Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 90 of 198
Found at i:28967974 original size:25 final size:25
Alignment explanation
Indices: 28967946--28968078 Score: 176
Period size: 25 Copynumber: 5.2 Consensus size: 25
28967936 CAAAAACAAA
28967946 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
28967971 AACTTACATAACCTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
*
28967996 AACTTACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAT
* * * *
28968021 AACTTACATAAGTTTCATAATCCAC
1 AACTTACATAACTTACATAATACAT
*
28968046 AACTTACACAACTTACATAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
28968073 AACTTA
1 AACTTA
28968079 TTCCTAAATC
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
25 84 0.90
27 9 0.10
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:28972736 original size:17 final size:17
Alignment explanation
Indices: 28972714--28972747 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28972704 TTTTGGCATT
28972714 CGAAGAAAGGCGAGGTA
1 CGAAGAAAGGCGAGGTA
28972731 CGAAGAAAGGCGAGGTA
1 CGAAGAAAGGCGAGGTA
28972748 TGACGTACTT
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:0.41, C:0.12, G:0.41, T:0.06
Consensus pattern (17 bp):
CGAAGAAAGGCGAGGTA
Found at i:28974119 original size:22 final size:22
Alignment explanation
Indices: 28974088--28974131 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28974078 TAGTGGCGTT
* *
28974088 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAGACCTA
28974110 AAAAAACGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAGACCTA
28974132 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAGACCTA
Found at i:28974230 original size:30 final size:31
Alignment explanation
Indices: 28974163--28974245 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
28974153 TTATAATCTA
*
28974163 ATATTATAGTAATAGTTATATATGTATTAAT
1 ATATTTTAGTAATAGTTATATATGTATTAAT
28974194 AT-TTTTAGTAATAGTTATATAT-TA-TAAT
1 ATATTTTAGTAATAGTTATATATGTATTAAT
* *
28974222 ATTATTTTATGTATTAGTAATATA
1 A-TATTTTA-GTAATAGTTATATA
28974246 CTAGCTTAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.11
29 3 0.07
30 24 0.52
31 14 0.30
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (31 bp):
ATATTTTAGTAATAGTTATATATGTATTAAT
Found at i:28978516 original size:24 final size:25
Alignment explanation
Indices: 28978424--28978516 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
28978414 TAGGGTTACC
* * *
28978424 TATTCTAGCTCTTATGAGCTTACTGA
1 TATTC-AGCTCGTATGAGCTTACCGT
* * *
28978450 TACTCATCTCGTATGAGATTACCGT
1 TATTCAGCTCGTATGAGCTTACCGT
* *
28978475 TATTCAGCTCGGAGGAGCTTACCGT
1 TATTCAGCTCGTATGAGCTTACCGT
28978500 T-TATCA-CTCGTATGAGC
1 TAT-TCAGCTCGTATGAGC
28978517 ATACATGTAC
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
24 10 0.19
25 39 0.74
26 4 0.08
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (25 bp):
TATTCAGCTCGTATGAGCTTACCGT
Found at i:28979187 original size:22 final size:23
Alignment explanation
Indices: 28979162--28979207 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
28979152 TGGTGTATGG
28979162 TGGCCATGTGAATTTT-TTTTTT
1 TGGCCATGTGAATTTTGTTTTTT
28979184 TGGCCATGTGAATTTTGTTTTTT
1 TGGCCATGTGAATTTTGTTTTTT
28979207 T
1 T
28979208 TTTGTGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.13, C:0.09, G:0.20, T:0.59
Consensus pattern (23 bp):
TGGCCATGTGAATTTTGTTTTTT
Found at i:28992887 original size:29 final size:29
Alignment explanation
Indices: 28992853--28992908 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
28992843 CGCATTGAAA
* *
28992853 ATTTTCAAGGTACAAGTATCACATTGGGC
1 ATTTTCAAAGTACAAGTACCACATTGGGC
* *
28992882 ATTTTCAAATTATAAGTACCACATTGG
1 ATTTTCAAAGTACAAGTACCACATTGG
28992909 AAATATTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (29 bp):
ATTTTCAAAGTACAAGTACCACATTGGGC
Found at i:28994109 original size:3 final size:3
Alignment explanation
Indices: 28994101--28994158 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
28994091 ATAAGAAGCA
* * *
28994101 AAG AAG AAG AAG AAA AAT AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
28994149 AAG AAG AAG A
1 AAG AAG AAG A
28994159 GAAATATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:28994124 original size:15 final size:15
Alignment explanation
Indices: 28994100--28994158 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
28994090 CATAAGAAGC
28994100 AAAGAAGAAGAAGAA
1 AAAGAAGAAGAAGAA
*
28994115 AAATAAGAAGAAGAA
1 AAAGAAGAAGAAGAA
*
28994130 GAAGAAGAAGAAGAA
1 AAAGAAGAAGAAGAA
28994145 AAAGAAGAAGAAGA
1 AAAGAAGAAGAAGA
28994159 GAAATATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
AAAGAAGAAGAAGAA
Found at i:28994269 original size:40 final size:42
Alignment explanation
Indices: 28994209--28994301 Score: 100
Period size: 42 Copynumber: 2.3 Consensus size: 42
28994199 TATGATTCGC
*
28994209 ATGTTAAGCATGCTCACTGTACT-AAT-TAAATCCGATTCAA
1 ATGTTAAGCATACTCACTGTACTGAATATAAATCCGATTCAA
** * * * **
28994249 ATGTTAAGCATACTGGCTGTATTGATTATAAATCTGATTCGC
1 ATGTTAAGCATACTCACTGTACTGAATATAAATCCGATTCAA
28994291 ATGTTAAGCAT
1 ATGTTAAGCAT
28994302 GCCCACTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 19 0.44
41 2 0.05
42 22 0.51
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (42 bp):
ATGTTAAGCATACTCACTGTACTGAATATAAATCCGATTCAA
Found at i:28994295 original size:42 final size:40
Alignment explanation
Indices: 28994201--28994301 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
28994191 AATTGATATA
*
28994201 TGATTCGCATGTTAAGCATGCTCACTGTACTAATTAAATC
1 TGATTCGCATGTTAAGCATACTCACTGTACTAATTAAATC
* ** ** * *
28994241 CGATTCAAATGTTAAGCATACTGGCTGTATTGATTATAAATC
1 TGATTCGCATGTTAAGCATACTCACTGTACT-AAT-TAAATC
28994283 TGATTCGCATGTTAAGCAT
1 TGATTCGCATGTTAAGCAT
28994302 GCCCACTAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 24 0.50
41 2 0.04
42 22 0.46
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (40 bp):
TGATTCGCATGTTAAGCATACTCACTGTACTAATTAAATC
Found at i:29000565 original size:23 final size:25
Alignment explanation
Indices: 29000551--29000603 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
29000541 AAGTTCAAGC
29000551 GAGCC-ATATCAGGAAGCTCACAAA
1 GAGCCTATATCAGGAAGCTCACAAA
*
29000575 GAGCCTATATCAGGACGCTCACAAA
1 GAGCCTATATCAGGAAGCTCACAAA
29000600 GAGC
1 GAGC
29000604 TGCATTTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.38, C:0.26, G:0.23, T:0.13
Consensus pattern (25 bp):
GAGCCTATATCAGGAAGCTCACAAA
Found at i:29004055 original size:35 final size:34
Alignment explanation
Indices: 29004009--29004074 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
29003999 ACTGGCATGC
*
29004009 TAGAGCAACACTGTGATGACAATCTATCGACTTTA
1 TAGAGCAACACTGCGATGACAAT-TATCGACTTTA
* *
29004044 TAGAGCGACACTGCGATGGCAATTATCGACT
1 TAGAGCAACACTGCGATGACAATTATCGACT
29004075 GGCTTGCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 8 0.29
35 20 0.71
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (34 bp):
TAGAGCAACACTGCGATGACAATTATCGACTTTA
Found at i:29004223 original size:22 final size:22
Alignment explanation
Indices: 29004198--29004245 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
29004188 TTCAAGGTGA
* *
29004198 CCTCGGAAGAGGTTTATTGATT
1 CCTCGAAAGAGGTTTATTAATT
*
29004220 CCTCGAAATAGGTTTATTAATT
1 CCTCGAAAGAGGTTTATTAATT
29004242 CCTC
1 CCTC
29004246 AGAATCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (22 bp):
CCTCGAAAGAGGTTTATTAATT
Found at i:29006492 original size:25 final size:25
Alignment explanation
Indices: 29006458--29006507 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
29006448 CAGAGCATCC
29006458 GAGGCATCTTGAGGATCCAATCAAT
1 GAGGCATCTTGAGGATCCAATCAAT
29006483 GAGGCATCTTGAGGATCCAATCAAT
1 GAGGCATCTTGAGGATCCAATCAAT
29006508 CTTTTATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (25 bp):
GAGGCATCTTGAGGATCCAATCAAT
Found at i:29013112 original size:3 final size:3
Alignment explanation
Indices: 29013106--29013165 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
29013096 TTTGAAGAGA
29013106 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29013154 ATT ATT ATT ATT
1 ATT ATT ATT ATT
29013166 GCCCATAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29013543 original size:31 final size:31
Alignment explanation
Indices: 29013508--29013571 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
29013498 ATTAGTTTTA
* * *
29013508 AAATTATTTGAAAGTTTTCATTTAAGTTATT
1 AAATTATTCGAAAGTTTTCACTTAAATTATT
*
29013539 AAATTATTCGAAAGTTTTTACTTAAATTATT
1 AAATTATTCGAAAGTTTTCACTTAAATTATT
29013570 AA
1 AA
29013572 GTTGTGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (31 bp):
AAATTATTCGAAAGTTTTCACTTAAATTATT
Found at i:29021366 original size:16 final size:16
Alignment explanation
Indices: 29021345--29021393 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 16
29021335 ATATCTAATC
29021345 ATATAATAAATTATTA
1 ATATAATAAATTATTA
29021361 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
29021374 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
29021391 ATA
1 ATA
29021394 ATTCATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
13 11 0.44
16 10 0.40
17 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:29029994 original size:95 final size:95
Alignment explanation
Indices: 29029891--29030160 Score: 283
Period size: 95 Copynumber: 2.8 Consensus size: 95
29029881 GCTTGTCAAT
* * * * ** * *
29029891 TAAATTAATTATAAATTTTTCAAAATTGGATT-AGTTTTCATG-TTTATTGTTTTTTAAGAAAAA
1 TAAATTAATTATAAATTTTTAAAAATTAGATTAAGGTTT-A-GAGTTAAGGGTTTTAAAGAAAAA
* *
29029954 ATCAATTAAATTAGGGTTTAGGGTTACTTGAG
64 ATCAAGTAAATTAGGGTTCAGGGTTACTTGAG
* * ** *
29029986 TAATTTAATTAAAAAAATTTAAAAATTAGATTAAGGTTTAGAGTTAAGGGTTTTAAAGGAAAAAT
1 TAAATTAATTATAAATTTTTAAAAATTAGATTAAGGTTTAGAGTTAAGGGTTTTAAAGAAAAAAT
29030051 CAAGTAAATTAGGGTTCAGGGTTACTTGAG
66 CAAGTAAATTAGGGTTCAGGGTTACTTGAG
* * * * * *
29030081 TAAATTAATTATAATTTTTTAAAAAATTAGTTTAGGGTTTAGTGTTTAGGGTTTTTAAGTAAAAA
1 TAAATTAATTATAAATTTTT-AAAAATTAGATTAAGGTTTAGAGTTAAGGGTTTTAAAG-AAAAA
* *
29030146 CTCAAATAAATTAGG
64 ATCAAGTAAATTAGG
29030161 CTTTGGCGTT
Statistics
Matches: 143, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
94 1 0.01
95 87 0.61
96 38 0.27
97 17 0.12
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (95 bp):
TAAATTAATTATAAATTTTTAAAAATTAGATTAAGGTTTAGAGTTAAGGGTTTTAAAGAAAAAAT
CAAGTAAATTAGGGTTCAGGGTTACTTGAG
Found at i:29030436 original size:126 final size:126
Alignment explanation
Indices: 29030204--29030631 Score: 669
Period size: 126 Copynumber: 3.4 Consensus size: 126
29030194 TTGTTAATTT
* *** *
29030204 AAAGAACCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAGAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAACCCCTGAAAAAATAATTTCGAGTAGAC
* *
29030269 GTTTCTGAGCAAACAGTGTTAAAAATGCTTTAAG-AATGATGCTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAA-GATGCTTTGTCAGCAGAAGTACTG
* * * * * *
29030330 AAAAAAGCTCCCACGTGGATGTGCTTTTACTACTGTAACCCTTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAACCCCTGAAAAAATAATTTCGAGTAGAC
* * *
29030395 GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAATCAGGATGCTTTGTCAGTAGAAGTACTG
66 GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTACTG
* *
29030456 AAAGAAGCTCCCACGTGGACACGCTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAACCCCTGAAAAAATAATTTCGAGTAGAC
*
29030521 GTTTCTGAGCAAACAATGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTACTG
29030582 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAACCCCTGAAAAAA
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAACCCCTGAAAAAA
29030632 GCTCCCACGT
Statistics
Matches: 271, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
126 270 1.00
127 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.25
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAACCCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTACTG
Found at i:29030634 original size:44 final size:44
Alignment explanation
Indices: 29030579--29030662 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
29030569 AGCAGAAGTA
* *
29030579 CTGAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAACCC
1 CTGAAAAAAGCTCCCACGTGGACGCACTTTTGCTACAGTAACCC
*
29030623 CTGAAAAAAGCTCCCACGTGGATGCACTTTTGCTACAGTA
1 CTGAAAAAAGCTCCCACGTGGACGCACTTTTGCTACAGTA
29030663 GCGCATGGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (44 bp):
CTGAAAAAAGCTCCCACGTGGACGCACTTTTGCTACAGTAACCC
Found at i:29031205 original size:7 final size:7
Alignment explanation
Indices: 29031193--29031217 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29031183 TATTAGTTAT
29031193 ATACATA
1 ATACATA
29031200 ATACATA
1 ATACATA
29031207 ATACATA
1 ATACATA
29031214 ATAC
1 ATAC
29031218 TAAATACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:29032223 original size:18 final size:18
Alignment explanation
Indices: 29032162--29032225 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
29032152 ATAAAAAATA
29032162 AAAAATT-AATAATTATTT
1 AAAAATTAAATAA-TATTT
* *
29032180 -AAAATTACATAA-A-TA
1 AAAAATTAAATAATATTT
29032195 AAAAATCTTAAATAATATTT
1 AAAAA--TTAAATAATATTT
29032215 AAAAATTAAAT
1 AAAAATTAAAT
29032226 TTAACACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 6 0.17
18 17 0.47
19 1 0.03
20 6 0.17
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAATTAAATAATATTT
Found at i:29032427 original size:21 final size:22
Alignment explanation
Indices: 29032395--29032439 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
29032385 TCTTTTAAAT
29032395 AGGAATTTGAGAGGAATTTGAG
1 AGGAATTTGAGAGGAATTTGAG
29032417 AGGAA-TTGAGAGGAATTTGAG
1 AGGAATTTGAGAGGAATTTGAG
29032438 AG
1 AG
29032440 AATATTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (22 bp):
AGGAATTTGAGAGGAATTTGAG
Found at i:29032442 original size:10 final size:11
Alignment explanation
Indices: 29032395--29032439 Score: 83
Period size: 11 Copynumber: 4.2 Consensus size: 11
29032385 TCTTTTAAAT
29032395 AGGAATTTGAG
1 AGGAATTTGAG
29032406 AGGAATTTGAG
1 AGGAATTTGAG
29032417 AGGAA-TTGAG
1 AGGAATTTGAG
29032427 AGGAATTTGAG
1 AGGAATTTGAG
29032438 AG
1 AG
29032440 AATATTAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.30
11 23 0.70
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (11 bp):
AGGAATTTGAG
Found at i:29032452 original size:12 final size:12
Alignment explanation
Indices: 29032435--29032462 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29032425 AGAGGAATTT
29032435 GAGAGAATATTA
1 GAGAGAATATTA
29032447 GAGAGAATATTA
1 GAGAGAATATTA
29032459 GAGA
1 GAGA
29032463 AAGGATTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (12 bp):
GAGAGAATATTA
Found at i:29034698 original size:26 final size:27
Alignment explanation
Indices: 29034667--29034731 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
29034657 AAAAAAAATC
* *
29034667 AGCATTAACTATAGGCAAGT-AAATAT
1 AGCATTAACTATACGAAAGTAAAATAT
* * *
29034693 GGCATTAACTATTCGAAATTAAAATAT
1 AGCATTAACTATACGAAAGTAAAATAT
29034720 AGCATTAACTAT
1 AGCATTAACTAT
29034732 TTCTGTTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 15 0.47
27 17 0.53
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (27 bp):
AGCATTAACTATACGAAAGTAAAATAT
Found at i:29034851 original size:2 final size:2
Alignment explanation
Indices: 29034844--29034868 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29034834 CATAAGAATT
29034844 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
29034869 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29035862 original size:10 final size:11
Alignment explanation
Indices: 29035827--29035868 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
29035817 ATCTATAATG
29035827 TTTTTAATATT
1 TTTTTAATATT
**
29035838 ATTTTTAAT-GC
1 -TTTTTAATATT
29035849 TTTTTAATATT
1 TTTTTAATATT
29035860 TTTTTAATA
1 TTTTTAATA
29035869 AAAAAAGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 9 0.36
12 8 0.32
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (11 bp):
TTTTTAATATT
Found at i:29035863 original size:21 final size:21
Alignment explanation
Indices: 29035808--29035867 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
29035798 TTTAAATGAC
* *
29035808 TTTTAA-ATTATCTATAATGT
1 TTTTAATATTATTTTTAATGT
29035828 TTTTAATATTATTTTTAATGCT
1 TTTTAATATTATTTTTAATG-T
29035850 TTTTAATATT-TTTTTAAT
1 TTTTAATATTATTTTTAAT
29035868 AAAAAAAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 6 0.17
21 19 0.53
22 11 0.31
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (21 bp):
TTTTAATATTATTTTTAATGT
Found at i:29041813 original size:67 final size:66
Alignment explanation
Indices: 29041723--29041920 Score: 174
Period size: 67 Copynumber: 3.0 Consensus size: 66
29041713 TTTTTAATAG
* * * *
29041723 ATTTAATATTAAATTAAAATTAATACTTATCTTAATAGTATTTATTAATTTAATATTAAAGTGAT
1 ATTTAATATCAAATTTAATTTAATATTTATCTTAATAGTATTTATTAATTTAATATTAAAGTGAT
29041788 T
66 T
* * * ** *
29041789 ATCTTAATGTCAAATTTAATTTAATGTTTATCTT-GTAGATAAATATT-CTATTAAT-TT-AA-T
1 AT-TTAATATCAAATTTAATTTAATATTTATCTTAATAG-TATTTATTAAT-TTAATATTAAAGT
**
29041849 -AAG
63 GATT
***
29041852 ATTTAATATTTTATTTAATTTAATATTTATCTTAATAAGTATTATATTAATTTAATATTAAAGTG
1 ATTTAATATCAAATTTAATTTAATATTTATCTTAAT-AGTATT-TATTAATTTAATATTAAAGTG
29041917 ATT
64 ATT
29041920 A
1 A
29041921 AGATTAATCA
Statistics
Matches: 98, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
62 26 0.27
63 6 0.06
64 12 0.12
65 5 0.05
66 10 0.10
67 37 0.38
68 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (66 bp):
ATTTAATATCAAATTTAATTTAATATTTATCTTAATAGTATTTATTAATTTAATATTAAAGTGAT
T
Found at i:29041872 original size:17 final size:17
Alignment explanation
Indices: 29041852--29041910 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
29041842 ATTTAATAAG
29041852 ATTTAATATTTTATTTA
1 ATTTAATATTTTATTTA
29041869 ATTTAATA-TTTATCTTA
1 ATTTAATATTTTAT-TTA
*
29041886 A--TAAGTATTATA-TTA
1 ATTTAA-TATTTTATTTA
29041901 ATTTAATATT
1 ATTTAATATT
29041911 AAAGTGATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
15 7 0.19
16 11 0.31
17 18 0.50
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTTAATATTTTATTTA
Found at i:29044441 original size:18 final size:17
Alignment explanation
Indices: 29044415--29044739 Score: 184
Period size: 18 Copynumber: 18.5 Consensus size: 17
29044405 TAAAATACAA
29044415 GAAATTTTTTAAAACAC
1 GAAATTTTTTAAAACAC
* *
29044432 GAAGA-TTTTTGAAACAA
1 GAA-ATTTTTTAAAACAC
** *
29044449 TTATTTTTTTGAAAACAC
1 GAAATTTTTT-AAAACAC
*
29044467 GAAAAATTTTTAAAACAC
1 G-AAATTTTTTAAAACAC
*
29044485 GAGAA--TTTTAGAGACAC
1 GA-AATTTTTTA-AAACAC
* *
29044502 GAAAATTCTTAAAAACAC
1 G-AAATTTTTTAAAACAC
*
29044520 GAAAATTTTTGAAAACAC
1 G-AAATTTTTTAAAACAC
29044538 GGAAA-TTTTTAAAACAC
1 -GAAATTTTTTAAAACAC
*
29044555 GGGAATTTTTTGAAAACAC
1 -GAAATTTTTT-AAAACAC
*
29044574 GAAAATTTTTAAAACACC
1 GAAATTTTTTAAAACA-C
*
29044592 GAAATTTTTGAAAACAC
1 GAAATTTTTTAAAACAC
* *
29044609 GAGGA--TTTTGAAACAC
1 GA-AATTTTTTAAAACAC
29044625 GAAATTTTCTTTGAAAACAC
1 GAAA-TTT-TTT-AAAACAC
** *
29044645 G-AATTTTTTTTATCACC
1 GAAATTTTTTAAAACA-C
*
29044662 AGAAA-TTTTGAAAACAC
1 -GAAATTTTTTAAAACAC
*
29044679 GAAAATTTTTGAAATAC-C
1 G-AAATTTTTTAAA-ACAC
* *
29044697 AAAATTTTTAAAAACAC
1 GAAATTTTTTAAAACAC
*
29044714 GGAAA-TTTATAAAACAC
1 -GAAATTTTTTAAAACAC
29044731 GGAAATTTT
1 -GAAATTTT
29044740 ATTTTCTGAA
Statistics
Matches: 240, Mismatches: 40, Indels: 55
0.72 0.12 0.16
Matches are distributed among these distances:
15 1 0.00
16 22 0.09
17 87 0.36
18 97 0.40
19 26 0.11
20 7 0.03
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (17 bp):
GAAATTTTTTAAAACAC
Found at i:29044607 original size:35 final size:35
Alignment explanation
Indices: 29044415--29044840 Score: 281
Period size: 36 Copynumber: 11.7 Consensus size: 35
29044405 TAAAATACAA
* * * **
29044415 GAAATTTTTTAAAACACGAAGATTTTTGAAACAAT
1 GAAATTTTTGAAAACACGAAAATTTTTAAAACACC
* **
29044450 TATTTTTTTGAAAACACGAAAAATTTTTAAAACA-C
1 GAAATTTTTGAAAACACG-AAAATTTTTAAAACACC
* * *
29044485 GAGAATTTTAG-AGACACGAAAATTCTTAAAA-ACAC
1 GA-AATTTTTGAAAACACGAAAATTTTTAAAACAC-C
* *
29044520 GAAAATTTTTGAAAACACGGAAATTTTTAAAACACGG
1 G-AAATTTTTGAAAACACGAAAATTTTTAAAACAC-C
*
29044557 GAATTTTTTGAAAACACGAAAATTTTTAAAACACC
1 GAAATTTTTGAAAACACGAAAATTTTTAAAACACC
** *
29044592 GAAATTTTTGAAAACACGAGGA-TTTTGAAACA-C
1 GAAATTTTTGAAAACACGAAAATTTTTAAAACACC
* ** *
29044625 GAAATTTTCTTTGAAAACACG-AATTTTTTTTATCACC
1 GAAA--TT-TTTGAAAACACGAAAATTTTTAAAACACC
* *
29044662 AGAAA-TTTTGAAAACACGAAAATTTTTGAAATACC
1 -GAAATTTTTGAAAACACGAAAATTTTTAAAACACC
* * * * *
29044697 AAAATTTTTAAAAACACGGAAATTTATAAAACACG
1 GAAATTTTTGAAAACACGAAAATTTTTAAAACACC
* * *
29044732 GAAATTTTATTTTCTGAAAATAAGAAAATTTTTGAAAACACAG
1 G-AA----ATTTT-TGAAAACACGAAAATTTTT-AAAACAC-C
* *
29044775 GAAAATTTTTTTGAAAACACGAAAATTTTTAAAATACA
1 G-AAA--TTTTTGAAAACACGAAAATTTTTAAAACACC
* *
29044813 AAAATTTATTTTGAAAACACAAAAATTT
1 GAAA--T-TTTTGAAAACACGAAAATTT
29044841 CGATAAATTA
Statistics
Matches: 309, Mismatches: 56, Indels: 49
0.75 0.14 0.12
Matches are distributed among these distances:
33 6 0.02
34 36 0.12
35 87 0.28
36 88 0.28
37 10 0.03
38 23 0.07
39 7 0.02
40 22 0.07
41 18 0.06
42 7 0.02
43 5 0.02
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (35 bp):
GAAATTTTTGAAAACACGAAAATTTTTAAAACACC
Found at i:29044652 original size:20 final size:19
Alignment explanation
Indices: 29044615--29044651 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
29044605 ACACGAGGAT
29044615 TTTGAAACACGAAATTTTC
1 TTTGAAACACGAAATTTTC
29044634 TTTGAAAACACG-AATTTT
1 TTTG-AAACACGAAATTTT
29044652 TTTTATCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (19 bp):
TTTGAAACACGAAATTTTC
Found at i:29044684 original size:17 final size:17
Alignment explanation
Indices: 29044455--29044819 Score: 202
Period size: 17 Copynumber: 20.2 Consensus size: 17
29044445 ACAATTATTT
29044455 TTTTGAAAACACGAAAAA
1 TTTTGAAAACACG-AAAA
* *
29044473 TTTTTAAAACACGAGAA
1 TTTTGAAAACACGAAAA
*
29044490 TTTT-AGAGACACGAAAA
1 TTTTGA-AAACACGAAAA
*
29044507 TTCTTAAAAACACGAAAA
1 TT-TTGAAAACACGAAAA
*
29044525 TTTTTGAAAACACGGAAA
1 -TTTTGAAAACACGAAAA
* **
29044543 TTTTTAAAACACGGGAATT
1 TTTTGAAAACAC--GAAAA
29044562 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
* *
29044579 TTTTTAAAACACCGAAAT
1 TTTTGAAAACA-CGAAAA
**
29044597 TTTTGAAAACACGAGGA
1 TTTTGAAAACACGAAAA
*
29044614 TTTTG-AAACACGAAATTT
1 TTTTGAAAACACGAAA--A
*
29044632 TCTTTGAAAACACG-AAT
1 T-TTTGAAAACACGAAAA
*** * *
29044649 TTTTTTTATCACCAGAAA
1 TTTTGAAAACACGA-AAA
29044667 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
29044684 TTTTTGAAATAC-C-AAAA
1 -TTTTGAAA-ACACGAAAA
* *
29044701 TTTTTAAAAACACGGAAA
1 -TTTTGAAAACACGAAAA
29044719 TTTAT-AAAACACGGAAATTTTA
1 TTT-TGAAAACAC-GAAA----A
* *
29044741 TTTTCTGAAAATAAGAAAA
1 -TTT-TGAAAACACGAAAA
29044760 TTTTTGAAAACACAGGAAAA
1 -TTTTGAAAACAC--GAAAA
29044780 TTTTTTTGAAAACACGAAAA
1 ---TTTTGAAAACACGAAAA
* * *
29044800 TTTTTAAAATACAAAAA
1 TTTTGAAAACACGAAAA
29044817 TTT
1 TTT
29044820 ATTTTGAAAA
Statistics
Matches: 273, Mismatches: 45, Indels: 59
0.72 0.12 0.16
Matches are distributed among these distances:
16 18 0.07
17 95 0.35
18 87 0.32
19 29 0.11
20 17 0.06
22 14 0.05
23 8 0.03
24 5 0.02
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.31
Consensus pattern (17 bp):
TTTTGAAAACACGAAAA
Found at i:29044741 original size:18 final size:17
Alignment explanation
Indices: 29044454--29044739 Score: 188
Period size: 18 Copynumber: 16.2 Consensus size: 17
29044444 AACAATTATT
*
29044454 TTTTTGAAAACACGAAAAA
1 TTTTT-AAAACACG-GAAA
29044473 TTTTTAAAACAC-GAGAA
1 TTTTTAAAACACGGA-AA
* *
29044490 -TTTTAGAGACACGAAAA
1 TTTTTA-AAACACGGAAA
* *
29044507 TTCTTAAAAACACGAAAA
1 TT-TTTAAAACACGGAAA
29044525 TTTTTGAAAACACGGAAA
1 TTTTT-AAAACACGGAAA
*
29044543 TTTTTAAAACACGGGAAT
1 TTTTTAAAACAC-GGAAA
*
29044561 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGGAAA
*
29044579 TTTTTAAAACACCGAAA
1 TTTTTAAAACACGGAAA
*
29044596 TTTTTGAAAACAC-GAGGA
1 TTTTT-AAAACACGGA-AA
*
29044614 -TTTTGAAACAC-GAAA
1 TTTTTAAAACACGGAAA
*
29044629 TTTTCTTTGAAAACAC-GAAT
1 --TT-TTT-AAAACACGGAAA
** * *
29044649 TTTTTTTATCACCAGAAA
1 TTTTTAAAACA-CGGAAA
* *
29044667 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGGAAA
* * **
29044684 TTTTTGAAATACCAAAA
1 TTTTTAAAACACGGAAA
29044701 TTTTTAAAAACACGGAAA
1 TTTTT-AAAACACGGAAA
*
29044719 TTTATAAAACACGGAAA
1 TTTTTAAAACACGGAAA
29044736 TTTT
1 TTTT
29044740 ATTTTCTGAA
Statistics
Matches: 212, Mismatches: 37, Indels: 38
0.74 0.13 0.13
Matches are distributed among these distances:
15 1 0.00
16 17 0.08
17 80 0.38
18 87 0.41
19 18 0.08
20 9 0.04
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGGAAA
Found at i:29044804 original size:21 final size:20
Alignment explanation
Indices: 29044760--29044840 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 20
29044750 AATAAGAAAA
29044760 TTTTTGAAAACACAGGAAAATT
1 TTTTTGAAAACACA--AAAATT
*
29044782 TTTTTGAAAACACGAAAA--
1 TTTTTGAAAACACAAAAATT
*
29044800 TTTTT-AAAATACAAAAATT
1 TTTTTGAAAACACAAAAATT
29044819 TATTTTGAAAACACAAAAATT
1 T-TTTTGAAAACACAAAAATT
29044840 T
1 T
29044841 CGATAAATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
17 10 0.20
18 5 0.10
19 1 0.02
20 8 0.16
21 14 0.27
22 13 0.25
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (20 bp):
TTTTTGAAAACACAAAAATT
Found at i:29044836 original size:20 final size:20
Alignment explanation
Indices: 29044451--29044840 Score: 159
Period size: 18 Copynumber: 21.2 Consensus size: 20
29044441 TGAAACAATT
29044451 ATTTTTTTGAAAACACGAAA
1 ATTTTTTTGAAAACACGAAA
* *
29044471 A-ATTTTT-AAAACACGAGA
1 ATTTTTTTGAAAACACGAAA
* *
29044489 A--TTTTAG-AGACACGAAA
1 ATTTTTTTGAAAACACGAAA
* *
29044506 A--TTCTTAAAAACACGAAA
1 ATTTTTTTGAAAACACGAAA
*
29044524 A--TTTTTGAAAACACGGAA
1 ATTTTTTTGAAAACACGAAA
**
29044542 A--TTTTT-AAAACACGGGA
1 ATTTTTTTGAAAACACGAAA
29044559 A-TTTTTTGAAAACACGAAA
1 ATTTTTTTGAAAACACGAAA
29044578 A--TTTTT-AAAACACCG-AA
1 ATTTTTTTGAAAACA-CGAAA
**
29044595 A--TTTTTGAAAACACGAGG
1 ATTTTTTTGAAAACACGAAA
29044613 A---TTTTG-AAACACG-AA
1 ATTTTTTTGAAAACACGAAA
29044628 ATTTTCTTTGAAAACACG--A
1 ATTTT-TTTGAAAACACGAAA
* * *
29044647 ATTTTTTT--TATCACCAGAA
1 ATTTTTTTGAAAACACGA-AA
29044666 A---TTTTGAAAACACGAAA
1 ATTTTTTTGAAAACACGAAA
29044683 A--TTTTTGAAATAC-C-AAA
1 ATTTTTTTGAAA-ACACGAAA
* *
29044700 A--TTTTTAAAAACACGGAA
1 ATTTTTTTGAAAACACGAAA
*
29044718 A--TTTAT-AAAACACGGAAA
1 ATTTTTTTGAAAACAC-GAAA
* * *
29044736 TTTTATTTTCTGAAAATAAGAAA
1 -ATT-TTTT-TGAAAACACGAAA
29044759 A--TTTTTGAAAACACAGGAAA
1 ATTTTTTTGAAAACAC--GAAA
29044779 ATTTTTTTGAAAACACGAAA
1 ATTTTTTTGAAAACACGAAA
* *
29044799 A--TTTTT-AAAATACAAAA
1 ATTTTTTTGAAAACACGAAA
*
29044816 ATTTATTTTGAAAACACAAAA
1 ATTT-TTTTGAAAACACGAAA
29044837 ATTT
1 ATTT
29044841 CGATAAATTA
Statistics
Matches: 295, Mismatches: 39, Indels: 71
0.73 0.10 0.18
Matches are distributed among these distances:
15 1 0.00
16 17 0.06
17 81 0.27
18 100 0.34
19 34 0.12
20 22 0.07
21 14 0.05
22 16 0.05
23 5 0.02
24 5 0.02
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (20 bp):
ATTTTTTTGAAAACACGAAA
Found at i:29044914 original size:17 final size:19
Alignment explanation
Indices: 29044882--29044925 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
29044872 AAACGAATAT
29044882 AAAACACGAGAAA-TTTTG
1 AAAACACGAGAAATTTTTG
*
29044900 AAAACAGGA-AAATTTTTG
1 AAAACACGAGAAATTTTTG
29044918 -AAACACGA
1 AAAACACGA
29044926 TTAGTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.52, C:0.11, G:0.16, T:0.20
Consensus pattern (19 bp):
AAAACACGAGAAATTTTTG
Found at i:29045293 original size:18 final size:20
Alignment explanation
Indices: 29045257--29045295 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
29045247 ATAAAATTTA
29045257 AAAAAACATAAATACAAAAT
1 AAAAAACATAAATACAAAAT
*
29045277 AAAAAA-ATAATTA-AAAAT
1 AAAAAACATAAATACAAAAT
29045295 A
1 A
29045296 TGCAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAAACATAAATACAAAAT
Found at i:29045826 original size:4 final size:4
Alignment explanation
Indices: 29045817--29045852 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
29045807 ATTTTTTCCC
29045817 TTCT TTCT TTCT TTC- TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
29045853 CCCCGTTCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTCT
Found at i:29045834 original size:15 final size:15
Alignment explanation
Indices: 29045816--29045848 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
29045806 TATTTTTTCC
29045816 CTTCTTTCTTTCTTT
1 CTTCTTTCTTTCTTT
29045831 CTTCTTTCTTTCTTT
1 CTTCTTTCTTTCTTT
29045846 CTT
1 CTT
29045849 TCTTCCCCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTCTTTCTTTCTTT
Found at i:29045841 original size:19 final size:19
Alignment explanation
Indices: 29045787--29045853 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
29045777 TTTAATTTTT
*
29045787 TTTCTTT-TTCTTTCCTT-
1 TTTCTTTCTTCTTTCTTTC
* * *
29045804 TTTATTTTTTCCCTTCTTTC
1 TTTCTTTCTT-CTTTCTTTC
29045824 TTTCTTTCTTCTTTCTTTC
1 TTTCTTTCTTCTTTCTTTC
29045843 TTTCTTTCTTC
1 TTTCTTTCTTC
29045854 CCCGTTCAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.15
18 2 0.05
19 25 0.61
20 8 0.20
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTCTTTCTTCTTTCTTTC
Found at i:29046033 original size:21 final size:20
Alignment explanation
Indices: 29045985--29046034 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
29045975 TGCTCTTTCC
29045985 TTTTTTTTCTCTTTTGCTTG
1 TTTTTTTTCTCTTTTGCTTG
* **
29046005 TTGCTTTTTCTCTTTGTTTTTG
1 TT-TTTTTTCTCTTT-TGCTTG
29046027 TTTTTTTT
1 TTTTTTTT
29046035 TTTTTGCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.67
22 6 0.25
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (20 bp):
TTTTTTTTCTCTTTTGCTTG
Found at i:29046377 original size:29 final size:30
Alignment explanation
Indices: 29046322--29046392 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
29046312 ATTCGGGGTA
29046322 AAAATGTAATTTTAAAAAAATATGA-GGCC
1 AAAATGTAATTTTAAAAAAATATGAGGGCC
* **
29046351 AAAATGTAATTTCT-AGAAAAT-TCGAGGGTT
1 AAAATGTAATTT-TAAAAAAATAT-GAGGGCC
29046381 AAAATGTAATTT
1 AAAATGTAATTT
29046393 ATTTTTTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.03
29 20 0.56
30 15 0.42
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.32
Consensus pattern (30 bp):
AAAATGTAATTTTAAAAAAATATGAGGGCC
Found at i:29046940 original size:76 final size:75
Alignment explanation
Indices: 29046716--29047839 Score: 1185
Period size: 76 Copynumber: 14.7 Consensus size: 75
29046706 GATCCGAAGT
* ** * *
29046716 TCAACTCACTTCTCAG-ATTATGAGTTGA--CCTTTGAAAAATAGATATTGAAAATACCTCAGCG
1 TCAACTCACCTCTC-GCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCG
* *
29046778 TGACTCGAGGC
65 TAACCCGAGGC
* *
29046789 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTGAAAATACCTTAGCGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
*
29046854 AACTCGAGGC
66 AACCCGAGGC
* *
29046864 TCAACCCACCTCTCGCATTATAAGTTGATTTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCG
1 TCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCG
*
29046929 TGACCCGAGGC
65 TAACCCGAGGC
* * *
29046940 TCAACTCACCTCTCGCATTATGAGTTTATTTTTTTTTTAAAAACAGAAATTGAAAACACCTCAGC
1 TCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTTGAAAAACAGAAATTGAAAATACCTCAGC
*
29047005 GTGACCCGAGGC
64 GTAACCCGAGGC
****** ***** **
29047017 TCAAC-CTACCTCTCGCATTATGAGTTGATTTCTTTTTTTCTTTCTTTTTTTTTGAAAA-ACAAA
1 TCAACTC-ACCTCTCGCATTATGAGTTGA-TT-TTTTTGAAAAAC--AGAAATTGAAAATAC-CT
* *** *
29047080 AATTGAAAATACCTCAGCGTGAC
60 CA--GCGTA-ACC-C-GAG-G-C
* * *** * * *
29047103 CCGAGGCTCAACCCACCTCTCGCATTATGAGTTGA-TTTTAAAAAAAATAGAAATTAAAAACACC
1 TC-A-ACT-----CACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACC
* *
29047167 ACAGGGTAACCCGAGGC
59 TCAGCGTAACCCGAGGC
* * *
29047184 TCAACTCACTTCTCGTATTATGAGTTGATTTTTTTGAAAAA-ACGAAAATTAAAAATACCTCAGC
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACA-G-AAATTGAAAATACCTCAGC
29047248 GTAACCCGAGGC
64 GTAACCCGAGGC
* * * *
29047260 TCAACTCACCTTTCGCATTATGAGTTGA-TTTTTTAAAAAATAGAAATTAAAAATACCTCAGCGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
29047324 AACCCGAGGC
66 AACCCGAGGC
* * *
29047334 TCAACTCACTTCTCGTATTATGAGTTGATTTTTTTGAAAAAACAGAAATTAAAAATACCTCAGCG
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG-AAAAACAGAAATTGAAAATACCTCAGCG
* *
29047399 TAACTCGTGGC
65 TAACCCGAGGC
* ** *
29047410 TCAACTCACCTCTCGCATTATGAGTTGA-TTGTTTGAAAAATGGAAATTAAAAATACCTCAGCGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
29047474 AACCCGAGGC
66 AACCCGAGGC
* * * *
29047484 TCAACTCACTTCTCGTATTATGAGTTGA-TTTTTTGAAAAACAGAAATTAAAAATACCTCAGTGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
29047548 AACCCGAGGC
66 AACCCGAGGC
* * *
29047558 TCAACTCACTTCTCGTATTATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATACCTCAGCGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
29047623 AACCCGAGGC
66 AACCCGAGGC
* * *
29047633 TCAACTCACCTCTCACAATATGAGTTAATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG-
1 TCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTTGAAAAACAGAAATTG-AAAATACCTCAGC
* *
29047697 GATGACCCGAGCC
64 G-TAACCCGAGGC
* *
29047710 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAATATCTCAG-GA
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCG-
*
29047774 TGACCCGAGGC
65 TAACCCGAGGC
*
29047785 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTT-AAAAACAAAAATTGAAAATA
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATA
29047840 TAATTCTTGA
Statistics
Matches: 901, Mismatches: 114, Indels: 71
0.83 0.10 0.07
Matches are distributed among these distances:
72 1 0.00
73 25 0.03
74 226 0.25
75 222 0.25
76 231 0.26
77 124 0.14
78 2 0.00
79 10 0.01
80 1 0.00
81 3 0.00
82 4 0.00
83 3 0.00
84 3 0.00
85 4 0.00
86 4 0.00
87 1 0.00
88 9 0.01
89 2 0.00
90 3 0.00
91 1 0.00
93 21 0.02
94 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (75 bp):
TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
AACCCGAGGC
Found at i:29047076 original size:93 final size:93
Alignment explanation
Indices: 29046968--29047140 Score: 310
Period size: 93 Copynumber: 1.9 Consensus size: 93
29046958 TATGAGTTTA
* * *
29046968 TTTTTTTTTTAAAAACAGAAATTGAAAACACCTCAGCGTGACCCGAGGCTCAACCTACCTCTCGC
1 TTTTTTTTTGAAAAACAAAAATTGAAAACACCTCAGCGTGACCCGAGGCTCAACCCACCTCTCGC
29047033 ATTATGAGTTGATTTCTTTTTTTCTTTC
66 ATTATGAGTTGATTTCTTTTTTTCTTTC
*
29047061 TTTTTTTTTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACCCACCTCTCGC
1 TTTTTTTTTGAAAAACAAAAATTGAAAACACCTCAGCGTGACCCGAGGCTCAACCCACCTCTCGC
29047126 ATTATGAGTTGATTT
66 ATTATGAGTTGATTT
29047141 TAAAAAAAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (93 bp):
TTTTTTTTTGAAAAACAAAAATTGAAAACACCTCAGCGTGACCCGAGGCTCAACCCACCTCTCGC
ATTATGAGTTGATTTCTTTTTTTCTTTC
Found at i:29047198 original size:74 final size:75
Alignment explanation
Indices: 29047063--29047839 Score: 1084
Period size: 74 Copynumber: 10.4 Consensus size: 75
29047053 TTTCTTTCTT
* * * *
29047063 TTTTTTTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACCCACCTCTCGCAT
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCAT
29047128 TATGAGTTGA
66 TATGAGTTGA
*** * * * * * *
29047138 -TTTTAAAAAAAATAGAAATTAAAAACACCACAGGGTAACCCGAGGCTCAACTCACTTCTCGTAT
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCAT
29047202 TATGAGTTGA
66 TATGAGTTGA
*
29047212 TTTTTTTGAAAAA-ACGAAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTTTCGC
1 TTTTTTTGAAAAACA-G-AAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGC
29047276 ATTATGAGTTGA
64 ATTATGAGTTGA
* * * *
29047288 -TTTTTTAAAAAATAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACTTCTCGTAT
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCAT
29047352 TATGAGTTGA
66 TATGAGTTGA
* *
29047362 TTTTTTTGAAAAAACAGAAATTAAAAATACCTCAGCGTAACTCGTGGCTCAACTCACCTCTCGCA
1 TTTTTTTG-AAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCA
29047427 TTATGAGTTGA
65 TTATGAGTTGA
* ** * *
29047438 -TTGTTTGAAAAATGGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACTTCTCGTAT
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCAT
29047502 TATGAGTTGA
66 TATGAGTTGA
* * *
29047512 -TTTTTTGAAAAACAGAAATTAAAAATACCTCAGTGTAACCCGAGGCTCAACTCACTTCTCGTAT
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCAT
29047576 TATGAGTTGA
66 TATGAGTTGA
* * * *
29047586 TTTTTTTGAAAAGCAGAAATTGAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCACAA
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCAT
*
29047651 TATGAGTTAA
66 TATGAGTTGA
* *
29047661 TTTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG-GATGACCCGAGCCTCAACTCACCTCTCG
1 -TTTTTTTGAAAAACAGAAATT-AAAAATACCTCAGCG-TAACCCGAGGCTCAACTCACCTCTCG
29047725 CATTATGAGTTGA
63 CATTATGAGTTGA
* *
29047738 TTTTTTTGAAAAACAGAAATTAAAAATATCTCAG-GATGACCCGAGGCTCAACTCACCTCTCGCA
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCG-TAACCCGAGGCTCAACTCACCTCTCGCA
29047802 TTATGAGTTGA
65 TTATGAGTTGA
* *
29047813 TTTTTTT-AAAAACAAAAATTGAAAATA
1 TTTTTTTGAAAAACAGAAATTAAAAATA
29047840 TAATTCTTGA
Statistics
Matches: 630, Mismatches: 62, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
74 267 0.42
75 159 0.25
76 158 0.25
77 46 0.07
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (75 bp):
TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCAT
TATGAGTTGA
Found at i:29047233 original size:150 final size:149
Alignment explanation
Indices: 29047063--29047839 Score: 1114
Period size: 150 Copynumber: 5.2 Consensus size: 149
29047053 TTTCTTTCTT
* * * *
29047063 TTTTTTTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACCCACCTCTCGCAT
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCAT
*** * * *
29047128 TATGAGTTGATTTTAAAAAAAATAGAAATTAAAAACACCACAGGGTAACCCGAGGCTCAACTCAC
66 TATGAGTTGATTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCAC
29047193 TTCTCGTATTATGAGTTGA
131 TTCTCGTATTATGAGTTGA
*
29047212 TTTTTTTGAAAAA-ACGAAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTTTCGC
1 TTTTTTTGAAAAACA-G-AAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGC
*
29047276 ATTATGAGTTGATTTTTTAAAAAATAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTC
64 ATTATGAGTTGATTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTC
29047341 ACTTCTCGTATTATGAGTTGA
129 ACTTCTCGTATTATGAGTTGA
* *
29047362 TTTTTTTGAAAAAACAGAAATTAAAAATACCTCAGCGTAACTCGTGGCTCAACTCACCTCTCGCA
1 TTTTTTTG-AAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCA
* *
29047427 TTATGAGTTGATTGTTTGAAAAATGGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCA
65 TTATGAGTTGATTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCA
29047492 CTTCTCGTATTATGAGTTGA
130 CTTCTCGTATTATGAGTTGA
* * *
29047512 -TTTTTTGAAAAACAGAAATTAAAAATACCTCAGTGTAACCCGAGGCTCAACTCACTTCTCGTAT
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCAT
** *
29047576 TATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATACCTCAGCGTAACCCGAGGCTCAACTCA
66 TATGAGTTGA-TTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCA
* ** * *
29047641 CCTCTCACAATATGAGTTAA
130 CTTCTCGTATTATGAGTTGA
* *
29047661 TTTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG-GATGACCCGAGCCTCAACTCACCTCTCG
1 -TTTTTTTGAAAAACAGAAATT-AAAAATACCTCAGCG-TAACCCGAGGCTCAACTCACCTCTCG
* * *
29047725 CATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAATATCTCAG-GATGACCCGAGGCTCAA
63 CATTATGAGTTGA-TTTTTTGAAAAATAGAAATTAAAAATACCTCAGCG-TAACCCGAGGCTCAA
* *
29047789 CTCACCTCTCGCATTATGAGTTGA
126 CTCACTTCTCGTATTATGAGTTGA
* *
29047813 TTTTTTT-AAAAACAAAAATTGAAAATA
1 TTTTTTTGAAAAACAGAAATTAAAAATA
29047840 TAATTCTTGA
Statistics
Matches: 574, Mismatches: 44, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
148 63 0.11
149 90 0.16
150 271 0.47
151 35 0.06
152 115 0.20
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (149 bp):
TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCAT
TATGAGTTGATTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCAC
TTCTCGTATTATGAGTTGA
Found at i:29047475 original size:224 final size:224
Alignment explanation
Indices: 29047064--29047839 Score: 1087
Period size: 224 Copynumber: 3.5 Consensus size: 224
29047054 TTCTTTCTTT
* * * *
29047064 TTTTTTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACCCACCTCTCGCATT
1 TTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCATT
*** * * * *
29047129 ATGAGTTGA-TTTTAAAAAAAATAGAAATTAAAAACACCACAGGGTAACCCGAGGCTCAACTCAC
66 ATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCAC
* * *
29047193 TTCTCGTATTATGAGTTGATTTTTTTGAAAAAACGAAAATTAAAAATACCTCAGCGTAACCCGAG
131 CTCTCGCATTATGAGTTGATTTTTTTG-AAAAACGGAAATTAAAAATACCTCAGCGTAACCCGAG
29047258 GCTCAACTCACCTTTCGCATTATGAGTTGA
195 GCTCAACTCACCTTTCGCATTATGAGTTGA
* * * *
29047288 TTTTTTAAAAAATAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACTTCTCGTATT
1 TTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCATT
* *
29047353 ATGAGTTGATTTTTTTGAAAAAACAGAAATTAAAAATACCTCAGCGTAACTCGTGGCTCAACTCA
66 ATGAGTTGATTTTTTTG-AAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCA
* *
29047418 CCTCTCGCATTATGAGTTGA-TTGTTTGAAAAATGGAAATTAAAAATACCTCAGCGTAACCCGAG
130 CCTCTCGCATTATGAGTTGATTTTTTTGAAAAACGGAAATTAAAAATACCTCAGCGTAACCCGAG
*
29047482 GCTCAACTCA-CTTCTCGTATTATGAGTTGA
195 GCTCAACTCACCTT-TCGCATTATGAGTTGA
* * *
29047512 TTTTTTGAAAAACAGAAATTAAAAATACCTCAGTGTAACCCGAGGCTCAACTCACTTCTCGTATT
1 TTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCATT
* *
29047577 ATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATACCTCAGCGTAACCCGAGGCTCAACTCAC
66 ATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCAC
* * * * *
29047642 CTCTCACAATATGAGTTAATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG-GATGACCCG
131 CTCTCGCATTATGAGTTGA-TTTTTTTGAAAAACGGAAATT-AAAAATACCTCAGCG-TAACCCG
* *
29047706 AGCCTCAACTCACCTCTCGCATTATGAGTTGA
193 AGGCTCAACTCACCTTTCGCATTATGAGTTGA
* *
29047738 TTTTTTTGAAAAACAGAAATTAAAAATATCTCAG-GATGACCCGAGGCTCAACTCACCTCTCGCA
1 -TTTTTTGAAAAACAGAAATTAAAAATACCTCAGCG-TAACCCGAGGCTCAACTCACCTCTCGCA
* *
29047802 TTATGAGTTGATTTTTTT-AAAAACAAAAATTGAAAATA
64 TTATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAATA
29047840 TAATTCTTGA
Statistics
Matches: 496, Mismatches: 46, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
223 63 0.13
224 205 0.41
225 28 0.06
226 123 0.25
227 77 0.16
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (224 bp):
TTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTCGCATT
ATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAACCCGAGGCTCAACTCAC
CTCTCGCATTATGAGTTGATTTTTTTGAAAAACGGAAATTAAAAATACCTCAGCGTAACCCGAGG
CTCAACTCACCTTTCGCATTATGAGTTGA
Found at i:29055871 original size:9 final size:9
Alignment explanation
Indices: 29055859--29055883 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29055849 TTTCTTTGGG
29055859 TCCTTTCCA
1 TCCTTTCCA
29055868 TCCTTTCCA
1 TCCTTTCCA
29055877 TCCTTTC
1 TCCTTTC
29055884 ATTGAGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (9 bp):
TCCTTTCCA
Found at i:29059618 original size:18 final size:17
Alignment explanation
Indices: 29059596--29059917 Score: 235
Period size: 18 Copynumber: 18.3 Consensus size: 17
29059586 ATAATTATTT
29059596 TTTTTCAAAACACGAAAAA
1 TTTTT-AAAACACG-AAAA
*
29059615 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAAAA
*
29059632 -TTTTAGAGACACGAAAA
1 TTTTTA-AAACACGAAAA
*
29059649 TTCTTAAAAACACGAAAA
1 TT-TTTAAAACACGAAAA
*
29059667 TTTTTGAAAACACGGAAA
1 TTTTT-AAAACACGAAAA
* *
29059685 TTTTTAAAACACGGGAAT
1 TTTTTAAAACAC-GAAAA
*
29059703 TTTTTGAAAACATGAAAA
1 TTTTT-AAAACACGAAAA
* *
29059721 TTTTTGAAACAC-AAAT
1 TTTTTAAAACACGAAAA
29059737 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
*
29059755 TTTTTAAAACACCG-GAA
1 TTTTTAAAACA-CGAAAA
**
29059772 TTTTTGAAAACACGAGGA
1 TTTTT-AAAACACGAAAA
*
29059790 TTTTTGAAACAC-AAAA
1 TTTTTAAAACACGAAAA
29059806 TTTTCTTTGAAAACACG-AAA
1 --TT-TTT-AAAACACGAAAA
** * *
29059826 TTTTTTTACCACCAGAAA
1 TTTTTAAAACACGA-AAA
*
29059844 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGAAAA
29059861 TTTTTGAAATAC-CG-AAA
1 TTTTT-AAA-ACACGAAAA
* *
29059878 TTTTTGAAAACGCGGAAA
1 TTTTT-AAAACACGAAAA
* *
29059896 TTTATAAAACACGGAAA
1 TTTTTAAAACACGAAAA
29059913 TTTTT
1 TTTTT
29059918 TTTTCTGAAA
Statistics
Matches: 246, Mismatches: 35, Indels: 46
0.75 0.11 0.14
Matches are distributed among these distances:
16 21 0.09
17 92 0.37
18 105 0.43
19 19 0.08
20 9 0.04
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.31
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:29059679 original size:53 final size:54
Alignment explanation
Indices: 29059602--29059914 Score: 230
Period size: 53 Copynumber: 5.9 Consensus size: 54
29059592 ATTTTTTTTC
* *
29059602 AAAACACGAAAAATTTTT-AAAACACGAGAA-TTTTAGAGACACGAAAATTCTTA
1 AAAACACG-AAAATTTTTGAAAACACGAGAATTTTTAGAAACACGAAAATTCTTG
* * *
29059655 AAAACACGAAAATTTTTGAAAACACG-GAAATTTTTA-AAACACGGGAATTTTTTG
1 AAAACACGAAAATTTTTGAAAACACGAG-AATTTTTAGAAACAC-GAAAATTCTTG
* * *
29059709 AAAACATGAAAATTTTTG-AAACAC-A-AATTTTTTGAAAACACGAAAATT-TTT
1 AAAACACGAAAATTTTTGAAAACACGAGAATTTTTAG-AAACACGAAAATTCTTG
* *
29059760 AAAACACCG-GAATTTTTGAAAACACGAGGATTTTT-GAAACAC-AAAATTTTCTTTG
1 AAAACA-CGAAAATTTTTGAAAACACGAGAATTTTTAGAAACACGAAAA--TTC-TTG
** * * * *
29059815 AAAACACG-AAATTTTT-TTACCACCAGAAATTTT-GAAAACACGAAAATTTTTG
1 AAAACACGAAAATTTTTGAAAACACGAGAATTTTTAG-AAACACGAAAATTCTTG
* * *
29059867 AAATAC-CG-AAATTTTTGAAAACGCG-GAAATTTATA-AAACACGGAAATT
1 AAA-ACACGAAAATTTTTGAAAACACGAG-AATTTTTAGAAACACGAAAATT
29059915 TTTTTTTCTG
Statistics
Matches: 209, Mismatches: 30, Indels: 43
0.74 0.11 0.15
Matches are distributed among these distances:
51 27 0.13
52 57 0.27
53 63 0.30
54 50 0.24
55 12 0.06
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (54 bp):
AAAACACGAAAATTTTTGAAAACACGAGAATTTTTAGAAACACGAAAATTCTTG
Found at i:29059821 original size:20 final size:19
Alignment explanation
Indices: 29059792--29059829 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
29059782 CACGAGGATT
29059792 TTTGAAACACAAAATTTTC
1 TTTGAAACACAAAATTTTC
*
29059811 TTTGAAAACACGAAATTTT
1 TTTG-AAACACAAAATTTT
29059830 TTTACCACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (19 bp):
TTTGAAACACAAAATTTTC
Found at i:29059964 original size:59 final size:58
Alignment explanation
Indices: 29059875--29060005 Score: 135
Period size: 57 Copynumber: 2.3 Consensus size: 58
29059865 TGAAATACCG
* *
29059875 AAATTTTTGAAA-ACGCGGAAATTTATAAAACAC-GGAAATTTTTTTTTCTGAAAACAAGA
1 AAATTTTTGAAATACGCGGAAATTTATAAAACACAAGAAA--TTCTTTT-TGAAAACAAGA
* * *
29059934 AAATTTTTGAAATATG-GG-AATTTTTGAAAACACAAGAAATTCTTTTTGAAAACACGA
1 AAATTTTTGAAATACGCGGAAATTTAT-AAAACACAAGAAATTCTTTTTGAAAACAAGA
* *
29059991 ACATTTTTAAAATAC
1 AAATTTTTGAAATAC
29060006 AAAAATTTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
57 22 0.36
58 12 0.20
59 21 0.34
60 6 0.10
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (58 bp):
AAATTTTTGAAATACGCGGAAATTTATAAAACACAAGAAATTCTTTTTGAAAACAAGA
Found at i:29059965 original size:35 final size:35
Alignment explanation
Indices: 29059596--29059917 Score: 273
Period size: 35 Copynumber: 9.1 Consensus size: 35
29059586 ATAATTATTT
* *
29059596 TTTTTCAAAACACGAAAAATTTTTAAAACA-CGAGAA
1 TTTTTGAAAACACG-AAAATTTTTGAAACACCGA-AA
* * * *
29059632 TTTTAG-AGACACGAAAATTCTT-AAAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACAC-CG-AAA
* * * *
29059667 TTTTTGAAAACACGGAAATTTTTAAAACACGGGAAT
1 TTTTTGAAAACACGAAAATTTTTGAAACAC-CGAAA
*
29059703 TTTTTGAAAACATGAAAATTTTTGAAACA-C-AAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* *
29059736 TTTTTTGAAAACACGAAAATTTTTAAAACACCGGAA
1 -TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
** *
29059772 TTTTTGAAAACACGAGGATTTTTGAAACA-CAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
** *
29059806 TTTTCTTTGAAAACACG-AAATTTTTTTACCACCAGAAA
1 --TT-TTTGAAAACACGAAAATTTTTGAAACACC-GAAA
*
29059844 -TTTTGAAAACACGAAAATTTTTGAAATACCGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* * * * *
29059878 TTTTTGAAAACGCGGAAATTTATAAAACACGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
29059913 TTTTT
1 TTTTT
29059918 TTTTCTGAAA
Statistics
Matches: 229, Mismatches: 42, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
33 6 0.03
34 54 0.24
35 88 0.38
36 59 0.26
37 19 0.08
38 3 0.01
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.31
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
Found at i:29059979 original size:21 final size:19
Alignment explanation
Indices: 29059954--29060035 Score: 78
Period size: 22 Copynumber: 4.2 Consensus size: 19
29059944 AATATGGGAA
29059954 TTTTTGAAAACACAAGAAATT
1 TTTTTGAAAACACAA-AAA-T
* *
29059975 CTTTTTGAAAACACGAACA-
1 -TTTTTGAAAACACAAAAAT
*
29059994 TTTTT-AAAATACAAAAATT
1 TTTTTGAAAACACAAAAA-T
29060013 TATTTTGAAAACACAAAAAT
1 T-TTTTGAAAACACAAAAAT
29060033 TTT
1 TTT
29060036 GATAAATTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
17 9 0.18
18 5 0.10
19 3 0.06
20 6 0.12
21 13 0.26
22 14 0.28
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (19 bp):
TTTTTGAAAACACAAAAAT
Found at i:29060019 original size:38 final size:40
Alignment explanation
Indices: 29059952--29060035 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 40
29059942 GAAATATGGG
*
29059952 AATTTTTGAAAACACAAGAAATTCTTTTTGAAAACACGAA
1 AATTTTTGAAAACACAAGAAATTCTTTTTGAAAACACAAA
* *
29059992 CATTTTT-AAAATACAA-AAATT-TATTTTGAAAACACAAA
1 AATTTTTGAAAACACAAGAAATTCT-TTTTGAAAACACAAA
29060030 AATTTT
1 AATTTT
29060036 GATAAATTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 1 0.03
38 24 0.62
39 8 0.21
40 6 0.15
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.35
Consensus pattern (40 bp):
AATTTTTGAAAACACAAGAAATTCTTTTTGAAAACACAAA
Found at i:29060036 original size:17 final size:17
Alignment explanation
Indices: 29059977--29060037 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
29059967 AAGAAATTCT
* *
29059977 TTTTGAAAACACGAACA
1 TTTTGAAAACACAAAAA
* *
29059994 TTTTTAAAATACAAAAATTTA
1 TTTTGAAAACAC-AAAA---A
29060015 TTTTGAAAACACAAAAA
1 TTTTGAAAACACAAAAA
29060032 TTTTGA
1 TTTTGA
29060038 TAAATTACGA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 17 0.50
18 2 0.06
20 4 0.12
21 11 0.32
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (17 bp):
TTTTGAAAACACAAAAA
Found at i:29060144 original size:17 final size:18
Alignment explanation
Indices: 29060099--29060148 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
29060089 TTTTATTATT
*
29060099 ATTTTTTAAACACGAGAA
1 ATTTTTGAAACACGAGAA
*
29060117 A-TTTTGAAAACAGGA-AA
1 ATTTTTG-AAACACGAGAA
29060134 ATTTTTGAAACACGA
1 ATTTTTGAAACACGA
29060149 TTAGTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (18 bp):
ATTTTTGAAACACGAGAA
Found at i:29060514 original size:18 final size:20
Alignment explanation
Indices: 29060478--29060516 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
29060468 ATAAAATTTA
29060478 AAAAAACATAAATACAAAAT
1 AAAAAACATAAATACAAAAT
*
29060498 AAAAAA-ATAATTA-AAAAT
1 AAAAAACATAAATACAAAAT
29060516 A
1 A
29060517 TGCAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAAACATAAATACAAAAT
Found at i:29061034 original size:4 final size:4
Alignment explanation
Indices: 29061019--29061086 Score: 70
Period size: 4 Copynumber: 17.5 Consensus size: 4
29061009 ATTTATTTTT
* * *
29061019 TTTC TTTT TTTC TTTC CTT- TTTC TTT- TTTCC CTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC
*
29061066 TTT- TGTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TT
29061087 CCCCATACAG
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
3 7 0.13
4 43 0.83
5 2 0.04
ACGTcount: A:0.00, C:0.24, G:0.01, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:29061056 original size:31 final size:32
Alignment explanation
Indices: 29061020--29061080 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
29061010 TTTATTTTTT
*
29061020 TTCTTTTTTTCTTTCCTTTT-TCTTT-TTTCCC
1 TTCTTTCTTTCTTT-CTTTTGTCTTTCTTTCCC
29061051 TTCTTTCTTTCTTTCTTTTGTCTTTCTTTC
1 TTCTTTCTTTCTTTCTTTTGTCTTTCTTTC
29061081 TTTCTTCCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
31 18 0.67
32 4 0.15
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.74
Consensus pattern (32 bp):
TTCTTTCTTTCTTTCTTTTGTCTTTCTTTCCC
Found at i:29061077 original size:23 final size:24
Alignment explanation
Indices: 29061027--29061086 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
29061017 TTTTTCTTTT
* *
29061027 TTTCTTTCCTT-TTTCTTTTTTCC
1 TTTCTTTCTTTCTTTCTTTTGTCC
*
29061050 CTTCTTTCTTTCTTTCTTTTGT-C
1 TTTCTTTCTTTCTTTCTTTTGTCC
29061073 TTTCTTTCTTTCTT
1 TTTCTTTCTTTCTT
29061087 CCCCATACAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 23 0.72
24 9 0.28
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTCTTTCTTTCTTTCTTTTGTCC
Found at i:29061083 original size:15 final size:15
Alignment explanation
Indices: 29061023--29061080 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
29061013 ATTTTTTTTC
29061023 TTTT-TTTCTTTCCT
1 TTTTCTTTCTTTCCT
29061037 TTTTCTTT-TTTCCCT
1 TTTTCTTTCTTT-CCT
29061052 TCTTTCTTTCTTT-CT
1 T-TTTCTTTCTTTCCT
29061067 TTTGTCTTTCTTTC
1 TTT-TCTTTCTTTC
29061081 TTTCTTCCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 9 0.24
15 19 0.50
16 7 0.18
17 3 0.08
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTCTTTCTTTCCT
Found at i:29066501 original size:35 final size:34
Alignment explanation
Indices: 29066452--29066599 Score: 154
Period size: 35 Copynumber: 4.2 Consensus size: 34
29066442 TTTGTTTTAA
*
29066452 TGTGTTTCGAAGGGATTACCTCTTTA-GAGCATTGG
1 TGTGTTTCG-AGGGATTAGCTC-TTACGAGCATTGG
* * *
29066487 TGTGTTTTGTAGGGATTAGTTCTTACAAGCATTGG
1 TGTGTTTCG-AGGGATTAGCTCTTACGAGCATTGG
*
29066522 TGTGCTTCGGAGGGATTAGCTCTTACGAGCATTGG
1 TGTGTTTC-GAGGGATTAGCTCTTACGAGCATTGG
* ** *
29066557 TGTGTTTCAGATGGATTAGCTCTTTTGAGCATCTAG
1 TGTGTTTC-GAGGGATTAGCTCTTACGAGCAT-TGG
29066593 TGTGTTT
1 TGTGTTT
29066600 TTGGTTGGAT
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
34 3 0.03
35 82 0.86
36 10 0.11
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.40
Consensus pattern (34 bp):
TGTGTTTCGAGGGATTAGCTCTTACGAGCATTGG
Found at i:29067127 original size:22 final size:22
Alignment explanation
Indices: 29067101--29067143 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
29067091 ATATTGGCTA
29067101 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
29067123 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
29067144 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:29070507 original size:22 final size:21
Alignment explanation
Indices: 29070482--29070549 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
29070472 TTGAGTATTA
29070482 TGATCTATGCTTGAATGTAATG
1 TGAT-TATGCTTGAATGTAATG
* *
29070504 TGATTAT--ATG-A-GTATTG
1 TGATTATGCTTGAATGTAATG
*
29070521 TGATATATGCTTGAATGTTATG
1 TGAT-TATGCTTGAATGTAATG
29070543 TGATTAT
1 TGATTAT
29070550 ATGAGTATTG
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
17 9 0.25
18 4 0.11
19 2 0.06
20 2 0.06
21 7 0.19
22 12 0.33
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (21 bp):
TGATTATGCTTGAATGTAATG
Found at i:29070530 original size:39 final size:39
Alignment explanation
Indices: 29070473--29070652 Score: 261
Period size: 39 Copynumber: 4.6 Consensus size: 39
29070463 AACATGTTTT
* * * *
29070473 TGAGTATTATGATCTATGCTTGAATGTAATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
29070512 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
29070551 TGAGTATTGTGATATATGCCTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
**
29070590 TGAGTATTGTGATATATGCTTAAATGTTACATGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
29070629 TGTGTAATGTGGTATATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
29070653 AGTGAATACC
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 130 1.00
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:29074119 original size:14 final size:14
Alignment explanation
Indices: 29074100--29074128 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29074090 AAATGTATTC
29074100 ATCCTAGGTCGTGG
1 ATCCTAGGTCGTGG
29074114 ATCCTAGGTCGTGG
1 ATCCTAGGTCGTGG
29074128 A
1 A
29074129 GCCATAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (14 bp):
ATCCTAGGTCGTGG
Found at i:29076218 original size:33 final size:34
Alignment explanation
Indices: 29076181--29076244 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
29076171 AGATTAATTG
*
29076181 TTAAAAAATAATA-TTATTTTAATAG-ATTTAATA
1 TTAAAAAA-AATACTTATCTTAATAGTATTTAATA
*
29076214 TTAAATAAAATACTTATCTTAATAGTATTTA
1 TTAAAAAAAATACTTATCTTAATAGTATTTA
29076245 TTAATTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 4 0.15
33 18 0.67
34 5 0.19
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (34 bp):
TTAAAAAAAATACTTATCTTAATAGTATTTAATA
Found at i:29077725 original size:11 final size:11
Alignment explanation
Indices: 29077694--29077728 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
29077684 TAACATTTTC
29077694 ATAAT-AAAAT
1 ATAATAAAAAT
29077704 ATCAATAAAAAT
1 AT-AATAAAAAT
29077716 ATAATAAAAAT
1 ATAATAAAAAT
29077727 AT
1 AT
29077729 TAATGTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 14 0.61
12 7 0.30
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATAAAAAT
Found at i:29077732 original size:12 final size:12
Alignment explanation
Indices: 29077695--29077732 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
29077685 AACATTTTCA
29077695 TAAT-AAAATAT
1 TAATAAAAATAT
*
29077706 CAATAAAAATA-
1 TAATAAAAATAT
29077717 TAATAAAAATAT
1 TAATAAAAATAT
29077729 TAAT
1 TAAT
29077733 GTTATAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (12 bp):
TAATAAAAATAT
Found at i:29081082 original size:21 final size:22
Alignment explanation
Indices: 29081058--29081099 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
29081048 TTTACGGTTT
*
29081058 AATTATTAAATT-TTTAAAAAA
1 AATTATAAAATTATTTAAAAAA
*
29081079 AATTATAAAATTATTTGAAAA
1 AATTATAAAATTATTTAAAAA
29081100 TTTTATCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTATAAAATTATTTAAAAAA
Found at i:29081626 original size:20 final size:20
Alignment explanation
Indices: 29081588--29081626 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29081578 TTTAAATATG
*
29081588 AAAAAAGAAATTTGAATTTT
1 AAAAAAGAAATTAGAATTTT
* *
29081608 AAAAAAGATATTAGTATTT
1 AAAAAAGAAATTAGAATTT
29081627 AGTCTATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAAAAGAAATTAGAATTTT
Found at i:29082030 original size:61 final size:58
Alignment explanation
Indices: 29081965--29082097 Score: 169
Period size: 61 Copynumber: 2.2 Consensus size: 58
29081955 TTTAATAAAT
* *
29081965 TTATTATTAAATATAATTTAATAAAAGTAATAATAAATAATTTAATCATATT-TTAACATAA
1 TTATTATTAAATATAATTTAATAAAA-TAAT-AT--ATAATTTAATAACATTCTTAACATAA
* * *
29082026 TTATTGTTAAATACAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATAA
1 TTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAACATTCTTAACATAA
*
29082084 TTATTATAAAATAT
1 TTATTATTAAATAT
29082098 GAAATAATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
57 14 0.22
58 19 0.30
59 2 0.03
60 4 0.06
61 24 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (58 bp):
TTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAACATTCTTAACATAA
Found at i:29083173 original size:15 final size:15
Alignment explanation
Indices: 29083153--29083183 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29083143 AAGACAGGAA
29083153 ATCATTCTTACACTT
1 ATCATTCTTACACTT
29083168 ATCATTCTTACACTT
1 ATCATTCTTACACTT
29083183 A
1 A
29083184 CATATGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (15 bp):
ATCATTCTTACACTT
Found at i:29087224 original size:38 final size:38
Alignment explanation
Indices: 29087170--29087621 Score: 530
Period size: 38 Copynumber: 11.9 Consensus size: 38
29087160 TGTTTGGAGT
* *
29087170 TTCGGTTGGACCAGCTCTTATGAGCTTCTATTTGGTGA
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
* * *
29087208 TTCGATTGTATTAGCTCTTATGAGCTTCTATTTGGCGA
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
* * *
29087246 TTCGGTTGGATCAGCTCTTATGAGCTTCTGTTTGACTA
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
* * * * * *
29087284 TTTGGTTGGATCAGCCCTTATGAACTTTTGTTTGGCGT
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
* *
29087322 TTTGGTTGGATAAGCTCTTATGAGCTTCTATTTGGCGA
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
* * * *
29087360 TCCTGTTGGATCAGCTATTATGAGCTTCTGTTTGGC--
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
* * *
29087396 TTCAGTTGCATCAGCTCTTATGAGCTTCTGTTTGGCGA
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
* * *
29087434 TTCTGTTGGATCAACTCTTATGAGCTTCTATTTGGCGT
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
* *
29087472 TTCGGTTGGATCATCTCTTATGAGCTTCTGTTTGGCGA
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
* * * * *
29087510 TTTGGTTGGATTAGCTCTTATGAGTTTCTATTTGGTGT
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
* * * * *
29087548 TTCAGTTGGATCAGTTCTTATGAGCTTCTGTTTGGTGTG
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCG-A
*
29087587 TTCAGTTGGATCAGCTCTTATGAGCTTCTATTTGG
1 TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGG
29087622 TGTGTTCGGT
Statistics
Matches: 352, Mismatches: 59, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
36 32 0.09
38 287 0.82
39 33 0.09
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.44
Consensus pattern (38 bp):
TTCGGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGA
Found at i:29087541 original size:188 final size:190
Alignment explanation
Indices: 29087174--29087621 Score: 607
Period size: 188 Copynumber: 2.4 Consensus size: 190
29087164 TGGAGTTTCG
* * * *
29087174 GTTGGACCAGCTCTTATGAGCTTCTATTTGGTGATTC-GATTGTATTAGCTCTTATGAGCTTCTA
1 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGATTCAG-TTGCATCAGCTCTTATGAGCTTCTA
* * *
29087238 TTTGGCGATTCGGTTGGATCAGCTCTTATGAGCTTCTGTTTGACTATTTGGTTGGATCAGCCCTT
65 TTTGGCGATTCGGTTGGATCAACTCTTATGAGCTTCTATTTGACTATTCGGTTGGATCAGCCCTT
* * *
29087303 ATGAACTTTTGTTTGGCGTTTTGGTTGGATAAGCTCTTATGAGCTTCTATTTGGCGATCCT
130 ATGAACTTCTGTTTGGCGATTTGGTTGGATAAGCTCTTATGAGCTTCTATTTGGCGATCCA
* * *
29087364 GTTGGATCAGCTATTATGAGCTTCTGTTT-G-GCTTCAGTTGCATCAGCTCTTATGAGCTTCTGT
1 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGATTCAGTTGCATCAGCTCTTATGAGCTTCTAT
* * * *
29087427 TTGGCGATTCTGTTGGATCAACTCTTATGAGCTTCTATTTGGCGT-TTCGGTTGGATCATCTCTT
66 TTGGCGATTCGGTTGGATCAACTCTTATGAGCTTCTATTTGAC-TATTCGGTTGGATCAGCCCTT
* * * * * *
29087491 ATGAGCTTCTGTTTGGCGATTTGGTTGGATTAGCTCTTATGAGTTTCTATTTGGTGTTTCA
130 ATGAACTTCTGTTTGGCGATTTGGTTGGATAAGCTCTTATGAGCTTCTATTTGGCGATCCA
* * *
29087552 GTTGGATCAGTTCTTATGAGCTTCTGTTTGGTGTGTTCAGTTGGATCAGCTCTTATGAGCTTCTA
1 GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG-ATTCAGTTGCATCAGCTCTTATGAGCTTCTA
29087617 TTTGG
65 TTTGG
29087622 TGTGTTCGGT
Statistics
Matches: 225, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
188 161 0.72
189 4 0.02
190 27 0.12
191 33 0.15
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.44
Consensus pattern (190 bp):
GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGATTCAGTTGCATCAGCTCTTATGAGCTTCTAT
TTGGCGATTCGGTTGGATCAACTCTTATGAGCTTCTATTTGACTATTCGGTTGGATCAGCCCTTA
TGAACTTCTGTTTGGCGATTTGGTTGGATAAGCTCTTATGAGCTTCTATTTGGCGATCCA
Found at i:29091221 original size:40 final size:40
Alignment explanation
Indices: 29091081--29091282 Score: 190
Period size: 40 Copynumber: 5.0 Consensus size: 40
29091071 ATAAGTGCTT
29091081 CTGATAGCACAACGGTGCTCCTGACAGTACTTTCGTACTC
1 CTGATAGCACAACGGTGCTCCTGACAGTACTTTCGTACTC
* **** ** *
29091121 CT-AGTTGCACTTTAGTGCTTTTGACAGTACTTTCATACTC
1 CTGA-TAGCACAACGGTGCTCCTGACAGTACTTTCGTACTC
* * * * *
29091161 CTTTGATATCATAATGATGCTTCTGACAGTACTTTCGTACTC
1 C--TGATAGCACAACGGTGCTCCTGACAGTACTTTCGTACTC
** * *
29091203 CTGATAGCACAACAATGCTCCTGACAGTACTTTCATACTT
1 CTGATAGCACAACGGTGCTCCTGACAGTACTTTCGTACTC
* * *
29091243 CTGATAGCACAACGGTGCTCCTAATAGTACTTTTGTACTC
1 CTGATAGCACAACGGTGCTCCTGACAGTACTTTCGTACTC
29091283 TTCTTAGCAC
Statistics
Matches: 127, Mismatches: 31, Indels: 8
0.77 0.19 0.05
Matches are distributed among these distances:
39 1 0.01
40 96 0.76
42 29 0.23
43 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (40 bp):
CTGATAGCACAACGGTGCTCCTGACAGTACTTTCGTACTC
Found at i:29094880 original size:3 final size:3
Alignment explanation
Indices: 29094872--29094910 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
29094862 TCCTTACCTT
29094872 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29094911 AAGACAAGAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29094953 original size:18 final size:18
Alignment explanation
Indices: 29094930--29094968 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29094920 AAATCATATG
*
29094930 TAAAATTTAATTTAAAAA
1 TAAAATTCAATTTAAAAA
* *
29094948 TAAAATTCACTTTAAATA
1 TAAAATTCAATTTAAAAA
29094966 TAA
1 TAA
29094969 TTAAAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTCAATTTAAAAA
Found at i:29097014 original size:12 final size:11
Alignment explanation
Indices: 29096990--29097032 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
29096980 GAATAGAAAG
29096990 AAGGAGAAAGGA
1 AAGGA-AAAGGA
29097002 AAGGAAAAGGGA
1 AAGGAAAA-GGA
*
29097014 AAGGGAAA-GA
1 AAGGAAAAGGA
29097024 AAGGAAAAG
1 AAGGAAAAG
29097033 AGGGAGGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.33
11 3 0.11
12 15 0.56
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (11 bp):
AAGGAAAAGGA
Found at i:29097810 original size:22 final size:22
Alignment explanation
Indices: 29097780--29097822 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29097770 TTTCTATTTT
* *
29097780 TTTTCAATTCTATATTTTTAAC
1 TTTTAAATTCTAAATTTTTAAC
29097802 TTTTAAATTCTAAATTTTTAA
1 TTTTAAATTCTAAATTTTTAA
29097823 ATTTATCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTAAATTCTAAATTTTTAAC
Found at i:29098791 original size:3 final size:3
Alignment explanation
Indices: 29098776--29098810 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
29098766 ATAAAGCTTT
* *
29098776 ATA ATA GTA ATA ATA ATA ATA ACA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
29098811 TAAAAGCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:29099683 original size:22 final size:23
Alignment explanation
Indices: 29099630--29099685 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
29099620 CCCGTTTTTA
* * *
29099630 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
29099653 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
29099675 ATTAAAATTAA
1 ATTAAAATTAA
29099686 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:29099698 original size:16 final size:16
Alignment explanation
Indices: 29099661--29099700 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29099651 TTAATAAAAT
* *
29099661 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
29099677 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
29099693 TAAAATTA
1 TAAAATTA
29099701 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:29099779 original size:59 final size:59
Alignment explanation
Indices: 29099711--29099880 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
29099701 TCAAATTATT
* *
29099711 AATTGTTAATTGTATTAATTGTTGTAATAAAATTTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
29099770 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
29099829 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
29099881 ACAAACTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 108 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:29099976 original size:24 final size:23
Alignment explanation
Indices: 29099947--29099991 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
29099937 AAATAAACTT
29099947 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTA-TATATTTTA
*
29099971 AAAATAAAAAAGTATATATTT
1 AAAATAAAAAACTATATATTT
29099992 AATATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAATAAAAAACTATATATTTTA
Found at i:29101923 original size:7 final size:7
Alignment explanation
Indices: 29101911--29101953 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
29101901 CGATTGGTAA
29101911 TTAGTAT
1 TTAGTAT
29101918 TTAGTAT
1 TTAGTAT
29101925 TTAGTAT
1 TTAGTAT
29101932 TTAGTAT
1 TTAGTAT
29101939 TTAGTAT
1 TTAGTAT
29101946 TTAGTAT
1 TTAGTAT
29101953 T
1 T
29101954 ATGTATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (7 bp):
TTAGTAT
Found at i:29101959 original size:21 final size:21
Alignment explanation
Indices: 29101910--29101959 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
29101900 TCGATTGGTA
29101910 ATTA-GTATTTAGTATTTAGT
1 ATTATGTATTTAGTATTTAGT
29101930 ATT-TAGTATTTAGTATTTAGT
1 ATTAT-GTATTTAGTATTTAGT
29101951 ATTATGTAT
1 ATTATGTAT
29101960 ATAACTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.11
21 23 0.85
22 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (21 bp):
ATTATGTATTTAGTATTTAGT
Found at i:29102627 original size:18 final size:18
Alignment explanation
Indices: 29102604--29102643 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
29102594 CAGGTGCGTT
*
29102604 TCCTAACCCTTTTATGTA
1 TCCTAACCCTTATATGTA
29102622 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
29102640 TCCT
1 TCCT
29102644 TTAACGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.05, T:0.42
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:29103248 original size:21 final size:21
Alignment explanation
Indices: 29103224--29103296 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
29103214 TAACCCTAAT
29103224 CCTAACCCTTAACTTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
* *
29103245 CCTACCCCTTAAATTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
* *
29103266 GCTAACCCTTAACTTAAAACC
1 CCTAACCCTTAACTTAAAAAC
29103287 CCTAAACCCT
1 CCT-AACCCT
29103297 AAACCCTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 38 0.86
22 6 0.14
ACGTcount: A:0.40, C:0.36, G:0.01, T:0.23
Consensus pattern (21 bp):
CCTAACCCTTAACTTAAAAAC
Found at i:29103308 original size:29 final size:29
Alignment explanation
Indices: 29103269--29103363 Score: 140
Period size: 29 Copynumber: 3.3 Consensus size: 29
29103259 TAAAAACGCT
* *
29103269 AACCCTTAACTT-AAAACCCCTAAACCCTA
1 AACCCTAAACTTAAAAACCAC-AAACCCTA
*
29103298 AACCCTAAACTTAAAAACCACAAGCCCTA
1 AACCCTAAACTTAAAAACCACAAACCCTA
29103327 AACCCTAAACTTAAAAACCACAAACCCTA
1 AACCCTAAACTTAAAAACCACAAACCCTA
29103356 AA-CCTAAA
1 AACCCTAAA
29103364 AACCTTAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
28 6 0.10
29 48 0.79
30 7 0.11
ACGTcount: A:0.48, C:0.35, G:0.01, T:0.16
Consensus pattern (29 bp):
AACCCTAAACTTAAAAACCACAAACCCTA
Found at i:29103315 original size:22 final size:22
Alignment explanation
Indices: 29103290--29103379 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 22
29103280 TAAAACCCCT
29103290 AAACCCTAAACCCTAAACTTAAAAA
1 AAACCCTAAACCCTAAACTT---AA
29103315 CCACAAGCCCTAAACCCTAAACTTAA
1 --A-AA-CCCTAAACCCTAAACTTAA
*
29103341 AAACCAC-AAACCCTAAACCTAA
1 AAACC-CTAAACCCTAAACTTAA
*
29103363 AAACCTTAAACCCTAAA
1 AAACCCTAAACCCTAAA
29103380 AACTTAACTT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
22 31 0.54
23 3 0.05
24 1 0.02
26 2 0.04
27 1 0.02
28 2 0.04
29 17 0.30
ACGTcount: A:0.51, C:0.33, G:0.01, T:0.14
Consensus pattern (22 bp):
AAACCCTAAACCCTAAACTTAA
Found at i:29103385 original size:15 final size:15
Alignment explanation
Indices: 29103348--29103400 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29103338 TAAAAACCAC
*
29103348 AAACCCTAAACCTAA
1 AAACCTTAAACCTAA
29103363 AAACCTTAAACCCTAA
1 AAACCTTAAA-CCTAA
* *
29103379 AAA-CTT-AACTTTA
1 AAACCTTAAACCTAA
29103392 AAACCTTAA
1 AAACCTTAA
29103401 CCCTTAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 6 0.19
14 5 0.16
15 13 0.41
16 8 0.25
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (15 bp):
AAACCTTAAACCTAA
Found at i:29103389 original size:51 final size:51
Alignment explanation
Indices: 29103297--29103396 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 51
29103287 CCTAAACCCT
* * **
29103297 AAACCCTAAACTTAAAAACCACAAGCCCTAAACCCTAAACTTAAAAACCAC
1 AAACCCTAAACCTAAAAACCACAAACCCTAAAAACTAAACTTAAAAACCAC
** * *
29103348 AAACCCTAAACCTAAAAACCTTAAACCCTAAAAACTTAACTTTAAAACC
1 AAACCCTAAACCTAAAAACCACAAACCCTAAAAACTAAACTTAAAAACC
29103397 TTAACCCTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.51, C:0.31, G:0.01, T:0.17
Consensus pattern (51 bp):
AAACCCTAAACCTAAAAACCACAAACCCTAAAAACTAAACTTAAAAACCAC
Found at i:29103399 original size:14 final size:14
Alignment explanation
Indices: 29103348--29103404 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
29103338 TAAAAACCAC
* *
29103348 AAACCCTAAACCTAA
1 AAACCTTAACCCT-A
29103363 AAACCTTAAACCCTA
1 AAACCTT-AACCCTA
* **
29103378 AAAACTTAACTTTA
1 AAACCTTAACCCTA
29103392 AAACCTTAACCCT
1 AAACCTTAACCCT
29103405 TAAGTTAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
14 15 0.45
15 13 0.39
16 5 0.15
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCTTAACCCTA
Found at i:29106138 original size:14 final size:15
Alignment explanation
Indices: 29106100--29106128 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29106090 CTAGAAAATT
29106100 AAAAAATTTATTTTC
1 AAAAAATTTATTTTC
29106115 AAAAAATTTATTTT
1 AAAAAATTTATTTT
29106129 AAAGATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAAATTTATTTTC
Found at i:29107473 original size:77 final size:78
Alignment explanation
Indices: 29107342--29107499 Score: 309
Period size: 77 Copynumber: 2.0 Consensus size: 78
29107332 TTTTTGCAAG
29107342 ATTGATATTATATGTACAAGAGTTGAACTTTTTATTGAATAATGGTAAGTAAGCATTTAGGTGGT
1 ATTGATATTATATGTACAAGAGTTGAACTTTTTATTGAATAATGGTAAGTAAGCATTTAGGTGGT
29107407 TTTGTGTAATTTA
66 TTTGTGTAATTTA
29107420 ATTGATATTATATGTACAAGAGTTGAA-TTTTTATTGAATAATGGTAAGTAAGCATTTAGGTGGT
1 ATTGATATTATATGTACAAGAGTTGAACTTTTTATTGAATAATGGTAAGTAAGCATTTAGGTGGT
29107484 TTTGTGTAATTTA
66 TTTGTGTAATTTA
29107497 ATT
1 ATT
29107500 AGGCTAATTA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 53 0.66
78 27 0.34
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.44
Consensus pattern (78 bp):
ATTGATATTATATGTACAAGAGTTGAACTTTTTATTGAATAATGGTAAGTAAGCATTTAGGTGGT
TTTGTGTAATTTA
Found at i:29108802 original size:20 final size:20
Alignment explanation
Indices: 29108773--29108846 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
29108763 CAATGGTCTT
*
29108773 CACACGGGCGTTTGCTTGTC
1 CACACGGGCGTGTGCTTGTC
*
29108793 CACACAGGCGTGTGCTTGTC
1 CACACGGGCGTGTGCTTGTC
*
29108813 CACACGGGCGTGTGCTTCTC
1 CACACGGGCGTGTGCTTGTC
29108833 CACACGGGCGTGTG
1 CACACGGGCGTGTG
29108847 GGTAAGTGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.12, C:0.31, G:0.32, T:0.24
Consensus pattern (20 bp):
CACACGGGCGTGTGCTTGTC
Found at i:29112133 original size:23 final size:23
Alignment explanation
Indices: 29112091--29112134 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
29112081 GATAAAAAAC
*
29112091 GCCGCTATAGATAGAGCATTAAT
1 GCCGCTATAGATAGACCATTAAT
* *
29112114 GCCGCTATAGGTTGACCATTA
1 GCCGCTATAGATAGACCATTA
29112135 GCGACGCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (23 bp):
GCCGCTATAGATAGACCATTAAT
Found at i:29112625 original size:22 final size:20
Alignment explanation
Indices: 29112550--29112632 Score: 58
Period size: 22 Copynumber: 3.9 Consensus size: 20
29112540 AAATACTATT
*
29112550 ATTATGGTTTAAGGTATATGG
1 ATTATGGTTTAAGGTTTA-GG
* * *
29112571 TTTAGGGTTTAAGATTTAGG
1 ATTATGGTTTAAGGTTTAGG
**
29112591 AGTTACTATTTTAAGGTTTAGGG
1 A-TTA-TGGTTTAAGGTTTA-GG
*
29112614 ATTATGGGTTTATGGTTTA
1 ATTAT-GGTTTAAGGTTTA
29112633 TGGTTTAATG
Statistics
Matches: 46, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
20 2 0.04
21 18 0.39
22 23 0.50
23 3 0.07
ACGTcount: A:0.25, C:0.01, G:0.28, T:0.46
Consensus pattern (20 bp):
ATTATGGTTTAAGGTTTAGG
Found at i:29112639 original size:14 final size:14
Alignment explanation
Indices: 29112551--29112690 Score: 61
Period size: 14 Copynumber: 9.8 Consensus size: 14
29112541 AATACTATTA
*
29112551 TTATGGTTTAAGGT
1 TTATGGTTTATGGT
* *
29112565 ATATGGTTTAGGGT
1 TTATGGTTTATGGT
* * *
29112579 TTAAGATTTAGGAGT
1 TTATGGTTTATG-GT
*
29112594 TACTAT--TTTAAGGT
1 T--TATGGTTTATGGT
* *
29112608 TTAGGGATTATGGGT
1 TTATGGTTTAT-GGT
29112623 TTATGGTTTATGGT
1 TTATGGTTTATGGT
**
29112637 TTAATGG-TTGGGGT
1 TT-ATGGTTTATGGT
* * * *
29112651 TTAAGATTTAAGGG
1 TTATGGTTTATGGT
*
29112665 TTAGGGGTTTATGGT
1 TTA-TGGTTTATGGT
29112680 TTATGGTTTAT
1 TTATGGTTTAT
29112691 AATTTAGGGT
Statistics
Matches: 93, Mismatches: 24, Indels: 18
0.69 0.18 0.13
Matches are distributed among these distances:
12 2 0.02
13 2 0.02
14 53 0.57
15 34 0.37
17 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (14 bp):
TTATGGTTTATGGT
Found at i:29112653 original size:21 final size:22
Alignment explanation
Indices: 29112627--29112687 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 22
29112617 ATGGGTTTAT
29112627 GGTTTATGGTTTAATGGTT-GG
1 GGTTTATGGTTTAATGGTTAGG
* * *
29112648 GGTTTAAGATTTAAGGGTTAGG
1 GGTTTATGGTTTAATGGTTAGG
29112670 GGTTTATGGTTT-ATGGTT
1 GGTTTATGGTTTAATGGTT
29112688 TATAATTTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (22 bp):
GGTTTATGGTTTAATGGTTAGG
Found at i:29112703 original size:7 final size:7
Alignment explanation
Indices: 29112600--29112733 Score: 58
Period size: 7 Copynumber: 18.7 Consensus size: 7
29112590 GAGTTACTAT
*
29112600 TTTAAGG
1 TTTAGGG
29112607 TTTAGGG
1 TTTAGGG
*
29112614 ATTATGGG
1 TTTA-GGG
*
29112622 TTTATGG
1 TTTAGGG
*
29112629 TTTATGG
1 TTTAGGG
*
29112636 TTTAATGG
1 TTT-AGGG
*
29112644 -TTGGGG
1 TTTAGGG
* *
29112650 TTTAAGA
1 TTTAGGG
29112657 TTTAAGGG
1 TTT-AGGG
29112665 -TTAGGGG
1 TTTA-GGG
*
29112672 TTTATGG
1 TTTAGGG
*
29112679 TTTATGG
1 TTTAGGG
***
29112686 TTTATAA
1 TTTAGGG
29112693 TTTAGGG
1 TTTAGGG
29112700 TTTAAGGG
1 TTT-AGGG
* *
29112708 ATAAGGG
1 TTTAGGG
29112715 -TTAGAGG
1 TTTAG-GG
29112722 TTTAGGG
1 TTTAGGG
29112729 TTTAG
1 TTTAG
29112734 ATTAATTAGT
Statistics
Matches: 98, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
6 6 0.06
7 68 0.69
8 24 0.24
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:29113003 original size:7 final size:7
Alignment explanation
Indices: 29112993--29113217 Score: 56
Period size: 7 Copynumber: 31.9 Consensus size: 7
29112983 TTTAGGGTGT
29112993 AGGTTTA
1 AGGTTTA
*
29113000 AGGTTTG
1 AGGTTTA
29113007 AGGTTTA
1 AGGTTTA
29113014 AGGTTT-
1 AGGTTTA
29113020 AGGATTTA
1 AGG-TTTA
* *
29113028 TGATTT-
1 AGGTTTA
29113034 A-GTGTTA
1 AGGT-TTA
*
29113041 AGAATTT-
1 AG-GTTTA
29113048 AGTGTTTA
1 AG-GTTTA
*
29113056 CGGTTT-
1 AGGTTTA
29113062 AGGTTGT-
1 AGGTT-TA
29113069 AGGTTTA
1 AGGTTTA
29113076 TA-GTTT-
1 -AGGTTTA
29113082 AGTGTTTA
1 AG-GTTTA
* *
29113090 TGATTTA
1 AGGTTTA
*
29113097 GGGTTTA
1 AGGTTTA
*
29113104 GGGTTTA
1 AGGTTTA
*
29113111 ATGTTTA
1 AGGTTTA
*
29113118 TGGTTTAA
1 AGGTTT-A
29113126 AGG-TTA
1 AGGTTTA
* *
29113132 GGGGATTA
1 -AGGTTTA
* *
29113140 GGGGATTA
1 -AGGTTTA
*
29113148 GGGTTTA
1 AGGTTTA
*
29113155 TGGTTTA
1 AGGTTTA
*
29113162 AAGTTTA
1 AGGTTTA
29113169 TA-GTTTA
1 -AGGTTTA
*
29113176 GGGTTTA
1 AGGTTTA
* *
29113183 TGGGCTTA
1 -AGGTTTA
*
29113191 AGGATTA
1 AGGTTTA
* *
29113198 TGATTTA
1 AGGTTTA
29113205 AGGTTTA
1 AGGTTTA
29113212 AGGTTT
1 AGGTTT
29113218 GATTTTAAAC
Statistics
Matches: 165, Mismatches: 34, Indels: 38
0.70 0.14 0.16
Matches are distributed among these distances:
5 2 0.01
6 11 0.07
7 124 0.75
8 27 0.16
9 1 0.01
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.45
Consensus pattern (7 bp):
AGGTTTA
Found at i:29113027 original size:14 final size:13
Alignment explanation
Indices: 29112981--29113130 Score: 81
Period size: 14 Copynumber: 10.8 Consensus size: 13
29112971 ATATATTTGG
* *
29112981 GGTTTAGGGTGTA
1 GGTTTAAGGTTTA
29112994 GGTTTAAGGTTTGA
1 GGTTTAAGGTTT-A
29113008 GGTTTAAGGTTTA
1 GGTTTAAGGTTTA
* *
29113021 GGATTTATGATTTA
1 GG-TTTAAGGTTTA
*
29113035 -GTGTTAAGAATTTA
1 GGT-TTAAG-GTTTA
*
29113049 GTGTTTACGGTTTA
1 G-GTTTAAGGTTTA
29113063 GGTTGT-AGGTTTA
1 GGTT-TAAGGTTTA
*
29113076 TAGTTT-AGTGTTTA
1 -GGTTTAAG-GTTTA
* *
29113090 TGATTTAGGGTTTA
1 -GGTTTAAGGTTTA
*
29113104 GGGTTTAATGTTTA
1 -GGTTTAAGGTTTA
29113118 TGGTTTAAAGGTT
1 -GGTTT-AAGGTT
29113131 AGGGGATTAG
Statistics
Matches: 108, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
12 1 0.01
13 30 0.28
14 65 0.60
15 10 0.09
16 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.47
Consensus pattern (13 bp):
GGTTTAAGGTTTA
Found at i:29113034 original size:21 final size:19
Alignment explanation
Indices: 29112993--29113124 Score: 70
Period size: 21 Copynumber: 6.4 Consensus size: 19
29112983 TTTAGGGTGT
*
29112993 AGGTTTAAGGTTTGAGGTTTA
1 AGGTTT-AGGTTT-ATGTTTA
29113014 AGGTTTAGGATTTATGATTT-
1 AGGTTTAGG-TTTATG-TTTA
* *
29113034 AGTGTTAAGAATTTAGTGTTTA
1 AG-GTTTAG-GTTTA-TGTTTA
* *
29113056 CGGTTTAGGTTGTAGGTTTA
1 AGGTTTAGGTT-TATGTTTA
29113076 TA-GTTTAGTGTTTATGATTTA
1 -AGGTTTAG-GTTTATG-TTTA
*
29113097 GGGTTTAGGGTTTAATGTTTA
1 AGGTTTA-GGTTT-ATGTTTA
*
29113118 TGGTTTA
1 AGGTTTA
29113125 AAGGTTAGGG
Statistics
Matches: 87, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
20 23 0.26
21 57 0.66
22 7 0.08
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.48
Consensus pattern (19 bp):
AGGTTTAGGTTTATGTTTA
Found at i:29113066 original size:48 final size:48
Alignment explanation
Indices: 29113008--29113110 Score: 122
Period size: 48 Copynumber: 2.1 Consensus size: 48
29112998 TAAGGTTTGA
*
29113008 GGTTTAAGGTT-TAGGATTTAT-GATTTAGTG-TTAAGAATTTAGTGTTTAC
1 GGTTT-AGGTTGTAGG-TTTATAG-TTTAGTGTTTAAG-ATTTAGGGTTTAC
* *
29113057 GGTTTAGGTTGTAGGTTTATAGTTTAGTGTTTATGATTTAGGGTTTAG
1 GGTTTAGGTTGTAGGTTTATAGTTTAGTGTTTAAGATTTAGGGTTTAC
29113105 GGTTTA
1 GGTTTA
29113111 ATGTTTATGG
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
48 34 0.71
49 14 0.29
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (48 bp):
GGTTTAGGTTGTAGGTTTATAGTTTAGTGTTTAAGATTTAGGGTTTAC
Found at i:29113169 original size:14 final size:14
Alignment explanation
Indices: 29113149--29113217 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
29113139 AGGGGATTAG
29113149 GGTTTATGGTTTAA
1 GGTTTATGGTTTAA
* * *
29113163 AGTTTATAGTTTAG
1 GGTTTATGGTTTAA
*
29113177 GGTTTATGGGCTTAA
1 GGTTTAT-GGTTTAA
* *
29113192 GGATTATGATTTAA
1 GGTTTATGGTTTAA
*
29113206 GGTTTAAGGTTT
1 GGTTTATGGTTT
29113218 GATTTTAAAC
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
14 31 0.76
15 10 0.24
ACGTcount: A:0.25, C:0.01, G:0.28, T:0.46
Consensus pattern (14 bp):
GGTTTATGGTTTAA
Found at i:29113204 original size:29 final size:28
Alignment explanation
Indices: 29113145--29113211 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
29113135 GATTAGGGGA
* *
29113145 TTAGGGTTTATGGTTTAAAGTTTATAGT
1 TTAGGGTTTATGGCTTAAAGATTATAGT
*
29113173 TTAGGGTTTATGGGCTTAAGGATTAT-GAT
1 TTAGGGTTTAT-GGCTTAAAGATTATAG-T
*
29113202 TTAAGGTTTA
1 TTAGGGTTTA
29113212 AGGTTTGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.46
Consensus pattern (28 bp):
TTAGGGTTTATGGCTTAAAGATTATAGT
Found at i:29114445 original size:3 final size:3
Alignment explanation
Indices: 29114437--29114480 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
29114427 AATCTATCCT
29114437 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29114481 TAACTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29120396 original size:98 final size:98
Alignment explanation
Indices: 29120178--29120375 Score: 357
Period size: 98 Copynumber: 2.0 Consensus size: 98
29120168 CCCATAAATT
29120178 GGTGGATTAATCTTTTATGTATC---TTATTATTATTATTTACTTAATTCTCATTGGTTGGGACA
1 GGTGGATTAATCTTTTATGTATCTTATTATTATTATTATTTACTTAATTCTCATTGGTTGGGACA
29120240 CATCACTTATGAGTTAAGTAATTTTATTGGTTA
66 CATCACTTATGAGTTAAGTAATTTTATTGGTTA
29120273 GGTGGATTAATCTTTTATGTATCTTATTATTATTATTATTTACTTAATTCTCATTGGTTGGGACA
1 GGTGGATTAATCTTTTATGTATCTTATTATTATTATTATTTACTTAATTCTCATTGGTTGGGACA
29120338 CATCACTTATGAGTTTTAAGTAATTTTATTGGTTA
66 CATCACTTATGAG--TTAAGTAATTTTATTGGTTA
29120373 GGT
1 GGT
29120376 TATTATTTAT
Statistics
Matches: 98, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
95 23 0.23
98 52 0.53
100 23 0.23
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (98 bp):
GGTGGATTAATCTTTTATGTATCTTATTATTATTATTATTTACTTAATTCTCATTGGTTGGGACA
CATCACTTATGAGTTAAGTAATTTTATTGGTTA
Found at i:29125538 original size:43 final size:42
Alignment explanation
Indices: 29125491--29125675 Score: 158
Period size: 43 Copynumber: 4.3 Consensus size: 42
29125481 AGAATTGTAC
* *
29125491 TTTTAGCGGCGTTTGTGATAAAAGTGTTGTTAAAGGTCATGAA
1 TTTTAGCGGCGTTTGTGATAAAAGCGTTGCTAAAGGTCATG-A
* * * *
29125534 TTTTAGTGGCGTTTGTGATAAAAGCGTCGCTAAAGGTTATGT
1 TTTTAGCGGCGTTTGTGATAAAAGCGTTGCTAAAGGTCATGA
* **
29125576 TCTTTAGCGGCGTTTGTGGAT-AAAGCGTTGCTAAAGGTTATTT
1 T-TTTAGCGGCGTTTGT-GATAAAAGCGTTGCTAAAGGTCATGA
* * * *** *
29125619 TATTTAGCGGCATTTTTTATAAAAGCACCGCTAAAGGTTATG-
1 T-TTTAGCGGCGTTTGTGATAAAAGCGTTGCTAAAGGTCATGA
29125661 TTCTGTAGCGGCGTT
1 TT-T-TAGCGGCGTT
29125676 GTCTATAACA
Statistics
Matches: 119, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 5 0.04
43 110 0.92
44 3 0.03
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.38
Consensus pattern (42 bp):
TTTTAGCGGCGTTTGTGATAAAAGCGTTGCTAAAGGTCATGA
Found at i:29125587 original size:86 final size:86
Alignment explanation
Indices: 29125492--29125675 Score: 228
Period size: 86 Copynumber: 2.1 Consensus size: 86
29125482 GAATTGTACT
* * * *
29125492 TTTAGCGGCGTTTGT-GATAAAAGTGTTGTTAAAGGTCATGAAT-TTTAGTGGCGTTTGTGATAA
1 TTTAGCGGCGTTTGTGGAT-AAAGCGTTGCTAAAGGTCAT-AATATTTAGCGGCATTTGTGATAA
**
29125555 AAGCGTCGCTAAAGGTTATGTTC
64 AAGCACCGCTAAAGGTTATGTTC
* ** * *
29125578 TTTAGCGGCGTTTGTGGATAAAGCGTTGCTAAAGGTTATTTTATTTAGCGGCATTTTTTATAAAA
1 TTTAGCGGCGTTTGTGGATAAAGCGTTGCTAAAGGTCATAATATTTAGCGGCATTTGTGATAAAA
29125643 GCACCGCTAAAGGTTATGTTC
66 GCACCGCTAAAGGTTATGTTC
*
29125664 TGTAGCGGCGTT
1 TTTAGCGGCGTT
29125676 GTCTATAACA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
85 1 0.01
86 80 0.95
87 3 0.04
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGGATAAAGCGTTGCTAAAGGTCATAATATTTAGCGGCATTTGTGATAAAA
GCACCGCTAAAGGTTATGTTC
Found at i:29125683 original size:43 final size:43
Alignment explanation
Indices: 29125551--29125689 Score: 154
Period size: 43 Copynumber: 3.2 Consensus size: 43
29125541 GGCGTTTGTG
**
29125551 ATAAAAGCGTCGCTAAAGGTTATGTTCTTTAGCGGCGTTTGTGG
1 ATAAAAGCGTCGCTAAAGGTTATGTTCTTTAGCGGCG-TTGTCT
* * * * * *
29125595 AT-AAAGCGTTGCTAAAGGTTATTTTATTTAGCGGCATTTTTT
1 ATAAAAGCGTCGCTAAAGGTTATGTTCTTTAGCGGCGTTGTCT
** *
29125637 ATAAAAGCACCGCTAAAGGTTATGTTCTGTAGCGGCGTTGTCT
1 ATAAAAGCGTCGCTAAAGGTTATGTTCTTTAGCGGCGTTGTCT
*
29125680 ATAACAGCGT
1 ATAAAAGCGT
29125690 TTTTTGTGGT
Statistics
Matches: 75, Mismatches: 19, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
42 5 0.07
43 68 0.91
44 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.35
Consensus pattern (43 bp):
ATAAAAGCGTCGCTAAAGGTTATGTTCTTTAGCGGCGTTGTCT
Found at i:29126668 original size:30 final size:32
Alignment explanation
Indices: 29126633--29126703 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
29126623 TCTAGGTCAA
* *
29126633 GACTAAAATTTCA-AAATTTGAAAAGT-ATAT
1 GACTAAAATTTCACAAATTCGAAAAGTAAAAT
* *
29126663 GACT-AAATTTGACCAATTCGAAAAGTAAAAT
1 GACTAAAATTTCACAAATTCGAAAAGTAAAAT
29126694 GACTAAAATT
1 GACTAAAATT
29126704 GGTCAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 7 0.21
30 15 0.44
31 7 0.21
32 5 0.15
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (32 bp):
GACTAAAATTTCACAAATTCGAAAAGTAAAAT
Found at i:29127035 original size:22 final size:24
Alignment explanation
Indices: 29127010--29127054 Score: 67
Period size: 22 Copynumber: 1.9 Consensus size: 24
29127000 TATGCAAATG
29127010 TAAATTAC-AATTTG-TAAATATA
1 TAAATTACAAATTTGTTAAATATA
29127032 TAAATTACATAATTTGTTAAATA
1 TAAATTACA-AATTTGTTAAATA
29127055 ATTATGGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (24 bp):
TAAATTACAAATTTGTTAAATATA
Done.