Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 105 of 145
Found at i:35235070 original size:27 final size:27
Alignment explanation
Indices: 35235032--35235100 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
35235022 AACATGCTAT
* * *
35235032 GAAAGGATTGCCTTTGTAGTAATATAC
1 GAAAGGAATGCCTTCGTAGCAATATAC
*
35235059 GAAAGGAATGCCTTCGTGGCAATATAC
1 GAAAGGAATGCCTTCGTAGCAATATAC
* *
35235086 GAAATGAACGCCTTC
1 GAAAGGAATGCCTTC
35235101 ATGGAAAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (27 bp):
GAAAGGAATGCCTTCGTAGCAATATAC
Found at i:35237196 original size:45 final size:46
Alignment explanation
Indices: 35237132--35237268 Score: 222
Period size: 45 Copynumber: 3.0 Consensus size: 46
35237122 AAATGTTTCG
*
35237132 AGCTATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTC-C
1 AGCTATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTCTA
35237177 AGCTATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTCTTA
1 AGCTATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTC-TA
** *
35237224 AATTATGGCATGTATAGGGACTTAGTCATTTCAATTGTATATTCT
1 AGCTATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTCT
35237269 TAAATTATGA
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
45 44 0.51
46 1 0.01
47 41 0.48
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (46 bp):
AGCTATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTCTA
Found at i:35237249 original size:47 final size:47
Alignment explanation
Indices: 35237135--35237277 Score: 236
Period size: 47 Copynumber: 3.1 Consensus size: 47
35237125 TGTTTCGAGC
* **
35237135 TATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTC--CAGC
1 TATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTCTTAAAT
35237180 TATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTCTTAAAT
1 TATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTCTTAAAT
*
35237227 TATGGCATGTATAGGGACTTAGTCATTTCAATTGTATATTCTTAAAT
1 TATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTCTTAAAT
35237274 TATG
1 TATG
35237278 ACCAAAAGAT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 41 0.45
47 51 0.55
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (47 bp):
TATGGCATGTATAGGGACTTAGTCATTTCGATTGTATATTCTTAAAT
Found at i:35240128 original size:20 final size:20
Alignment explanation
Indices: 35240081--35240128 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
35240071 GTTAGTTAGA
35240081 AATTGTTTA-TTAATCTTTTG
1 AATT-TTTATTTAATCTTTTG
*
35240101 AA-TTTTATTTAATTTTTTG
1 AATTTTTATTTAATCTTTTG
35240120 AATTTTTAT
1 AATTTTTAT
35240129 AATTTCTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 13 0.52
20 8 0.32
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (20 bp):
AATTTTTATTTAATCTTTTG
Found at i:35240140 original size:18 final size:19
Alignment explanation
Indices: 35240100--35240150 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
35240090 TTAATCTTTT
* * *
35240100 GAATTTTATTTAATTTTTT
1 GAATTTTATATAATTTCTA
35240119 GAATTTT-TATAATTTCTA
1 GAATTTTATATAATTTCTA
**
35240137 GAATACTATATAAT
1 GAATTTTATATAAT
35240151 ATTTTTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (19 bp):
GAATTTTATATAATTTCTA
Found at i:35240566 original size:13 final size:13
Alignment explanation
Indices: 35240550--35240575 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35240540 TAAAACAGAC
35240550 ATAAAAAATAAAA
1 ATAAAAAATAAAA
35240563 ATAAAAAATAAAA
1 ATAAAAAATAAAA
35240576 TTTCTCTTTT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:35242982 original size:20 final size:20
Alignment explanation
Indices: 35242959--35242996 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35242949 AATATTATAT
*
35242959 TAATTATATATGTTAAATAA
1 TAATTATATATATTAAATAA
35242979 TAATTATATATATTAAAT
1 TAATTATATATATTAAAT
35242997 CACTAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TAATTATATATATTAAATAA
Found at i:35246552 original size:51 final size:50
Alignment explanation
Indices: 35246461--35246592 Score: 133
Period size: 51 Copynumber: 2.6 Consensus size: 50
35246451 GTTCATATAG
** ***
35246461 TAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACATG-TAA
1 TAGCCTGCACATAGTACTACACACATGACCAAGCTCATCCGAT--ATGATAA
* * *
35246512 TAGCCTGCACATAGTACTACACACATGATCGAAGCT-ATCCGGTATGCATAG
1 TAGCCTGCACATAGTACTACACACATGA-CCAAGCTCATCCGATATG-ATAA
*
35246563 TAGCCTGCACATAGTACTACACACGTGACC
1 TAGCCTGCACATAGTACTACACACATGACC
35246593 TAGCAACTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
49 3 0.04
50 1 0.01
51 61 0.90
52 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGCCTGCACATAGTACTACACACATGACCAAGCTCATCCGATATGATAA
Found at i:35253055 original size:28 final size:27
Alignment explanation
Indices: 35253001--35253055 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
35252991 GATGCAACTA
* *
35253001 TGGTTTCTTCCATGTAGCTTCCTTTGT
1 TGGTTTCTTCCAAGTAACTTCCTTTGT
*
35253028 TGGTTTTTTCCCAAGTAACTTCCTTTGT
1 TGGTTTCTT-CCAAGTAACTTCCTTTGT
35253056 CTTTTCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.11, C:0.22, G:0.16, T:0.51
Consensus pattern (27 bp):
TGGTTTCTTCCAAGTAACTTCCTTTGT
Found at i:35253670 original size:22 final size:21
Alignment explanation
Indices: 35253634--35253677 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
35253624 TTAATAAATG
*
35253634 AAAAGAAAAAATTGATCTGTT
1 AAAAGAAAAAATTGAACTGTT
*
35253655 AAAAGAAAAATTTTGAACTGTT
1 AAAAGAAAAA-ATTGAACTGTT
35253677 A
1 A
35253678 TTTCCCTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (21 bp):
AAAAGAAAAAATTGAACTGTT
Found at i:35253806 original size:11 final size:11
Alignment explanation
Indices: 35253790--35253842 Score: 72
Period size: 11 Copynumber: 4.6 Consensus size: 11
35253780 CATAAGCTTG
35253790 TAGAAAATATT
1 TAGAAAATATT
35253801 TAGAAAA-AGCTT
1 TAGAAAATA--TT
35253813 GTAGAAAATATT
1 -TAGAAAATATT
35253825 TAGAAAATATT
1 TAGAAAATATT
35253836 TAGAAAA
1 TAGAAAA
35253843 AACTTTATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.03
11 25 0.66
12 4 0.11
13 7 0.18
14 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.30
Consensus pattern (11 bp):
TAGAAAATATT
Found at i:35253815 original size:24 final size:24
Alignment explanation
Indices: 35253783--35253831 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
35253773 GTAAAAACAT
35253783 AAGCTTGTAGAAAATATTTAGAAA
1 AAGCTTGTAGAAAATATTTAGAAA
35253807 AAGCTTGTAGAAAATATTTAGAAA
1 AAGCTTGTAGAAAATATTTAGAAA
35253831 A
1 A
35253832 TATTTAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (24 bp):
AAGCTTGTAGAAAATATTTAGAAA
Found at i:35258042 original size:36 final size:36
Alignment explanation
Indices: 35257995--35258067 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
35257985 AAAGAAATGA
35257995 AATATTAGGAATTAAGGAATTTAATAGATTTCGAGT
1 AATATTAGGAATTAAGGAATTTAATAGATTTCGAGT
35258031 AATATTAGGAATTAAGGAATTTAATAGATTTCGAGT
1 AATATTAGGAATTAAGGAATTTAATAGATTTCGAGT
35258067 A
1 A
35258068 TCATGGGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (36 bp):
AATATTAGGAATTAAGGAATTTAATAGATTTCGAGT
Found at i:35272352 original size:38 final size:38
Alignment explanation
Indices: 35272308--35272414 Score: 151
Period size: 38 Copynumber: 2.8 Consensus size: 38
35272298 ATTCAAATTG
*
35272308 GGTGTTATTCAGGCTTAGTGCCTAGTAGGCTCAGTGTC
1 GGTGTTATTCAGGCTTAGTGCCTAGTAGGCTCAGTGCC
* * * *
35272346 GGTGTTATTTAGGCTTAGTGCCTAGCAGACTTAGTGCC
1 GGTGTTATTCAGGCTTAGTGCCTAGTAGGCTCAGTGCC
* *
35272384 TGTGTTATTCAGGCTTAGCGCCTAGTAGGCT
1 GGTGTTATTCAGGCTTAGTGCCTAGTAGGCT
35272415 TTCTGCTGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.35
Consensus pattern (38 bp):
GGTGTTATTCAGGCTTAGTGCCTAGTAGGCTCAGTGCC
Found at i:35275083 original size:43 final size:43
Alignment explanation
Indices: 35275010--35275093 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
35275000 TGCATGATAA
***
35275010 GATAATACGAAGGAAATATACTGGTGCATGTTA-TGCATCACCG
1 GATAATACGAAGGAAATATACTGACACATG-TAGTGCATCACCG
*
35275053 GATAA-ACTGAAGGAAATATATTGACACATGTAGTGCATCAC
1 GATAATAC-GAAGGAAATATACTGACACATGTAGTGCATCAC
35275094 TATATTAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
42 4 0.11
43 31 0.89
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (43 bp):
GATAATACGAAGGAAATATACTGACACATGTAGTGCATCACCG
Found at i:35275195 original size:43 final size:43
Alignment explanation
Indices: 35275114--35275429 Score: 296
Period size: 43 Copynumber: 7.4 Consensus size: 43
35275104 AAAGAAATTT
* * * * *
35275114 TACTGGCAAATACAGTTCATCATCAGATAAA-TCGAAGCATATG
1 TACTGGCACACACAGTGCATCATCGGATAAACT-GAAGCATATA
* * * *
35275157 TAGTGGCACACAAAGTGCATCATCGGATAAACTAAAGCATCTA
1 TACTGGCACACACAGTGCATCATCGGATAAACTGAAGCATATA
* * * * *
35275200 TACTCGCACACATAGTGCATCATTGGATGAACTGAAGCATTTA
1 TACTGGCACACACAGTGCATCATCGGATAAACTGAAGCATATA
* * * * * *
35275243 TACTGGTACACATAGTGTATCATCAGATAATCTGAAGCATCTA
1 TACTGGCACACACAGTGCATCATCGGATAAACTGAAGCATATA
* * * * *
35275286 TACTGACACACACAGTACATCACCGGATAAACTAAAACA-ACTA
1 TACTGGCACACACAGTGCATCATCGGATAAACTGAAGCATA-TA
* *
35275329 TACTGGCACACACAGTGCATCATTGGATAAGCTGAAGCATATA
1 TACTGGCACACACAGTGCATCATCGGATAAACTGAAGCATATA
* * * * *
35275372 CACT-GCACACACAGTTCAACATCGGATAAACCGAAGCATTTA
1 TACTGGCACACACAGTGCATCATCGGATAAACTGAAGCATATA
*
35275414 TATTGGCACACACAGT
1 TACTGGCACACACAGT
35275430 TCTTCATTGA
Statistics
Matches: 218, Mismatches: 51, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
42 34 0.16
43 182 0.83
44 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (43 bp):
TACTGGCACACACAGTGCATCATCGGATAAACTGAAGCATATA
Found at i:35275216 original size:129 final size:129
Alignment explanation
Indices: 35275083--35275350 Score: 283
Period size: 129 Copynumber: 2.1 Consensus size: 129
35275073 TTGACACATG
* * *
35275083 TAGTGCATCACTATATTAA-TCAAAGAAATTT-TACTGGCAAATACAGT-TCATCATCAGATAAA
1 TAGTGCATCACTAGATGAACT-AAAG-AATTTATACTGGCAAACACAGTGT-ATCATCAGAT-AA
* * * * * * *
35275145 TC-GAAGCATATGTAGTGGCACACAAAGTGCATCATCGGATAAACTAAAGCATCTATACTCGCAC
62 TCTGAAGCATATATACTGACACACAAAGTACATCACCGGATAAACTAAAACAACTATACTCGCAC
35275209 ACA
127 ACA
* * * * * * *
35275212 TAGTGCATCATTGGATGAACTGAAGCATTTATACTGGTACACATAGTGTATCATCAGATAATCTG
1 TAGTGCATCACTAGATGAACTAAAGAATTTATACTGGCAAACACAGTGTATCATCAGATAATCTG
* * *
35275277 AAGCATCTATACTGACACACACAGTACATCACCGGATAAACTAAAACAACTATACTGGCACACA
66 AAGCATATATACTGACACACAAAGTACATCACCGGATAAACTAAAACAACTATACTCGCACACA
*
35275341 CAGTGCATCA
1 TAGTGCATCA
35275351 TTGGATAAGC
Statistics
Matches: 114, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
128 8 0.07
129 104 0.91
130 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (129 bp):
TAGTGCATCACTAGATGAACTAAAGAATTTATACTGGCAAACACAGTGTATCATCAGATAATCTG
AAGCATATATACTGACACACAAAGTACATCACCGGATAAACTAAAACAACTATACTCGCACACA
Found at i:35275351 original size:129 final size:127
Alignment explanation
Indices: 35275125--35275429 Score: 362
Period size: 129 Copynumber: 2.4 Consensus size: 127
35275115 ACTGGCAAAT
* * * * *
35275125 ACAGTTCATCATCAGATAAATCGAAGCATATGTAGTGGCACACAAAGTGCATCATCGGATAAACT
1 ACAGTTCATCATCAGAT-AATCGAAGCATATATACTGGCACACACAGTACATCACCGGATAAACT
* * * * * *
35275190 AAAGCATCTATACTCGCACACATAGTGCATCATTGGATGAA-CTGAAGCATTTATACTGGTACAC
65 AAAACAACTATACTCGCACACACAGTGCATCATTGGAT-AAGCTGAAGCATATACACT-GCACAC
* * *
35275254 ATAGTGT-ATCATCAGATAATCTGAAGCATCTATACTGACACACACAGTACATCACCGGATAAAC
1 ACAGT-TCATCATCAGATAATC-GAAGCATATATACTGGCACACACAGTACATCACCGGATAAAC
*
35275318 TAAAACAACTATACTGGCACACACAGTGCATCATTGGATAAGCTGAAGCATATACACTGCACAC
64 TAAAACAACTATACTCGCACACACAGTGCATCATTGGATAAGCTGAAGCATATACACTGCACAC
* * * * *
35275382 ACAGTTCAACATCGGATAAACCGAAGCATTTATATTGGCACACACAGT
1 ACAGTTCATCATCAGAT-AATCGAAGCATATATACTGGCACACACAGT
35275430 TCTTCATTGA
Statistics
Matches: 149, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
127 1 0.01
128 46 0.31
129 101 0.68
130 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (127 bp):
ACAGTTCATCATCAGATAATCGAAGCATATATACTGGCACACACAGTACATCACCGGATAAACTA
AAACAACTATACTCGCACACACAGTGCATCATTGGATAAGCTGAAGCATATACACTGCACAC
Found at i:35277246 original size:43 final size:43
Alignment explanation
Indices: 35277181--35277302 Score: 163
Period size: 43 Copynumber: 2.8 Consensus size: 43
35277171 AACACTACTT
* *
35277181 ATAAAAGCGCCGCTAAAAATCATGTTCTATAGCGGCATTTTTA
1 ATAAAAGCGCCGCTAAAGATCATGTTCTATAGCGGCATTTGTA
* * *
35277224 GTAAAAGCGCCGCTAAAGATCATGTTCTATAGCAGCGTTTGTA
1 ATAAAAGCGCCGCTAAAGATCATGTTCTATAGCGGCATTTGTA
* ** *
35277267 ATAAAAGTGTTGCTAAAGATCATGTTCTTTAGCGGC
1 ATAAAAGCGCCGCTAAAGATCATGTTCTATAGCGGC
35277303 GCTATAGACC
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (43 bp):
ATAAAAGCGCCGCTAAAGATCATGTTCTATAGCGGCATTTGTA
Found at i:35277325 original size:25 final size:25
Alignment explanation
Indices: 35277278--35277326 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
35277268 TAAAAGTGTT
* **
35277278 GCTAAAGATCATGTTCTTTAGCGGC
1 GCTAAAGACCATGTTCTAGAGCGGC
*
35277303 GCTATAGACCATGTTCTAGAGCGG
1 GCTAAAGACCATGTTCTAGAGCGG
35277327 TGTTTGTGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (25 bp):
GCTAAAGACCATGTTCTAGAGCGGC
Found at i:35295690 original size:51 final size:51
Alignment explanation
Indices: 35295634--35295761 Score: 150
Period size: 51 Copynumber: 2.5 Consensus size: 51
35295624 TTTTATGATT
* *
35295634 ATTATGAAATATGATTATTTAATTAAATAAT-AGAAAATTAAATATTTAAAA
1 ATTATGAAATATGATTATTTATTTAAATAATCA-AAAATTAAATAATTAAAA
* * ** * **
35295685 ATTATGAATTATGAATATTTATTTATTTAATCAAAAATTAATTAATTAATT
1 ATTATGAAATATGATTATTTATTTAAATAATCAAAAATTAAATAATTAAAA
*
35295736 ATTATGAAACATGATTATTTATTTAA
1 ATTATGAAATATGATTATTTATTTAA
35295762 TTTTATCCAC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
51 62 0.98
52 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (51 bp):
ATTATGAAATATGATTATTTATTTAAATAATCAAAAATTAAATAATTAAAA
Found at i:35295883 original size:17 final size:16
Alignment explanation
Indices: 35295857--35295902 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 16
35295847 CTATTGTTTA
*
35295857 ATTATATAATTAATACT
1 ATTATTTAATTAATA-T
35295874 ATTATTTAATTAA-AT
1 ATTATTTAATTAATAT
35295889 -TTATTTAATTAATA
1 ATTATTTAATTAATA
35295903 AAAAATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 12 0.44
15 2 0.07
16 1 0.04
17 12 0.44
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATTTAATTAATAT
Found at i:35295991 original size:12 final size:12
Alignment explanation
Indices: 35295974--35296000 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
35295964 ACCTTTTTGA
35295974 TTTTAATACTAG
1 TTTTAATACTAG
35295986 TTTTAATACTAG
1 TTTTAATACTAG
35295998 TTT
1 TTT
35296001 AAAACTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (12 bp):
TTTTAATACTAG
Found at i:35296039 original size:185 final size:186
Alignment explanation
Indices: 35295701--35296064 Score: 613
Period size: 185 Copynumber: 2.0 Consensus size: 186
35295691 AATTATGAAT
* * * *
35295701 ATTTATTTATTTAATCAAAAATTAATTAATTAATTATTATGAAACATGATTATTTATTTAATTTT
1 ATTTATTTAATTAATAAAAAATTAATTAACTAATTATTATGAAACATGATTATTTATTTAATGTT
* *
35295766 ATCCACCACCACTTCCCTTTCGATTTTAGTACTAGTTTTAATACTAGTTTAAAACTGGTTTAGTA
66 ATCCACCACCACTACCCTTTCGATTTTAATACTAGTTTTAATACTAGTTTAAAACTGGTTTAGTA
* *
35295831 AATCATTTAAAATCAGCTATTGTTTAATTATATAATTAATACTATTATTTAATTAA
131 AATCATTTAAAATAAACTATTGTTTAATTATATAATTAATACTATTATTTAATTAA
*
35295887 ATTTATTTAATTAATAAAAAATTAATTAACTAATTATTATGAAATATGATTATTTATTTAATGTT
1 ATTTATTTAATTAATAAAAAATTAATTAACTAATTATTATGAAACATGATTATTTATTTAATGTT
* *
35295952 ATCCACCA-CACTACCTTTTTGATTTTAATACTAGTTTTAATACTAGTTTAAAACTGGTTTAGTA
66 ATCCACCACCACTACCCTTTCGATTTTAATACTAGTTTTAATACTAGTTTAAAACTGGTTTAGTA
*
35296016 AATCATTTAAAATAAACTATTGTTTAATTATATAATTAATACTGTTATT
131 AATCATTTAAAATAAACTATTGTTTAATTATATAATTAATACTATTATT
35296065 GTTTATGTGT
Statistics
Matches: 166, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
185 98 0.59
186 68 0.41
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (186 bp):
ATTTATTTAATTAATAAAAAATTAATTAACTAATTATTATGAAACATGATTATTTATTTAATGTT
ATCCACCACCACTACCCTTTCGATTTTAATACTAGTTTTAATACTAGTTTAAAACTGGTTTAGTA
AATCATTTAAAATAAACTATTGTTTAATTATATAATTAATACTATTATTTAATTAA
Found at i:35301764 original size:82 final size:82
Alignment explanation
Indices: 35301645--35301876 Score: 302
Period size: 82 Copynumber: 2.8 Consensus size: 82
35301635 AATAAAAATA
* *
35301645 TTTGCGGCATTTATGGGAAAAACGCCGCTATTGCTTTAACTTTAGTGGCGTTTATGGGAAAAACG
1 TTTGCGGCGTTTAT-GGAAAAACGCCGCTATTGCTTTAACTTTAGCGGCGTTTATGGGAAAAACG
* * *
35301710 CCGCTATTGTTTTAACCT
65 CCACTATCGTTTTAAACT
* * * * * **
35301728 TTTGCGGCGTTTATGCAAAAATGCTGCCATTGCTTTACCTTTAGCGGCGTTTATGAAAAAAACGC
1 TTTGCGGCGTTTATGGAAAAACGCCGCTATTGCTTTAACTTTAGCGGCGTTTATGGGAAAAACGC
35301793 CACTATCGTTTTAAACT
66 CACTATCGTTTTAAACT
* * * * *
35301810 TTTACGGCGTTTATGGAAAAACGCCGCTGTTGCTTGAACTTTTGCGGCGTTTATGGGAAAAATGC
1 TTTGCGGCGTTTATGGAAAAACGCCGCTATTGCTTTAACTTTAGCGGCGTTTATGGGAAAAACGC
35301875 CA
66 CA
35301877 GTAACACTAC
Statistics
Matches: 125, Mismatches: 24, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
82 112 0.90
83 13 0.10
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (82 bp):
TTTGCGGCGTTTATGGAAAAACGCCGCTATTGCTTTAACTTTAGCGGCGTTTATGGGAAAAACGC
CACTATCGTTTTAAACT
Found at i:35301822 original size:42 final size:41
Alignment explanation
Indices: 35301691--35301864 Score: 119
Period size: 40 Copynumber: 4.2 Consensus size: 41
35301681 TAACTTTAGT
** * * *
35301691 GGCGTTTATGGGAAAAACGCCGCTATTGTTTTAACCTTTTGC
1 GGCGTTTATGAAAAAAACGCCACTA-TGTTTTAAACTTTTAC
** * *
35301733 GGCGTTTATGCAAAAATGCTGCCA-T-TGCTTT--ACCTTTAGC
1 GGCGTTTATG-AAAAAAAC-GCCACTATGTTTTAAACTTTTA-C
35301773 GGCGTTTATGAAAAAAACGCCACTATCGTTTTAAACTTTTAC
1 GGCGTTTATGAAAAAAACGCCACTAT-GTTTTAAACTTTTAC
* * * *
35301815 GGCGTTTATG-GAAAAACGCCGC--TGTTGCTTGAACTTTTGC
1 GGCGTTTATGAAAAAAACGCCACTATGTT--TTAAACTTTTAC
35301855 GGCGTTTATG
1 GGCGTTTATG
35301865 GGAAAAATGC
Statistics
Matches: 105, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
38 7 0.07
39 12 0.11
40 32 0.30
41 19 0.18
42 21 0.20
43 11 0.10
44 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (41 bp):
GGCGTTTATGAAAAAAACGCCACTATGTTTTAAACTTTTAC
Found at i:35301828 original size:123 final size:123
Alignment explanation
Indices: 35301648--35301874 Score: 307
Period size: 123 Copynumber: 1.8 Consensus size: 123
35301638 AAAAATATTT
** * * *
35301648 GCGGCATTTATGGGAAAAACGCCGCTATTGCTTTAACTTTAGTGGCGTTTATGGGAAAAACGCCG
1 GCGGCATTTATGAAAAAAACGCCACTATCGCTTTAACTTTAGCGGCGTTTATGGGAAAAACGCCG
* *
35301713 CTATTGTTTTAACCTTTTGCGGCGTTTAT-GCAAAAATGCTGCCATTGCTTTACCTTTA
66 CTATTGCTTGAA-CTTTTGCGGCGTTTATGGCAAAAATGCTGCCATTGCTTTACCTTTA
* *
35301771 GCGGCGTTTATGAAAAAAACGCCACTATCGTTTTAAACTTTTA-CGGCGTTTAT-GGAAAAACGC
1 GCGGCATTTATGAAAAAAACGCCACTATCGCTTT-AAC-TTTAGCGGCGTTTATGGGAAAAACGC
* *
35301834 CGCTGTTGCTTGAACTTTTGCGGCGTTTATGGGAAAAATGC
64 CGCTATTGCTTGAACTTTTGCGGCGTTTATGGCAAAAATGC
35301875 CAGTAACACT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
122 16 0.18
123 58 0.64
124 12 0.13
125 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (123 bp):
GCGGCATTTATGAAAAAAACGCCACTATCGCTTTAACTTTAGCGGCGTTTATGGGAAAAACGCCG
CTATTGCTTGAACTTTTGCGGCGTTTATGGCAAAAATGCTGCCATTGCTTTACCTTTA
Found at i:35301865 original size:40 final size:41
Alignment explanation
Indices: 35301645--35301871 Score: 260
Period size: 41 Copynumber: 5.5 Consensus size: 41
35301635 AATAAAAATA
*
35301645 TTTGCGGCATTTATGGGAAAAACGCCGCTATTGCTTTAACT
1 TTTGCGGCGTTTATGGGAAAAACGCCGCTATTGCTTTAACT
* * *
35301686 TTAGTGGCGTTTATGGGAAAAACGCCGCTATTGTTTTAACCT
1 TTTGCGGCGTTTATGGGAAAAACGCCGCTATTGCTTTAA-CT
* * * * *
35301728 TTTGCGGCGTTTAT-GCAAAAATGCTGCCATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAACGCCGCTATTGCTTTAACT
* ** * * *
35301768 TTAGCGGCGTTTATGAAAAAAACGCCACTATCGTTTTAAACT
1 TTTGCGGCGTTTATGGGAAAAACGCCGCTATTGCTTT-AACT
* * *
35301810 TTTACGGCGTTTAT-GGAAAAACGCCGCTGTTGCTTGAACT
1 TTTGCGGCGTTTATGGGAAAAACGCCGCTATTGCTTTAACT
35301850 TTTGCGGCGTTTATGGGAAAAA
1 TTTGCGGCGTTTATGGGAAAAA
35301872 TGCCAGTAAC
Statistics
Matches: 150, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
40 32 0.21
41 89 0.59
42 29 0.19
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (41 bp):
TTTGCGGCGTTTATGGGAAAAACGCCGCTATTGCTTTAACT
Found at i:35304004 original size:15 final size:15
Alignment explanation
Indices: 35303979--35304022 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
35303969 TAGTTTCATT
35303979 AAAGT-ACTAAAGTA
1 AAAGTAACTAAAGTA
35303993 AAAGTAACTAAAGTA
1 AAAGTAACTAAAGTA
**
35304008 AATTTAACTAAAGTA
1 AAAGTAACTAAAGTA
35304023 TACATACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.57, C:0.07, G:0.11, T:0.25
Consensus pattern (15 bp):
AAAGTAACTAAAGTA
Found at i:35305562 original size:29 final size:29
Alignment explanation
Indices: 35305530--35305585 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
35305520 TTCAGCTGTG
*
35305530 TGACCCACA-TAGTCTGCCACATGGCCATA
1 TGACCCACACT-GTCTGCCACACGGCCATA
*
35305559 TGACCCACACTGTCTGCCCCACGGCCA
1 TGACCCACACTGTCTGCCACACGGCCA
35305586 CATGGCTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.23, C:0.41, G:0.18, T:0.18
Consensus pattern (29 bp):
TGACCCACACTGTCTGCCACACGGCCATA
Found at i:35308340 original size:43 final size:43
Alignment explanation
Indices: 35308282--35308575 Score: 268
Period size: 43 Copynumber: 6.8 Consensus size: 43
35308272 GAAGCAATTT
* * * *
35308282 TACTGGCGCATACAATTCATCATCGGATGAACTGAAGCA-CATA
1 TACTGGCACACACAATTCATCATCGGATAAACCGAAGCATC-TA
* * * * *
35308325 TACTGGAACACACAATGCATCAGCGGATAAACCAAAACATCTA
1 TACTGGCACACACAATTCATCATCGGATAAACCGAAGCATCTA
*** * ** *
35308368 TACTGGCACACATTGTGCATCATTAGATAAATCGAAGCATCTA
1 TACTGGCACACACAATTCATCATCGGATAAACCGAAGCATCTA
** * * * * *
35308411 TACTGGCACACAGTATGCATCATCTGATAAATCAAAGCAACTA
1 TACTGGCACACACAATTCATCATCGGATAAACCGAAGCATCTA
* * *
35308454 TACTGGCACACAC-ATTACGTCATCGAATAAACCGAAGCATATA
1 TACTGGCACACACAATT-CATCATCGGATAAACCGAAGCATCTA
* * *
35308497 TACTGGCACACATAGTGCATCATCGGATAAACCGAAGCATCTA
1 TACTGGCACACACAATTCATCATCGGATAAACCGAAGCATCTA
* * *
35308540 TATTGGCACACACAGTTCATCATCAGATAAACCGAA
1 TACTGGCACACACAATTCATCATCGGATAAACCGAA
35308576 ATATAACCTA
Statistics
Matches: 204, Mismatches: 44, Indels: 6
0.80 0.17 0.02
Matches are distributed among these distances:
42 2 0.01
43 200 0.98
44 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (43 bp):
TACTGGCACACACAATTCATCATCGGATAAACCGAAGCATCTA
Found at i:35308386 original size:129 final size:129
Alignment explanation
Indices: 35308236--35308570 Score: 325
Period size: 129 Copynumber: 2.6 Consensus size: 129
35308226 ACGAAAGGAA
** * * * * *
35308236 ATATACTGGCACATGTAGTGCATCACCAGATTAATAGAAGCAAT-TTTACTGGCGCATACAATTC
1 ATATACTGGCACACATAGTGCATCACCAGATAAATAGAAGC-ATCTATACTGGCACACACAATGC
* * * *
35308300 ATCATCGGATGAA-CTGAAGC-ACATATACTGGAACACACAATGCATCAGCGGATAAACCAAAAC
65 ATCATCGGATAAATC-AAAGCAAC-TATACTGGAACACACAATACATCAGCGAATAAACCAAAAC
35308363 AT
128 AT
* * ** * **
35308365 CTATACTGGCACACATTGTGCATCATTAGATAAATCGAAGCATCTATACTGGCACACAGTATGCA
1 ATATACTGGCACACATAGTGCATCACCAGATAAATAGAAGCATCTATACTGGCACACACAATGCA
* * * * * * *
35308430 TCATCTGATAAATCAAAGCAACTATACTGGCACACACATTACGTCATCGAATAAACCGAAGCAT
66 TCATCGGATAAATCAAAGCAACTATACTGGAACACACAATACATCAGCGAATAAACCAAAACAT
* * ** * * *
35308494 ATATACTGGCACACATAGTGCATCATCGGATAAACCGAAGCATCTATATTGGCACACACAGTTCA
1 ATATACTGGCACACATAGTGCATCACCAGATAAATAGAAGCATCTATACTGGCACACACAATGCA
*
35308559 TCATCAGATAAA
66 TCATCGGATAAA
35308571 CCGAAATATA
Statistics
Matches: 167, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
128 2 0.01
129 162 0.97
130 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (129 bp):
ATATACTGGCACACATAGTGCATCACCAGATAAATAGAAGCATCTATACTGGCACACACAATGCA
TCATCGGATAAATCAAAGCAACTATACTGGAACACACAATACATCAGCGAATAAACCAAAACAT
Found at i:35308570 original size:86 final size:86
Alignment explanation
Indices: 35308213--35308575 Score: 324
Period size: 86 Copynumber: 4.2 Consensus size: 86
35308203 ACATGTAGTG
* * * ** * * * *
35308213 CATCATCGGATAAA-CGAAAGGAAATATACTGGCACATGTAGTGCATCACCAGATTAA-TAGAAG
1 CATCATCAGATAAACCG-AAGCATATATACTGGCACACATAGTGCATCATCGGATAAACCA-AAG
* * * *
35308276 CAAT-TTTACTGGCGCATACAATT
64 C-ATCTATACTGGCACACACAGTT
* * * * * * * * *
35308299 CATCATCGGATGAACTGAAGCACATATACTGGAACACACAATGCATCAGCGGATAAACCAAAACA
1 CATCATCAGATAAACCGAAGCATATATACTGGCACACATAGTGCATCATCGGATAAACCAAAGCA
** *
35308364 TCTATACTGGCACACATTGTG
66 TCTATACTGGCACACACAGTT
* * * * *
35308385 CATCATTAGATAAATCGAAGCATCTATACTGGCACACAGTA-TGCATCATCTGATAAATCAAAGC
1 CATCATCAGATAAACCGAAGCATATATACTGGCACACA-TAGTGCATCATCGGATAAACCAAAGC
*
35308449 AACTATACTGGCACACACA-TT
65 ATCTATACTGGCACACACAGTT
* *
35308470 ACGTCATC-GAATAAACCGAAGCATATATACTGGCACACATAGTGCATCATCGGATAAACCGAAG
1 -CATCATCAG-ATAAACCGAAGCATATATACTGGCACACATAGTGCATCATCGGATAAACCAAAG
*
35308534 CATCTATATTGGCACACACAGTT
64 CATCTATACTGGCACACACAGTT
35308557 CATCATCAGATAAACCGAA
1 CATCATCAGATAAACCGAA
35308576 ATATAACCTA
Statistics
Matches: 220, Mismatches: 48, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
85 6 0.03
86 208 0.95
87 6 0.03
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (86 bp):
CATCATCAGATAAACCGAAGCATATATACTGGCACACATAGTGCATCATCGGATAAACCAAAGCA
TCTATACTGGCACACACAGTT
Found at i:35340855 original size:12 final size:12
Alignment explanation
Indices: 35340838--35340862 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35340828 TTAAGCTAAG
35340838 TCAAAGTACAAC
1 TCAAAGTACAAC
35340850 TCAAAGTACAAC
1 TCAAAGTACAAC
35340862 T
1 T
35340863 ATAGTTAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (12 bp):
TCAAAGTACAAC
Found at i:35342492 original size:20 final size:20
Alignment explanation
Indices: 35342469--35342507 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35342459 AAATATTAAA
35342469 TTTAAT-TTAATATTTATCTT
1 TTTAATCTT-ATATTTATCTT
35342489 TTTAATCTTATATTTATCT
1 TTTAATCTTATATTTATCT
35342508 CGATAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTAATCTTATATTTATCTT
Found at i:35349096 original size:36 final size:37
Alignment explanation
Indices: 35349034--35349124 Score: 105
Period size: 36 Copynumber: 2.4 Consensus size: 37
35349024 ATTTCAAAAA
*
35349034 TAATATTATTTTAATAGTTTAATATTAAATTAA-ATT
1 TAATATTATCTTAATAGTTTAATATTAAATTAATATT
* *
35349070 TAATATTATCTTAATAGTATT-TTATTAATTTAATATT
1 TAATATTATCTTAATAGT-TTAATATTAAATTAATATT
*
35349107 AAAGTGATTATCTTAATA
1 TAA-T-ATTATCTTAATA
35349125 TTGAATTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
36 27 0.57
37 7 0.15
38 1 0.02
39 12 0.26
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAAATTAATATT
Found at i:35349108 original size:11 final size:11
Alignment explanation
Indices: 35349034--35349108 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
35349024 ATTTCAAAAA
*
35349034 TAATATTATTT
1 TAATATTAATT
35349045 TAATAGTTTAATAT
1 TAATA--TTAAT-T
35349059 TAA-ATTAAATT
1 TAATATT-AATT
35349070 TAATATT-ATCT
1 TAATATTAAT-T
*
35349081 TAATAGT-ATT
1 TAATATTAATT
35349091 T--TATTAATT
1 TAATATTAATT
35349100 TAATATTAA
1 TAATATTAA
35349109 AGTGATTATC
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 4 0.08
11 26 0.50
12 6 0.12
13 5 0.10
14 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (11 bp):
TAATATTAATT
Found at i:35349195 original size:21 final size:22
Alignment explanation
Indices: 35349171--35349217 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
35349161 TTCTATTATT
35349171 TTAATA-AGATTAAATTTAATA
1 TTAATAGAGATTAAATTTAATA
* *
35349192 TTAA-AGTGATTAAGTTTAATA
1 TTAATAGAGATTAAATTTAATA
*
35349213 ATAAT
1 TTAAT
35349218 TGAACTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (22 bp):
TTAATAGAGATTAAATTTAATA
Found at i:35358208 original size:33 final size:33
Alignment explanation
Indices: 35358151--35358235 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
35358141 TTCGCCCAAA
*
35358151 GATGAGATTGAATTAGTTTCGCTATG-CGGTAGG
1 GATGACATTGAATTAGTTTCGCTATGAC-GTAGG
* * *
35358184 GGTGACATTGTATTGGTTTCGCTATGACGTAGG
1 GATGACATTGAATTAGTTTCGCTATGACGTAGG
*
35358217 GATGACAGTGAATTAGTTT
1 GATGACATTGAATTAGTTT
35358236 AAGCCTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 42 0.98
34 1 0.02
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (33 bp):
GATGACATTGAATTAGTTTCGCTATGACGTAGG
Found at i:35359788 original size:31 final size:31
Alignment explanation
Indices: 35359753--35359814 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
35359743 ATAAACAACC
* *
35359753 CAATGATTTAAAT-AAAATTTTTTGAATAGTT
1 CAATGACTTAAATGAAAA-ATTTTGAATAGTT
35359784 CAATGACTTAAATGAAAAATTTTGAATAGTT
1 CAATGACTTAAATGAAAAATTTTGAATAGTT
35359815 AAAAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (31 bp):
CAATGACTTAAATGAAAAATTTTGAATAGTT
Found at i:35360360 original size:3 final size:3
Alignment explanation
Indices: 35360352--35360385 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
35360342 ATACATCTCA
35360352 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
35360386 GAGACCTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35363347 original size:17 final size:17
Alignment explanation
Indices: 35363325--35363358 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35363315 TTATATGATC
35363325 ATACAAATGCTTTAAAG
1 ATACAAATGCTTTAAAG
35363342 ATACAAATGCTTTAAAG
1 ATACAAATGCTTTAAAG
35363359 TCAACCCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
ATACAAATGCTTTAAAG
Found at i:35364158 original size:172 final size:176
Alignment explanation
Indices: 35363869--35364219 Score: 602
Period size: 172 Copynumber: 2.0 Consensus size: 176
35363859 CCCTTTCAGG
*
35363869 AAAAAAACCACGGGTAGAGGAGAAGATAATTCATTATGTTGAATTCGAATGATTACAAGAGGAGT
1 AAAAAAACCACGGGTAGAGGAGAAGATAATTCACTATGTTGAATTCGAATGATTACAAGAGGAGT
35363934 AGACTATATCTATTTATAGGCTTGTAAAACCATATTCTAATAGAAAGAGTGTAGTAA-G-G-TTG
66 AGACTATATCTATTTATAGGCTTGTAAAACCATATTCTAATAGAAAGAGTGTAGTAAGGTGATTG
*
35363996 AAACACCTTATTCT-AAAAAACTAAATAAAAGAAGTGCAGTTCTAA
131 AAACACCTTATTCTAAAAAAAATAAATAAAAGAAGTGCAGTTCTAA
*
35364041 AAAAAAACCACGGGTAGAGGAGAAGATAATTCACTATGTTGAATTCGAATGATTACACGAGGAGT
1 AAAAAAACCACGGGTAGAGGAGAAGATAATTCACTATGTTGAATTCGAATGATTACAAGAGGAGT
*
35364106 AGACTATATCTATTTATAGGCTTGTAAAACCATATTCTAATAGAAGGAGTGTAGTAAGGTTGAAA
66 AGACTATATCTATTTATAGGCTTGTAAAACCATATTCTAATAGAAAGAGTGTAGTAAGG-TG--A
35364171 CTTGAAACACCTTATTCTAAAAAAAATAAATAAAAGAAGTGCAGTTCTA
128 -TTGAAACACCTTATTCTAAAAAAAATAAATAAAAGAAGTGCAGTTCTA
35364220 TATGGATTTA
Statistics
Matches: 167, Mismatches: 4, Indels: 8
0.93 0.02 0.04
Matches are distributed among these distances:
172 119 0.71
173 1 0.01
175 1 0.01
179 17 0.10
180 29 0.17
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (176 bp):
AAAAAAACCACGGGTAGAGGAGAAGATAATTCACTATGTTGAATTCGAATGATTACAAGAGGAGT
AGACTATATCTATTTATAGGCTTGTAAAACCATATTCTAATAGAAAGAGTGTAGTAAGGTGATTG
AAACACCTTATTCTAAAAAAAATAAATAAAAGAAGTGCAGTTCTAA
Found at i:35369748 original size:20 final size:20
Alignment explanation
Indices: 35369723--35369857 Score: 96
Period size: 20 Copynumber: 6.8 Consensus size: 20
35369713 AATACCCAAG
* *
35369723 GTATCGCTAGTTTACTCAAA
1 GTATCGATACTTTACTCAAA
*
35369743 GTATCGATACTTTTCTCAAA
1 GTATCGATACTTTACTCAAA
* *
35369763 GTATCTATACTTCGA-TCAAA
1 GTATCGATACTT-TACTCAAA
** *
35369783 GTATTTATACTTTACTAAAA
1 GTATCGATACTTTACTCAAA
* ** *
35369803 GTATCTATACTTTGGTC-TA
1 GTATCGATACTTTACTCAAA
**
35369822 GTTATTTATACTTT-CTTCAAA
1 G-TATCGATACTTTAC-TCAAA
35369843 GTATCGATACTTTAC
1 GTATCGATACTTTAC
35369858 CCTTGGTATT
Statistics
Matches: 90, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.03
20 84 0.93
21 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (20 bp):
GTATCGATACTTTACTCAAA
Found at i:35369828 original size:40 final size:39
Alignment explanation
Indices: 35369738--35369855 Score: 130
Period size: 40 Copynumber: 2.9 Consensus size: 39
35369728 GCTAGTTTAC
** *
35369738 TCAAAGTATCGATACTTTTCTCAAAGTATCTATACTTCGA
1 TCAAAGTATTTATAC-TTTCTCAAAGTATCTATACTTTGA
* *
35369778 TCAAAGTATTTATACTTTACTAAAAGTATCTATACTTTGG
1 TCAAAGTATTTATACTTT-CTCAAAGTATCTATACTTTGA
* *
35369818 TC-TAGTTATTTATACTTTCTTCAAAGTATCGATACTTT
1 TCAAAG-TATTTATACTTTC-TCAAAGTATCTATACTTT
35369856 ACCCTTGGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 6 0.09
40 61 0.91
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.43
Consensus pattern (39 bp):
TCAAAGTATTTATACTTTCTCAAAGTATCTATACTTTGA
Found at i:35369832 original size:60 final size:60
Alignment explanation
Indices: 35369723--35369857 Score: 139
Period size: 60 Copynumber: 2.2 Consensus size: 60
35369713 AATACCCAAG
* * * *
35369723 GTATCGCTAGTTTACTCAAAGTATCGATACTTTTCTCAAAGTATCTATAC-TTCGATCAAA
1 GTATCGATACTTTACTAAAAGTATCGATACTTTGCTCAAAGTATCTATACTTTC-ATCAAA
** * * * * *
35369783 GTATTTATACTTTACTAAAAGTATCTATACTTTGGTC-TAGTTATTTATACTTTCTTCAAA
1 GTATCGATACTTTACTAAAAGTATCGATACTTTGCTCAAAG-TATCTATACTTTCATCAAA
35369843 GTATCGATACTTTAC
1 GTATCGATACTTTAC
35369858 CCTTGGTATT
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
59 2 0.03
60 55 0.92
61 3 0.05
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (60 bp):
GTATCGATACTTTACTAAAAGTATCGATACTTTGCTCAAAGTATCTATACTTTCATCAAA
Found at i:35371782 original size:23 final size:23
Alignment explanation
Indices: 35371756--35371805 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
35371746 GCTAAAGCAT
* *
35371756 ATAATTGAACACTGCCGAAGTGG
1 ATAACTGAACACCGCCGAAGTGG
*
35371779 ATAACTGAGCACCGCCGAAGTGG
1 ATAACTGAACACCGCCGAAGTGG
35371802 ATAA
1 ATAA
35371806 ATAATAAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (23 bp):
ATAACTGAACACCGCCGAAGTGG
Found at i:35377201 original size:20 final size:20
Alignment explanation
Indices: 35377152--35377201 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
35377142 TAAGCTAAAA
**
35377152 TAAGTAAATATAATGGAAAG
1 TAAGTAAATGCAATGGAAAG
35377172 TAAGTAAATGCAATGGAAAG
1 TAAGTAAATGCAATGGAAAG
35377192 TAAGTAAATG
1 TAAGTAAATG
35377202 GAAGGGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.22, T:0.24
Consensus pattern (20 bp):
TAAGTAAATGCAATGGAAAG
Found at i:35381219 original size:27 final size:27
Alignment explanation
Indices: 35381181--35381322 Score: 207
Period size: 27 Copynumber: 5.3 Consensus size: 27
35381171 AGAGGTCAAG
35381181 AAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCTCATAGGGTA
35381208 AAATGACCGAAATACCACT-ATAGGGTA
1 AAATGACCGAAATACC-CTCATAGGGTA
* * *
35381235 AAATAATCGAAATACCATCATAGGGTA
1 AAATGACCGAAATACCCTCATAGGGTA
*
35381262 AAATGACCGAAATATCCC-CATAGGATA
1 AAATGACCGAAATA-CCCTCATAGGGTA
*
35381289 AAATGACCGAAATACTCTCATAGGGTA
1 AAATGACCGAAATACCCTCATAGGGTA
35381316 AAATGAC
1 AAATGAC
35381323 TGTTATACCC
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
26 3 0.03
27 95 0.93
28 4 0.04
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCATAGGGTA
Found at i:35381347 original size:54 final size:52
Alignment explanation
Indices: 35381181--35381349 Score: 180
Period size: 54 Copynumber: 3.1 Consensus size: 52
35381171 AGAGGTCAAG
* *
35381181 AAATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATA-CCACTATAGGGTA
1 AAATGACCGAAATA-CCTCATAGGGTAAAATGACCGATATACCCA-TA-AGGATA
* * *
35381235 AAATAATCGAAATACCATCATAGGGTAAAATGACCGAAATATCCCCAT-AGGATA
1 AAATGACCGAAATACC-TCATAGGGTAAAATGACCG--ATATACCCATAAGGATA
* * *
35381289 AAATGACCGAAATACTCTCATAGGGTAAAATGACTGTTATACCCATAAGAGATG
1 AAATGACCGAAATAC-CTCATAGGGTAAAATGACCGATATACCCATAAG-GATA
35381343 AAATGAC
1 AAATGAC
35381350 TAATATGGCC
Statistics
Matches: 97, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
52 8 0.08
53 4 0.04
54 77 0.79
55 1 0.01
56 4 0.04
57 3 0.03
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (52 bp):
AAATGACCGAAATACCTCATAGGGTAAAATGACCGATATACCCATAAGGATA
Found at i:35381529 original size:26 final size:26
Alignment explanation
Indices: 35381493--35381624 Score: 131
Period size: 26 Copynumber: 5.1 Consensus size: 26
35381483 TTGAGGAAGT
* *
35381493 ATACTGTTATTGGCAGCT-TCGCTGCA
1 ATACTGTTACTGGCAGCTCT-GCTGCG
*
35381519 ATACTGTTATTGGCAGCTCTGCTGCG
1 ATACTGTTACTGGCAGCTCTGCTGCG
*
35381545 ATATTGTTACTGGCAGCTCTGCTGCG
1 ATACTGTTACTGGCAGCTCTGCTGCG
* * * *
35381571 ATATTGTTACGGGCAGCTTTGTTGCG
1 ATACTGTTACTGGCAGCTCTGCTGCG
* * * * *
35381597 ACACTATTAGTGACAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTCTGCTGCG
35381623 AT
1 AT
35381625 GTTGGTGTGT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 90 0.99
27 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTCTGCTGCG
Found at i:35389074 original size:27 final size:27
Alignment explanation
Indices: 35389033--35389171 Score: 188
Period size: 27 Copynumber: 5.1 Consensus size: 27
35389023 AGAGGTCAAG
*
35389033 AAATGATCGACATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
35389060 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*** * *
35389087 AAATGATCGAAATACAATCATTGGGTT
1 AAATGATCGAAATACCCCCATAGGGTA
*
35389114 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * *
35389141 AAATAACCGAAATACCCTCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
35389168 AAAT
1 AAAT
35389172 AACTGTTATA
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 98 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:35389369 original size:26 final size:26
Alignment explanation
Indices: 35389340--35389414 Score: 132
Period size: 26 Copynumber: 2.9 Consensus size: 26
35389330 GAGGAAGTAG
*
35389340 ACTGTTACTGGCAGCTTTGCTGCGAT
1 ACTGTTACTGGCAGCTTTGCTGCGAC
35389366 ACTGTTACTGGCAGCTTTGCTGCGAC
1 ACTGTTACTGGCAGCTTTGCTGCGAC
*
35389392 ACTATTACTGGCAGCTTTGCTGC
1 ACTGTTACTGGCAGCTTTGCTGC
35389415 AATATTGGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (26 bp):
ACTGTTACTGGCAGCTTTGCTGCGAC
Found at i:35405072 original size:494 final size:495
Alignment explanation
Indices: 35404139--35405129 Score: 1975
Period size: 494 Copynumber: 2.0 Consensus size: 495
35404129 TATTTATTAA
35404139 AAATTAAAAACCTTTATTTTAGTTGTTTTAAAAATATTTATAGAAAAAATAAAACTAACTTCATT
1 AAATTAAAAACCTTTATTTTAGTTGTTTTAAAAATATTTATAGAAAAAATAAAACTAACTTCATT
35404204 ATTTATATAAAGAATAGCCAATTATTGTAAATTATTCAATTTAAGTACCTAGATTTAAAAATAAT
66 ATTTATATAAAGAATAGCCAATTATTGTAAATTATTCAATTTAAGTACCTAGATTTAAAAATAAT
35404269 TTGAAAATTGAGCTGCAAATTAAAAATTGGATTAAAATTGACCCTTTTATTTTAAAATTTAAAAA
131 TTGAAAATTGAGCTGCAAATTAAAAATTGGATTAAAATTGACCCTTTTATTTTAAAATTTAAAAA
35404334 TTTATTTAACACTTAAGAAATATTTCTCTGAATATTATGTTAAAATAAATTCTCAGGAAAGATTG
196 TTTATTTAACACTTAAGAAATATTTCTCTGAATATTATGTTAAAATAAATTCTCAGGAAAGATTG
35404399 AAGGGGCCACAAGTGGTCCCACTTAAGTTCCAATCTCCTAGACAGAATTTATTTGAACATACGAA
261 AAGGGGCCACAAGTGGTCCCACTTAAGTTCCAATCTCCTAGACAGAATTTATTTGAACATACGAA
35404464 TTCAAAAAATACAGCCCAAGTCATTTATTAAAAAGAAGAATAAAAATTTAAGTATCTGATTAAAT
326 TTCAAAAAATACAGCCCAAGTCATTTATTAAAAAGAAGAATAAAAATTTAAGTATCTGATTAAAT
35404529 GAACGAGATTTTATCCCCCCAATAGTGTTTCAAGCGTTGAACGTTAACTATGAAATTACCTCTCT
391 GAACGAGATTTTATCCCCCCAATAGTGTTTCAAGCGTTGAACGTTAACTATGAAATTACCTCTCT
35404594 TACCATGAAGTTCAACAACCCCGTATGGGAAGACTTGATG
456 TACCATGAAGTTCAACAACCCCGTATGGGAAGACTTGATG
35404634 AAATT-AAAACCTTTATTTTAGTTGTTTTAAAAATATTTATAGAAAAAATAAAACTAACTTCATT
1 AAATTAAAAACCTTTATTTTAGTTGTTTTAAAAATATTTATAGAAAAAATAAAACTAACTTCATT
35404698 ATTTATATAAAGAATAGCCAATTATTGTAAATTATTCAATTTAAGTACCTAGATTTAAAAATAAT
66 ATTTATATAAAGAATAGCCAATTATTGTAAATTATTCAATTTAAGTACCTAGATTTAAAAATAAT
35404763 TTGAAAATTGAGCTGCAAATTAAAAATTGGATTAAAATTGACCCTTTTATTTTAAAATTTAAAAA
131 TTGAAAATTGAGCTGCAAATTAAAAATTGGATTAAAATTGACCCTTTTATTTTAAAATTTAAAAA
35404828 TTTATTTAACACTTAAGAAATATTTCTCTGAATATTATGTTAAAATAAATTCTCAGGAAAGATTG
196 TTTATTTAACACTTAAGAAATATTTCTCTGAATATTATGTTAAAATAAATTCTCAGGAAAGATTG
35404893 AAGGGGCCACAAGTGGTCCCACTTAAGTTCCAATCTCCTAGACAGAATTTATTTGAACATACGAA
261 AAGGGGCCACAAGTGGTCCCACTTAAGTTCCAATCTCCTAGACAGAATTTATTTGAACATACGAA
35404958 TTCAAAAAATACAGCCCAAGTCATTTATTAAAAAGAAGAATAAAAATTTAAGTATCTGATTAAAT
326 TTCAAAAAATACAGCCCAAGTCATTTATTAAAAAGAAGAATAAAAATTTAAGTATCTGATTAAAT
35405023 GAACGAGATTTTATCCCCCCAATAGTGTTTCAAGCGTTGAACGTTAACTATGAAATTACCTCTCT
391 GAACGAGATTTTATCCCCCCAATAGTGTTTCAAGCGTTGAACGTTAACTATGAAATTACCTCTCT
35405088 TACCATGAAGTTCAACAACCCCGTATGGGAAGACTTGATG
456 TACCATGAAGTTCAACAACCCCGTATGGGAAGACTTGATG
35405128 AA
1 AA
35405130 TAGTGAATGG
Statistics
Matches: 496, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
494 491 0.99
495 5 0.01
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (495 bp):
AAATTAAAAACCTTTATTTTAGTTGTTTTAAAAATATTTATAGAAAAAATAAAACTAACTTCATT
ATTTATATAAAGAATAGCCAATTATTGTAAATTATTCAATTTAAGTACCTAGATTTAAAAATAAT
TTGAAAATTGAGCTGCAAATTAAAAATTGGATTAAAATTGACCCTTTTATTTTAAAATTTAAAAA
TTTATTTAACACTTAAGAAATATTTCTCTGAATATTATGTTAAAATAAATTCTCAGGAAAGATTG
AAGGGGCCACAAGTGGTCCCACTTAAGTTCCAATCTCCTAGACAGAATTTATTTGAACATACGAA
TTCAAAAAATACAGCCCAAGTCATTTATTAAAAAGAAGAATAAAAATTTAAGTATCTGATTAAAT
GAACGAGATTTTATCCCCCCAATAGTGTTTCAAGCGTTGAACGTTAACTATGAAATTACCTCTCT
TACCATGAAGTTCAACAACCCCGTATGGGAAGACTTGATG
Found at i:35413364 original size:20 final size:20
Alignment explanation
Indices: 35413305--35413374 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
35413295 AAGAGCATCA
*
35413305 AAATGCTAACAGAGGCACCG
1 AAATGCAAACAGAGGCACCG
* * *
35413325 TAGTGCAAATACAAAGGCACCG
1 AAATGC-AA-ACAGAGGCACCG
35413347 AAATGCAAACAGAGGCACC-
1 AAATGCAAACAGAGGCACCG
35413366 AAAGTGCAA
1 AAA-TGCAA
35413375 TCCCGCACAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 3 0.08
20 19 0.47
21 3 0.08
22 15 0.38
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (20 bp):
AAATGCAAACAGAGGCACCG
Found at i:35414381 original size:19 final size:22
Alignment explanation
Indices: 35414357--35414402 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
35414347 ATGATGATAA
35414357 TTTTATT-TTAT-CTTT-TTAC
1 TTTTATTATTATGCTTTATTAC
*
35414376 TTTTATTATTATGTTTTATTAC
1 TTTTATTATTATGCTTTATTAC
35414398 TTTTA
1 TTTTA
35414403 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 4 0.17
21 3 0.13
22 9 0.39
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTATTATTATGCTTTATTAC
Found at i:35418145 original size:32 final size:32
Alignment explanation
Indices: 35418085--35418147 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
35418075 ATTAATCAGT
* * *
35418085 ATGAGTTATTAAATTAAATTCATTAATTTATC
1 ATGAGTTATTAAATTAAAGTAATCAATTTATC
*
35418117 ATGAGTTATTAAATTCAAGTAATCAATTTAT
1 ATGAGTTATTAAATTAAAGTAATCAATTTAT
35418148 ATGTTTATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.44
Consensus pattern (32 bp):
ATGAGTTATTAAATTAAAGTAATCAATTTATC
Found at i:35418926 original size:14 final size:16
Alignment explanation
Indices: 35418891--35418920 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35418881 TTAGAATCGA
35418891 AATATTTATAATTTTT
1 AATATTTATAATTTTT
35418907 AATATTTAT-ATTTT
1 AATATTTATAATTTT
35418921 ATTATTCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATATTTATAATTTTT
Found at i:35432379 original size:23 final size:23
Alignment explanation
Indices: 35432352--35432397 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35432342 ACAAAAGATT
35432352 AAATGTTTCATGAGAGAACAAAG
1 AAATGTTTCATGAGAGAACAAAG
35432375 AAATGTTTCATGAGAGAACAAAG
1 AAATGTTTCATGAGAGAACAAAG
35432398 CACATTGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.22
Consensus pattern (23 bp):
AAATGTTTCATGAGAGAACAAAG
Found at i:35439999 original size:53 final size:55
Alignment explanation
Indices: 35439930--35440076 Score: 201
Period size: 53 Copynumber: 2.7 Consensus size: 55
35439920 TTCTTAATTG
35439930 CTTCTTTTGAATCGATTGTTTATATGTTTAAATTGATTGTCATGTTGGAATACTA
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATTGATTGTCATGTTGGAATACTA
* ** * * *
35439985 CTTCTTTTG-A-CGATTATTTATATGTTTAAATCAATTGTTATGTTGGAATATTG
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATTGATTGTCATGTTGGAATACTA
* *
35440038 CTTATTTTGAATCGATTGTTTATATGTTT-AATTGGTTGT
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATTGATTGT
35440077 TACATAGCAT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
53 45 0.57
54 9 0.11
55 25 0.32
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.52
Consensus pattern (55 bp):
CTTCTTTTGAATCGATTGTTTATATGTTTAAATTGATTGTCATGTTGGAATACTA
Found at i:35442071 original size:10 final size:10
Alignment explanation
Indices: 35442056--35442103 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
35442046 ACTTTTAAAA
*
35442056 ATTAAAAATC
1 ATTAAAAATT
35442066 ATT-AAAATT
1 ATTAAAAATT
*
35442075 ATTAAAAAGT
1 ATTAAAAATT
35442085 A-TAAAAATT
1 ATTAAAAATT
35442094 ATTAAAAATT
1 ATTAAAAATT
35442104 TAATAGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:35442078 original size:19 final size:18
Alignment explanation
Indices: 35442056--35442102 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
35442046 ACTTTTAAAA
*
35442056 ATTAAAAATCATTAAAATT
1 ATTAAAAAT-ATAAAAATT
35442075 ATTAAAAAGTATAAAAATT
1 ATTAAAAA-TATAAAAATT
35442094 ATTAAAAAT
1 ATTAAAAAT
35442103 TTAATAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 24 0.92
20 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
ATTAAAAATATAAAAATT
Found at i:35442277 original size:19 final size:19
Alignment explanation
Indices: 35442225--35442290 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
35442215 TTTTTTAAAA
35442225 TTTTAAAAATATTTTTTAAT
1 TTTTAAAAATA-TTTTTAAT
* **
35442245 ATTT-CTAATGATTTTTAAT
1 TTTTAAAAAT-ATTTTTAAT
35442264 TTTTAAAAATATTTTTATTAT
1 TTTTAAAAATATTTTTA--AT
35442285 TTTTAA
1 TTTTAA
35442291 TTTTTAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 21 0.58
20 7 0.19
21 8 0.22
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTAAAAATATTTTTAAT
Found at i:35442277 original size:29 final size:28
Alignment explanation
Indices: 35442242--35442299 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
35442232 AATATTTTTT
35442242 AATATTTCTAATGATTTTTAATTTTTAAA
1 AATATTT-TAATGATTTTTAATTTTTAAA
* *
35442271 AATATTTTTATTATTTTTAATTTTTAAA
1 AATATTTTAATGATTTTTAATTTTTAAA
35442299 A
1 A
35442300 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (28 bp):
AATATTTTAATGATTTTTAATTTTTAAA
Found at i:35442279 original size:38 final size:40
Alignment explanation
Indices: 35442216--35442309 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 40
35442206 TTAATTAAGT
35442216 TTTTTAAAATTTTAAAAATATTTTTTAATATTTCTAATGA
1 TTTTTAAAATTTTAAAAATATTTTTTAATATTTCTAATGA
* * *
35442256 TTTTT-AATTTTTAAAAATA-TTTTTATTATTT-T--TAA
1 TTTTTAAAATTTTAAAAATATTTTTTAATATTTCTAATGA
*
35442291 TTTTTAAAATTTAAAAAAT
1 TTTTTAAAATTTTAAAAAT
35442310 CTAATTAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
35 7 0.15
36 11 0.23
37 1 0.02
38 11 0.23
39 13 0.27
40 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (40 bp):
TTTTTAAAATTTTAAAAATATTTTTTAATATTTCTAATGA
Found at i:35442443 original size:22 final size:21
Alignment explanation
Indices: 35442418--35442471 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
35442408 ATTTTTAAAC
* *
35442418 TTAAAAATCATTAAAATTATTT
1 TTAAAAAT-ATAAAAAATATTT
35442440 TTAAAAAGTATAAAAAATATTT
1 TTAAAAA-TATAAAAAATATTT
*
35442462 TAAAAAATAT
1 TTAAAAATAT
35442472 TTTTTTAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 24 0.86
23 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TTAAAAATATAAAAAATATTT
Found at i:35442467 original size:12 final size:12
Alignment explanation
Indices: 35442450--35442474 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35442440 TTAAAAAGTA
35442450 TAAAAAATATTT
1 TAAAAAATATTT
35442462 TAAAAAATATTT
1 TAAAAAATATTT
35442474 T
1 T
35442475 TTTAGTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATATTT
Found at i:35443671 original size:18 final size:17
Alignment explanation
Indices: 35443650--35443684 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35443640 AAAAATGTGT
35443650 TTTAATTGAAAATAAGGA
1 TTTAATTGAAAA-AAGGA
*
35443668 TTTATTTGAAAAAAGGA
1 TTTAATTGAAAAAAGGA
35443685 AGAAACTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
TTTAATTGAAAAAAGGA
Found at i:35457020 original size:20 final size:20
Alignment explanation
Indices: 35456991--35457032 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
35456981 CACATAATTT
35456991 TCTTGCATCACCATTACTGA
1 TCTTGCATCACCATTACTGA
* *
35457011 TCTTGTATCACCATTATTGA
1 TCTTGCATCACCATTACTGA
35457031 TC
1 TC
35457033 AACTCAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (20 bp):
TCTTGCATCACCATTACTGA
Found at i:35465889 original size:3 final size:3
Alignment explanation
Indices: 35465881--35465923 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
35465871 GAAGTGTTTA
35465881 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
35465924 GCTGAGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:35468985 original size:8 final size:8
Alignment explanation
Indices: 35468972--35469026 Score: 65
Period size: 9 Copynumber: 6.5 Consensus size: 8
35468962 TAGTTTAATT
35468972 ATTTTTTA
1 ATTTTTTA
35468980 ATTTTTTAA
1 ATTTTTT-A
35468989 ATTTTTTAA
1 ATTTTTT-A
*
35468998 ATTTTTAA
1 ATTTTTTA
*
35469006 ATTTTTAA
1 ATTTTTTA
35469014 ATTTTTTTA
1 A-TTTTTTA
35469023 ATTT
1 ATTT
35469027 AACATAATGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
8 20 0.47
9 23 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
ATTTTTTA
Found at i:35468991 original size:9 final size:9
Alignment explanation
Indices: 35468972--35469026 Score: 80
Period size: 8 Copynumber: 6.4 Consensus size: 9
35468962 TAGTTTAATT
35468972 ATTTTTT-A
1 ATTTTTTAA
35468980 ATTTTTTAA
1 ATTTTTTAA
35468989 ATTTTTTAA
1 ATTTTTTAA
35468998 A-TTTTTAA
1 ATTTTTTAA
35469006 A-TTTTTAA
1 ATTTTTTAA
*
35469014 ATTTTTTTA
1 ATTTTTTAA
35469023 ATTT
1 ATTT
35469027 AACATAATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
8 23 0.52
9 21 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:35468994 original size:17 final size:17
Alignment explanation
Indices: 35468972--35469026 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
35468962 TAGTTTAATT
35468972 ATTTTTTAATTTTTTAA
1 ATTTTTTAATTTTTTAA
*
35468989 ATTTTTTAAATTTTTAA
1 ATTTTTTAATTTTTTAA
* *
35469006 ATTTTTAAATTTTTTTA
1 ATTTTTTAATTTTTTAA
35469023 ATTT
1 ATTT
35469027 AACATAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATTTTTTAA
Found at i:35470073 original size:20 final size:20
Alignment explanation
Indices: 35470026--35470064 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35470016 ATCTGGGCAT
*
35470026 CAATACTTATTAAAATATAC
1 CAATACTTATTAAAAAATAC
35470046 CAATACTTATTAAAAAATA
1 CAATACTTATTAAAAAATA
35470065 TTGATACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (20 bp):
CAATACTTATTAAAAAATAC
Found at i:35470144 original size:22 final size:21
Alignment explanation
Indices: 35470099--35470163 Score: 80
Period size: 22 Copynumber: 3.1 Consensus size: 21
35470089 TTTTCACTTG
* *
35470099 TTTCACTTGATAT-AAAATTG
1 TTTCACTTGATTTAAAAATTA
35470119 TTTCACTTGATTTTAAAAATTA
1 TTTCACTTGA-TTTAAAAATTA
*
35470141 TTTCACTTGAGTTAAAAA-TA
1 TTTCACTTGATTTAAAAATTA
35470161 TTT
1 TTT
35470164 GAAGTGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
20 15 0.38
21 9 0.22
22 16 0.40
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.48
Consensus pattern (21 bp):
TTTCACTTGATTTAAAAATTA
Found at i:35470162 original size:20 final size:19
Alignment explanation
Indices: 35470099--35470163 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
35470089 TTTTCACTTG
* *
35470099 TTTCACTTGATATAAAATTG
1 TTTCACTTGAT-TAAAAATA
35470119 TTTCACTTGATTTTAAAAATTA
1 TTTCACTTGA--TTAAAAA-TA
35470141 TTTCACTTGAGTTAAAAATA
1 TTTCACTTGA-TTAAAAATA
35470161 TTT
1 TTT
35470164 GAAGTGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
20 15 0.38
21 12 0.31
22 12 0.31
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.48
Consensus pattern (19 bp):
TTTCACTTGATTAAAAATA
Found at i:35470295 original size:16 final size:17
Alignment explanation
Indices: 35470266--35470300 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
35470256 TGATTCTTTG
35470266 TTCAAAAACAATTTTTA
1 TTCAAAAACAATTTTTA
35470283 TTCAAAAAC-ATTTTTA
1 TTCAAAAACAATTTTTA
35470299 TT
1 TT
35470301 TGTTATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
TTCAAAAACAATTTTTA
Found at i:35472360 original size:20 final size:19
Alignment explanation
Indices: 35472332--35472413 Score: 85
Period size: 20 Copynumber: 4.2 Consensus size: 19
35472322 TAACAATATT
*
35472332 TTTTGTTAAGTATCGATAC
1 TTTTGTTAAATATCGATAC
* *
35472351 TTTTGATTAAATATCAATAG
1 TTTTG-TTAAATATCGATAC
35472371 TTTTGTTAAAATATCGATAC
1 TTTTGTT-AAATATCGATAC
* *
35472391 TTGTTCTTAAGTATCGATA-
1 TT-TTGTTAAATATCGATAC
35472410 TTTT
1 TTTT
35472414 AACAAAAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.04
19 9 0.17
20 38 0.72
21 4 0.08
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (19 bp):
TTTTGTTAAATATCGATAC
Found at i:35473823 original size:19 final size:19
Alignment explanation
Indices: 35473801--35473839 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
35473791 ATTTGTACTA
35473801 CTAACAAATCTTTGTCCTT
1 CTAACAAATCTTTGTCCTT
35473820 CTAACAAATCTTTGTCCTT
1 CTAACAAATCTTTGTCCTT
35473839 C
1 C
35473840 ATTTTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.28, G:0.05, T:0.41
Consensus pattern (19 bp):
CTAACAAATCTTTGTCCTT
Found at i:35478352 original size:66 final size:66
Alignment explanation
Indices: 35478226--35478358 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
35478216 AATATCAAAA
* * ** *
35478226 TCAAGCATGACAAAGGTACCATTCCCGTCTAGGTTAGATAACAAACAAAAGAGGGGTGAAGTTGA
1 TCAAGCATGACAAAGGTACCATTCACGTCTAGGTTAGACAACAAACAAAAGAGGAATGAAGCTGA
35478291 T
66 T
*
35478292 TCAAGCATGACAAAGGTACCATTCACGTCTAGGTTAGACAATAAACAAAAGAGGAATGAAGCTGA
1 TCAAGCATGACAAAGGTACCATTCACGTCTAGGTTAGACAACAAACAAAAGAGGAATGAAGCTGA
35478357 T
66 T
35478358 T
1 T
35478359 TTGTAAGTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (66 bp):
TCAAGCATGACAAAGGTACCATTCACGTCTAGGTTAGACAACAAACAAAAGAGGAATGAAGCTGA
T
Found at i:35482069 original size:18 final size:16
Alignment explanation
Indices: 35482027--35482069 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
35482017 TGTCGTTCGT
35482027 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
35482044 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
35482063 TTTCAAA
1 TTTCAAA
35482070 ACGTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:35492923 original size:98 final size:98
Alignment explanation
Indices: 35492802--35493027 Score: 425
Period size: 98 Copynumber: 2.3 Consensus size: 98
35492792 ACATGCCAAA
35492802 GCCATGTCCTAGACATGGTCCTACATGGGATGTTTTTTGTACTGCCAATGCCATATCCCAGAATG
1 GCCATGTCCTAGACATGGTCCTACATGGGATGTTTTTTGTACTGCCAATGCCATATCCCAGAATG
35492867 ATCTTACATGGGAGTTCTCATATCGGTGCCCAT
66 ATCTTACATGGGAGTTCTCATATCGGTGCCCAT
35492900 GCCATGTCCTAGACATGGTCCTACATGGGATGTTTTTTGTACTGCCAATGCCATATCCCAGAATG
1 GCCATGTCCTAGACATGGTCCTACATGGGATGTTTTTTGTACTGCCAATGCCATATCCCAGAATG
35492965 ATCTTACATGGGAGTTCTCATATCGGTGCCCAT
66 ATCTTACATGGGAGTTCTCATATCGGTGCCCAT
* * *
35492998 GCCATGTCCCAGACATGGTCTTACAGGGGA
1 GCCATGTCCTAGACATGGTCCTACATGGGA
35493028 CCTCTCATAT
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 125 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (98 bp):
GCCATGTCCTAGACATGGTCCTACATGGGATGTTTTTTGTACTGCCAATGCCATATCCCAGAATG
ATCTTACATGGGAGTTCTCATATCGGTGCCCAT
Found at i:35492928 original size:50 final size:50
Alignment explanation
Indices: 35492795--35493130 Score: 283
Period size: 50 Copynumber: 6.7 Consensus size: 50
35492785 GATAATAACA
* * * ** *
35492795 TGCCAAAGCCATGTCCTAGACATGGTCCTACATGGGATGTT-TTTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* *
35492844 TGCCAATGCCATATCCCAGA-ATGATCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * * ** *
35492893 TGCCCATGCCATGTCCTAGACATGGTCCTACATGGGATGTT-TTTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* *
35492942 TGCCAATGCCATATCCCAGA-ATGATCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * **
35492991 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * * ** * *
35493041 TGCCAACGCCATGTCCTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-A--TC---GG
35493097 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
35493131 AGATCTCTTT
Statistics
Matches: 230, Mismatches: 41, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
47 8 0.03
48 34 0.15
49 69 0.30
50 80 0.35
51 5 0.02
53 2 0.01
56 32 0.14
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:35492977 original size:48 final size:49
Alignment explanation
Indices: 35492795--35492977 Score: 194
Period size: 49 Copynumber: 3.8 Consensus size: 49
35492785 GATAATAACA
* * * *
35492795 TGCCAAAGCCATGTCCTAGACATGGTCCTACATGGGATGTTTTTTGTAC
1 TGCCAATGCCATATCCCAGACATGATCCTACATGGGATGTTTTTTGTAC
* * **
35492844 TGCCAATGCCATATCCCAGA-ATGATCTTACATGGGA-G-TTCTCATATC
1 TGCCAATGCCATATCCCAGACATGATCCTACATGGGATGTTTTTTGTA-C
* * * *
35492891 GGTGCCCATGCCATGTCCTAGACATGGTCCTACATGGGATGTTTTTTGTAC
1 --TGCCAATGCCATATCCCAGACATGATCCTACATGGGATGTTTTTTGTAC
*
35492942 TGCCAATGCCATATCCCAGA-ATGATCTTACATGGGA
1 TGCCAATGCCATATCCCAGACATGATCCTACATGGGA
35492978 GTTCTCATAT
Statistics
Matches: 107, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
46 5 0.05
47 2 0.02
48 28 0.26
49 51 0.48
50 14 0.13
51 2 0.02
52 5 0.05
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (49 bp):
TGCCAATGCCATATCCCAGACATGATCCTACATGGGATGTTTTTTGTAC
Found at i:35504939 original size:20 final size:23
Alignment explanation
Indices: 35504892--35504956 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
35504882 ATACAACGAT
35504892 TGAGAAAAGAAATAAAAGAGAAA
1 TGAGAAAAGAAATAAAAGAGAAA
*
35504915 TGAGAAAAGAAA-AGAAGA-AAA
1 TGAGAAAAGAAATAAAAGAGAAA
*
35504936 -GAGAAAAGAAATGAGAAGAGA
1 TGAGAAAAGAAAT-AAAAGAGA
35504957 GGGAGACACC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
20 11 0.29
21 3 0.08
22 11 0.29
23 13 0.34
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (23 bp):
TGAGAAAAGAAATAAAAGAGAAA
Found at i:35517114 original size:98 final size:98
Alignment explanation
Indices: 35516945--35517143 Score: 362
Period size: 98 Copynumber: 2.0 Consensus size: 98
35516935 AATCCTCCTC
*
35516945 TGAAAACTATGCAACAATTTGCTTCATAGTGGCCCATTCATTTGGAATAACATCTTCATTGGCCT
1 TGAAAACTATGCAACAATTTGCTTCATAATGGCCCATTCATTTGGAATAACATCTTCATTGGCCT
35517010 GGACAAAGACATTCATACGCTAGCATAGCGCGG
66 GGACAAAGACATTCATACGCTAGCATAGCGCGG
* *
35517043 TGAAAACTTTGCAACAATTTGCTTCATAATGGCCCCTTCATTTGGAATAACATCTTCATTGGCCT
1 TGAAAACTATGCAACAATTTGCTTCATAATGGCCCATTCATTTGGAATAACATCTTCATTGGCCT
*
35517108 GGACAAAGACATTCATACGCTAGCATGGCGCGG
66 GGACAAAGACATTCATACGCTAGCATAGCGCGG
35517141 TGA
1 TGA
35517144 TGAGAGAGGG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (98 bp):
TGAAAACTATGCAACAATTTGCTTCATAATGGCCCATTCATTTGGAATAACATCTTCATTGGCCT
GGACAAAGACATTCATACGCTAGCATAGCGCGG
Found at i:35522833 original size:27 final size:27
Alignment explanation
Indices: 35522792--35522843 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
35522782 GATGATACCT
*
35522792 GGGCTATTAACGAAGTGATTTCATCAA
1 GGGCTATTAACGAAGTGATTGCATCAA
*
35522819 GGGCTATTAATGAAGTGATTGCATC
1 GGGCTATTAACGAAGTGATTGCATC
35522844 GAGCTCCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (27 bp):
GGGCTATTAACGAAGTGATTGCATCAA
Found at i:35526372 original size:15 final size:15
Alignment explanation
Indices: 35526344--35526384 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
35526334 GTACAAATCA
*
35526344 TAAGTATTGGAAAAT
1 TAAGTATTGAAAAAT
*
35526359 TAAGTGTTGAAAAAT
1 TAAGTATTGAAAAAT
*
35526374 TAAATATTGAA
1 TAAGTATTGAA
35526385 TTTAGGTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (15 bp):
TAAGTATTGAAAAAT
Found at i:35532434 original size:15 final size:15
Alignment explanation
Indices: 35532396--35532437 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35532386 ATAATTTTTT
35532396 AAATAAAAATA-A-A
1 AAATAAAAATATATA
* *
35532409 ATATAACAATATATA
1 AAATAAAAATATATA
35532424 AAATAAAAATATAT
1 AAATAAAAATATAT
35532438 TTTGAAATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 9 0.39
14 1 0.04
15 13 0.57
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAAAATATATA
Found at i:35532932 original size:5 final size:5
Alignment explanation
Indices: 35532922--35532954 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
35532912 AGTAATCTCG
35532922 AATTT AATTT AATTT AATTT AATTT AA-TT AATT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATT
35532955 AAGTCTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:35537679 original size:28 final size:28
Alignment explanation
Indices: 35537639--35537713 Score: 132
Period size: 28 Copynumber: 2.7 Consensus size: 28
35537629 TAGAACATCT
* *
35537639 AATAATTGTTCTTGAGTTGATTCCATAA
1 AATAATCGTTCTTGAGTTGATTCAATAA
35537667 AATAATCGTTCTTGAGTTGATTCAATAA
1 AATAATCGTTCTTGAGTTGATTCAATAA
35537695 AATAATCGTTCTTGAGTTG
1 AATAATCGTTCTTGAGTTG
35537714 GGATGTATGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (28 bp):
AATAATCGTTCTTGAGTTGATTCAATAA
Found at i:35539162 original size:16 final size:16
Alignment explanation
Indices: 35539125--35539156 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35539115 TTTGGTTCGC
35539125 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
35539141 TGTAATGGAATGGAGG
1 TGTAATGGAATAGAGG
35539157 GTTAATAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.41, T:0.25
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:35539237 original size:44 final size:46
Alignment explanation
Indices: 35539144--35539239 Score: 117
Period size: 44 Copynumber: 2.1 Consensus size: 46
35539134 ATAGAGGTGT
* * * * *
35539144 AATGGAATGGAGGGTTAATAGGTAATTTTTTTGTTTGTTTGAATGG
1 AATGGAATAGAGGGTTAATAGGTAATTTTTGTGTTTGGTTAAATAG
35539190 AATGGAATAGA-GGTGTAATA-GT-ATTTTTGTGTTTGGTTAAATAG
1 AATGGAATAGAGGGT-TAATAGGTAATTTTTGTGTTTGGTTAAATAG
35539234 AATGGA
1 AATGGA
35539240 GGTGTAATAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
44 24 0.55
45 5 0.11
46 15 0.34
ACGTcount: A:0.30, C:0.00, G:0.29, T:0.41
Consensus pattern (46 bp):
AATGGAATAGAGGGTTAATAGGTAATTTTTGTGTTTGGTTAAATAG
Found at i:35539431 original size:27 final size:27
Alignment explanation
Indices: 35539396--35539455 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
35539386 GTTATTATTA
35539396 AATATATTTTAATTAAAATATAT-ATTTT
1 AATA-ATTTTAATTAAAATATATGA-TTT
35539424 AATAATTTTAATTAAAATATATGATTT
1 AATAATTTTAATTAAAATATATGATTT
35539451 AATAA
1 AATAA
35539456 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
AATAATTTTAATTAAAATATATGATTT
Found at i:35539574 original size:91 final size:90
Alignment explanation
Indices: 35539475--35539680 Score: 274
Period size: 91 Copynumber: 2.3 Consensus size: 90
35539465 TAATTATAAC
* *
35539475 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATACTA-ATTATTACATATAATTTAATAA
1 TAATAAATTAT-TTTTATGAATTTGTATAATTTAAAATAATATA-TATTAAATATAATTTAATAA
* *
35539539 TAATATATAATTTCATAAAATTCTTGA
64 TAACATATAATTTCATAAAATTCTTAA
*
35539566 TAATAAATT-TTCTTATATGAATTTGTATAATTTAAAATAATTTATATTAAATATAATTTAATAA
1 TAATAAATTATT-TT-TATGAATTTGTATAATTTAAAATAATATATATTAAATATAATTTAATAA
* *
35539630 TGACATATAATTTCATAAAATTTTTAA
64 TAACATATAATTTCATAAAATTCTTAA
35539657 TAATAAA-TATTCTTATATGAATTT
1 TAATAAATTATT-TT-TATGAATTT
35539681 ACTAAAATCA
Statistics
Matches: 104, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
89 1 0.01
90 4 0.04
91 98 0.94
92 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (90 bp):
TAATAAATTATTTTTATGAATTTGTATAATTTAAAATAATATATATTAAATATAATTTAATAATA
ACATATAATTTCATAAAATTCTTAA
Found at i:35539666 original size:47 final size:45
Alignment explanation
Indices: 35539525--35539666 Score: 114
Period size: 47 Copynumber: 3.1 Consensus size: 45
35539515 TAATTATTAC
*
35539525 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAAT-ATATATAATTTCATAAAATT-TTTATAATAA
* * * * *
35539572 AT-T-TTCTTATATGAATTTGTATAA-TT--TAAAATAATTTATATTAA
1 ATATAAT-TTA-AT-AATATATATAATTTCATAAAAT-TTTTATAATAA
*
35539616 ATATAATTTAATAATGACATATAATTTCATAAAATTTTTAATAATAA
1 ATATAATTTAATAAT-ATATATAATTTCATAAAATTTTT-ATAATAA
35539663 ATAT
1 ATAT
35539667 TCTTATATGA
Statistics
Matches: 72, Mismatches: 12, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
43 3 0.04
44 23 0.32
45 7 0.10
46 10 0.14
47 26 0.36
48 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (45 bp):
ATATAATTTAATAATATATATAATTTCATAAAATTTTTATAATAA
Found at i:35548324 original size:3 final size:3
Alignment explanation
Indices: 35548316--35548354 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
35548306 CATTCCCTCA
35548316 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
35548355 ATTAAGATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:35549562 original size:20 final size:22
Alignment explanation
Indices: 35549517--35549562 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
35549507 AAAGAGAGAA
* *
35549517 ATGTCGTGACATCAGCCCTTGG
1 ATGTCGCGACATCAGCCCTCGG
35549539 -TGTCGCGACA-CAG-CCTCGG
1 ATGTCGCGACATCAGCCCTCGG
35549558 ATGTC
1 ATGTC
35549563 TTAACACACC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.24
20 7 0.33
21 9 0.43
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.24
Consensus pattern (22 bp):
ATGTCGCGACATCAGCCCTCGG
Found at i:35557511 original size:6 final size:6
Alignment explanation
Indices: 35557499--35557533 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
35557489 GCAAATGAAT
* *
35557499 CATTTC TATTTC TATTTC CATTTC CATTTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
35557534 TGGAAACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.26, G:0.00, T:0.57
Consensus pattern (6 bp):
CATTTC
Found at i:35560381 original size:17 final size:18
Alignment explanation
Indices: 35560359--35560401 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
35560349 ATTGTTATTT
35560359 TTTTTAAAAAATTTAT-A
1 TTTTTAAAAAATTTATAA
* * *
35560376 TTTTTAATAATTTTTTAA
1 TTTTTAAAAAATTTATAA
35560394 TTTTTAAA
1 TTTTTAAA
35560402 TGTTTTTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTAAAAAATTTATAA
Found at i:35560408 original size:19 final size:18
Alignment explanation
Indices: 35560386--35560440 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
35560376 TTTTTAATAA
35560386 TTTTTTAATTTTTAAATGT
1 TTTTTTAATTTTTAAAT-T
**
35560405 TTTTGGAATTTATTAATATT
1 TTTTTTAATTT-TTAA-ATT
*
35560425 TTTTTTCATTTTTAAA
1 TTTTTTAATTTTTAAA
35560441 GAATTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 13 0.45
20 13 0.45
21 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTTTAATTTTTAAATT
Found at i:35562993 original size:19 final size:20
Alignment explanation
Indices: 35562949--35562993 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
35562939 GCAGGGAAAA
*
35562949 AGAAAAATAAAAGAACAATG
1 AGAAAAATAAAAGAACAAGG
*
35562969 ACAAAAA-AAAAGAACAAGG
1 AGAAAAATAAAAGAACAAGG
*
35562988 GGAAAA
1 AGAAAA
35562994 TGACGAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.71, C:0.07, G:0.18, T:0.04
Consensus pattern (20 bp):
AGAAAAATAAAAGAACAAGG
Found at i:35564748 original size:25 final size:24
Alignment explanation
Indices: 35564678--35564765 Score: 72
Period size: 25 Copynumber: 3.6 Consensus size: 24
35564668 TCAGAGTTAC
*
35564678 CCGTTAT-AGGCTCGCATGAGCTT
1 CCGTTATAAGGCTCACATGAGCTT
* ** *
35564701 CCGTTATACGGC-CTGGATAAGCTT
1 CCGTTATAAGGCTC-ACATGAGCTT
35564725 CCTGTTATAAGGCTCACATGAGCTT
1 CC-GTTATAAGGCTCACATGAGCTT
* *
35564750 CCCATTATATGGCTCA
1 -CCGTTATAAGGCTCA
35564766 AGAGTGTGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
23 8 0.16
24 13 0.25
25 27 0.53
26 3 0.06
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (24 bp):
CCGTTATAAGGCTCACATGAGCTT
Found at i:35565727 original size:13 final size:13
Alignment explanation
Indices: 35565709--35565733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35565699 ACATCTAATT
35565709 TTTGGTCGTGTGG
1 TTTGGTCGTGTGG
35565722 TTTGGTCGTGTG
1 TTTGGTCGTGTG
35565734 TCTCGTGCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.44, T:0.48
Consensus pattern (13 bp):
TTTGGTCGTGTGG
Found at i:35571824 original size:25 final size:24
Alignment explanation
Indices: 35571796--35571849 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
35571786 GAGCTTTTCA
*
35571796 TTATATGGTTCTT-GCGAGCTTCCCG
1 TTATATGG-TCTTCG-GAGCGTCCCG
35571821 TTATA-GGTCTTCGGAGCGTCCCG
1 TTATATGGTCTTCGGAGCGTCCCG
35571844 TTATAT
1 TTATAT
35571850 TGTGATCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 18 0.69
24 3 0.12
25 5 0.19
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (24 bp):
TTATATGGTCTTCGGAGCGTCCCG
Found at i:35584338 original size:14 final size:15
Alignment explanation
Indices: 35584309--35584340 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35584299 AAAAACATCA
35584309 TAATTTTATCTATTT
1 TAATTTTATCTATTT
35584324 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
35584338 TAA
1 TAA
35584341 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:35585522 original size:56 final size:56
Alignment explanation
Indices: 35585436--35585547 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
35585426 CATGTAATTC
35585436 AGTTGAGCTCCTGTCAGAGTCCGACTCGCATAGTAGATGGGATGAAAAAATTTGTT
1 AGTTGAGCTCCTGTCAGAGTCCGACTCGCATAGTAGATGGGATGAAAAAATTTGTT
35585492 AGTTGAGCTCCTGTCAGAGTCCGACTCGCATAGTAGATGGGATGAAAAAATTTGTT
1 AGTTGAGCTCCTGTCAGAGTCCGACTCGCATAGTAGATGGGATGAAAAAATTTGTT
35585548 CTTTCGCTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (56 bp):
AGTTGAGCTCCTGTCAGAGTCCGACTCGCATAGTAGATGGGATGAAAAAATTTGTT
Found at i:35597805 original size:50 final size:53
Alignment explanation
Indices: 35597737--35597861 Score: 166
Period size: 50 Copynumber: 2.4 Consensus size: 53
35597727 ATGGCACTGA
* * *
35597737 AAGAATACCATATCGTGTAAGACCATAATTGGTGGGTTAT-G-A-CATGTAGG
1 AAGAAGACCATATCGTGTAAGACCATAACTGGTGGGTTATGGAATCATATAGG
* *
35597787 AAGAAGACCATATTGTGTAAGACCGTAACTGGTGGGTTATGGAATCATATAGG
1 AAGAAGACCATATCGTGTAAGACCATAACTGGTGGGTTATGGAATCATATAGG
* *
35597840 CAGAAGACCATATCATGTAAGA
1 AAGAAGACCATATCGTGTAAGA
35597862 GTTGGAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 36 0.56
51 1 0.02
52 1 0.02
53 26 0.41
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.26
Consensus pattern (53 bp):
AAGAAGACCATATCGTGTAAGACCATAACTGGTGGGTTATGGAATCATATAGG
Found at i:35602783 original size:11 final size:10
Alignment explanation
Indices: 35602767--35602802 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
35602757 TTTTTGAAAA
35602767 TTTTATATATT
1 TTTTATA-ATT
35602778 TTTTATAATT
1 TTTTATAATT
35602788 TTTTATAAATT
1 TTTTAT-AATT
35602799 TTTT
1 TTTT
35602803 CACTGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATAATT
Found at i:35607327 original size:20 final size:19
Alignment explanation
Indices: 35607281--35607329 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
35607271 AAATTACAAT
* * *
35607281 AATTCAAAACATTTTTTAA
1 AATTCAAAATATTTATAAA
35607300 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
35607319 AATTTCAAAAT
1 AA-TTCAAAAT
35607330 TTATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:35607364 original size:18 final size:18
Alignment explanation
Indices: 35607298--35607365 Score: 50
Period size: 18 Copynumber: 3.7 Consensus size: 18
35607288 AACATTTTTT
35607298 AAAA-TTCAAAATATTTATA
1 AAAATTTCAAAA-A-TTATA
*
35607317 AAAATTTCAAAATTTAT-
1 AAAATTTCAAAAATTATA
*** *
35607334 ATTTTTTAAAAAAATTATA
1 AAAATTT-CAAAAATTATA
35607353 AAAATTTCAAAAA
1 AAAATTTCAAAAA
35607366 AAAATCTACA
Statistics
Matches: 36, Mismatches: 10, Indels: 7
0.68 0.19 0.13
Matches are distributed among these distances:
17 4 0.11
18 17 0.47
19 8 0.22
20 7 0.19
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTTCAAAAATTATA
Found at i:35612010 original size:68 final size:67
Alignment explanation
Indices: 35611901--35612093 Score: 233
Period size: 68 Copynumber: 2.8 Consensus size: 67
35611891 TTGGAATTGA
* * * *
35611901 GAGTCCTCCAGGAAAATAAACATGAGGTTACATTGTGTAAGACCATAGCTCTACTATGGTAACAT
1 GAGTCCGCCAGGAAAATAAACATG-GGTTACATTGTGTAAGACCATAGCTCGACTATAGCAACAT
35611966 ATG
65 ATG
* * * * *
35611969 GAGTCCGCCAAGATAATAAACATAGGGTTACATTGTATAAGACCATAGTTCGGCTATAGCAACAT
1 GAGTCCGCCAGGAAAATAAACAT-GGGTTACATTGTGTAAGACCATAGCTCGACTATAGCAACAT
35612034 ATG
65 ATG
* * * * *
35612037 GAGTCTGCTAGGACAATAAACATTGGGTTACATTATGTAAGACCATAGCTCGGCTAT
1 GAGTCCGCCAGGAAAATAAACA-TGGGTTACATTGTGTAAGACCATAGCTCGACTAT
35612094 GGAAACAAAT
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
68 105 0.98
69 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (67 bp):
GAGTCCGCCAGGAAAATAAACATGGGTTACATTGTGTAAGACCATAGCTCGACTATAGCAACATA
TG
Found at i:35627419 original size:77 final size:77
Alignment explanation
Indices: 35627281--35627435 Score: 238
Period size: 77 Copynumber: 2.0 Consensus size: 77
35627271 ATAATTGGGT
* * * * *
35627281 CCAATACAATAAGAGGTCTGAATCCATATCATAATACATAAGAGGGGAAGCAAACCTTATTAGCC
1 CCAATACAATAAGAGGCCCGAATCCACATCATAATACATAAGAGGGGAAACAAACCCTATTAGCC
35627346 CCTCTCCCTCTC
66 CCTCTCCCTCTC
* * *
35627358 CCAATACAATAAGAGGCCCGAATCCCCATCATAATACATAAGAGGGGAAACACACCCTATTAGCT
1 CCAATACAATAAGAGGCCCGAATCCACATCATAATACATAAGAGGGGAAACAAACCCTATTAGCC
35627423 CCTCTCCCTCTC
66 CCTCTCCCTCTC
35627435 C
1 C
35627436 TAGTTGGACT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (77 bp):
CCAATACAATAAGAGGCCCGAATCCACATCATAATACATAAGAGGGGAAACAAACCCTATTAGCC
CCTCTCCCTCTC
Found at i:35629898 original size:19 final size:19
Alignment explanation
Indices: 35629849--35629890 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
35629839 CTTTTATACA
*
35629849 TTAATTAACTTTTAATTAATC
1 TTAATTAA--TTTAATTAACC
35629870 TTAATTAATTTAATTAACC
1 TTAATTAATTTAATTAACC
35629889 TT
1 TT
35629891 CAATAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
21 8 0.40
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATTAATTTAATTAACC
Found at i:35631438 original size:16 final size:16
Alignment explanation
Indices: 35631404--35631438 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35631394 AGCATTACGA
*
35631404 TAACATTTCAAACATT
1 TAACATTTCAAACAAT
*
35631420 TAACATTTCATACAAT
1 TAACATTTCAAACAAT
35631436 TAA
1 TAA
35631439 ATATGCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (16 bp):
TAACATTTCAAACAAT
Found at i:35632376 original size:24 final size:23
Alignment explanation
Indices: 35632342--35632389 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
35632332 AACATTTACT
*
35632342 TATATAAACATAATTATATCAAAA
1 TATATAAACATAATT-TACCAAAA
* *
35632366 TATATATACATCATTTACCAAAA
1 TATATAAACATAATTTACCAAAA
35632389 T
1 T
35632390 TTTAACTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (23 bp):
TATATAAACATAATTTACCAAAA
Found at i:35632949 original size:39 final size:39
Alignment explanation
Indices: 35632906--35633045 Score: 105
Period size: 39 Copynumber: 3.7 Consensus size: 39
35632896 GGAAGTTGCA
*
35632906 CCCAACGCTAGTCGGATA-ATCCAACGAATAAATAGTGAG
1 CCCAACTCTAGTCGGATATA-CCAACGAATAAATAGTGAG
* * * *
35632945 CCCAATTCTAGTTGGATATACCAACG-AT--AT-TTGCG
1 CCCAACTCTAGTCGGATATACCAACGAATAAATAGTGAG
* * * *
35632980 CCCAGCACTAGTCAGATA-ATCCGAC-AATAAATAGTGAG
1 CCCAACTCTAGTCGGATATA-CCAACGAATAAATAGTGAG
* * *
35633018 CCTAGCTCTAGTTGGATATACCAACGAA
1 CCCAACTCTAGTCGGATATACCAACGAA
35633046 ATGTAGTTAT
Statistics
Matches: 75, Mismatches: 18, Indels: 16
0.69 0.17 0.15
Matches are distributed among these distances:
34 1 0.01
35 22 0.29
36 2 0.03
37 2 0.03
38 23 0.31
39 24 0.32
40 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (39 bp):
CCCAACTCTAGTCGGATATACCAACGAATAAATAGTGAG
Found at i:35637208 original size:2 final size:2
Alignment explanation
Indices: 35637201--35637233 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
35637191 ATAATTATCT
*
35637201 TA TA TA TA AA 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 TA TA TA TA T
35637234 CTTTAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:35637358 original size:2 final size:2
Alignment explanation
Indices: 35637340--35637383 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
35637330 TGTTAAATTT
*
35637340 TA TA TT TA TA T- 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
35637381 TA T
1 TA T
35637384 TTAAAAGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:35639351 original size:15 final size:16
Alignment explanation
Indices: 35639319--35639362 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
35639309 GAAGTAGAAG
*
35639319 AGAATAAAAA-AT-AA
1 AGAAGAAAAATATAAA
35639333 AGAA-AAAAATATAAA
1 AGAAGAAAAATATAAA
35639348 AGAAGAAAAAT-TAAA
1 AGAAGAAAAATATAAA
35639363 TTGCTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.19
14 6 0.22
15 10 0.37
16 6 0.22
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (16 bp):
AGAAGAAAAATATAAA
Done.