Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 68 of 168
Found at i:19908800 original size:136 final size:136
Alignment explanation
Indices: 19908556--19908828 Score: 501
Period size: 136 Copynumber: 2.0 Consensus size: 136
19908546 ATAGAGGAGG
19908556 TAGTGCCCACTACCATTGTCCTTTCAAAGCCTCAAGGGAGCCAACTAGTGGACAAGAAGGAAAGT
1 TAGTGCCCACTACCATTGTCCTTTCAAAGCCTCAAGGGAGCCAACTAGTGGACAAGAAGGAAAGT
* *
19908621 GTAGATATCTCTATTCAAGAAGCCTTAGTAGAGATCGATAAGCTAATTGCTTATCCTTCAATTCT
66 GTAGATATCTCTATTCAAGAAGCCTTAGCAGAGATCGATAAGCTAATTGCTTATCCTCCAATTCT
19908686 AGAACA
131 AGAACA
* * *
19908692 TAGTGTCCACTACCATTGTCCTTTCAAAGCCTCAAGGGAGCCAACTAGTGGACAAGGAGGAAGGT
1 TAGTGCCCACTACCATTGTCCTTTCAAAGCCTCAAGGGAGCCAACTAGTGGACAAGAAGGAAAGT
19908757 GTAGATATCTCTATTCAAGAAGCCTTAGCAGAGATCGATAAGCTAATTGCTTATCCTCCAATTCT
66 GTAGATATCTCTATTCAAGAAGCCTTAGCAGAGATCGATAAGCTAATTGCTTATCCTCCAATTCT
19908822 AGAACA
131 AGAACA
19908828 T
1 T
19908829 CAATGACCAC
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 132 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (136 bp):
TAGTGCCCACTACCATTGTCCTTTCAAAGCCTCAAGGGAGCCAACTAGTGGACAAGAAGGAAAGT
GTAGATATCTCTATTCAAGAAGCCTTAGCAGAGATCGATAAGCTAATTGCTTATCCTCCAATTCT
AGAACA
Found at i:19913209 original size:54 final size:54
Alignment explanation
Indices: 19913151--19913284 Score: 171
Period size: 54 Copynumber: 2.5 Consensus size: 54
19913141 CTAGCGGACC
* * * *
19913151 CTAGCTTGCTAAACAGACTGGTGAAC-TTCTAGTTCGCAACTCAACTAGTAAACA
1 CTAGCTTGCCAAACAGACTGGTGAACTTTC-AATTCGCAACCCAACTAGAAAACA
* * * *
19913205 CTAGCTCGCCAAACAGACTAGTGAACTTTCAATTTGCAACCCAACTGGAAAACA
1 CTAGCTTGCCAAACAGACTGGTGAACTTTCAATTCGCAACCCAACTAGAAAACA
*
19913259 CTAGCTTGCCAAACAGACTGGCGAAC
1 CTAGCTTGCCAAACAGACTGGTGAAC
19913285 CCACTTGCAA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 65 0.96
55 3 0.04
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (54 bp):
CTAGCTTGCCAAACAGACTGGTGAACTTTCAATTCGCAACCCAACTAGAAAACA
Found at i:19915233 original size:18 final size:18
Alignment explanation
Indices: 19915212--19915247 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19915202 AGATTTGCCA
*
19915212 ATCATGTTATTATTGATT
1 ATCAAGTTATTATTGATT
19915230 ATCAAGTTATTATTGATT
1 ATCAAGTTATTATTGATT
19915248 CCATTTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (18 bp):
ATCAAGTTATTATTGATT
Found at i:19939158 original size:7 final size:6
Alignment explanation
Indices: 19939137--19939177 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
19939127 TTACAACATA
* *
19939137 TTTTGT TTTTGT TTTTGT TTTTGGT TTTGGT TTTGGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTT-GT TTTTGT TTTTGT TTTT
19939178 CTTTACCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (6 bp):
TTTTGT
Found at i:19939169 original size:19 final size:18
Alignment explanation
Indices: 19939137--19939177 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
19939127 TTACAACATA
* *
19939137 TTTTGTTTTTGTTTTTGT
1 TTTTGGTTTTGTTTTGGT
19939155 TTTTGGTTTTGGTTTTGGT
1 TTTTGGTTTT-GTTTTGGT
19939174 TTTT
1 TTTT
19939178 CTTTACCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (18 bp):
TTTTGGTTTTGTTTTGGT
Found at i:19951749 original size:363 final size:362
Alignment explanation
Indices: 19951120--19951848 Score: 1206
Period size: 363 Copynumber: 2.0 Consensus size: 362
19951110 ATAGCACCAC
*
19951120 TATTAGGATACCATGCCTAATCGATAACCGTTCGACAAGTAGCAACCATCGCAACAATGTTTCCG
1 TATTAGGATACCATGCCTAATCGATAACCGTTCGACAAGTAGCAACCATCGCAACAATGTTTCCA
* *
19951185 TGAGAGTAAGAACCATTGTAATCTGCATATGGCACTCTAGAAACAAAACTAGATACAGACCCTAA
66 TGAGAATAAGAACCATTGTAATCTGCATATAGCACTCTAGAAACAAAACTAGATACAGACCCTAA
* * * *
19951250 AGAGTTGAGCGGTGGAGATGAAGAGACATTAGGGGGAGATGAGGAGACACAAGAAAATGACCCAC
131 AGAGTTGAACGGTGGAGATGAAGAGACATTAAGAGGAGATGAGGAGACACAAGAAAATGAACCAC
19951315 CAAAAAATGGTAGAAGAAAAGGCACGAGCAGACGGTAAGAAAGAAACACGAGCAGACCCAAACCC
196 CAAAAAATGGTAGAAGAAAAGGCACGAGCAGACGGTAAGAAAGAAACACGAGCAGACCCAAACCC
** * * **
19951380 TAATGAATTATGTGGATCACGCTCAGTGTAACAATATTGGGGCAAAATGGGCTAAGAAGAACGAG
261 TAATGAATTATGTGGATCACGCTCAGCATAAAAATATTGGGCCAAAACAGGCTAAGAAGAACGAG
* *
19951445 CTTGGAAATTACTACCTAAATTGGGCTCAACATAACAA
326 CCT-GAAATTACTACCTAAATTGAGCTCAACATAACAA
* * *
19951483 TATTAGGATACCATGCCTGATCGATAACCGTTCGACAAGTAGCAACCGTCGTAACAATGTTTCCA
1 TATTAGGATACCATGCCTAATCGATAACCGTTCGACAAGTAGCAACCATCGCAACAATGTTTCCA
**
19951548 TGAGAATAAGAACCATTGTAATCTGCATATAGCACTCTAGAAACAAAACTAGATATGGACCCTAA
66 TGAGAATAAGAACCATTGTAATCTGCATATAGCACTCTAGAAACAAAACTAGATACAGACCCTAA
**
19951613 AGAGTTGAACGGTGGAGATGAAGAGACATTAAGAGGAGATGAGGAGACACGGGAAAATGAACCAC
131 AGAGTTGAACGGTGGAGATGAAGAGACATTAAGAGGAGATGAGGAGACACAAGAAAATGAACCAC
* *
19951678 CAAAAAATGGTAGAAGAAAAGGCACGAGCAGACGGTAAGAAAGAAACATGAGCAGACCCAAACCT
196 CAAAAAATGGTAGAAGAAAAGGCACGAGCAGACGGTAAGAAAGAAACACGAGCAGACCCAAACCC
* * *
19951743 TAATGAATTATGTGGATCACGCTCAGCATAAAAATATTGGGCCGAAACAGGCTGAGAAGAACGGG
261 TAATGAATTATGTGGATCACGCTCAGCATAAAAATATTGGGCCAAAACAGGCTAAGAAGAACGAG
19951808 CCTGAAATTACTACCTAAATTGAGCTCAACATAACAA
326 CCTGAAATTACTACCTAAATTGAGCTCAACATAACAA
19951845 TATT
1 TATT
19951849 GAGCCAATGT
Statistics
Matches: 339, Mismatches: 27, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
362 37 0.11
363 302 0.89
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (362 bp):
TATTAGGATACCATGCCTAATCGATAACCGTTCGACAAGTAGCAACCATCGCAACAATGTTTCCA
TGAGAATAAGAACCATTGTAATCTGCATATAGCACTCTAGAAACAAAACTAGATACAGACCCTAA
AGAGTTGAACGGTGGAGATGAAGAGACATTAAGAGGAGATGAGGAGACACAAGAAAATGAACCAC
CAAAAAATGGTAGAAGAAAAGGCACGAGCAGACGGTAAGAAAGAAACACGAGCAGACCCAAACCC
TAATGAATTATGTGGATCACGCTCAGCATAAAAATATTGGGCCAAAACAGGCTAAGAAGAACGAG
CCTGAAATTACTACCTAAATTGAGCTCAACATAACAA
Found at i:19953846 original size:26 final size:26
Alignment explanation
Indices: 19953810--19953862 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
19953800 TTGAATAAAA
19953810 AGGGGTCGCTAAGTG-TAGATTCCCCG
1 AGGGGTCGCTAAGTGCT-GATTCCCCG
*
19953836 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTCGCTAAGTGCTGATTCCCCG
19953862 A
1 A
19953863 ATTATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.25
Consensus pattern (26 bp):
AGGGGTCGCTAAGTGCTGATTCCCCG
Found at i:19953895 original size:42 final size:43
Alignment explanation
Indices: 19953839--19953990 Score: 152
Period size: 42 Copynumber: 3.6 Consensus size: 43
19953829 TTCCCCGAGG
*
19953839 GGTTGCTAAGTGCTGATTCC-CCGAATTATTAACTTTAAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTAACTTTAAAGGT
* * * * *
19953881 TGTTGCTAAGTGCTGATTCCACCGTATCCTTGACTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTAACT-TTAAAGGT
* * *
19953924 GGTTGATATGTGCTGATTCC-CCGTAATCACTGAA-TTT-AAGGT
1 GGTTGCTAAGTGCTGATTCCACCG-AATCA-TTAACTTTAAAGGT
*
19953966 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCCACCGA
19953991 GTTACGGATA
Statistics
Matches: 87, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
41 4 0.05
42 41 0.47
43 34 0.39
44 8 0.09
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGAATCATTAACTTTAAAGGT
Found at i:19957434 original size:33 final size:34
Alignment explanation
Indices: 19957397--19957463 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
19957387 GGATTTTTGA
* * *
19957397 CACTG-TACTGAGATGGGCTAATGCCCAA-ACTGT
1 CACTGATACTGAAAAGGGCT-AGGCCCAAGACTGT
19957430 CACTGATACTGAAAAGGGCTAGGCCCAAGACTGT
1 CACTGATACTGAAAAGGGCTAGGCCCAAGACTGT
19957464 TCAACTGTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 12 0.41
34 17 0.59
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (34 bp):
CACTGATACTGAAAAGGGCTAGGCCCAAGACTGT
Found at i:19960236 original size:20 final size:20
Alignment explanation
Indices: 19960160--19960247 Score: 81
Period size: 20 Copynumber: 4.3 Consensus size: 20
19960150 TTTTTTATAA
*
19960160 AATTTTTAAAATATAATTTTTGG
1 AATTTTTAAAA-ATTA-TTTT-G
* *
19960183 AATTTCTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
*
19960202 TA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
* *
19960221 AATTTTTGAAATTTATTTTG
1 AATTTTTAAAAATTATTTTG
19960241 AATTTTT
1 AATTTTT
19960248 TTGTAACTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
18 7 0.13
19 10 0.19
20 26 0.48
21 1 0.02
22 1 0.02
23 9 0.17
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:19967409 original size:16 final size:17
Alignment explanation
Indices: 19967375--19967410 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19967365 ATGTGCACTC
19967375 TCTTTGCTCTTTCATTA
1 TCTTTGCTCTTTCATTA
*
19967392 TCTTTGTTCTTT-ATTA
1 TCTTTGCTCTTTCATTA
19967408 TCT
1 TCT
19967411 ATCTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.11, C:0.19, G:0.06, T:0.64
Consensus pattern (17 bp):
TCTTTGCTCTTTCATTA
Found at i:19970095 original size:34 final size:34
Alignment explanation
Indices: 19970057--19970137 Score: 144
Period size: 34 Copynumber: 2.4 Consensus size: 34
19970047 CATCAGCTTA
*
19970057 GGCCTTAGCCCATTTCAGTAACAGTAAGTATTAG
1 GGCCTTAGCCCATTTCAGTAACAGTAAGCATTAG
*
19970091 GGCCTTAGCCCATTTCAGTAATAGTAAGCATTAG
1 GGCCTTAGCCCATTTCAGTAACAGTAAGCATTAG
19970125 GGCCTTAGCCCAT
1 GGCCTTAGCCCAT
19970138 CATAGTACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (34 bp):
GGCCTTAGCCCATTTCAGTAACAGTAAGCATTAG
Found at i:19970143 original size:28 final size:30
Alignment explanation
Indices: 19970079--19970144 Score: 73
Period size: 34 Copynumber: 2.1 Consensus size: 30
19970069 TTTCAGTAAC
*
19970079 AGTAAGTATTAGGGCCTTAGCCCATTTCAGTAAT
1 AGTAAGCATTAGGGCCTTAGCCCA-TTC---AAT
19970113 AGTAAGCATTAGGGCCTTAGCCCA-TC-AT
1 AGTAAGCATTAGGGCCTTAGCCCATTCAAT
19970141 AGTA
1 AGTA
19970145 CAGTAACAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 6 0.19
32 2 0.06
34 23 0.74
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (30 bp):
AGTAAGCATTAGGGCCTTAGCCCATTCAAT
Found at i:19970642 original size:18 final size:17
Alignment explanation
Indices: 19970619--19970654 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19970609 TGTGTTGAAT
19970619 GCCCATATGGGCCCACAC
1 GCCCATAT-GGCCCACAC
*
19970637 GCCCATGTGGCCCACAC
1 GCCCATATGGCCCACAC
19970654 G
1 G
19970655 GCTCAAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.19, C:0.44, G:0.25, T:0.11
Consensus pattern (17 bp):
GCCCATATGGCCCACAC
Found at i:19972176 original size:15 final size:15
Alignment explanation
Indices: 19972156--19972188 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19972146 ATGTACATCC
*
19972156 TCTACTCTGTTCTAT
1 TCTACTCTGTTATAT
19972171 TCTACTCTGTTATAT
1 TCTACTCTGTTATAT
19972186 TCT
1 TCT
19972189 GTTATGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.06, T:0.55
Consensus pattern (15 bp):
TCTACTCTGTTATAT
Found at i:19977110 original size:29 final size:29
Alignment explanation
Indices: 19977056--19977112 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
19977046 TCAATACAGT
**
19977056 TTAAATTATATGACTATCGATAAATATTA
1 TTAAATTATATGACTATAAATAAATATTA
*
19977085 TTAAATTATATGATTA-AAATATAATATT
1 TTAAATTATATGACTATAAATA-AATATT
19977113 GTGATGTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (29 bp):
TTAAATTATATGACTATAAATAAATATTA
Found at i:19977390 original size:105 final size:105
Alignment explanation
Indices: 19977249--19977458 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 105
19977239 GTAACGCCCC
19977249 TAACCCGAATCCGTCGCCAGAATAGGGTTACGGAGCATTACCGGAGTTTACAATTTAATTATCAG
1 TAACCCGAATCCGTCGCCAGAATAGGGTTACGGAGCATTACCGGAGTTTACAATTTAATTATCAG
*
19977314 ACATTTCATTTCATCTAGCATTCATATTTGAAACCAATCA
66 ACATTTCATTTCATCGAGCATTCATATTTGAAACCAATCA
19977354 TAACCCGAATCCGTCGCCAGAATAGGGTTACGGAGCATTACCGGAGTTTACAATTTAATTATCAG
1 TAACCCGAATCCGTCGCCAGAATAGGGTTACGGAGCATTACCGGAGTTTACAATTTAATTATCAG
*
19977419 ACATTTCATTTCATCGAGCATTCATATTTGAAACTAATCA
66 ACATTTCATTTCATCGAGCATTCATATTTGAAACCAATCA
19977459 AAATCAAAAC
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (105 bp):
TAACCCGAATCCGTCGCCAGAATAGGGTTACGGAGCATTACCGGAGTTTACAATTTAATTATCAG
ACATTTCATTTCATCGAGCATTCATATTTGAAACCAATCA
Found at i:19981642 original size:26 final size:26
Alignment explanation
Indices: 19981604--19981653 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
19981594 TCTCATCCTT
19981604 ATTTTAACCCTAGTAAAATTTTGACG
1 ATTTTAACCCTAGTAAAATTTTGACG
19981630 ATTTT-ACCTCTAGTAAAATTTTGA
1 ATTTTAACC-CTAGTAAAATTTTGA
19981654 GAAAATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (26 bp):
ATTTTAACCCTAGTAAAATTTTGACG
Found at i:19985410 original size:21 final size:20
Alignment explanation
Indices: 19985380--19985418 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
19985370 ACCAAAAATT
19985380 TATTTTAAAAATAAAAAAAG
1 TATTTTAAAAATAAAAAAAG
19985400 TATTTTAAAAATAAAAAAA
1 TATTTTAAAAATAAAAAAA
19985419 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
TATTTTAAAAATAAAAAAAG
Found at i:19986072 original size:48 final size:46
Alignment explanation
Indices: 19986002--19986092 Score: 137
Period size: 48 Copynumber: 1.9 Consensus size: 46
19985992 AAAAATAATT
* *
19986002 TTATTTTAATAATTTAATATTAAATTAAATTTAATGTTTATCTACA
1 TTATTTTAATAATTTAATATTAAATTAAATCTAATATTTATCTACA
*
19986048 TTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCT
1 TTATTTTAAT-A-ATTTAATATTAAATTAAATCTAATATTTATCT
19986093 TGATAAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 10 0.25
47 1 0.03
48 29 0.73
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (46 bp):
TTATTTTAATAATTTAATATTAAATTAAATCTAATATTTATCTACA
Found at i:19990138 original size:25 final size:25
Alignment explanation
Indices: 19990106--19990156 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
19990096 AGATGTCAAA
19990106 TAGTAAGTATGTATTAAACTGAAAG
1 TAGTAAGTATGTATTAAACTGAAAG
19990131 TAGTAAGTATGTATTAAACTGAAAG
1 TAGTAAGTATGTATTAAACTGAAAG
19990156 T
1 T
19990157 GTCCTTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (25 bp):
TAGTAAGTATGTATTAAACTGAAAG
Found at i:19996752 original size:73 final size:74
Alignment explanation
Indices: 19996637--19996782 Score: 258
Period size: 73 Copynumber: 2.0 Consensus size: 74
19996627 CATCAGTGGT
*
19996637 AATGTTATGCATTATTTCTTTTGGCTATTTCTTGGTTTCTTCTAAGCACTATTATGGTGATGGTA
1 AATGTTATGCATTATTTCTTTTGCCTATTTCTTGGTTTCTTCTAAGCACTATTATGGTGATGGTA
19996702 ATAATTTTC
66 ATAATTTTC
**
19996711 AATGTTATGTTTTATTTC-TTTGCCTATTTCTTGGTTTCTTCTAAGCACTATTATGGTGATGGTA
1 AATGTTATGCATTATTTCTTTTGCCTATTTCTTGGTTTCTTCTAAGCACTATTATGGTGATGGTA
19996775 ATAATTTT
66 ATAATTTT
19996783 TAAGTTTGCC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 53 0.77
74 16 0.23
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (74 bp):
AATGTTATGCATTATTTCTTTTGCCTATTTCTTGGTTTCTTCTAAGCACTATTATGGTGATGGTA
ATAATTTTC
Found at i:20000696 original size:2 final size:2
Alignment explanation
Indices: 20000691--20000715 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20000681 ATATATATAT
20000691 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
20000716 AATTATGCTC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20007179 original size:23 final size:25
Alignment explanation
Indices: 20007149--20007203 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 25
20007139 TTCAAAAGAT
20007149 ATTTTTTTTAAAA-TA-TATTTTGA
1 ATTTTTTTTAAAATTATTATTTTGA
*
20007172 A-TTTTTTTAAAATTATTATTTTTA
1 ATTTTTTTTAAAATTATTATTTTGA
*
20007196 ATTGTTTT
1 ATTTTTTT
20007204 CAAACATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 11 0.41
23 3 0.11
24 8 0.30
25 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (25 bp):
ATTTTTTTTAAAATTATTATTTTGA
Found at i:20007191 original size:24 final size:22
Alignment explanation
Indices: 20007151--20007203 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
20007141 CAAAAGATAT
20007151 TTTTTTTAAAATATATTTTGAA
1 TTTTTTTAAAATATATTTTGAA
*
20007173 TTTTTTTAAAATTATTATTTTTAA
1 TTTTTTTAAAA-TA-TATTTTGAA
*
20007197 TTGTTTT
1 TTTTTTT
20007204 CAAACATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 11 0.41
23 2 0.07
24 14 0.52
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (22 bp):
TTTTTTTAAAATATATTTTGAA
Found at i:20011708 original size:25 final size:25
Alignment explanation
Indices: 20011647--20011713 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
20011637 ATTCGGGAGT
* *
20011647 GCTCATACGAGCAAATAAATGGGAA
1 GCTCATGCGAGCCAATAAATGGGAA
* * * * *
20011672 GCTCAAGAGAGCCATTAATTGGGGA
1 GCTCATGCGAGCCAATAAATGGGAA
20011697 GCTCATGCGAGCCAATA
1 GCTCATGCGAGCCAATA
20011714 TCGGGAAGCT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (25 bp):
GCTCATGCGAGCCAATAAATGGGAA
Found at i:20011748 original size:25 final size:25
Alignment explanation
Indices: 20011717--20011801 Score: 100
Period size: 25 Copynumber: 3.3 Consensus size: 25
20011707 GCCAATATCG
20011717 GGAAGCTCCGAAGAGCCATTAATCA
1 GGAAGCTCCGAAGAGCCATTAATCA
* * *
20011742 GGAAGCTCATGAAAGAGCCTTTAATTA
1 GGAAGCTC-CG-AAGAGCCATTAATCA
20011769 GGAAGCTCCGAAGAGCCA-TATATCA
1 GGAAGCTCCGAAGAGCCATTA-ATCA
*
20011794 GGACGCTC
1 GGAAGCTC
20011802 ATAAGAGCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
24 2 0.04
25 25 0.50
26 2 0.04
27 21 0.42
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (25 bp):
GGAAGCTCCGAAGAGCCATTAATCA
Found at i:20011807 original size:25 final size:26
Alignment explanation
Indices: 20011705--20011809 Score: 94
Period size: 25 Copynumber: 4.2 Consensus size: 26
20011695 GAGCTCATGC
* *
20011705 GAGCCA-AT-ATCGGGAAGCTCCGAA
1 GAGCCATATAATCAGGAAGCTCAGAA
20011729 GAGCCAT-TAATCAGGAAGCTCATGAAA
1 GAGCCATATAATCAGGAAGCTCA-G-AA
* * *
20011756 GAGCC-TTTAATTAGGAAGCTCCGAA
1 GAGCCATATAATCAGGAAGCTCAGAA
* *
20011781 GAGCCATAT-ATCAGGACGCTCATAA
1 GAGCCATATAATCAGGAAGCTCAGAA
20011806 GAGC
1 GAGC
20011810 TACGGTGTGT
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
24 7 0.11
25 34 0.52
26 5 0.08
27 20 0.30
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
GAGCCATATAATCAGGAAGCTCAGAA
Found at i:20016231 original size:27 final size:27
Alignment explanation
Indices: 20016174--20016231 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
20016164 TCAATAGATT
* *
20016174 AAAAAAGTTCACGTTTTTTTTAAGTAA
1 AAAAAAGTTCAAGTTTTTTTTAAGAAA
20016201 AAAAAAGTT-AAGTTTTTTAATTAA-AAA
1 AAAAAAGTTCAAGTTTTTT--TTAAGAAA
20016228 AAAA
1 AAAA
20016232 CTTTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.30
27 15 0.56
28 4 0.15
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (27 bp):
AAAAAAGTTCAAGTTTTTTTTAAGAAA
Found at i:20027849 original size:28 final size:28
Alignment explanation
Indices: 20027817--20027882 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
20027807 ATTATAGTAC
*
20027817 TCAGGTAGCAGAGCCGACCATATATCAT
1 TCAGGCAGCAGAGCCGACCATATATCAT
* * *
20027845 TCAGGCGGCAGAGTCGATCATATATCAT
1 TCAGGCAGCAGAGCCGACCATATATCAT
20027873 TCAGGCAGCA
1 TCAGGCAGCA
20027883 AAATCGATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (28 bp):
TCAGGCAGCAGAGCCGACCATATATCAT
Found at i:20027889 original size:28 final size:28
Alignment explanation
Indices: 20027835--20027897 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
20027825 CAGAGCCGAC
* * *
20027835 CATATATCATTCAGGCGGCAGAGTCGAT
1 CATATATCATTCAGGCAGCAAAATCGAT
20027863 CATATATCATTCAGGCAGCAAAATCGAT
1 CATATATCATTCAGGCAGCAAAATCGAT
*
20027891 TATATAT
1 CATATAT
20027898 TCAAACTAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (28 bp):
CATATATCATTCAGGCAGCAAAATCGAT
Found at i:20032501 original size:5 final size:5
Alignment explanation
Indices: 20032491--20032523 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
20032481 CCCTAAAATT
20032491 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATA
20032524 GTACAGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:20034706 original size:58 final size:58
Alignment explanation
Indices: 20034632--20034750 Score: 166
Period size: 58 Copynumber: 2.1 Consensus size: 58
20034622 TATAAATATT
* * *
20034632 AAGGTCCAAGGTATGAACTTCTACTACTAAAAGTGATATTGCATAATAATGATTGATG
1 AAGGTCCAAGGCATGAACTCCTACTACTAAAAGTGATATTGCATAATAATGATTAATG
* ** * *
20034690 AAGGTCCAAGGCATGAACTCCTATTGTTAAAAGTGTTATTGCGTAATAATGATTAATG
1 AAGGTCCAAGGCATGAACTCCTACTACTAAAAGTGATATTGCATAATAATGATTAATG
20034748 AAG
1 AAG
20034751 TCATGACAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (58 bp):
AAGGTCCAAGGCATGAACTCCTACTACTAAAAGTGATATTGCATAATAATGATTAATG
Found at i:20042664 original size:29 final size:29
Alignment explanation
Indices: 20042631--20042693 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
20042621 TTGTGAAGAA
*
20042631 CCTAACCTTAGAACTCTTTGAAGAGAGCT
1 CCTAACCTTAGAACTCGTTGAAGAGAGCT
* *
20042660 CCTAACCTTGGAACTCGTTGAAGGGAGCT
1 CCTAACCTTAGAACTCGTTGAAGAGAGCT
*
20042689 TCTAA
1 CCTAA
20042694 TCATGAATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.27
Consensus pattern (29 bp):
CCTAACCTTAGAACTCGTTGAAGAGAGCT
Found at i:20043276 original size:29 final size:29
Alignment explanation
Indices: 20043218--20043276 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
20043208 TGAATATATA
*
20043218 TGGAACCTGTTGAAAGGAGCTCCTACCCT
1 TGGAACCTGTTGAAAGGAGCTCCTAACCT
* * *
20043247 TGGAACTTGTTGAAGGGAGCTCTTAACCT
1 TGGAACCTGTTGAAAGGAGCTCCTAACCT
20043276 T
1 T
20043277 AAACTCATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (29 bp):
TGGAACCTGTTGAAAGGAGCTCCTAACCT
Found at i:20043420 original size:15 final size:15
Alignment explanation
Indices: 20043396--20043425 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20043386 TAAGAATGAG
*
20043396 AACTATAATTAAGGA
1 AACTAAAATTAAGGA
20043411 AACTAAAATTAAGGA
1 AACTAAAATTAAGGA
20043426 CTTCTAATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (15 bp):
AACTAAAATTAAGGA
Found at i:20046832 original size:13 final size:13
Alignment explanation
Indices: 20046814--20046839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20046804 TTGAAGCTTT
20046814 TTTTTAATTAATA
1 TTTTTAATTAATA
20046827 TTTTTAATTAATA
1 TTTTTAATTAATA
20046840 AATATATTGT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAATTAATA
Found at i:20050847 original size:52 final size:50
Alignment explanation
Indices: 20050783--20050899 Score: 137
Period size: 50 Copynumber: 2.3 Consensus size: 50
20050773 ATGAACAAAT
* *
20050783 GAGTTACTTAATGCAAGAC-TTAATTTAATGATGCAGGCTTAAACTAACATGG
1 GAGTTACATAATGCAAGACATT-ATTT-ATGATGCAGACTT-AACTAACATGG
* * * *
20050835 GAGTTACATAATGCATGTCATTATTTATGATGCATACTTAACTAGCATGG
1 GAGTTACATAATGCAAGACATTATTTATGATGCAGACTTAACTAACATGG
*
20050885 AAGTTACATAATGCA
1 GAGTTACATAATGCA
20050900 CAACTTTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 24 0.42
51 11 0.19
52 20 0.35
53 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (50 bp):
GAGTTACATAATGCAAGACATTATTTATGATGCAGACTTAACTAACATGG
Found at i:20059622 original size:19 final size:19
Alignment explanation
Indices: 20059600--20059637 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20059590 TCAATCATCC
20059600 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
20059619 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
20059638 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:20065236 original size:26 final size:26
Alignment explanation
Indices: 20065200--20065250 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
20065190 TTGAATAAAA
*
20065200 AGGGGTTGCTAATTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
20065226 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
20065251 AAATTATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:20065369 original size:85 final size:84
Alignment explanation
Indices: 20065226--20065545 Score: 365
Period size: 85 Copynumber: 3.8 Consensus size: 84
20065216 TGATTCCCCG
* * * * *
20065226 AGGGGTTGCTAAGTGCTGATTCCCC-AAATTATTGACTCTAAAGGTGGTTGCTAAGTGCTGATCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTAA-CACTGAATATAAAGGTGGTTGCTAAGTGCTGATC-
*
20065290 CACCGTATTTTTAACTGTGAA
64 CACCGTATTTTTAATTGTGAA
* * ** * *
20065311 AGGGGTTGCTAAGTGTTGGTTCCCCGTAACGTTGAATATAAATGTGGTTGCTATGTGCTGAATCC
1 AGGGGTTGCTAAGTGCTGATTCCCCGTAACACTGAATATAAAGGTGGTTGCTAAGTGCTG-ATCC
20065376 ACCGTATTTTTAATTGTGAA
65 ACCGTATTTTTAATTGTGAA
* * * *
20065396 TGGGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATACAAAGGTGGTTGCTAAATGCTGATTCC
1 AGGGGTTGCTAAGTGCTGATTCCCCGTAACACTGAATATAAAGGTGGTTGCTAAGTGCTGA-TCC
* **
20065461 ACCGAATCCTTAATTGTGAA
65 ACCGTATTTTTAATTGTGAA
* * * * *
20065481 AGGGGTTGCTATGTGCTGATTCCCTGTATCACTGAAT-TTATGGTGGTTGCTAAGTGCTGAATCC
1 AGGGGTTGCTAAGTGCTGATTCCCCGTAACACTGAATATAAAGGTGGTTGCTAAGTGCTG-ATCC
20065545 A
65 A
20065546 TCGAGTAACG
Statistics
Matches: 201, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
84 23 0.11
85 173 0.86
86 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (84 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGTAACACTGAATATAAAGGTGGTTGCTAAGTGCTGATCCA
CCGTATTTTTAATTGTGAA
Found at i:20065403 original size:43 final size:42
Alignment explanation
Indices: 20065226--20065503 Score: 192
Period size: 43 Copynumber: 6.5 Consensus size: 42
20065216 TGATTCCCCG
** * * *
20065226 AGGGGTTGCTAAGTGCTGATTCC-CCAAATTATTGACTCT-AA
1 AGGGGTTGCTAAGTGCTGATTCCACCGTATT-TTTAATGTGAA
20065267 AGGTGGTTGCTAAGTGCTGA-TCACACCGTATTTTTAACTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTC-CACCGTATTTTTAA-TGTGAA
* * ** * *
20065311 AGGGGTTGCTAAGTGTTGGTTCC-CCGTAACGTTGAATAT-AA
1 AGGGGTTGCTAAGTGCTGATTCCACCGT-ATTTTTAATGTGAA
* * *
20065352 ATGTGGTTGCTATGTGCTGAATCCACCGTATTTTTAATTGTGAA
1 A-GGGGTTGCTAAGTGCTGATTCCACCGTATTTTTAA-TGTGAA
* ** * **
20065396 TGGGGTTGCTAAGTGCTGATTCC-CCGTATCACTGAAT-ACAA
1 AGGGGTTGCTAAGTGCTGATTCCACCGTAT-TTTTAATGTGAA
* * **
20065437 AGGTGGTTGCTAAATGCTGATTCCACCGAATCCTTAATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCCACCGTATTTTTAA-TGTGAA
*
20065481 AGGGGTTGCTATGTGCTGATTCC
1 AGGGGTTGCTAAGTGCTGATTCC
20065504 CTGTATCACT
Statistics
Matches: 183, Mismatches: 38, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
41 12 0.07
42 78 0.43
43 79 0.43
44 14 0.08
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
AGGGGTTGCTAAGTGCTGATTCCACCGTATTTTTAATGTGAA
Found at i:20068028 original size:23 final size:23
Alignment explanation
Indices: 20067998--20068044 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
20067988 CAACCTCGAA
20067998 TCCCGAAAGAAACCCTAGTTCTT
1 TCCCGAAAGAAACCCTAGTTCTT
20068021 TCCCGAAAGAAACCCTAGTTCTT
1 TCCCGAAAGAAACCCTAGTTCTT
20068044 T
1 T
20068045 TCTTCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.28
Consensus pattern (23 bp):
TCCCGAAAGAAACCCTAGTTCTT
Found at i:20071250 original size:14 final size:14
Alignment explanation
Indices: 20071215--20071250 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20071205 ATAAAATATA
*
20071215 AATTTATATTTAAT
1 AATTTATTTTTAAT
20071229 AATTTATTTTTAAT
1 AATTTATTTTTAAT
*
20071243 ATTTTATT
1 AATTTATT
20071251 AATAAATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTTATTTTTAAT
Found at i:20077120 original size:69 final size:70
Alignment explanation
Indices: 20077003--20077167 Score: 224
Period size: 69 Copynumber: 2.4 Consensus size: 70
20076993 ATCATCAGAA
* * * *
20077003 TGCCATAGCCTAGCTATAGTCCTACATATATACACTGCCATGGTCCAACCATGGTCTTACGTCAG
1 TGCCATAGCCTTGCTATGGTCTTACA-ATATACACTGCCATGGTCCAACCATGGTCTTACATCAG
*
20077068 AACAAT
65 AACAAC
* * * * *
20077074 TGTCATAGCCTTGCTATGGTCTTAC-ATATACATTGCCATGGTCCAACCATGGTTTTATATCCGA
1 TGCCATAGCCTTGCTATGGTCTTACAATATACACTGCCATGGTCCAACCATGGTCTTACATCAGA
20077138 ACAAC
66 ACAAC
20077143 TGCCATAGCCTTGCTATGGTCTTAC
1 TGCCATAGCCTTGCTATGGTCTTAC
20077168 GTTTATACTT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
69 62 0.75
71 21 0.25
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (70 bp):
TGCCATAGCCTTGCTATGGTCTTACAATATACACTGCCATGGTCCAACCATGGTCTTACATCAGA
ACAAC
Found at i:20080150 original size:50 final size:50
Alignment explanation
Indices: 20080084--20080325 Score: 277
Period size: 50 Copynumber: 4.7 Consensus size: 50
20080074 TTCATGAACA
* * * **
20080084 GCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
* * ** * *
20080134 GCCCATGCCATGTCCCAGACATTGTCTTACGGGGGACCTCTCATCTCGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
* * *
20080184 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTTGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
* * *
20080234 ACTAATGCTATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG-T
20080290 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
20080326 TCACTTTACC
Statistics
Matches: 159, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
50 122 0.77
53 1 0.01
55 2 0.01
56 34 0.21
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
Found at i:20085457 original size:14 final size:14
Alignment explanation
Indices: 20085438--20085464 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20085428 ATCAATACTT
20085438 TTTTTTCTTATTCC
1 TTTTTTCTTATTCC
20085452 TTTTTTCTTATTC
1 TTTTTTCTTATTC
20085465 TTATTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTCTTATTCC
Found at i:20088576 original size:20 final size:21
Alignment explanation
Indices: 20088539--20088598 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
20088529 TTCGGGTGGA
20088539 TCAGCTCTT-TCGAGCTTCTAT
1 TCAGCTCTTAT-GAGCTTCTAT
*
20088560 TCAGCTCTTAT-AGCTTCTGT
1 TCAGCTCTTATGAGCTTCTAT
*
20088580 TTAGCTCTTATGAGCTTCT
1 TCAGCTCTTATGAGCTTCT
20088599 GTTGGCGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 18 0.51
21 16 0.46
22 1 0.03
ACGTcount: A:0.15, C:0.25, G:0.15, T:0.45
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTAT
Found at i:20088599 original size:21 final size:21
Alignment explanation
Indices: 20088539--20088601 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
20088529 TTCGGGTGGA
*
20088539 TCAGCTCTT-TCGAGCTTCTAT
1 TCAGCTCTTAT-GAGCTTCTGT
20088560 TCAGCTCTTAT-AGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
*
20088580 TTAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
20088601 T
1 T
20088602 GGCGTATTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.47
21 19 0.50
22 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.46
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:20094266 original size:48 final size:48
Alignment explanation
Indices: 20094196--20094315 Score: 172
Period size: 48 Copynumber: 2.5 Consensus size: 48
20094186 AGAACATATA
*
20094196 TGGACAAAGCCACCAAATTTGTAGACAAGCTGCCAATATACATAGTTG
1 TGGACAAAGCCACCAAATTTGTAGACAAGCTGCCAATACACATAGTTG
* * *
20094244 TGGACAAAGTCATCGAAA-TTGTAGACAAGCTGCCAATACACATAGTTT
1 TGGACAAAGCCA-CCAAATTTGTAGACAAGCTGCCAATACACATAGTTG
*
20094292 TGGATAAA-CCACCAAATTTGTAGA
1 TGGACAAAGCCACCAAATTTGTAGA
20094316 TTATTCAACT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
46 4 0.06
47 9 0.14
48 46 0.73
49 4 0.06
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.24
Consensus pattern (48 bp):
TGGACAAAGCCACCAAATTTGTAGACAAGCTGCCAATACACATAGTTG
Found at i:20102712 original size:26 final size:25
Alignment explanation
Indices: 20102673--20102746 Score: 103
Period size: 26 Copynumber: 2.9 Consensus size: 25
20102663 TGGAGGAAGT
20102673 ATACTATACTGGCAGCTTTGCTGCG
1 ATACTATACTGGCAGCTTTGCTGCG
*
20102698 ATACTGATATTGGCAGCTTTGCTGCG
1 ATACT-ATACTGGCAGCTTTGCTGCG
* *
20102724 TTACTATTACTGGCAGATTTGCT
1 ATACTA-TACTGGCAGCTTTGCT
20102747 ACAATATTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 6 0.14
26 37 0.86
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (25 bp):
ATACTATACTGGCAGCTTTGCTGCG
Found at i:20102892 original size:9 final size:9
Alignment explanation
Indices: 20102878--20102908 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20102868 GTTAAACGAA
20102878 TCGAGTTAT
1 TCGAGTTAT
*
20102887 TCGAGTTAA
1 TCGAGTTAT
20102896 TCGAGTTAT
1 TCGAGTTAT
20102905 TCGA
1 TCGA
20102909 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:20103232 original size:29 final size:31
Alignment explanation
Indices: 20103200--20103258 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
20103190 AAACCTTTTA
*
20103200 TTTTCCCC-CAAAATTTTACTCCC-TCCCAC
1 TTTTCCCCTAAAAATTTTACTCCCTTCCCAC
*
20103229 TTTTCCCCTAAAAATTTTATTCCCTTCCCA
1 TTTTCCCCTAAAAATTTTACTCCCTTCCCA
20103259 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 13 0.50
31 5 0.19
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (31 bp):
TTTTCCCCTAAAAATTTTACTCCCTTCCCAC
Found at i:20104153 original size:29 final size:29
Alignment explanation
Indices: 20104108--20104190 Score: 127
Period size: 27 Copynumber: 3.0 Consensus size: 29
20104098 ACTGTATTGA
*
20104108 TACTGTAATGGGCTAAGGCCCACACTGTT
1 TACTGTATTGGGCTAAGGCCCACACTGTT
*
20104137 TACTGTATTGGGTTAAGGCCC-CACTG-T
1 TACTGTATTGGGCTAAGGCCCACACTGTT
20104164 TACTGTATTGGGCTAAGG-CCACACTGT
1 TACTGTATTGGGCTAAGGCCCACACTGT
20104191 ACTATTACTG
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 2 0.04
27 23 0.47
28 5 0.10
29 19 0.39
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (29 bp):
TACTGTATTGGGCTAAGGCCCACACTGTT
Found at i:20104199 original size:32 final size:30
Alignment explanation
Indices: 20104108--20104215 Score: 100
Period size: 27 Copynumber: 3.7 Consensus size: 30
20104098 ACTGTATTGA
*
20104108 TACTGTAATGGGCTAAGGCCCACACTG--TT
1 TACTGTATTGGGCTAAGG-CCACACTGACTT
* *
20104137 TACTGTATTGGGTTAAGGCCCCACTG---T
1 TACTGTATTGGGCTAAGGCCACACTGACTT
20104164 TACTGTATTGGGCTAAGGCCACACTGTACTAT
1 TACTGTATTGGGCTAAGGCCACACTG-ACT-T
* * *
20104196 TACTGAATAGGGCTCAGGCC
1 TACTGTATTGGGCTAAGGCC
20104216 CAGACTATTA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
27 25 0.38
28 7 0.11
29 16 0.24
32 18 0.27
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (30 bp):
TACTGTATTGGGCTAAGGCCACACTGACTT
Found at i:20107587 original size:20 final size:21
Alignment explanation
Indices: 20107549--20107588 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20107539 TTATATTTTA
20107549 TTTTTATTTTTTTATTATATG
1 TTTTTATTTTTTTATTATATG
20107570 TTTTT-TTTGTTTTA-TATAT
1 TTTTTATTT-TTTTATTATAT
20107589 TTCATTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTATTTTTTTATTATATG
Found at i:20119483 original size:45 final size:45
Alignment explanation
Indices: 20119427--20119952 Score: 718
Period size: 45 Copynumber: 11.8 Consensus size: 45
20119417 GTCTGAAAAG
* * *
20119427 AGCAGGTCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAATAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* * *
20119472 AGTATATCTTGTCTTCCTATATT----GCGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* * * * *
20119513 AGCAGATCTTGTCTTCCTATATGGGTAGCGAAGTATATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* *
20119558 AACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* *
20119603 AGCAGACCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* * * *
20119648 AGCAGATCTTGTCTTCCTATATGGGTAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* *
20119693 AGCAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGATTAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* * *
20119738 AGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* * *
20119783 AACATATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* * *
20119828 AGCAGATCTTATCTTCCTGTATTGGTAGTGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* *
20119873 AACAGATCTTGTCTTCCTGTATTGGCAGAGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
* *
20119918 AGCAGATCTTGTCTGCCTGTATTGGCAGTGAAGTA
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTA
20119953 AATCGAAGCC
Statistics
Matches: 425, Mismatches: 52, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
41 36 0.08
45 389 0.92
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (45 bp):
AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGAT
Found at i:20120505 original size:22 final size:22
Alignment explanation
Indices: 20120461--20120510 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
20120451 TTTGTACAAG
20120461 CCCAATAACCCTAAACCTAAAA
1 CCCAATAACCCTAAACCTAAAA
* *
20120483 CCCAACTAACCC-AAGCCTGAAA
1 CCCAA-TAACCCTAAACCTAAAA
20120505 -CCAATA
1 CCCAATA
20120511 GCAGAGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.08
21 4 0.16
22 13 0.52
23 6 0.24
ACGTcount: A:0.46, C:0.38, G:0.04, T:0.12
Consensus pattern (22 bp):
CCCAATAACCCTAAACCTAAAA
Found at i:20130367 original size:48 final size:48
Alignment explanation
Indices: 20130314--20130409 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
20130304 TTGTTGAGAT
*
20130314 TGTCAAATTGCATAGGGTACCAGTTTTTATTATTTTTTATAAAGATCC
1 TGTCAAATTGCACAGGGTACCAGTTTTTATTATTTTTTATAAAGATCC
* *
20130362 TGTCAAATTGCACGGGGTACCAGTTTTTATTATTTTTTATATAGATCC
1 TGTCAAATTGCACAGGGTACCAGTTTTTATTATTTTTTATAAAGATCC
20130410 GCAATTTACA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.44
Consensus pattern (48 bp):
TGTCAAATTGCACAGGGTACCAGTTTTTATTATTTTTTATAAAGATCC
Found at i:20133725 original size:12 final size:12
Alignment explanation
Indices: 20133708--20133737 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20133698 TCAGATAATT
20133708 ACACGGCCTAGC
1 ACACGGCCTAGC
*
20133720 ACACGGCCTGGC
1 ACACGGCCTAGC
20133732 ACACGG
1 ACACGG
20133738 GCGTGTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:20139413 original size:30 final size:27
Alignment explanation
Indices: 20139358--20139414 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
20139348 TAAAACAATT
*
20139358 ATAGAAAAATAATTAAATTAAAATTAA
1 ATAGAAAAATAATAAAATTAAAATTAA
20139385 ATAGAAAAATAATCCAAAATTCAAAATTAA
1 ATAGAAAAATAAT--AAAATT-AAAATTAA
20139415 CAATTTCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 13 0.50
29 5 0.19
30 8 0.31
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.26
Consensus pattern (27 bp):
ATAGAAAAATAATAAAATTAAAATTAA
Found at i:20142407 original size:35 final size:35
Alignment explanation
Indices: 20142262--20142408 Score: 145
Period size: 35 Copynumber: 4.2 Consensus size: 35
20142252 TGTTTTAAAA
*
20142262 GCAAAGCTTTTTGATAATCCAAGCTCACCTTGAAG
1 GCAAAGCTTTTTGATAATCCGAGCTCACCTTGAAG
* * * ** *
20142297 GTAGAG--TTTTAATAAAACGAAGCTCGCCTTGAAG
1 GCAAAGCTTTTTGATAATCCG-AGCTCACCTTGAAG
* * ** *
20142331 GCAAAGATTTTTTATAATCCGAGCTTGCATTGAAG
1 GCAAAGCTTTTTGATAATCCGAGCTCACCTTGAAG
* *
20142366 GCAAAGCTTTTTGATAATCTGAGCTTACCTTGAAG
1 GCAAAGCTTTTTGATAATCCGAGCTCACCTTGAAG
20142401 GCAAAGCT
1 GCAAAGCT
20142409 GTAATAGAAC
Statistics
Matches: 90, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
33 9 0.10
34 17 0.19
35 54 0.60
36 10 0.11
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (35 bp):
GCAAAGCTTTTTGATAATCCGAGCTCACCTTGAAG
Found at i:20144027 original size:35 final size:35
Alignment explanation
Indices: 20143982--20144175 Score: 124
Period size: 34 Copynumber: 5.6 Consensus size: 35
20143972 AATAAAATGA
* * *
20143982 AGCTCTCCTTGAAGGCAAAGCTTTTTGATAATTTG
1 AGCTCGCCTTGAAGGTAAAGCTTTTTGATAATTCG
* * *
20144017 AGCTCGCCTTGAAGGTAATGTTTTTTTGATAATTCA
1 AGCTCGCCTTGAAGGTAAAG-CTTTTTGATAATTCG
*** * * * **
20144053 AGCTCATTTTGAAGATAAAG--TTGTAATAAAACG
1 AGCTCGCCTTGAAGGTAAAGCTTTTTGATAATTCG
* * * * * *
20144086 AAGCTAGCCTTGAAGATAAAGATTTTTTATGATCCG
1 -AGCTCGCCTTGAAGGTAAAGCTTTTTGATAATTCG
* * **
20144122 AGCTTG-CTTGAAGGAAAAGCTTTTTGATAATTTA
1 AGCTCGCCTTGAAGGTAAAGCTTTTTGATAATTCG
*
20144156 AGCTCGCCTTGAAGATAAAG
1 AGCTCGCCTTGAAGGTAAAG
20144176 TTGTAATAGA
Statistics
Matches: 117, Mismatches: 37, Indels: 10
0.71 0.23 0.06
Matches are distributed among these distances:
33 8 0.07
34 41 0.35
35 33 0.28
36 35 0.30
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (35 bp):
AGCTCGCCTTGAAGGTAAAGCTTTTTGATAATTCG
Found at i:20144099 original size:34 final size:34
Alignment explanation
Indices: 20144061--20144259 Score: 127
Period size: 34 Copynumber: 5.8 Consensus size: 34
20144051 CAAGCTCATT
*
20144061 TTGAAGATAAAGTTGTAATAAAACGAAGCTAGCC
1 TTGAAGATAAAGTTGTAATAAAACAAAGCTAGCC
** * * ** *
20144095 TTGAAGATAAAGATT-TTTTATGATCCGAGCTTG-C
1 TTGAAGATAAAG-TTGTAATA-AAACAAAGCTAGCC
* * *** *
20144129 TTGAAGGA-AAAGCTTTTTGATAATTTAA-GCTCGCC
1 TTGAA-GATAAAG--TTGTAATAAAACAAAGCTAGCC
* * *
20144164 TTGAAGATAAAGTTGTAATAGAACAAAGTTAACC
1 TTGAAGATAAAGTTGTAATAAAACAAAGCTAGCC
* *
20144198 TTGAAGTTAAAGTTGTAATAAAACAAAGCTTGCC
1 TTGAAGATAAAGTTGTAATAAAACAAAGCTAGCC
** *
20144232 TTGAAGGCAAAGTTGTAATAAAAAAAAG
1 TTGAAGATAAAGTTGTAATAAAACAAAG
20144260 TATAGGTAAT
Statistics
Matches: 124, Mismatches: 33, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
33 8 0.06
34 89 0.72
35 24 0.19
36 3 0.02
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.29
Consensus pattern (34 bp):
TTGAAGATAAAGTTGTAATAAAACAAAGCTAGCC
Found at i:20144235 original size:103 final size:103
Alignment explanation
Indices: 20144039--20144243 Score: 234
Period size: 103 Copynumber: 2.0 Consensus size: 103
20144029 AGGTAATGTT
** * *
20144039 TTTTTGATAATTCAAGCTCATTTTGAAGATAAAGTTGTAATAAAACGAAGCTAGCCTTGAAGATA
1 TTTTTGATAATTCAAGCTCACCTTGAAGATAAAGTTGTAATAAAACAAAGCTAACCTTGAAGATA
** * * **
20144104 AAGATTTTTTATGATCCGAGCTTGCTTGAAGGAAAAGC
66 AAGATTTAATATAAACAAAGCTTGCTTGAAGGAAAAGC
* * * * *
20144142 TTTTTGATAATTTAAGCTCGCCTTGAAGATAAAGTTGTAATAGAACAAAGTTAACCTTGAAGTTA
1 TTTTTGATAATTCAAGCTCACCTTGAAGATAAAGTTGTAATAAAACAAAGCTAACCTTGAAGATA
*
20144207 AAG-TTGTAATA-AAACAAAGCTTGCCTTGAAGGCAAAG
66 AAGATT-TAATATAAACAAAGCTTG-CTTGAAGGAAAAG
20144244 TTGTAATAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
102 10 0.12
103 74 0.88
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (103 bp):
TTTTTGATAATTCAAGCTCACCTTGAAGATAAAGTTGTAATAAAACAAAGCTAACCTTGAAGATA
AAGATTTAATATAAACAAAGCTTGCTTGAAGGAAAAGC
Found at i:20147663 original size:7 final size:6
Alignment explanation
Indices: 20147629--20147662 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
20147619 TGAAAGTTAC
20147629 TTTCTTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT TTT
20147663 TTGCTTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:20154023 original size:14 final size:14
Alignment explanation
Indices: 20154004--20154033 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20153994 ATTGCGTTCG
20154004 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
*
20154018 TAGTTAATTTAGAT
1 TAGTTAAATTAGAT
20154032 TA
1 TA
20154034 AAAACAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TAGTTAAATTAGAT
Found at i:20160999 original size:27 final size:26
Alignment explanation
Indices: 20160973--20161036 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
20160963 CTTTCCTTTC
*
20160973 CTTTA-TTTTATTTTATTTCTTTATTT
1 CTTTATTTTTATTAT-TTTCTTTATTT
*
20160999 CTTTATCTTTTATTATTTTGTTTATTT
1 CTTTAT-TTTTATTATTTTCTTTATTT
*
20161026 TTTTATTTTTA
1 CTTTATTTTTA
20161037 GTTTCTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 10 0.30
27 15 0.45
28 8 0.24
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.77
Consensus pattern (26 bp):
CTTTATTTTTATTATTTTCTTTATTT
Found at i:20161034 original size:8 final size:8
Alignment explanation
Indices: 20160983--20161035 Score: 61
Period size: 8 Copynumber: 6.2 Consensus size: 8
20160973 CTTTATTTTA
20160983 TTTTATTT
1 TTTTATTT
*
20160991 CTTTATTT
1 TTTTATTT
*
20160999 CTTTATCTT
1 TTTTAT-TT
20161008 TTATTATTT
1 TT-TTATTT
20161017 TGTTTATTT
1 T-TTTATTT
20161026 TTTTATTT
1 TTTTATTT
20161034 TT
1 TT
20161036 AGTTTCTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
8 22 0.55
9 13 0.32
10 5 0.12
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTATTT
Found at i:20161035 original size:18 final size:17
Alignment explanation
Indices: 20160974--20161034 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
20160964 TTTCCTTTCC
* *
20160974 TTTATTTTATTTTATTTC
1 TTTATTTT-GTTTATTTT
*
20160992 TTTA-TTTCTTTATCTTT
1 TTTATTTTGTTTAT-TTT
20161009 TATTATTTTGTTTATTTT
1 T-TTATTTTGTTTATTTT
20161027 TTTATTTT
1 TTTATTTT
20161035 TAGTTTCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.14
17 13 0.35
18 11 0.30
19 8 0.22
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTATTTTGTTTATTTT
Found at i:20164063 original size:11 final size:14
Alignment explanation
Indices: 20164028--20164054 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20164018 TTAAAAATGT
20164028 TCATCTTTAGTGTA
1 TCATCTTTAGTGTA
20164042 TCATCTTTAGTGT
1 TCATCTTTAGTGT
20164055 TCTTTTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.52
Consensus pattern (14 bp):
TCATCTTTAGTGTA
Found at i:20165278 original size:14 final size:14
Alignment explanation
Indices: 20165259--20165288 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20165249 ATTGTGTTCG
20165259 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
*
20165273 TAGTTAATTTAGAT
1 TAGTTAAATTAGAT
20165287 TA
1 TA
20165289 AAAACAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TAGTTAAATTAGAT
Found at i:20167855 original size:20 final size:20
Alignment explanation
Indices: 20167830--20167872 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
20167820 CTAGGAGTTC
20167830 ATTTTTCTAGTAGAAATAAA
1 ATTTTTCTAGTAGAAATAAA
20167850 ATTTTTCTAGTAGAAATAAA
1 ATTTTTCTAGTAGAAATAAA
20167870 ATT
1 ATT
20167873 CTACAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (20 bp):
ATTTTTCTAGTAGAAATAAA
Found at i:20182252 original size:72 final size:72
Alignment explanation
Indices: 20182131--20182264 Score: 205
Period size: 72 Copynumber: 1.9 Consensus size: 72
20182121 AAAAGTTTTT
* * *
20182131 TCAAAATGTCAAAGTAATATTATCTTTCATTAAACATTGCATCACAGTGTCATACAATCATATCC
1 TCAAAATGCCAAAGTAACATTATCTTTCAATAAACATTGCATCACAGTGTCATACAATCATATCC
20182196 AATACTA
66 AATACTA
* * * *
20182203 TCAAAATGCCAATGTAACATTATCTTTCAATAAACATTGCATCATAGTGTTATACCATCATA
1 TCAAAATGCCAAAGTAACATTATCTTTCAATAAACATTGCATCACAGTGTCATACAATCATA
20182265 CCATGGATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (72 bp):
TCAAAATGCCAAAGTAACATTATCTTTCAATAAACATTGCATCACAGTGTCATACAATCATATCC
AATACTA
Found at i:20187996 original size:2 final size:2
Alignment explanation
Indices: 20187989--20188013 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20187979 AAAACTTTAA
20187989 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20188014 AACAAGATTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20189523 original size:47 final size:44
Alignment explanation
Indices: 20189456--20189546 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 44
20189446 GCTTAGTCCC
20189456 TAGGGTTTTTTGGTTTAGGGTTTTAAGGG-TTTGTT-AAAATAATT
1 TAGGGTTTTTTGGTTTAGGG-TTT-AGGGTTTTGTTAAAAATAATT
*
20189500 TAGGGTTTTTGGTAGGTTTAGGGTTTAGGGTTTTTTTAAAAATAATT
1 TAGGGTTTTT--T-GGTTTAGGGTTTAGGGTTTTGTTAAAAATAATT
20189547 AAATTAGGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
44 10 0.24
45 4 0.10
46 9 0.22
47 18 0.44
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.49
Consensus pattern (44 bp):
TAGGGTTTTTTGGTTTAGGGTTTAGGGTTTTGTTAAAAATAATT
Found at i:20189560 original size:33 final size:31
Alignment explanation
Indices: 20189517--20189640 Score: 142
Period size: 33 Copynumber: 3.9 Consensus size: 31
20189507 TTTGGTAGGT
20189517 TTAGGGTTTAGGGTTTTTTTAAAAATAATTAAA
1 TTAGGGTTTAGGG--TTTTTAAAAATAATTAAA
* *
20189550 TTAGGTTTTAGGGTTTTAAATAAATAAATTAAA
1 TTAGGGTTTAGGGTTTTTAA-AAAT-AATTAAA
* *
20189583 TTAGGGATTAGGGTTTTTAAGAA-AATTAAA
1 TTAGGGTTTAGGGTTTTTAAAAATAATTAAA
* **
20189613 TTATGGTTTAGTTTTTTTAAAAATAATT
1 TTAGGGTTTAGGGTTTTTAAAAATAATT
20189641 TTGTATTTAG
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
30 25 0.32
31 10 0.13
32 6 0.08
33 36 0.47
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (31 bp):
TTAGGGTTTAGGGTTTTTAAAAATAATTAAA
Found at i:20189569 original size:30 final size:29
Alignment explanation
Indices: 20189533--20189640 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 29
20189523 TTTAGGGTTT
20189533 TTTTAAAAATAATTAAATTAGGTTTTAGGG
1 TTTTAAAAATAATTAAATTAGG-TTTAGGG
*
20189563 TTTTAAATAAATAAATTAAATTAGGGATTAGGG
1 TTTT-AA-AAAT-AATTAAATTA-GGTTTAGGG
* **
20189596 TTTTTAAGAA-AATTAAATTATGGTTTAGTTT
1 -TTTTAAAAATAATTAAATTA-GGTTTAG-GG
20189627 TTTTAAAAATAATT
1 TTTTAAAAATAATT
20189641 TTGTATTTAG
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
30 28 0.44
31 6 0.09
32 6 0.09
33 18 0.28
34 6 0.09
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (29 bp):
TTTTAAAAATAATTAAATTAGGTTTAGGG
Found at i:20189919 original size:125 final size:125
Alignment explanation
Indices: 20189692--20189958 Score: 342
Period size: 125 Copynumber: 2.1 Consensus size: 125
20189682 ACTTTTTTTC
*
20189692 TTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGCTCTGAAAAGATAATGAAAAAAC
1 TTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGCTCTGAAAAGATAATGAAAAAAC
* * * *
20189757 GCTTCAAGCAGAATGCGCTGTCAGTAAAATTACTGAAAAAAGCTCCCACGTGGACGTTCT
66 GCTTCAAGCAGAAGGCACTATCAGTAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCT
* * * ** *
20189817 TTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGAGGGTTCTGAACAA-A-GGTGTCAAAA
1 TTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGCTCTGAA-AAGATAATG-AAAAA
* * *
20189880 ATGCTTCAAGCAGGAGGCACTATCAGTAAAATTGA-TGAAAAAAGCTTCCACGTGGACGCTCTT
64 ACGCTTCAAGCAGAAGGCACTATCAGTAAAATT-ACTGAAAAAAGCTCCCACGTGGACGCTC-T
*
20189943 TTTTCTACAATAGTTC
1 TTTTCTACAGTAGTTC
20189959 TTATTTGGCA
Statistics
Matches: 122, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
124 2 0.02
125 102 0.84
126 18 0.15
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28
Consensus pattern (125 bp):
TTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGCTCTGAAAAGATAATGAAAAAAC
GCTTCAAGCAGAAGGCACTATCAGTAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCT
Found at i:20190072 original size:28 final size:28
Alignment explanation
Indices: 20190040--20190093 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
20190030 AGGAGGCTAA
20190040 GTAGAATAGAAATTGAAGATGAGTGAAC
1 GTAGAATAGAAATTGAAGATGAGTGAAC
20190068 GTAGAATAGAAATTGAAGATGAGTGA
1 GTAGAATAGAAATTGAAGATGAGTGA
20190094 CTTTATTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (28 bp):
GTAGAATAGAAATTGAAGATGAGTGAAC
Found at i:20193188 original size:21 final size:21
Alignment explanation
Indices: 20193129--20193188 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
20193119 AAATAGGCCA
* *
20193129 GCCCATGTGGCTACCCCACAC
1 GCCCGTGTGGCTAACCCACAC
* * *
20193150 GCTCGTGTGGATATCCCACAC
1 GCCCGTGTGGCTAACCCACAC
20193171 GCCCGTGTGGCTAACCCA
1 GCCCGTGTGGCTAACCCA
20193189 TATGCCCATG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.18, C:0.40, G:0.23, T:0.18
Consensus pattern (21 bp):
GCCCGTGTGGCTAACCCACAC
Found at i:20193195 original size:21 final size:21
Alignment explanation
Indices: 20193129--20193200 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
20193119 AAATAGGCCA
*
20193129 GCCCATGTGGCTACCCCACAC
1 GCCCATGTGGCTAACCCACAC
* * * *
20193150 GCTCGTGTGGATATCCCACAC
1 GCCCATGTGGCTAACCCACAC
* * *
20193171 GCCCGTGTGGCTAACCCATAT
1 GCCCATGTGGCTAACCCACAC
20193192 GCCCATGTG
1 GCCCATGTG
20193201 CTCAGACCGT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.18, C:0.38, G:0.24, T:0.21
Consensus pattern (21 bp):
GCCCATGTGGCTAACCCACAC
Found at i:20197659 original size:23 final size:23
Alignment explanation
Indices: 20197633--20197676 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
20197623 TAAAAACCGA
20197633 AAATAAAC-TAAAATGAAAATAGG
1 AAATAAACATAAAA-GAAAATAGG
*
20197656 AAATAAACATACAAGAAAATA
1 AAATAAACATAAAAGAAAATA
20197677 AAATGTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.68, C:0.07, G:0.09, T:0.16
Consensus pattern (23 bp):
AAATAAACATAAAAGAAAATAGG
Found at i:20200196 original size:37 final size:37
Alignment explanation
Indices: 20200146--20200216 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
20200136 TTTAAATTAC
20200146 AAGTATATGGTTATTTGATATGTGAACGAAAATGATT
1 AAGTATATGGTTATTTGATATGTGAACGAAAATGATT
* *
20200183 AAGTATATGGTTATTTGATATGTGTATGAAAATG
1 AAGTATATGGTTATTTGATATGTGAACGAAAATG
20200217 TTCAAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.39
Consensus pattern (37 bp):
AAGTATATGGTTATTTGATATGTGAACGAAAATGATT
Found at i:20204340 original size:41 final size:41
Alignment explanation
Indices: 20204286--20204378 Score: 159
Period size: 41 Copynumber: 2.2 Consensus size: 41
20204276 TGGGATTAGG
20204286 ATTTTGAATTATTCAACTTGTTTTTGGACTTTGGATGAGGTTA
1 ATTTTG-A-TATTCAACTTGTTTTTGGACTTTGGATGAGGTTA
*
20204329 ATTTTGATATTCAACTTGTTTTTGGACTTTGGATGTGGTTA
1 ATTTTGATATTCAACTTGTTTTTGGACTTTGGATGAGGTTA
20204370 ATTTTGATA
1 ATTTTGATA
20204379 CTTGATATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 42 0.86
42 1 0.02
43 6 0.12
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51
Consensus pattern (41 bp):
ATTTTGATATTCAACTTGTTTTTGGACTTTGGATGAGGTTA
Found at i:20207103 original size:2 final size:2
Alignment explanation
Indices: 20207096--20207125 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20207086 TCAAAATTTG
20207096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20207126 TCAATTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20209352 original size:30 final size:30
Alignment explanation
Indices: 20209318--20209382 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
20209308 TGACAAACTT
* *
20209318 TTTTTTGTTCATATTATATTTGACTT-TAAA
1 TTTTTTATTCATATTATATCTGACTTCT-AA
*
20209348 TTTTTTATTCGTATTATATCTGACTTCTAA
1 TTTTTTATTCATATTATATCTGACTTCTAA
20209378 TTTTT
1 TTTTT
20209383 GTTTTTGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.09, G:0.06, T:0.62
Consensus pattern (30 bp):
TTTTTTATTCATATTATATCTGACTTCTAA
Found at i:20209540 original size:9 final size:9
Alignment explanation
Indices: 20209497--20209609 Score: 69
Period size: 9 Copynumber: 12.4 Consensus size: 9
20209487 TGTGTATTAC
20209497 TGTTATGTA
1 TGTTATGTA
20209506 TGTTA-GTA
1 TGTTATGTA
* *
20209514 TTATGTCTGCTA
1 -TGT-TATG-TA
*
20209526 TG-TATGTT
1 TGTTATGTA
20209534 TGTTATGTA
1 TGTTATGTA
20209543 TGTTATGAATA
1 TGTTATG--TA
*
20209554 TG-TATGCA
1 TGTTATGTA
20209562 TGTTATGTA
1 TGTTATGTA
20209571 TGTCTAT-TA
1 TGT-TATGTA
20209580 TGTCTAT-TA
1 TGT-TATGTA
20209589 TGTCTAT-TA
1 TGT-TATGTA
20209598 TG-TATGTA
1 TGTTATGTA
20209606 TGTT
1 TGTT
20209610 GTGAATATGT
Statistics
Matches: 85, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
7 3 0.04
8 13 0.15
9 53 0.62
10 8 0.09
11 6 0.07
12 2 0.02
ACGTcount: A:0.22, C:0.05, G:0.19, T:0.53
Consensus pattern (9 bp):
TGTTATGTA
Found at i:20209556 original size:37 final size:37
Alignment explanation
Indices: 20209497--20209582 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 37
20209487 TGTGTATTAC
* * *
20209497 TGTTATGTATGTTAGTATTATGTCTGCTATG-TATGTT
1 TGTTATGTATGTTAGTAATATGTATGC-ATGTTATGTA
20209534 TGTTATGTATGTTA-TGAATATGTATGCATGTTATGTA
1 TGTTATGTATGTTAGT-AATATGTATGCATGTTATGTA
20209571 TGTCTAT-TATGT
1 TGT-TATGTATGT
20209583 CTATTATGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
36 4 0.09
37 36 0.84
38 3 0.07
ACGTcount: A:0.22, C:0.05, G:0.21, T:0.52
Consensus pattern (37 bp):
TGTTATGTATGTTAGTAATATGTATGCATGTTATGTA
Found at i:20209604 original size:63 final size:62
Alignment explanation
Indices: 20209497--20209653 Score: 163
Period size: 63 Copynumber: 2.5 Consensus size: 62
20209487 TGTGTATTAC
* * *
20209497 TGTTATGTATGTTAGTATTATGTCTGCTATGTATGTTTGTTATGTATGTTATGAATATGTATGCA
1 TGTTATGTATG-T-CTATTATGTCT-ATATGTATATTTGTTATGTATGTTATGAATATGTATGCA
* * **
20209562 TGTTATGTATGTCTATTATGTCTATTATGTCTATTATG-TATGTATGTTGTGAATATGTATGTT
1 TGTTATGTATGTCTATTATGTCTA-TATGTATATT-TGTTATGTATGTTATGAATATGTATGCA
* * * *
20209625 TGTGATTTATGACTATTATGTATATATGT
1 TGTTATGTATGTCTATTATGTCTATATGT
20209654 TGTGAATATT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
62 5 0.06
63 60 0.76
64 3 0.04
65 11 0.14
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.52
Consensus pattern (62 bp):
TGTTATGTATGTCTATTATGTCTATATGTATATTTGTTATGTATGTTATGAATATGTATGCA
Found at i:20209620 original size:15 final size:16
Alignment explanation
Indices: 20209600--20209629 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20209590 GTCTATTATG
20209600 TATGTATG-TTGTGAA
1 TATGTATGTTTGTGAA
20209615 TATGTATGTTTGTGA
1 TATGTATGTTTGTGA
20209630 TTTATGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (16 bp):
TATGTATGTTTGTGAA
Found at i:20209734 original size:15 final size:16
Alignment explanation
Indices: 20209702--20209736 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
20209692 TTACTGTGAA
*
20209702 GTATATTATTGTTTAT
1 GTATACTATTGTTTAT
20209718 GTATACTATTG-TTAT
1 GTATACTATTGTTTAT
20209733 GTAT
1 GTAT
20209737 GTATGTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (16 bp):
GTATACTATTGTTTAT
Found at i:20209791 original size:69 final size:69
Alignment explanation
Indices: 20209714--20209898 Score: 282
Period size: 69 Copynumber: 2.7 Consensus size: 69
20209704 ATATTATTGT
* * * *
20209714 TTATGTATACTATTGTTATGTATGTATGTTATGTGGTATATTATTGTTTATTATTGTATATCATG
1 TTATGTATATTAATATTATGTATGTTTGTTATGTGGTATATTATTGTTTATTATTGTATATCATG
20209779 TATG
66 TATG
* * * * *
20209783 TTATGTATATTACTATTATGTATGTTTGTTATATGGAATATTACTGTTTATTATTGTATATTATG
1 TTATGTATATTAATATTATGTATGTTTGTTATGTGGTATATTATTGTTTATTATTGTATATCATG
20209848 TATG
66 TATG
20209852 TTATGTATATTAATATTATGTATGTTTGTTATGT-GTATATTATTGTT
1 TTATGTATATTAATATTATGTATGTTTGTTATGTGGTATATTATTGTT
20209899 ATTTATGTAT
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
68 11 0.11
69 93 0.89
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (69 bp):
TTATGTATATTAATATTATGTATGTTTGTTATGTGGTATATTATTGTTTATTATTGTATATCATG
TATG
Found at i:20209803 original size:24 final size:25
Alignment explanation
Indices: 20209771--20209908 Score: 111
Period size: 24 Copynumber: 5.8 Consensus size: 25
20209761 TTATTATTGT
*
20209771 ATATCATGTATGTTATGTATAT-TA
1 ATATTATGTATGTTATGTATATGTA
* *
20209795 CTATTATGTATGTT-TGTTATATGGA
1 ATATTATGTATGTTATG-TATATGTA
20209820 ATATTACTG--T-TTAT-TAT-TGT-
1 ATATTA-TGTATGTTATGTATATGTA
20209840 ATATTATGTATGTTATGTATAT-TA
1 ATATTATGTATGTTATGTATATGTA
*
20209864 ATATTATGTATGTT-TGT-TATGTGT
1 ATATTATGTATGTTATGTATATGT-A
20209888 ATATTATTGTTAT-TTATGTAT
1 ATATTA-TG-TATGTTATGTAT
20209909 GCTATGTTGA
Statistics
Matches: 92, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
19 2 0.02
20 6 0.07
21 3 0.03
22 10 0.11
23 12 0.13
24 40 0.43
25 10 0.11
26 8 0.09
27 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (25 bp):
ATATTATGTATGTTATGTATATGTA
Found at i:20209855 original size:9 final size:9
Alignment explanation
Indices: 20209702--20209908 Score: 77
Period size: 9 Copynumber: 23.4 Consensus size: 9
20209692 TTACTGTGAA
20209702 GTATATTAT
1 GTATATTAT
*
20209711 -TGT-TTAT
1 GTATATTAT
*
20209718 GTATACTATT
1 GTATATTA-T
20209728 GT-TATGTAT
1 GTATAT-TAT
*
20209737 GTATGTTATGT
1 GTATATTA--T
20209748 GGTATATTATT
1 -GTATATTA-T
*
20209759 GTTTATTATT
1 GTATATTA-T
*
20209769 GTATATCAT
1 GTATATTAT
*
20209778 GTATGTTAT
1 GTATATTAT
20209787 GTATATTA-
1 GTATATTAT
*
20209795 --CTATTAT
1 GTATATTAT
*
20209802 GTATGTT-T
1 GTATATTAT
20209810 GT-TA-TAT
1 GTATATTAT
*
20209817 GGAATATTACT
1 -GTATATTA-T
*
20209828 GTTTATTATT
1 GTATATTA-T
20209838 GTATATTAT
1 GTATATTAT
*
20209847 GTATGTTAT
1 GTATATTAT
20209856 GTATATTA-
1 GTATATTAT
20209864 --ATATTAT
1 GTATATTAT
*
20209871 GTATGTT-T
1 GTATATTAT
*
20209879 GT-TA-TGT
1 GTATATTAT
20209886 GTATATTATT
1 GTATATTA-T
20209896 GT-TATTTAT
1 GTATA-TTAT
20209905 GTAT
1 GTAT
20209909 GCTATGTTGA
Statistics
Matches: 146, Mismatches: 27, Indels: 49
0.66 0.12 0.22
Matches are distributed among these distances:
6 13 0.09
7 10 0.07
8 13 0.09
9 55 0.38
10 45 0.31
11 3 0.02
12 7 0.05
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (9 bp):
GTATATTAT
Found at i:20209951 original size:13 final size:13
Alignment explanation
Indices: 20209933--20209957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20209923 TATTTAAAAT
20209933 ATGTATGTATATC
1 ATGTATGTATATC
20209946 ATGTATGTATAT
1 ATGTATGTATAT
20209958 TATAGTTTAT
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:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (13 bp):
ATGTATGTATATC
Found at i:20212532 original size:20 final size:20
Alignment explanation
Indices: 20212506--20212553 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
20212496 GAGCTCAAAC
*
20212506 GAGCTGAATTAAGCTCATGT
1 GAGCTGAATTAAACTCATGT
*
20212526 GATCTGAATTAAACTCATGT
1 GAGCTGAATTAAACTCATGT
20212546 GAGCTGAA
1 GAGCTGAA
20212554 CCGAGCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (20 bp):
GAGCTGAATTAAACTCATGT
Found at i:20214358 original size:18 final size:18
Alignment explanation
Indices: 20214337--20214379 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
20214327 TTTTTACTCA
20214337 CTTTTTCAATTTCCTTTT
1 CTTTTTCAATTTCCTTTT
* *
20214355 CTTTTGCAATTTCTTTTT
1 CTTTTTCAATTTCCTTTT
20214373 CTTTTTC
1 CTTTTTC
20214380 TTTTTCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.67
Consensus pattern (18 bp):
CTTTTTCAATTTCCTTTT
Found at i:20214373 original size:6 final size:6
Alignment explanation
Indices: 20214364--20214406 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
20214354 TCTTTTGCAA
** *
20214364 TTTCTT TTTCTT TTTCTT TTTCTT TTTCAA TGTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
20214407 CATTTCTCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:20214385 original size:18 final size:18
Alignment explanation
Indices: 20214337--20214406 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 18
20214327 TTTTTACTCA
* *
20214337 CTTTTTCAATTTCCTTTT
1 CTTTTTCAATGTCTTTTT
* *
20214355 CTTTTGCAATTTCTTTTT
1 CTTTTTCAATGTCTTTTT
20214373 C--TTT---T-TCTTTTT
1 CTTTTTCAATGTCTTTTT
20214385 CTTTTTCAATGTCTTTTT
1 CTTTTTCAATGTCTTTTT
20214403 CTTT
1 CTTT
20214407 CATTTCTCCA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 8 0.19
13 1 0.02
14 3 0.07
16 2 0.05
17 1 0.02
18 28 0.65
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.70
Consensus pattern (18 bp):
CTTTTTCAATGTCTTTTT
Found at i:20214406 original size:30 final size:30
Alignment explanation
Indices: 20214283--20214403 Score: 118
Period size: 30 Copynumber: 3.9 Consensus size: 30
20214273 TTTCCCACTC
20214283 TTTCTTTTTCTTCTCTTTCAATTTCTTTTTCAA
1 TTTCTTTTTC-T-T-TTTCAATTTCTTTTTCAA
* * **
20214316 TCTCTTTTTCCTTTTT-ACTCACTTTTTCAA
1 TTTCTTTTT-CTTTTTCAATTTCTTTTTCAA
* * **
20214346 TTTCCTTTTCTTTTGCAATTTCTTTTTCTT
1 TTTCTTTTTCTTTTTCAATTTCTTTTTCAA
*
20214376 TTTCTTTTTCTTTTTCAATGTCTTTTTC
1 TTTCTTTTTCTTTTTCAATTTCTTTTTC
20214404 TTTCATTTCT
Statistics
Matches: 71, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
29 5 0.07
30 52 0.73
31 3 0.04
32 1 0.01
33 9 0.13
34 1 0.01
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.67
Consensus pattern (30 bp):
TTTCTTTTTCTTTTTCAATTTCTTTTTCAA
Found at i:20214743 original size:14 final size:15
Alignment explanation
Indices: 20214716--20214744 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20214706 TAAGAAACTC
20214716 TTTCATCTCTTCGTG
1 TTTCATCTCTTCGTG
20214731 TTTCATC-CTTCGTG
1 TTTCATCTCTTCGTG
20214745 GACGAGTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.07, C:0.28, G:0.14, T:0.52
Consensus pattern (15 bp):
TTTCATCTCTTCGTG
Found at i:20217199 original size:20 final size:20
Alignment explanation
Indices: 20217174--20217217 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
20217164 TCAAACGAGT
*
20217174 TGAATTAAGCTCATGTGAGC
1 TGAATTAAACTCATGTGAGC
20217194 TGAATTAAACTCATGTGAGC
1 TGAATTAAACTCATGTGAGC
20217214 TGAA
1 TGAA
20217218 CCGAGCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (20 bp):
TGAATTAAACTCATGTGAGC
Found at i:20218686 original size:40 final size:40
Alignment explanation
Indices: 20218642--20218719 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
20218632 CCTCTGTTTG
20218642 CACTTCGGTGCCTCTGATTGCACATTTGTGCCTTTTCCTA
1 CACTTCGGTGCCTCTGATTGCACATTTGTGCCTTTTCCTA
20218682 CACTTCGGTGCCTCTGATTGCACATTTGTGCCTTTTCC
1 CACTTCGGTGCCTCTGATTGCACATTTGTGCCTTTTCC
20218720 AACTTTGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.12, C:0.31, G:0.18, T:0.40
Consensus pattern (40 bp):
CACTTCGGTGCCTCTGATTGCACATTTGTGCCTTTTCCTA
Found at i:20218714 original size:20 final size:21
Alignment explanation
Indices: 20218617--20218707 Score: 77
Period size: 20 Copynumber: 4.5 Consensus size: 21
20218607 GCTTGTATGG
* *
20218617 GATTACAC-TTCGATGCCTCT
1 GATTGCACATTCGGTGCCTCT
*
20218637 GTTTGCAC-TTCGGTGCCTCT
1 GATTGCACATTCGGTGCCTCT
*
20218657 GATTGCACATT-TGTGCCT-T
1 GATTGCACATTCGGTGCCTCT
*
20218676 --TTCCTACACTTCGGTGCCTCT
1 GATTGC-ACA-TTCGGTGCCTCT
20218697 GATTGCACATT
1 GATTGCACATT
20218708 TGTGCCTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.05
18 3 0.05
19 3 0.05
20 36 0.64
21 5 0.09
22 3 0.05
23 3 0.05
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (21 bp):
GATTGCACATTCGGTGCCTCT
Found at i:20219150 original size:13 final size:13
Alignment explanation
Indices: 20219124--20219180 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
20219114 CTTATGAGTT
20219124 AAATGTGTAA-ATG
1 AAATG-GTAAGATG
20219137 AAATGGTAAGATG
1 AAATGGTAAGATG
** *
20219150 AAATATTTAGATG
1 AAATGGTAAGATG
* *
20219163 AAATGGTTATATG
1 AAATGGTAAGATG
20219176 AAATG
1 AAATG
20219181 CTTATATGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
12 4 0.11
13 33 0.89
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.32
Consensus pattern (13 bp):
AAATGGTAAGATG
Found at i:20221295 original size:29 final size:29
Alignment explanation
Indices: 20221258--20221326 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
20221248 TGAATCATTA
20221258 TGATGGTTGTATTTTGATGGACAATTTAT
1 TGATGGTTGTATTTTGATGGACAATTTAT
*
20221287 TGATAGTTGTATTTTGATGGACAATTTAT
1 TGATGGTTGTATTTTGATGGACAATTTAT
20221316 TGATGGTTGTA
1 TGATGGTTGTA
20221327 ATGGATGGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.48
Consensus pattern (29 bp):
TGATGGTTGTATTTTGATGGACAATTTAT
Found at i:20238272 original size:15 final size:16
Alignment explanation
Indices: 20238233--20238274 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
20238223 TAATAATAAC
20238233 ATATGAAATAT-AAAAA
1 ATATGAAA-ATGAAAAA
*
20238249 ATATTAAAATGAAAAA
1 ATATGAAAATGAAAAA
20238265 A-ATGAAAATG
1 ATATGAAAATG
20238275 TGAGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (16 bp):
ATATGAAAATGAAAAA
Found at i:20243383 original size:45 final size:45
Alignment explanation
Indices: 20243314--20243431 Score: 141
Period size: 45 Copynumber: 2.6 Consensus size: 45
20243304 TTGCTTGAAT
* *
20243314 GAAACGAATAAGATCATAGTTGAAAGACACTATAGCA-CTATACC-
1 GAAATGAATAAGACCATAGTTGAAAGACACTATAGCATC-ATACCG
* *
20243358 GAAATTGAATAAGACCATAGTTGAAAGAAACTATGGCATCATACCG
1 GAAA-TGAATAAGACCATAGTTGAAAGACACTATAGCATCATACCG
* * *
20243404 GAAATGAGTAAGACCATAGCTAAAAGAC
1 GAAATGAATAAGACCATAGTTGAAAGAC
20243432 GTTATGGCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
44 4 0.06
45 54 0.86
46 5 0.08
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (45 bp):
GAAATGAATAAGACCATAGTTGAAAGACACTATAGCATCATACCG
Found at i:20244809 original size:42 final size:42
Alignment explanation
Indices: 20244747--20244836 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
20244737 ATGGCCTGGC
* * *
20244747 ACACGGTCTGCGACACGGCCGTGTGTATC-AAGTTAGAGAGTT
1 ACACGGCCTACGACACGGCCGTGTG-ATCTAAGTCAGAGAGTT
* *
20244789 ACACGGCCTACGACATGGCCGTGTGATCTAAGTCAGTGAGTT
1 ACACGGCCTACGACACGGCCGTGTGATCTAAGTCAGAGAGTT
20244831 ACACGG
1 ACACGG
20244837 TTTAAGACAC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 3 0.07
42 39 0.93
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.22
Consensus pattern (42 bp):
ACACGGCCTACGACACGGCCGTGTGATCTAAGTCAGAGAGTT
Found at i:20250437 original size:10 final size:11
Alignment explanation
Indices: 20250424--20250471 Score: 64
Period size: 10 Copynumber: 4.5 Consensus size: 11
20250414 ATAAAAATAA
20250424 ATAAAATAC-T
1 ATAAAATACAT
*
20250434 ATAAAATACTT
1 ATAAAATACAT
20250445 ATAAAATACAT
1 ATAAAATACAT
*
20250456 ATAAAA-AGAT
1 ATAAAATACAT
20250466 ATAAAA
1 ATAAAA
20250472 GTATTTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (11 bp):
ATAAAATACAT
Found at i:20250449 original size:11 final size:10
Alignment explanation
Indices: 20250424--20250461 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
20250414 ATAAAAATAA
20250424 ATAAAATACT
1 ATAAAATACT
20250434 ATAAAATACTT
1 ATAAAATAC-T
20250445 ATAAAATACAT
1 ATAAAATAC-T
20250456 ATAAAA
1 ATAAAA
20250462 AGATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAAAATACT
Found at i:20250468 original size:21 final size:20
Alignment explanation
Indices: 20250414--20250471 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
20250404 TTAGTTTTCA
* *
20250414 ATAAAAATAAATAAAATACT
1 ATAAAAACATATAAAATACT
*
20250434 ATAAAATACTTATAAAATACAT
1 ATAAAA-ACATATAAAATAC-T
*
20250456 ATAAAAAGATATAAAA
1 ATAAAAACATATAAAA
20250472 GTATTTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 6 0.19
21 18 0.58
22 7 0.23
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (20 bp):
ATAAAAACATATAAAATACT
Found at i:20255807 original size:3 final size:3
Alignment explanation
Indices: 20255799--20255937 Score: 120
Period size: 3 Copynumber: 44.7 Consensus size: 3
20255789 TGTCGTTGTT
* *
20255799 TTC TTC TTC TTA TTC -TC TTTC TTC TTC TTC TTT TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC
* ** * * * *
20255844 -CC CCC AATTT TTT TATC ATTC TTT TTT TTCC TTC TTTC TTC TTC TTC
1 TTC TTC --TTC TTC T-TC -TTC TTC TTC TT-C TTC -TTC TTC TTC TTC
20255891 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
20255938 TTTCGTCATC
Statistics
Matches: 116, Mismatches: 11, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.03
3 102 0.88
4 10 0.09
5 1 0.01
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:20259721 original size:20 final size:20
Alignment explanation
Indices: 20259685--20259723 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20259675 TGGTAACGAA
*
20259685 TTTCTTGATGTTGCTTGATG
1 TTTCTTGATGCTGCTTGATG
20259705 TTTCTTGATAGCT-CTTGAT
1 TTTCTTGAT-GCTGCTTGAT
20259724 CTCTTGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.54
Consensus pattern (20 bp):
TTTCTTGATGCTGCTTGATG
Found at i:20263550 original size:44 final size:44
Alignment explanation
Indices: 20263460--20263550 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
20263450 TGTCTAGACA
* * *
20263460 GTGTAACTCTCTGACTTGGGTCACACGGGTGTATGTCAGGCCGT
1 GTGTAACTCTCTGACTTGGGTCACACGGGTGTATGACAGACAGT
*
20263504 GTGTAACTCTCTGACTTGGGTCACAC-GGTCGTGTGACAGACAGT
1 GTGTAACTCTCTGACTTGGGTCACACGGGT-GTATGACAGACAGT
20263548 GTG
1 GTG
20263551 AGGCACTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 3 0.07
44 39 0.93
ACGTcount: A:0.18, C:0.22, G:0.32, T:0.29
Consensus pattern (44 bp):
GTGTAACTCTCTGACTTGGGTCACACGGGTGTATGACAGACAGT
Found at i:20264166 original size:22 final size:22
Alignment explanation
Indices: 20264138--20264196 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
20264128 GGGGTAAGAA
**
20264138 TCTGCATCTGTATCTGATTTGT
1 TCTGCATCTGTATCTGACATGT
* *
20264160 TCTGCATTTGTATATGACATGT
1 TCTGCATCTGTATCTGACATGT
* *
20264182 TCTACAACTGTATCT
1 TCTGCATCTGTATCT
20264197 AATATCTTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (22 bp):
TCTGCATCTGTATCTGACATGT
Found at i:20275268 original size:21 final size:21
Alignment explanation
Indices: 20275244--20275295 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
20275234 GCGGTGGCGG
*
20275244 TGAGATTAGTTACTGTAGCGA
1 TGAGATTAGATACTGTAGCGA
* *
20275265 TGAGATTGGATACTGTAGCGG
1 TGAGATTAGATACTGTAGCGA
20275286 TGAGATTAGA
1 TGAGATTAGA
20275296 AACAATGGTG
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:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (21 bp):
TGAGATTAGATACTGTAGCGA
Found at i:20276572 original size:21 final size:21
Alignment explanation
Indices: 20276546--20276601 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
20276536 AACAGCGGTG
*
20276546 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
20276567 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
20276588 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
20276602 AACAGCGGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:20276610 original size:18 final size:19
Alignment explanation
Indices: 20276546--20276611 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
20276536 AACAGCGGTG
**
20276546 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGAAAC--TA
*
20276567 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGAAAC--TA
20276588 GCGGTGAGATTAGAAAC-A
1 GCGGTGAGATTAGAAACTA
20276606 GCGGTG
1 GCGGTG
20276612 GAGTGTGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 7 0.16
21 36 0.84
ACGTcount: A:0.27, C:0.11, G:0.36, T:0.26
Consensus pattern (19 bp):
GCGGTGAGATTAGAAACTA
Done.