCCGAGCCTAGGGCAGGGCAGATTGCAGCCATC---C
1 AATCTCTTACCCCGAG-CT--TG--GGGCAGA-T-CA-CCATCAGTC
* * * * * * *
12811515 GATCTCTTACCCCGAGCCTAGGGTAGATAATCATTAG-C
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
* * * * *
12811553 AAATCTCTTACCCCGAGCTT-GGGAAGATTA-TAGCCATTC
1 -AATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGTC
* * *
12811592 GATCTCTTACCCCAAGCTTGAGGCAGATCACCATCAG-C
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
* * * * * * * *
12811630 GTATCTTTTACCCCGATCATGGGGCAGATTA-CAGTTATTT
1 -AATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGTC
* *
12811670 GATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGTC
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
* * * ** * * *
12811709 AATCTCTTACCCCGAGCCTGAGGTAGATTGCAACCATTC
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
* * ** * * *
12811748 GATCTTTTACCTTGAGCCTAGGGCAGATCATCATCAGTC
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
* *
12811787 AATCTCTTACCCCGAGCTTGGGGTAGATCACCATCAGCC
1 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
* * * *
12811826 AGTCTCTTACTCCGATCATGGGGCAGAT
1 AATCTCTTACCCCGAGCTTGGGGCAGAT
12811854 GGTAGTCATT
Statistics
Matches: 432, Mismatches: 112, Indels: 66
0.71 0.18 0.11
Matches are distributed among these distances:
36 11 0.03
37 6 0.01
38 55 0.13
39 311 0.72
40 9 0.02
41 6 0.01
42 4 0.01
43 1 0.00
44 22 0.05
45 1 0.00
46 2 0.00
47 4 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.26
Consensus pattern (39 bp):
AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGTC
Found at i:12812286 original size:17 final size:17
Alignment explanation
Indices: 12812264--12812332 Score: 102
Period size: 17 Copynumber: 4.1 Consensus size: 17
12812254 CCCATTTTTA
*
12812264 AAATTTATTTTAAGGTT
1 AAATTTATTTTAAGTTT
*
12812281 AAATTTATTTTAAATTT
1 AAATTTATTTTAAGTTT
12812298 AAATTTATTTTAAGTTT
1 AAATTTATTTTAAGTTT
* *
12812315 AAATTTAATTTAAATTT
1 AAATTTATTTTAAGTTT
12812332 A
1 A
12812333 TTTTTAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
AAATTTATTTTAAGTTT
Found at i:12812295 original size:11 final size:11
Alignment explanation
Indices: 12812279--12812345 Score: 73
Period size: 11 Copynumber: 5.9 Consensus size: 11
12812269 TATTTTAAGG
*
12812279 TTAAATTTATT
1 TTAAATTTAAT
12812290 TTAAATTTAAAT
1 TTAAATTT-AAT
*
12812302 TT-ATTTTAAGT
1 TTAAATTTAA-T
12812313 TTAAATTTAAT
1 TTAAATTTAAT
*
12812324 TTAAATTTATTT
1 TTAAATTTA-AT
12812336 TTAAATTTAA
1 TTAAATTTAA
12812346 AATTATTCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
10 2 0.04
11 25 0.53
12 20 0.43
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:12812298 original size:6 final size:6
Alignment explanation
Indices: 12812279--12812365 Score: 76
Period size: 6 Copynumber: 15.2 Consensus size: 6
12812269 TATTTTAAGG
* * *
12812279 TTAAAT TT-ATT TTAAAT TTAAAT TT-ATT TTAAGT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
** *
12812324 TTAAAT TTATTT TTAAAT TTAAAA TT--AT TCTAAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT T
12812366 GATAATGTCA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
4 2 0.03
5 14 0.22
6 45 0.70
7 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:12812303 original size:34 final size:34
Alignment explanation
Indices: 12812264--12812332 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
12812254 CCCATTTTTA
*
12812264 AAATTTATTTTAAGGTTAAATTTATTTTAAATTT
1 AAATTTATTTTAAGGTTAAATTTAATTTAAATTT
*
12812298 AAATTTATTTTAAGTTTAAATTTAATTTAAATTT
1 AAATTTATTTTAAGGTTAAATTTAATTTAAATTT
12812332 A
1 A
12812333 TTTTTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (34 bp):
AAATTTATTTTAAGGTTAAATTTAATTTAAATTT
Found at i:12812315 original size:23 final size:23
Alignment explanation
Indices: 12812279--12812346 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
12812269 TATTTTAAGG
12812279 TTAAATTTATTTTAAATTTAAAT
1 TTAAATTTATTTTAAATTTAAAT
* *
12812302 TT-ATTTTAAGTTTAAATTT-AAT
1 TTAAATTT-ATTTTAAATTTAAAT
12812324 TTAAATTTATTTTTAAATTTAAA
1 TTAAATTTA-TTTTAAATTTAAA
12812347 ATTATTCTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 10 0.27
23 25 0.68
24 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (23 bp):
TTAAATTTATTTTAAATTTAAAT
Found at i:12812338 original size:17 final size:16
Alignment explanation
Indices: 12812264--12812365 Score: 88
Period size: 17 Copynumber: 6.3 Consensus size: 16
12812254 CCCATTTTTA
*
12812264 AAATTTATTTTAAGGTT
1 AAATTTATTTTAA-TTT
12812281 AAATTTATTTTAAATTT
1 AAATTTATTTT-AATTT
12812298 AAATTTATTTTAAGTTT
1 AAATTTATTTTAA-TTT
12812315 -AA---A-TTTAATTT
1 AAATTTATTTTAATTT
12812326 AAATTTATTTTTAAATTT
1 AAATTTA-TTTT-AATTT
* *
12812344 AAAATTATTCTAAATTT
1 AAATTTATT-TTAATTT
12812361 AAATT
1 AAATT
12812366 GATAATGTCA
Statistics
Matches: 71, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
11 3 0.04
12 7 0.10
13 1 0.01
15 1 0.01
16 4 0.06
17 41 0.58
18 14 0.20
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (16 bp):
AAATTTATTTTAATTT
Found at i:12812361 original size:23 final size:22
Alignment explanation
Indices: 12812279--12812365 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 22
12812269 TATTTTAAGG
12812279 TTAAATTTATTTTAAATTTAAAT
1 TTAAATTTA-TTTAAATTTAAAT
*
12812302 TT-ATTTTAAGTTTAAATTT-AAT
1 TTAAATTT-A-TTTAAATTTAAAT
12812324 TTAAATTTA-TT---TTTAAAT
1 TTAAATTTATTTAAATTTAAAT
*
12812342 TTAAAATTATTCTAAATTTAAAT
1 TTAAATTTATT-TAAATTTAAAT
12812365 T
1 T
12812366 GATAATGTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
17 3 0.06
18 11 0.21
19 1 0.02
20 3 0.06
22 10 0.19
23 24 0.46
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (22 bp):
TTAAATTTATTTAAATTTAAAT
Found at i:12814055 original size:30 final size:30
Alignment explanation
Indices: 12813989--12814218 Score: 118
Period size: 30 Copynumber: 7.8 Consensus size: 30
12813979 TTGAACAATC
* *
12813989 CAAAAATCATATTTTGACCCCTACACTTTT
1 CAAAAATCATATTTTGACCCCTAAACTTCT
** *
12814019 TTAAAATCATATTTTGACCCCTAAACTTGT
1 CAAAAATCATATTTTGACCCCTAAACTTCT
* * * *
12814049 CAAAAATTACATTTTTACCTCTAAACTTCT
1 CAAAAATCATATTTTGACCCCTAAACTTCT
* * * *
12814079 CAAAAATTACATTTTTA-CCCTCGAACTTC-
1 CAAAAATCATATTTTGACCCCT-AAACTTCT
* * * **
12814108 CAAAAATTACATTCT-ACCCCCGAACTT-T
1 CAAAAATCATATTTTGACCCCTAAACTTCT
* *
12814136 CAAAAATTACATATTTTG--CCCTCGAACTT-A
1 CAAAAA-T-CATATTTTGACCCCT-AAACTTCT
* * **
12814166 CAAAAATCATGTTTT-ACCCCGAATTTTC-
1 CAAAAATCATATTTTGACCCCTAAACTTCT
* * *
12814194 CTAAAATGATATTTTTACCCCTAAA
1 CAAAAATCATATTTTGACCCCTAAA
12814219 ACTTTTTAAA
Statistics
Matches: 159, Mismatches: 30, Indels: 23
0.75 0.14 0.11
Matches are distributed among these distances:
28 35 0.22
29 35 0.22
30 89 0.56
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
CAAAAATCATATTTTGACCCCTAAACTTCT
Found at i:12814126 original size:28 final size:29
Alignment explanation
Indices: 12814049--12814213 Score: 160
Period size: 30 Copynumber: 5.7 Consensus size: 29
12814039 CTAAACTTGT
*
12814049 CAAAAATTACATTTTTA-CCTCTAAACTTC
1 CAAAAATTACATTTTTACCCTC-GAACTTC
12814078 TCAAAAATTACATTTTTACCCTCGAACTTC
1 -CAAAAATTACATTTTTACCCTCGAACTTC
* * *
12814108 CAAAAATTACA-TTCTACCCCCGAACTTT
1 CAAAAATTACATTTTTACCCTCGAACTTC
* *
12814136 CAAAAATTACATATTTTGCCCTCGAACTTA
1 CAAAAATTACAT-TTTTACCCTCGAACTTC
*
12814166 CAAAAA-T-CATGTTTTACCC-CGAATTTTC
1 CAAAAATTACAT-TTTTACCCTCGAA-CTTC
* * *
12814194 CTAAAATGATATTTTTACCC
1 CAAAAATTACATTTTTACCC
12814214 CTAAAACTTT
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
27 4 0.04
28 42 0.37
29 20 0.18
30 44 0.39
31 4 0.04
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCGAACTTC
Found at i:12814170 original size:58 final size:59
Alignment explanation
Indices: 12814049--12814172 Score: 171
Period size: 58 Copynumber: 2.1 Consensus size: 59
12814039 CTAAACTTGT
* * * *
12814049 CAAAAATTACATTTTTACCTCTAAACTTCTCAAAAATTACATTTTTACCCTCGAACTTC
1 CAAAAATTACATTTCTACCCCCAAACTTCTCAAAAATTACATTTTTACCCTCGAACTTA
* *
12814108 CAAAAATTACA-TTCTACCCCCGAACTT-TCAAAAATTACATATTTTGCCCTCGAACTTA
1 CAAAAATTACATTTCTACCCCCAAACTTCTCAAAAATTACAT-TTTTACCCTCGAACTTA
12814166 CAAAAAT
1 CAAAAAT
12814173 CATGTTTTAC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
57 13 0.22
58 34 0.59
59 11 0.19
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (59 bp):
CAAAAATTACATTTCTACCCCCAAACTTCTCAAAAATTACATTTTTACCCTCGAACTTA
Found at i:12814184 original size:58 final size:56
Alignment explanation
Indices: 12814072--12814213 Score: 158
Period size: 58 Copynumber: 2.5 Consensus size: 56
12814062 TTTACCTCTA
* *
12814072 AACTTCTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTACATTCTACCCCCG
1 AACTT-TCAAAAATTACATTTTTACCCTCGAACTTACAAAAATCACATTCTA-CCCCG
* ** *
12814130 AACTTTCAAAAATTACATATTTTGCCCTCGAACTTACAAAAATCATGTTTTACCCCG
1 AACTTTCAAAAATTACAT-TTTTACCCTCGAACTTACAAAAATCACATTCTACCCCG
* * * *
12814187 AATTTTCCTAAAATGATATTTTTACCC
1 AACTTT-CAAAAATTACATTTTTACCC
12814214 CTAAAACTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
57 30 0.42
58 41 0.58
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.35
Consensus pattern (56 bp):
AACTTTCAAAAATTACATTTTTACCCTCGAACTTACAAAAATCACATTCTACCCCG
Found at i:12814238 original size:30 final size:29
Alignment explanation
Indices: 12814029--12814238 Score: 153
Period size: 30 Copynumber: 7.2 Consensus size: 29
12814019 TTAAAATCAT
*
12814029 ATTTTGACCCCTAAACTTGTCAAAAATTAC
1 ATTTTTACCCCTAAACTT-TCAAAAATTAC
*
12814059 ATTTTTACCTCTAAACTTCTCAAAAATTAC
1 ATTTTTACCCCTAAACTT-TCAAAAATTAC
* *
12814089 ATTTTTA-CCCTCGAACTTCCAAAAATTAC
1 ATTTTTACCCCT-AAACTTTCAAAAATTAC
* **
12814118 A-TTCTACCCCCGAACTTTCAAAAATTAC
1 ATTTTTACCCCTAAACTTTCAAAAATTAC
* * *
12814146 ATATTTT-GCCCTCGAACTTACAAAAA-T-C
1 AT-TTTTACCCCT-AAACTTTCAAAAATTAC
* * * * *
12814174 ATGTTTTACCCC-GAATTTTCCTAAAATGAT
1 AT-TTTTACCCCTAAACTTT-CAAAAATTAC
**
12814204 ATTTTTACCCCTAAAACTTTTTAAAATTAC
1 ATTTTTACCCCT-AAACTTTCAAAAATTAC
12814234 ATTTT
1 ATTTT
12814239 AACTCCAACC
Statistics
Matches: 144, Mismatches: 25, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
27 5 0.03
28 33 0.23
29 33 0.23
30 68 0.47
31 5 0.03
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (29 bp):
ATTTTTACCCCTAAACTTTCAAAAATTAC
Found at i:12814687 original size:97 final size:97
Alignment explanation
Indices: 12814521--12814808 Score: 459
Period size: 97 Copynumber: 3.0 Consensus size: 97
12814511 AAAATATTTA
* * * * * *
12814521 AAATCGAGGCAATATTCCTTTGTTTCGGGTTTTAAAAATTTGTGCCTTAACTTACTAGGCGCGAT
1 AAATCGAGGCAATGTTCTTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
*
12814586 TTTTCTTCAAACCGAGATAATCGAATACCCTT
66 TTTTCTTCAAACCGGGATAATCGAATACCCTT
*
12814618 AAATCGAGGCAATGTTCTTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGTGCGAT
1 AAATCGAGGCAATGTTCTTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
* *
12814683 TTTTCTTCAAACTGGGACAATCGAATACCCTT
66 TTTTCTTCAAACCGGGATAATCGAATACCCTT
* *
12814715 AAATCGAGGCAATGTTCTTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGTGAC
1 AAATCGAGGCAATGTTCTTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
*
12814780 TTTTCTTCAAACCGGGATAATCGGATACC
66 TTTTCTTCAAACCGGGATAATCGAATACC
12814809 TTTTTTCATG
Statistics
Matches: 175, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 175 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (97 bp):
AAATCGAGGCAATGTTCTTTTATCTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
TTTTCTTCAAACCGGGATAATCGAATACCCTT
Found at i:12818955 original size:5 final size:5
Alignment explanation
Indices: 12818945--12818971 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12818935 ATAAAAACCA
12818945 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
12818972 TTTAACTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:12821207 original size:21 final size:21
Alignment explanation
Indices: 12821160--12821229 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
12821150 AATAGTACAG
*
12821160 ACTTCTACTGATACAAGTGAT
1 ACTTCTACCGATACAAGTGAT
*
12821181 AATTCTACCGATACAAGTGACT
1 ACTTCTACCGATACAAGTGA-T
* **
12821203 -CTTCTACCAATACAAGTCTT
1 ACTTCTACCGATACAAGTGAT
12821223 ACTTCTA
1 ACTTCTA
12821230 TCAGTATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.95
22 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAT
Found at i:12835735 original size:22 final size:21
Alignment explanation
Indices: 12835691--12835740 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
12835681 TAAACTCGCC
* *
12835691 AATA-TTATTTTAATTTTTTT
1 AATATTTATATTAATTATTTT
12835711 AATATTTATATTATATTATTTT
1 AATATTTATATTA-ATTATTTT
12835733 AATATTTA
1 AATATTTA
12835741 ATGATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 4 0.15
21 7 0.27
22 15 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
AATATTTATATTAATTATTTT
Found at i:12843734 original size:36 final size:36
Alignment explanation
Indices: 12843687--12843775 Score: 142
Period size: 36 Copynumber: 2.4 Consensus size: 36
12843677 GGTAACAGGC
*
12843687 ATGACCTTTGGGTCAACATGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGAAAAATGAGCATA
* *
12843723 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAACAGGGAGAAAAATGAGCATA
12843759 ATGACCTTTGAGGTCAA
1 ATGACCTTTG-GGTCAA
12843776 TAAAGAGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 43 0.88
37 6 0.12
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.24
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGAAAAATGAGCATA
Found at i:12843784 original size:37 final size:36
Alignment explanation
Indices: 12843686--12843787 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
12843676 TGGTAACAGG
* *
12843686 CATGACCTTTGGGTCAACATGGAGAAAAATGAGCAT
1 CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAT
* *
12843722 AATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAT
* *
12843758 CATGACCTTTGAGGTCAATAAAGAGTAAAA
1 CATGACCTTTG-GGTCAACAAGGAGTAAAA
12843788 CGAATAACGA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 43 0.74
37 15 0.26
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAT
Found at i:12848204 original size:60 final size:61
Alignment explanation
Indices: 12848140--12848257 Score: 157
Period size: 61 Copynumber: 2.0 Consensus size: 61
12848130 ACAAAAAATT
* * **
12848140 AATTTATTGACTTTTTT-GAATTAGAATTAAATTAACAAATTTTGTAAATTTTGAGGGCTA
1 AATTTATTGACTTTTTTAGAATTAGAACTAAAATAACAAATTTTGTAAACATTGAGGGCTA
* * * *
12848200 AATTTATTGAGTTTTTTAGAATTCGAACTAAAATGATAAATTTTGTAAACATTGAGGG
1 AATTTATTGACTTTTTTAGAATTAGAACTAAAATAACAAATTTTGTAAACATTGAGGG
12848258 TTAATTTTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 16 0.33
61 33 0.67
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.42
Consensus pattern (61 bp):
AATTTATTGACTTTTTTAGAATTAGAACTAAAATAACAAATTTTGTAAACATTGAGGGCTA
Found at i:12851647 original size:15 final size:15
Alignment explanation
Indices: 12851627--12851658 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12851617 TTATGAACCC
*
12851627 TTTTTAAATTTTTTA
1 TTTTTAAATATTTTA
12851642 TTTTTAAATATTTTA
1 TTTTTAAATATTTTA
12851657 TT
1 TT
12851659 ATTTTTTTTG
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTAAATATTTTA
Found at i:12857986 original size:6 final size:6
Alignment explanation
Indices: 12857985--12858023 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
12857975 ACTTTTTATT
*
12857985 TTTTAA TTTTAA TTTTGA -TTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
12858024 TATAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:12858008 original size:17 final size:17
Alignment explanation
Indices: 12857986--12858022 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12857976 CTTTTTATTT
*
12857986 TTTAATTTTAATTTTGA
1 TTTAATTTTAATTTTAA
12858003 TTTAATTTTAATTTTAA
1 TTTAATTTTAATTTTAA
12858020 TTT
1 TTT
12858023 TTATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTAATTTTAATTTTAA
Found at i:12858038 original size:23 final size:23
Alignment explanation
Indices: 12857984--12858035 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
12857974 AACTTTTTAT
*
12857984 TTTTTAATTTTAATTTTGATTTAA
1 TTTTTAATTTTAATTTT-ATATAA
12858008 -TTTTAATTTTAATTTT-TATAA
1 TTTTTAATTTTAATTTTATATAA
12858029 TTTTTAA
1 TTTTTAA
12858036 ATTATTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 4 0.15
22 6 0.23
23 16 0.62
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTAATTTTAATTTTATATAA
Found at i:12862242 original size:41 final size:42
Alignment explanation
Indices: 12862180--12862322 Score: 134
Period size: 41 Copynumber: 3.5 Consensus size: 42
12862170 CTTGATGTTT
* *
12862180 AAAAGGAAGACTCATGTCTCGAGATAAGAATGAGAAT-G-TG
1 AAAAGGAAGACTCATGACTCGAAATAAGAATGAGAATGGTTG
* *
12862220 ATAAAGGAAGACTCATGACTCGAAATTAGCATGAGAATGGTTG
1 A-AAAGGAAGACTCATGACTCGAAATAAGAATGAGAATGGTTG
* * * * * *
12862263 AAAAGGAAGCCTTATGACTCG--ATAGAGCATAAG-ATTGTTA
1 AAAAGGAAGACTCATGACTCGAAATA-AGAATGAGAATGGTTG
*
12862303 AAAAGGAAGACTTATGACTC
1 AAAAGGAAGACTCATGACTC
12862323 AGTAGAGCAT
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
40 27 0.31
41 39 0.44
42 19 0.22
43 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.22
Consensus pattern (42 bp):
AAAAGGAAGACTCATGACTCGAAATAAGAATGAGAATGGTTG
Found at i:12862317 original size:40 final size:40
Alignment explanation
Indices: 12862222--12862342 Score: 145
Period size: 40 Copynumber: 3.0 Consensus size: 40
12862212 AGAATGTGAT
* * * * * *
12862222 AAAGGAAGACTCATGACTCGAAATTAGCATGAGAATGGTTGA
1 AAAGGAAGACTTATGACTCGATA-GAGCATAAG-ATTGTTAA
*
12862264 AAAGGAAGCCTTATGACTCGATAGAGCATAAGATTGTTAA
1 AAAGGAAGACTTATGACTCGATAGAGCATAAGATTGTTAA
12862304 AAAGGAAGACTTATGACTC-AGTAGAGCATAAGATTGTTA
1 AAAGGAAGACTTATGACTCGA-TAGAGCATAAGATTGTTA
12862343 TAACGAAGAC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 42 0.60
41 7 0.10
42 20 0.29
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (40 bp):
AAAGGAAGACTTATGACTCGATAGAGCATAAGATTGTTAA
Found at i:12863066 original size:21 final size:21
Alignment explanation
Indices: 12863042--12863088 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
12863032 AAGTAAGACA
*
12863042 TGTATCGGTAAAACTGTCACT
1 TGTATCGGTAAAACGGTCACT
12863063 TGTATCGGTAAAACGGTCACT
1 TGTATCGGTAAAACGGTCACT
12863084 TGTAT
1 TGTAT
12863089 TAGTAGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (21 bp):
TGTATCGGTAAAACGGTCACT
Found at i:12873725 original size:18 final size:18
Alignment explanation
Indices: 12873679--12873725 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
12873669 GCATTCGAGC
*
12873679 ATGTGATTGCATCTGATT
1 ATGTGATTGCATCTGAGT
* *
12873697 ATATGACTGCATCTGAGT
1 ATGTGATTGCATCTGAGT
12873715 ATGTGATTGCA
1 ATGTGATTGCA
12873726 ATTGATCAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (18 bp):
ATGTGATTGCATCTGAGT
Found at i:12875300 original size:15 final size:15
Alignment explanation
Indices: 12875282--12875313 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12875272 TTAGAGTCTA
12875282 TATGAAAAGAATTGT
1 TATGAAAAGAATTGT
12875297 TATGAAAAGAATTGT
1 TATGAAAAGAATTGT
12875312 TA
1 TA
12875314 AGAGTAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (15 bp):
TATGAAAAGAATTGT
Found at i:12877674 original size:21 final size:21
Alignment explanation
Indices: 12877650--12877702 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
12877640 TGTAAATTTT
12877650 TATGGCTGCATCCGATTCT-A
1 TATGGCTGCATCCGATTCTGA
* *
12877670 GTATGGCTGTATCTGATTCTGA
1 -TATGGCTGCATCCGATTCTGA
*
12877692 TGTGGCTGCAT
1 TATGGCTGCAT
12877703 TTGGCTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (21 bp):
TATGGCTGCATCCGATTCTGA
Found at i:12880153 original size:15 final size:16
Alignment explanation
Indices: 12880125--12880154 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12880115 AAGTCTTTGA
12880125 TTGTTCTGTTTTGTAT
1 TTGTTCTGTTTTGTAT
12880141 TTGTTCT-TTTTGTA
1 TTGTTCTGTTTTGTA
12880155 GGAGCGATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.70
Consensus pattern (16 bp):
TTGTTCTGTTTTGTAT
Found at i:12885086 original size:24 final size:24
Alignment explanation
Indices: 12885031--12885087 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
12885021 GGCGTGATAA
12885031 TTAGCACTT-GTGTGCCCATGTTT
1 TTAGCACTTCGTGTGCCCATGTTT
* *
12885054 CTAGCACTTCG-GTGCTCATGATTT
1 TTAGCACTTCGTGTGCCCATG-TTT
12885078 TTAGCACTTC
1 TTAGCACTTC
12885088 CATGATCGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (24 bp):
TTAGCACTTCGTGTGCCCATGTTT
Found at i:12889218 original size:39 final size:39
Alignment explanation
Indices: 12889168--12889262 Score: 190
Period size: 39 Copynumber: 2.4 Consensus size: 39
12889158 TAGATATATT
12889168 TCCATTCAATTTGAACTCTCAAATGCATAGGATTTGATA
1 TCCATTCAATTTGAACTCTCAAATGCATAGGATTTGATA
12889207 TCCATTCAATTTGAACTCTCAAATGCATAGGATTTGATA
1 TCCATTCAATTTGAACTCTCAAATGCATAGGATTTGATA
12889246 TCCATTCAATTTGAACT
1 TCCATTCAATTTGAACT
12889263 ATCCAAAACC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (39 bp):
TCCATTCAATTTGAACTCTCAAATGCATAGGATTTGATA
Found at i:12893111 original size:49 final size:48
Alignment explanation
Indices: 12893058--12893325 Score: 172
Period size: 49 Copynumber: 5.5 Consensus size: 48
12893048 CTTAAACCGA
* * * *
12893058 TCCCTTGGCATCTTCGTGGTATTGGATTCACCGTTGCAGCTTAAATCTT
1 TCCCTT-GCATCTTCGTGGTAATGGATTCGCCATTGCGGCTTAAATCTT
* * * * * *
12893107 TCCCTT-CATTTTTGAGGTACAAGG-TTCGCCATTGCGGCTTAAACCTC
1 TCCCTTGCATCTTCGTGGTA-ATGGATTCGCCATTGCGGCTTAAATCTT
*
12893154 TCCCTTTGCATCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTT
1 TCCC-TTGCATCTTCGTGGTAATGGATTCGCCATTGCGGCTTAAATCTT
* * * * * * *
12893203 TCCCTT-CGTGCTT-TTGAAGTACAAGG-TTCGTCGTTGCGACTTAAACCTT
1 TCCCTTGCAT-CTTCGTG--GTA-ATGGATTCGCCATTGCGGCTTAAATCTT
* * * *
12893252 TCCCTCCAT-TATCTTTGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTT
1 TCCCT---TGCATCTTCGTGGTAATGGATTCGCCATTGCGGCTTAAATCTT
*
12893302 TCCCTT-CATGTCTTCATGGTAATG
1 TCCCTTGCA--TCTTCGTGGTAATG
12893326 AAACCTATAG
Statistics
Matches: 167, Mismatches: 37, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
47 38 0.23
48 11 0.07
49 81 0.49
50 30 0.18
51 3 0.02
52 4 0.02
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (48 bp):
TCCCTTGCATCTTCGTGGTAATGGATTCGCCATTGCGGCTTAAATCTT
Found at i:12893165 original size:96 final size:97
Alignment explanation
Indices: 12893045--12893310 Score: 349
Period size: 96 Copynumber: 2.7 Consensus size: 97
12893035 TTTGCCGTTA
* * * * *
12893045 CGACTTAAACCGATCCCTTGGCATCTTCGTGGTATTGGATTCACCGTTGCAGCTTAAATCTTTCC
1 CGACTTAAACCTATCCCTTTGCATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCC
*
12893110 CTTCAT-TTTTGAGGTACAAGGTTCGCCATTG
66 CTTCATCTTTTGAAGTACAAGGTTCGCCATTG
* * *
12893141 CGGCTTAAACCTCTCCCTTTGCATCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCC
1 CGACTTAAACCTATCCCTTTGCATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCC
* * *
12893206 CTTCGTGCTTTTGAAGTACAAGGTTCGTCGTTG
66 CTTCAT-CTTTTGAAGTACAAGGTTCGCCATTG
* *
12893239 CGACTTAAACCTTTCCCTCCATT--ATCTTTGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTT
1 CGACTTAAACCTATCCCT---TTGCATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTT
12893302 TCCCTTCAT
63 TCCCTTCAT
12893311 GTCTTCATGG
Statistics
Matches: 148, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
96 62 0.42
98 38 0.26
99 46 0.31
101 2 0.01
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (97 bp):
CGACTTAAACCTATCCCTTTGCATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCC
CTTCATCTTTTGAAGTACAAGGTTCGCCATTG
Found at i:12906562 original size:37 final size:38
Alignment explanation
Indices: 12906511--12906586 Score: 136
Period size: 37 Copynumber: 2.0 Consensus size: 38
12906501 GAGAATTACA
*
12906511 TAGTTCACTGTTCTTTTCTCCTA-TTGTTGCTCTCTAT
1 TAGTTCACTATTCTTTTCTCCTATTTGTTGCTCTCTAT
12906548 TAGTTCACTATTCTTTTCTCCTATTTGTTGCTCTCTAT
1 TAGTTCACTATTCTTTTCTCCTATTTGTTGCTCTCTAT
12906586 T
1 T
12906587 GTCTCTGTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 22 0.59
38 15 0.41
ACGTcount: A:0.12, C:0.24, G:0.09, T:0.55
Consensus pattern (38 bp):
TAGTTCACTATTCTTTTCTCCTATTTGTTGCTCTCTAT
Found at i:12910626 original size:21 final size:21
Alignment explanation
Indices: 12910597--12910673 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
12910587 GGAGTTTTTA
* *
12910597 GTATCGGTAGAAGTAAGACTT
1 GTATCGGTAGAAGTGACACTT
* * *
12910618 GTTTCGGTAGATGTGCCACTT
1 GTATCGGTAGAAGTGACACTT
* *
12910639 GTATCGGTAGAACTGTCACTT
1 GTATCGGTAGAAGTGACACTT
12910660 GTATCGGTAGAAGT
1 GTATCGGTAGAAGT
12910674 CAGCATTACA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAAGTGACACTT
Found at i:12916525 original size:2 final size:2
Alignment explanation
Indices: 12916518--12916553 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12916508 AAATCCAAGG
12916518 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12916554 TTGTTTCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12924721 original size:116 final size:116
Alignment explanation
Indices: 12924506--12924730 Score: 301
Period size: 116 Copynumber: 1.9 Consensus size: 116
12924496 TAATTATAAA
* * * *
12924506 GTAGGAGAGAAGTTGTTCACTGACTTGGGTTGTATCGGTAGATGAATAACAAGTATTGGTAGTCA
1 GTAGGAAAGAAGTTGTTCACTAACTTGGGTTGTATCGGTAGAGGAATAACAAGTATCGGTAGTCA
* * * ** *
12924571 TGTGTTTAGAAGTATCAGTATTTTGCATATTTGTA-TCGGTAGAAATACATG
66 TGTATTTAGAAATATCAGTAGTTCACATACTTGTACT-GGTAGAAATACATG
*
12924622 GTAGGAAAGAGGTTGTAT-ACTAACTTGGGTTGTATCGGTAGAGGAATAACAAGTATCGGTAGTC
1 GTAGGAAAGAAGTTGT-TCACTAACTTGGGTTGTATCGGTAGAGGAATAACAAGTATCGGTAGTC
* *
12924686 ATGTATTTAGAAATATCGGTGGTTCACATACTTGTACTGGTAGAA
65 ATGTATTTAGAAATATCAGTAGTTCACATACTTGTACTGGTAGAA
12924731 GTAGTAGGGT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
116 92 0.98
117 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.33
Consensus pattern (116 bp):
GTAGGAAAGAAGTTGTTCACTAACTTGGGTTGTATCGGTAGAGGAATAACAAGTATCGGTAGTCA
TGTATTTAGAAATATCAGTAGTTCACATACTTGTACTGGTAGAAATACATG
Found at i:12932012 original size:116 final size:117
Alignment explanation
Indices: 12931866--12932082 Score: 292
Period size: 116 Copynumber: 1.9 Consensus size: 117
12931856 GTGTTCACTA
* * * * * * * *
12931866 ACTTGGGTTGTATCGACAGATGAATAACAAGTATCAGTAGTCATGTGTTTAGAAGTATCAGTATT
1 ACTTGGGTTATATCAACAGAGGAATAACAAGTATCAGTAGTCATGTATTTAAAAATATCAATAGT
* *
12931931 TTACATATTTGTATCGGTAGAAGTA-CAAGGTAAGAGAGAGATTGTATATTG
66 TTACATACTTGTATCAGTAGAAGTAGCAAGGTAAGAGAGAGATTGTATATTG
* *
12931982 ACTTGGGTTATATCAATAGAGGGATAACAAGTATCAGTAGTCATGTATTTAAAAATATCAATAGT
1 ACTTGGGTTATATCAACAGAGGAATAACAAGTATCAGTAGTCATGTATTTAAAAATATCAATAGT
* * *
12932047 TTGCATACTTGTATCATTAGAAGTAGCAGGGTAAGA
66 TTACATACTTGTATCAGTAGAAGTAGCAAGGTAAGA
12932083 TTTCTAGCTC
Statistics
Matches: 85, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
116 76 0.89
117 9 0.11
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (117 bp):
ACTTGGGTTATATCAACAGAGGAATAACAAGTATCAGTAGTCATGTATTTAAAAATATCAATAGT
TTACATACTTGTATCAGTAGAAGTAGCAAGGTAAGAGAGAGATTGTATATTG
Found at i:12935411 original size:18 final size:16
Alignment explanation
Indices: 12935380--12935413 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
12935370 GTGAAATCTT
12935380 CAAATTAAGTTTTAAA
1 CAAATTAAGTTTTAAA
12935396 CAAATCTAATGTTTTAAA
1 CAAAT-TAA-GTTTTAAA
12935414 AATAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (16 bp):
CAAATTAAGTTTTAAA
Found at i:12942033 original size:34 final size:34
Alignment explanation
Indices: 12941995--12942062 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
12941985 GTATGATGTA
12941995 TTGATGGTTTAATGATGATAATGAGAGAGAGAAT
1 TTGATGGTTTAATGATGATAATGAGAGAGAGAAT
12942029 TTGATGGTTTAATGATGATAATGAGAGAGAGAAT
1 TTGATGGTTTAATGATGATAATGAGAGAGAGAAT
12942063 ATTAGTGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.32
Consensus pattern (34 bp):
TTGATGGTTTAATGATGATAATGAGAGAGAGAAT
Found at i:12949843 original size:13 final size:13
Alignment explanation
Indices: 12949825--12949850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12949815 TTGTAGTTTG
12949825 TAGGAAATTATGA
1 TAGGAAATTATGA
12949838 TAGGAAATTATGA
1 TAGGAAATTATGA
12949851 AAGGTGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
TAGGAAATTATGA
Found at i:12957610 original size:3 final size:3
Alignment explanation
Indices: 12957604--12957644 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
12957594 GTAGTAGTAG
*
12957604 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12957645 CAAATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:12960313 original size:238 final size:229
Alignment explanation
Indices: 12959904--12960335 Score: 569
Period size: 238 Copynumber: 1.8 Consensus size: 229
12959894 TCTCTGAACC
* * * *
12959904 ATATGATGGTACCTTGGAGTTTCCTGAACGAGAACTTGGCTGAGCAGTCATAAAACTATATTCCA
1 ATATGATGATACCTTGGAGTTCCCTGAACAAGAACTTGGCTGAGCAGTCAGAAAACTATATTCCA
* * * * *
12959969 TATGTTCCAAGTTATCTGATGATAAACCTGATTCATTGCTGCACTTCCCACTAATGTTGAACATT
66 TATGTTCCAAGCTACCAGATGATAAACCTGATTCACTGCTGCACTTCCCACTAATGTCGAACATT
* * ** *
12960034 TCACTTTGACCCTGTCCATTATGACAAAATTGCAGTAAAATTTCATCAAGCAAACTACCACTAAT
131 TCACTTTCACCCTATCCATTACAACAAAATTGCAGTAAAATTTCATCAAGCAAACTAACACTAAT
12960099 TCATTTTTAAGCATTTATTTACAGCCTCTCAATT
196 TCATTTTTAAGCATTTATTTACAGCCTCTCAATT
* *
12960133 ATATGATGATACCTTGGAGTTCCCTGAACAAGAACTTGGTTGAGCAGTCAGAAAATTATATTCCA
1 ATATGATGATACCTTGGAGTTCCCTGAACAAGAACTTGGCTGAGCAGTCAGAAAACTATATTCCA
* * * *
12960198 TATGTTCTATGCTCCCAGATTGCAGCCCTTCAAAACCTGATAT-ACTGCTGCACTTTCCACTAAT
66 TATGTTCCAAGCTACCAGA-TG-A-----T--AAACCTGAT-TCACTGCTGCACTTCCCACTAAT
* *
12960262 GTCGAACATTTCAGTTTCACCCTATCCATTACAACAAAATTGCAGTAAAATTTCATTAAGCAAAC
121 GTCGAACATTTCACTTTCACCCTATCCATTACAACAAAATTGCAGTAAAATTTCATCAAGCAAAC
12960327 TAACACTAA
186 TAACACTAA
12960336 CTTATTTATT
Statistics
Matches: 171, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
229 72 0.42
230 2 0.01
231 1 0.01
236 1 0.01
238 94 0.55
239 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.32
Consensus pattern (229 bp):
ATATGATGATACCTTGGAGTTCCCTGAACAAGAACTTGGCTGAGCAGTCAGAAAACTATATTCCA
TATGTTCCAAGCTACCAGATGATAAACCTGATTCACTGCTGCACTTCCCACTAATGTCGAACATT
TCACTTTCACCCTATCCATTACAACAAAATTGCAGTAAAATTTCATCAAGCAAACTAACACTAAT
TCATTTTTAAGCATTTATTTACAGCCTCTCAATT
Found at i:12970290 original size:28 final size:28
Alignment explanation
Indices: 12970235--12970295 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
12970225 CATTTAGAAT
* * *
12970235 TCAGCTTGCATGCATAGCTCGCACTTCA
1 TCAGCTAGCATACATAGCTCACACTTCA
* *
12970263 TCAGCTAGCATACGTAGCTCACATTTCA
1 TCAGCTAGCATACATAGCTCACACTTCA
*
12970291 CCAGC
1 TCAGC
12970296 CGCTCAACTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (28 bp):
TCAGCTAGCATACATAGCTCACACTTCA
Found at i:12987676 original size:19 final size:19
Alignment explanation
Indices: 12987652--12987694 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12987642 AAACATAACT
12987652 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
12987671 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
12987690 TAAAT
1 TAAAT
12987695 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:12988467 original size:109 final size:111
Alignment explanation
Indices: 12988289--12988493 Score: 274
Period size: 109 Copynumber: 1.9 Consensus size: 111
12988279 TACATTGGAC
* * **
12988289 CTTTTGACGCAAAATGAAATGACATCCAAGCACTCCATCCCGGTTACTCAGCCCAACATGCTCTC
1 CTTTTGACGCAAAATGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGCCCAACACACTCTC
12988354 AATTT-TTT-TCTTC-TCTTTTCTTTTTTTTGTAGAATGTGTTAGCT
66 AATTTATTTAT-TTCATCTTTTCTTTTTTTTGTAGAATGTGTTAGCT
* * * *
12988398 CTTTTGACGCGAAGTGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGTCTAACACACTC-C
1 CTTTTGACGCAAAATGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGCCCAACACACTCTC
*
12988462 GAATTTATTTATTTCTATTTTTTCTTTTTTTT
66 -AATTTATTTATTTC-ATCTTTTCTTTTTTTT
12988494 TCGGGTTAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
108 1 0.01
109 60 0.73
110 6 0.07
111 1 0.01
112 14 0.17
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (111 bp):
CTTTTGACGCAAAATGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGCCCAACACACTCTC
AATTTATTTATTTCATCTTTTCTTTTTTTTGTAGAATGTGTTAGCT
Found at i:12992043 original size:22 final size:21
Alignment explanation
Indices: 12992003--12992045 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12991993 CGATCTGAGG
*
12992003 AAAAATAAAAGAAATAGAATT
1 AAAAATAAAAGAAACAGAATT
12992024 AAAAATAAAAGAAAACAGAATT
1 AAAAATAAAAG-AAACAGAATT
12992046 GAAAGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAGAAACAGAATT
Found at i:12993163 original size:14 final size:14
Alignment explanation
Indices: 12993144--12993177 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
12993134 CAAGTTTAAC
12993144 CAAAAGAAGTCCAA
1 CAAAAGAAGTCCAA
12993158 CAAAAGAAGTCCAA
1 CAAAAGAAGTCCAA
12993172 CAAAAG
1 CAAAAG
12993178 TGACCCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.21, G:0.15, T:0.06
Consensus pattern (14 bp):
CAAAAGAAGTCCAA
Found at i:12997749 original size:24 final size:24
Alignment explanation
Indices: 12997711--12997761 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
12997701 TAGACAAAAA
*
12997711 TTAGCTCATATGAGCCCAAAATGG
1 TTAGCTCATACGAGCCCAAAATGG
*
12997735 TTAGCTCTTACGAGCCCAAAATGG
1 TTAGCTCATACGAGCCCAAAATGG
12997759 TTA
1 TTA
12997762 ACCAGTATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (24 bp):
TTAGCTCATACGAGCCCAAAATGG
Found at i:13013227 original size:30 final size:30
Alignment explanation
Indices: 13013191--13013250 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
13013181 ATAATTGTTT
*
13013191 TATCATAAATTTCAAGTCACAATCATCTAA
1 TATCATAAATGTCAAGTCACAATCATCTAA
*
13013221 TATCATAAATGTCAAGTCACGATCATCTAA
1 TATCATAAATGTCAAGTCACAATCATCTAA
13013251 ACTTTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (30 bp):
TATCATAAATGTCAAGTCACAATCATCTAA
Found at i:13014115 original size:39 final size:39
Alignment explanation
Indices: 13014061--13014135 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
13014051 ATCCGATCTC
13014061 TATGTCAAATGTTTATGACTAACAGATTTTATAAATGAA
1 TATGTCAAATGTTTATGACTAACAGATTTTATAAATGAA
*
13014100 TATGTCAACTGTTTATGACTAACAGATTTTATAAAT
1 TATGTCAAATGTTTATGACTAACAGATTTTATAAAT
13014136 CAATCATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (39 bp):
TATGTCAAATGTTTATGACTAACAGATTTTATAAATGAA
Found at i:13023545 original size:66 final size:66
Alignment explanation
Indices: 13023436--13023593 Score: 171
Period size: 66 Copynumber: 2.4 Consensus size: 66
13023426 CTTATTCTAA
* * * * *
13023436 CGCCATAGCTC-AACTATGGTCTTACACAGTTTACCCTTTTTTAATGTCCTGGCGAA-CTCCATA
1 CGCCATAG-TCGAGCTATGGTATTACACAGTTTACCCATGTTTAATGTCCTGAC-AAGCTCCATA
13023499 TGT
64 TGT
* * * *
13023502 CGCCATAGTCGAGCTATGGTTTTACATA-TTATACCCATGTTTAATTTTCTGACAAGCTCCATAT
1 CGCCATAGTCGAGCTATGGTATTACACAGTT-TACCCATGTTTAATGTCCTGACAAGCTCCATAT
13023566 GT
65 GT
*
13023568 CACCATAG-CGAGCTATGGTATTACAC
1 CGCCATAGTCGAGCTATGGTATTACAC
13023594 CTTAAACCTC
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
65 22 0.28
66 56 0.72
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (66 bp):
CGCCATAGTCGAGCTATGGTATTACACAGTTTACCCATGTTTAATGTCCTGACAAGCTCCATATG
T
Found at i:13030616 original size:9 final size:9
Alignment explanation
Indices: 13030604--13030708 Score: 72
Period size: 9 Copynumber: 11.4 Consensus size: 9
13030594 AAAAAATCGA
13030604 AAAAATTAT
1 AAAAATTAT
* *
13030613 AAAAAATCT
1 AAAAATTAT
*
13030622 GAAAATTA-
1 AAAAATTAT
13030630 AAAAGA-TATT
1 AAAA-ATTA-T
*
13030640 AAAATTTAT
1 AAAAATTAT
*
13030649 ATAAACTTAT
1 A-AAAATTAT
*
13030659 TAAAATTAT
1 AAAAATTAT
13030668 AAAAACTTAT
1 AAAAA-TTAT
*
13030678 AAATATTAT
1 AAAAATTAT
13030687 AAAAATCTA-
1 AAAAAT-TAT
*
13030696 ATAAATTAT
1 AAAAATTAT
13030705 AAAA
1 AAAA
13030709 TTTGTAAACC
Statistics
Matches: 73, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
8 7 0.10
9 43 0.59
10 23 0.32
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:13030673 original size:19 final size:19
Alignment explanation
Indices: 13030636--13030708 Score: 80
Period size: 19 Copynumber: 3.8 Consensus size: 19
13030626 ATTAAAAAGA
*
13030636 TATTAAAATTTATATAAACT
1 TATTAAAA-TTATAAAAACT
13030656 TATTAAAATTATAAAAACT
1 TATTAAAATTATAAAAACT
13030675 TA-TAAATATTATAAAAA-T
1 TATTAAA-ATTATAAAAACT
*
13030693 CTAAT-AAATTATAAAA
1 -TATTAAAATTATAAAA
13030709 TTTGTAAACC
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
18 14 0.29
19 26 0.53
20 9 0.18
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
TATTAAAATTATAAAAACT
Found at i:13036919 original size:23 final size:23
Alignment explanation
Indices: 13036893--13037013 Score: 163
Period size: 23 Copynumber: 5.2 Consensus size: 23
13036883 ACACTAGCGC
13036893 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
13036916 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
*
13036939 GCTCTCTGTTATTAGCACTGCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
13036964 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
13036987 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
13037010 GCTC
1 GCTC
13037014 AGTACTTTGT
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
22 3 0.03
23 65 0.75
25 17 0.20
26 2 0.02
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:13036964 original size:48 final size:46
Alignment explanation
Indices: 13036893--13037013 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
13036883 ACACTAGCGC
*
13036893 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCAC-TCTGCGT
* * *
13036939 GCTCTCTGTTATTAGCACTGCGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTCTGCGT
*
13036987 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
13037014 AGTACTTTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
46 25 0.38
47 2 0.03
48 39 0.59
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTCTGCGT
Found at i:13037032 original size:39 final size:39
Alignment explanation
Indices: 13036978--13037052 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
13036968 TCTGATTAGC
*
13036978 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
*
13037017 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTC
13037053 TCTGTTGCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (39 bp):
ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:13037047 original size:23 final size:23
Alignment explanation
Indices: 13037012--13037105 Score: 84
Period size: 23 Copynumber: 4.0 Consensus size: 23
13037002 CTTTGTGTGC
*
13037012 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
13037035 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
13037058 TGCCCAGCA-TTTATGTGCTCTCTGT
1 T---CAGCACTTTGTGTACTCTCTGT
* *
13037083 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
13037105 T
1 T
13037106 TGTTCCGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
22 15 0.26
23 23 0.40
25 16 0.28
26 4 0.07
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:13040182 original size:18 final size:18
Alignment explanation
Indices: 13040159--13040210 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
13040149 CGATCCAGAA
13040159 ATGCTCTAACGAGCCAGT
1 ATGCTCTAACGAGCCAGT
* *
13040177 ATGCTCAAACAAGCCAGT
1 ATGCTCTAACGAGCCAGT
*
13040195 ATGCTCTAATGAGCCA
1 ATGCTCTAACGAGCCA
13040211 AATGCTCTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (18 bp):
ATGCTCTAACGAGCCAGT
Found at i:13045363 original size:83 final size:84
Alignment explanation
Indices: 13045223--13045383 Score: 200
Period size: 83 Copynumber: 1.9 Consensus size: 84
13045213 GTATTTGAGG
* * * * *
13045223 TTAGTTCTAAAACATTAGTGTAAAGGTTTTACTTGAGCGGATCAAACAAAATGATTCTCAGACAG
1 TTAGTTCTAAAACATTAATGGAAAGGTCTTACTTGAGCGGACCAAACAAAATGATTCTAAGACAG
13045288 TA-AACAAAAGCATTTGAC
66 TACAACAAAAGCATTTGAC
* * * * *
13045306 TTAGTTCTATAACATTAATGGACAGGTCTTATTTTG-GCGGACCAAACAAATTTATTCTAAGACA
1 TTAGTTCTAAAACATTAATGGAAAGGTCTTA-CTTGAGCGGACCAAACAAAATGATTCTAAGACA
*
13045370 GTACAACAGAAGCA
65 GTACAACAAAAGCA
13045384 GACAAGGTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
83 53 0.82
84 12 0.18
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (84 bp):
TTAGTTCTAAAACATTAATGGAAAGGTCTTACTTGAGCGGACCAAACAAAATGATTCTAAGACAG
TACAACAAAAGCATTTGAC
Found at i:13045753 original size:3 final size:3
Alignment explanation
Indices: 13045738--13045775 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
13045728 AAAGGGAGAG
*
13045738 GAA GAA CAA GAA GAA GATA -AA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA GA
13045776 GGGAAGAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 29 0.94
4 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:13046867 original size:30 final size:32
Alignment explanation
Indices: 13046833--13046899 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
13046823 AAACCAAACT
* *
13046833 TAAATATCAA-ATTGAAAA-AAACTTAAATAC
1 TAAATATAAACATTAAAAATAAACTTAAATAC
*
13046863 TAAAT-TAAACATTAAAAATAAATTTAAATAC
1 TAAATATAAACATTAAAAATAAACTTAAATAC
13046894 TAAATA
1 TAAATA
13046900 ATATATTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.10
30 12 0.39
31 16 0.52
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.30
Consensus pattern (32 bp):
TAAATATAAACATTAAAAATAAACTTAAATAC
Found at i:13058769 original size:68 final size:68
Alignment explanation
Indices: 13058652--13058787 Score: 209
Period size: 68 Copynumber: 2.0 Consensus size: 68
13058642 GAGAAGATAA
* * *
13058652 AGTTAAAATGGAATATTCAGAACATATAGAGACAATAAACCCAAGAAACATTTAAGATTTTATCC
1 AGTTAAAATGGAAAATTCAAAACATATAAAGACAATAAACCCAAGAAACATTTAAGATTTTATCC
13058717 TAT
66 TAT
* * * *
13058720 AGTTAAAATGGAAAATTCAAAACATATAAAGACAATAAGCCTAATAAACATTTAGGATTTTATCC
1 AGTTAAAATGGAAAATTCAAAACATATAAAGACAATAAACCCAAGAAACATTTAAGATTTTATCC
13058785 TAT
66 TAT
13058788 GTCTCTTGGT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (68 bp):
AGTTAAAATGGAAAATTCAAAACATATAAAGACAATAAACCCAAGAAACATTTAAGATTTTATCC
TAT
Found at i:13059662 original size:122 final size:122
Alignment explanation
Indices: 13059445--13059689 Score: 490
Period size: 122 Copynumber: 2.0 Consensus size: 122
13059435 AACACTACAG
13059445 AAAAATAATAATAACTAATCACCTGAAATGTTACACCCTTTTCAGTGATGTCAGCTAAATGCAGC
1 AAAAATAATAATAACTAATCACCTGAAATGTTACACCCTTTTCAGTGATGTCAGCTAAATGCAGC
13059510 AGTGAAACCTATAAAGTAACCAGCAAGAGAGATTGTCATCTTCAACATACCACACAC
66 AGTGAAACCTATAAAGTAACCAGCAAGAGAGATTGTCATCTTCAACATACCACACAC
13059567 AAAAATAATAATAACTAATCACCTGAAATGTTACACCCTTTTCAGTGATGTCAGCTAAATGCAGC
1 AAAAATAATAATAACTAATCACCTGAAATGTTACACCCTTTTCAGTGATGTCAGCTAAATGCAGC
13059632 AGTGAAACCTATAAAGTAACCAGCAAGAGAGATTGTCATCTTCAACATACCACACAC
66 AGTGAAACCTATAAAGTAACCAGCAAGAGAGATTGTCATCTTCAACATACCACACAC
13059689 A
1 A
13059690 TATTATCTAT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 123 1.00
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (122 bp):
AAAAATAATAATAACTAATCACCTGAAATGTTACACCCTTTTCAGTGATGTCAGCTAAATGCAGC
AGTGAAACCTATAAAGTAACCAGCAAGAGAGATTGTCATCTTCAACATACCACACAC
Found at i:13064093 original size:59 final size:60
Alignment explanation
Indices: 13064016--13064140 Score: 200
Period size: 59 Copynumber: 2.1 Consensus size: 60
13064006 CATTGGACCT
* *
13064016 TTTTTTCTTGTCCAAATTAGTCTTTGAACTTGGCAATTG-CTCTCACATTAGGGTTTAAAC
1 TTTTTTCTTGTCCAAATTAGTCCTTGAACTTGGCAATTGTCTC-CACATTAGGGCTTAAAC
*
13064076 TTTTTT-TTGTCCAAATTAGTCCTTGAACTTGGCAATTGTTTCCACATTAGGGCTTAAAC
1 TTTTTTCTTGTCCAAATTAGTCCTTGAACTTGGCAATTGTCTCCACATTAGGGCTTAAAC
13064135 TTTTTT
1 TTTTTT
13064141 AATCCAAGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
59 53 0.87
60 8 0.13
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (60 bp):
TTTTTTCTTGTCCAAATTAGTCCTTGAACTTGGCAATTGTCTCCACATTAGGGCTTAAAC
Found at i:13064751 original size:43 final size:43
Alignment explanation
Indices: 13064688--13064776 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
13064678 CATAACATTT
13064688 GTATGCTTTGTATATAACATAATAGTTCTCTTTTTTATCCTTA
1 GTATGCTTTGTATATAACATAATAGTTCTCTTTTTTATCCTTA
*
13064731 GTATGCTTTGTATATGACATAATAGTTCTCTTTTTTATCCTTA
1 GTATGCTTTGTATATAACATAATAGTTCTCTTTTTTATCCTTA
13064774 GTA
1 GTA
13064777 AACTAAAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (43 bp):
GTATGCTTTGTATATAACATAATAGTTCTCTTTTTTATCCTTA
Found at i:13076544 original size:18 final size:18
Alignment explanation
Indices: 13076521--13076557 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13076511 TTTGTGATCA
13076521 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
13076539 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
13076557 A
1 A
13076558 TATGAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:13077524 original size:19 final size:19
Alignment explanation
Indices: 13077500--13077541 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
13077490 TTAGAACAGA
*
13077500 GGTATCAATATTTTATGGT
1 GGTATCAATATTTTAAGGT
*
13077519 GGTATCGATATTTTAAGGT
1 GGTATCAATATTTTAAGGT
13077538 GGTA
1 GGTA
13077542 ACGATGCCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.43
Consensus pattern (19 bp):
GGTATCAATATTTTAAGGT
Found at i:13077546 original size:19 final size:19
Alignment explanation
Indices: 13077507--13077546 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
13077497 AGAGGTATCA
* *
13077507 ATATTTTATGGTGGTATCG
1 ATATTTTAAGGTGGTAACG
13077526 ATATTTTAAGGTGGTAACG
1 ATATTTTAAGGTGGTAACG
13077545 AT
1 AT
13077547 GCCAGAGTTC
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:0.28, C:0.05, G:0.25, T:0.42
Consensus pattern (19 bp):
ATATTTTAAGGTGGTAACG
Found at i:13079065 original size:29 final size:30
Alignment explanation
Indices: 13079013--13079069 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
13079003 AAATTGAATC
* *
13079013 AAATCAAAATTTTATATATAAAATTACATA
1 AAATCAAAAGTTTAAATATAAAATTACATA
13079043 AAATC-AAAGTTTAAATATAAAATTACA
1 AAATCAAAAGTTTAAATATAAAATTACA
13079070 CAATAAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (30 bp):
AAATCAAAAGTTTAAATATAAAATTACATA
Found at i:13082037 original size:3 final size:3
Alignment explanation
Indices: 13082029--13082073 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
13082019 GTTTTTGTTA
13082029 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13082074 GCTTGTACTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:13083204 original size:17 final size:17
Alignment explanation
Indices: 13083169--13083215 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
13083159 TCAAGTTAAC
**
13083169 AAATAATTTAAAATTATA
1 AAATAA-TTAAAACAATA
13083187 AAATAATTAAAACAATA
1 AAATAATTAAAACAATA
13083204 AAA-AATTCAAAA
1 AAATAATT-AAAA
13083216 AAATTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 4 0.15
17 16 0.62
18 6 0.23
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAATTAAAACAATA
Found at i:13084329 original size:28 final size:24
Alignment explanation
Indices: 13084289--13084346 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 24
13084279 TTTCATTTTC
13084289 ATTTAATAAAATATAATTAATAAGTTT
1 ATTTAAT-AAA-ATAATT-ATAAGTTT
* *
13084316 ATTTATATGAAATAATTATAATTTT
1 ATTTA-ATAAAATAATTATAAGTTT
13084341 ATTTAA
1 ATTTAA
13084347 ATTTTGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 1 0.04
25 12 0.43
26 6 0.21
27 7 0.25
28 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (24 bp):
ATTTAATAAAATAATTATAAGTTT
Found at i:13093163 original size:25 final size:25
Alignment explanation
Indices: 13093116--13093163 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
13093106 TTATTTTATA
* *
13093116 ATAATAATTTGTATATTTTAAAATT
1 ATAAAAATTTGTATATTTCAAAATT
13093141 ATAAAAATTTGTAT-TTTACAAAA
1 ATAAAAATTTGTATATTT-CAAAA
13093164 AAAATAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
ATAAAAATTTGTATATTTCAAAATT
Done.