Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 116 of 135
Found at i:34826597 original size:17 final size:17
Alignment explanation
Indices: 34826577--34826611 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34826567 TATACTTTTT
*
34826577 TAAAAAAATTAAAAATA
1 TAAAAAAATAAAAAATA
*
34826594 TAAAAATATAAAAAATA
1 TAAAAAAATAAAAAATA
34826611 T
1 T
34826612 TTTTAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAAATAAAAAATA
Found at i:34827034 original size:12 final size:12
Alignment explanation
Indices: 34827018--34827062 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
34827008 CACGAACAAG
*
34827018 CTCGTTTATTGG
1 CTCGTTTATTGA
**
34827030 CTCGTTTATAAA
1 CTCGTTTATTGA
34827042 CTCGTTTATTGA
1 CTCGTTTATTGA
*
34827054 CTCATTTAT
1 CTCGTTTAT
34827063 GAATTAATGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:34827170 original size:12 final size:12
Alignment explanation
Indices: 34827142--34827217 Score: 66
Period size: 12 Copynumber: 6.3 Consensus size: 12
34827132 TTGTTTATTA
*
34827142 TTCATTAACATTG
1 TTCATGAACA-TG
34827155 TTCATGAACATG
1 TTCATGAACATG
* *
34827167 TTCAAT-TATATG
1 TTC-ATGAACATG
34827179 TTCATGAACATG
1 TTCATGAACATG
* **
34827191 TTCGTTTA-ATG
1 TTCATGAACATG
34827202 TTCATGAACATG
1 TTCATGAACATG
34827214 TTCA
1 TTCA
34827218 ATTAAGTTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 7
0.73 0.16 0.10
Matches are distributed among these distances:
11 10 0.20
12 28 0.57
13 11 0.22
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:34827206 original size:23 final size:23
Alignment explanation
Indices: 34827153--34827239 Score: 122
Period size: 23 Copynumber: 3.7 Consensus size: 23
34827143 TCATTAACAT
34827153 TGTTCATGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
**
34827177 TGTTCATGAACATGTTCGTTTAA
1 TGTTCATGAACATGTTCAATTAA
34827200 TGTTCATGAACATGTTCAATTAA
1 TGTTCATGAACATGTTCAATTAA
*
34827223 -GTTAAATGAACATGTTC
1 TGTT-CATGAACATGTTC
34827240 GTGAACATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
22 3 0.05
23 34 0.60
24 20 0.35
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:34836552 original size:2 final size:2
Alignment explanation
Indices: 34836505--34836533 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34836495 TTATAGGGTT
34836505 TA TA 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 TA TA T
34836534 TGAGAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34838831 original size:17 final size:18
Alignment explanation
Indices: 34838809--34838848 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
34838799 TATGCATATT
*
34838809 TTATTTTTAAAT-TATAA
1 TTATTTTTAAATGAATAA
34838826 TTATTTTTAAATGAATAA
1 TTATTTTTAAATGAATAA
34838844 TTATT
1 TTATT
34838849 ACAATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTATTTTTAAATGAATAA
Found at i:34843518 original size:22 final size:22
Alignment explanation
Indices: 34843485--34843536 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
34843475 AAAAATATAT
34843485 AAAC-ATATTAAATA-TTAAAATA
1 AAACAATA-TAAATATTTAAAA-A
34843507 AAACAATATAAATATTTAAAAA
1 AAACAATATAAATATTTAAAAA
34843529 AAA-AATAT
1 AAACAATAT
34843537 GGACAGACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.18
22 14 0.50
23 9 0.32
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AAACAATATAAATATTTAAAAA
Found at i:34846875 original size:339 final size:338
Alignment explanation
Indices: 34846255--34847270 Score: 1710
Period size: 339 Copynumber: 3.0 Consensus size: 338
34846245 GTGTGGATGA
* ** *
34846255 AACCTCTCGGAGTTTGTCTTCTGATAGAAATAAGAGATCAATTGCTACGAAAAGGATGCCCGATG
1 AACCTCTCGGAGTTTGTCTTCTGATAGAAATAAGAGATCAACTGCTGGGAAAAGGATGGCCGATG
* *
34846320 GGGAAATAAACGTTCCAGGAGAACATTCTGAATTGGAAAGTAATAAACATAAAGATGTTGCTCAC
66 GGGGAATAAACGTTCCAGGAGAACATTCTGAATTGGAAACTAATAAACATAAAGATGTTGCTCAC
* * * *
34846385 AAGGACCTGGAACATGAGTCAAAAGATGATTCCTTTCAATCTCGTCCTGTATCAAAGAAAAAGCG
131 AAGGACCAGGAACATGAGTCAAAAGAAGATTCCTTTCAATCTCGGCCTGCATCAAAGAAAAAGCG
* *
34846450 CAAAGGCGAGAAGAAAGATTTTACTGACAATTCTTTAATAGAAAATGGAGAACAAGCTGCTGATC
196 CAAAGCCGAGAAGAAAGATTTAAC-GACAATTCTTTAATAGAAAATGGAGAACAAGCTGCTGATC
*
34846515 TCAATACTGCAACCTCTGAGTGCACTTTAGGTCAGAAACTGGAAAATACGGGGGCTGTCGCAGAC
260 TCAATACTGCAACCTCTGAGTGCACTTTAGGTCAGAAACTGGAAAATACGGGGGCTGTCGTAGAC
*
34846580 CCCTTGAATATTGC
325 CCCTTGAATACTGC
* *
34846594 AACCTCTCGGAGTTTGTCTTCTAATAGAAATAAGAGCTCAACTGCTGGGAAAAGGATGGCCGATG
1 AACCTCTCGGAGTTTGTCTTCTGATAGAAATAAGAGATCAACTGCTGGGAAAAGGATGGCCGATG
*
34846659 GGGGAATAAACGTTCCAGGAGAACATTCTGAATTGGAAACTAAAAAACATAAAGATGTTGCTCAC
66 GGGGAATAAACGTTCCAGGAGAACATTCTGAATTGGAAACTAATAAACATAAAGATGTTGCTCAC
* *
34846724 AAGGACCAGGAACATGAGTCAAAAGAAGATTCCTTTCAATCTCGGCCTGCATCAAAGAAGAGGCG
131 AAGGACCAGGAACATGAGTCAAAAGAAGATTCCTTTCAATCTCGGCCTGCATCAAAGAAAAAGCG
*
34846789 CAAAGCCGAGAAGAAAGATTGTAACGACAGTTCTTTAATAGAAAATGGAGAACAAGCTGCTGATC
196 CAAAGCCGAGAAGAAAGATT-TAACGACAATTCTTTAATAGAAAATGGAGAACAAGCTGCTGATC
* * *
34846854 TCAATACTGCAACCTCTGAGTGCACTTTAGGTCAGAAACTGGAAAAGACGAGGGCTGTTGTAGAC
260 TCAATACTGCAACCTCTGAGTGCACTTTAGGTCAGAAACTGGAAAATACGGGGGCTGTCGTAGAC
34846919 CCCTTGAATACTGC
325 CCCTTGAATACTGC
* * *
34846933 AACCTCTCGGAGTTTGTCTTCTGATAGAAATAAGAGGTCAACTGCTGGGAAAAGAATGGCTGATG
1 AACCTCTCGGAGTTTGTCTTCTGATAGAAATAAGAGATCAACTGCTGGGAAAAGGATGGCCGATG
**
34846998 GGGGAATAAACAATCCAGGAGAACATTCTGAATTGGAAACTAATAAACATAAAGATGTTGCTCAC
66 GGGGAATAAACGTTCCAGGAGAACATTCTGAATTGGAAACTAATAAACATAAAGATGTTGCTCAC
34847063 AAGGACCAGGAACATGAGTCAAAAGAAGATTCCTTTCAATCTCGGCCTGCATCAAAGAAAAAGCG
131 AAGGACCAGGAACATGAGTCAAAAGAAGATTCCTTTCAATCTCGGCCTGCATCAAAGAAAAAGCG
* * *
34847128 CAAAGCCGAGAAGAAAGCTTTTAATGACAATTCTTTAATAGAAAATGGAGAACAAGCTACTGATC
196 CAAAGCCGAGAAGAAAG-ATTTAACGACAATTCTTTAATAGAAAATGGAGAACAAGCTGCTGATC
34847193 TCAATACTGCAACCTCTGAGTGCACTTTAGGTCAGAAACTGGAAAATA-GGAGGGCTGTCGTAGA
260 TCAATACTGCAACCTCTGAGTGCACTTTAGGTCAGAAACTGGAAAATACGG-GGGCTGTCGTAGA
34847257 CCCCTTGAATACTG
324 CCCCTTGAATACTG
34847271 AATCCGTAAA
Statistics
Matches: 635, Mismatches: 39, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
338 1 0.00
339 629 0.99
340 5 0.01
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (338 bp):
AACCTCTCGGAGTTTGTCTTCTGATAGAAATAAGAGATCAACTGCTGGGAAAAGGATGGCCGATG
GGGGAATAAACGTTCCAGGAGAACATTCTGAATTGGAAACTAATAAACATAAAGATGTTGCTCAC
AAGGACCAGGAACATGAGTCAAAAGAAGATTCCTTTCAATCTCGGCCTGCATCAAAGAAAAAGCG
CAAAGCCGAGAAGAAAGATTTAACGACAATTCTTTAATAGAAAATGGAGAACAAGCTGCTGATCT
CAATACTGCAACCTCTGAGTGCACTTTAGGTCAGAAACTGGAAAATACGGGGGCTGTCGTAGACC
CCTTGAATACTGC
Found at i:34850783 original size:28 final size:28
Alignment explanation
Indices: 34850752--34850813 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
34850742 AATGCACTAT
* * * *
34850752 AGAATAAAAATCAAGGTATTGATTTCAA
1 AGAAGAAAAATCAAAGCATTGATATCAA
34850780 AGAAGAAAAATCAAAGCATTGATATCAA
1 AGAAGAAAAATCAAAGCATTGATATCAA
*
34850808 ATAAGA
1 AGAAGA
34850814 GGTATCAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.15, T:0.23
Consensus pattern (28 bp):
AGAAGAAAAATCAAAGCATTGATATCAA
Found at i:34856313 original size:9 final size:10
Alignment explanation
Indices: 34856291--34856344 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
34856281 ATAACAAATT
34856291 TTTTATATAA
1 TTTTATATAA
34856301 TTTTATA-AA
1 TTTTATATAA
34856310 TTTT-TAATAA
1 TTTTAT-ATAA
34856320 TTTTA-ATAA
1 TTTTATATAA
34856329 TTTTATA-ATA
1 TTTTATATA-A
34856339 TTTTAT
1 TTTTAT
34856345 CAATATACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 1 0.03
9 17 0.44
10 21 0.54
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTATATAA
Found at i:34856319 original size:19 final size:20
Alignment explanation
Indices: 34856290--34856344 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
34856280 AATAACAAAT
34856290 TTTTTATATAATTTTATA-AA
1 TTTTTA-ATAATTTTATATAA
34856310 TTTTTAATAATTTTA-ATAA
1 TTTTTAATAATTTTATATAA
34856329 TTTTATAAT-ATTTTAT
1 TTTT-TAATAATTTTAT
34856345 CAATATACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.03
19 21 0.66
20 10 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAATAATTTTATATAA
Found at i:34856625 original size:21 final size:20
Alignment explanation
Indices: 34856599--34856648 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
34856589 TAAAGATAGT
*
34856599 TTTTTTTAATAATTTCATATA
1 TTTTTTTAATAATTTAATA-A
* *
34856620 TTTTTTATATTATTTTAATAA
1 TTTTTT-TAATAATTTAATAA
34856641 TTTTTTTA
1 TTTTTTTA
34856649 CATCAAACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 13 0.52
22 10 0.40
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTTAATAATTTAATAA
Found at i:34856625 original size:22 final size:21
Alignment explanation
Indices: 34856598--34856647 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
34856588 GTAAAGATAG
*
34856598 TTTTTTTTAATAATTTCATATA
1 TTTTTTTTAATAATTTAATA-A
* * *
34856620 TTTTTTATATTATTTTAATAA
1 TTTTTTTTAATAATTTAATAA
34856641 TTTTTTT
1 TTTTTTT
34856648 ACATCAAACG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTTTAATAATTTAATAA
Found at i:34858824 original size:23 final size:23
Alignment explanation
Indices: 34858798--34858844 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
34858788 GAAAATGAGA
34858798 AAAAAAAATCATTTAATCCTTGT
1 AAAAAAAATCATTTAATCCTTGT
*
34858821 AAAAAAAATCATTTAATTCTTGT
1 AAAAAAAATCATTTAATCCTTGT
34858844 A
1 A
34858845 TTAAATTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (23 bp):
AAAAAAAATCATTTAATCCTTGT
Found at i:34859035 original size:10 final size:9
Alignment explanation
Indices: 34858985--34859114 Score: 54
Period size: 9 Copynumber: 14.3 Consensus size: 9
34858975 ATAAAATGAT
*
34858985 TAAAAATCA
1 TAAAAATTA
34858994 TAAAAATTA
1 TAAAAATTA
*
34859003 TAAAAA-GA
1 TAAAAATTA
*
34859011 TAAAAA-AA
1 TAAAAATTA
34859019 TATAAAATTA
1 TA-AAAATTA
*
34859029 TTAAAAA--C
1 -TAAAAATTA
*
34859037 CAAAAA-TA
1 TAAAAATTA
*
34859045 TTAAAATTGA
1 TAAAAATT-A
*
34859055 TATAAACTTA
1 TA-AAAATTA
*
34859065 TGAAAATTA
1 TAAAAATTA
*
34859074 TACAAAATAA
1 TA-AAAATTA
**
34859084 TAAATTGTTA
1 TAAA-AATTA
*
34859094 TAAATATTA
1 TAAAAATTA
*
34859103 TAAAAAATA
1 TAAAAATTA
34859112 TAA
1 TAA
34859115 CATTAATAAT
Statistics
Matches: 91, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
7 5 0.05
8 14 0.15
9 42 0.46
10 23 0.25
11 7 0.08
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:34859041 original size:26 final size:26
Alignment explanation
Indices: 34858986--34859052 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 26
34858976 TAAAATGATT
*
34858986 AAAAATCATAAAAATTATAAAAAGATAA
1 AAAAAT-AT-AAAATTATAAAAAGACAA
* *
34859014 AAAAATATAAAATTATTAAAA-AC-C
1 AAAAATATAAAATTATAAAAAGACAA
34859038 AAAAATATTAAAATT
1 AAAAATA-TAAAATT
34859053 GATATAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 7 0.20
25 8 0.23
26 12 0.34
27 2 0.06
28 6 0.17
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.25
Consensus pattern (26 bp):
AAAAATATAAAATTATAAAAAGACAA
Found at i:34859185 original size:20 final size:20
Alignment explanation
Indices: 34859162--34859199 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34859152 AAAAAAAACA
* *
34859162 TATTAAAATTCTTAAAAAAT
1 TATTAAAAATCATAAAAAAT
34859182 TATTAAAAATCATAAAAA
1 TATTAAAAATCATAAAAA
34859200 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TATTAAAAATCATAAAAAAT
Found at i:34859245 original size:9 final size:9
Alignment explanation
Indices: 34859176--34859248 Score: 56
Period size: 10 Copynumber: 7.6 Consensus size: 9
34859166 AAAATTCTTA
34859176 AAAAATTATT
1 AAAAATTA-T
*
34859186 AAAAATCAT
1 AAAAATTAT
*
34859195 AAAAATATAA
1 AAAAAT-TAT
34859205 AAAAATATAT
1 AAAAAT-TAT
*
34859215 TAAAATTGAT
1 AAAAATT-AT
**
34859225 ATAATCTTAT
1 A-AAAATTAT
34859235 AAAAATTAT
1 AAAAATTAT
34859244 AAAAA
1 AAAAA
34859249 CTTGAACCAA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
9 19 0.38
10 27 0.54
11 4 0.08
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:34863098 original size:18 final size:18
Alignment explanation
Indices: 34863075--34863110 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
34863065 GTGGAGTTTC
34863075 ATTGACCACATGCGTCAT
1 ATTGACCACATGCGTCAT
34863093 ATTGACCACATGCGTCAT
1 ATTGACCACATGCGTCAT
34863111 CCTTTGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
ATTGACCACATGCGTCAT
Found at i:34871381 original size:29 final size:30
Alignment explanation
Indices: 34871349--34871630 Score: 82
Period size: 29 Copynumber: 9.6 Consensus size: 30
34871339 GGAAGTTTGG
34871349 GGGT-AAAATGGTAATTTTTGGTGAAATCA
1 GGGTAAAAATGGTAATTTTTGGTGAAATCA
* * **
34871378 GGGTTGAAAATGG-AA-TTTT-G-GAAGTTTGG
1 GGG-TAAAAATGGTAATTTTTGGTGAA--ATCA
* * *
34871407 GGGT-AAAATGGTAAATTTTAGTGAAATTA
1 GGGTAAAAATGGTAATTTTTGGTGAAATCA
* * *
34871436 GGGTTAAAAAT--TAAATTTT--AGAAGTTCGA
1 GGG-TAAAAATGGTAATTTTTGGTGAA-ATC-A
* * *
34871465 GGGT-AAAATGGTAATTTTGGGTAAAATTA
1 GGGTAAAAATGGTAATTTTTGGTGAAATCA
* ** *
34871494 GGGTTAAAAATGG-AATTTTAGAAG-GATCGA
1 GGG-TAAAAATGGTAATTTTTGGTGAAATC-A
* *
34871524 GGGT-AAAATAGTAATTTTTGATGAAATCGA
1 GGGTAAAAATGGTAATTTTTGGTGAAATC-A
* * *
34871554 GGTTAAAAATGGT-A-TTTT--AGAAAGTTCGC
1 GGGTAAAAATGGTAATTTTTGGTGAAA--TC-A
* * *
34871583 GGGT-AAAATGGTAATTTTCGGTAAAATTA
1 GGGTAAAAATGGTAATTTTTGGTGAAATCA
34871612 GGGTTAAAAATGG-AATTTT
1 GGG-TAAAAATGGTAATTTT
34871631 AAAAGGTTCG
Statistics
Matches: 188, Mismatches: 35, Indels: 59
0.67 0.12 0.21
Matches are distributed among these distances:
27 22 0.12
28 20 0.11
29 67 0.36
30 38 0.20
31 38 0.20
32 3 0.02
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (30 bp):
GGGTAAAAATGGTAATTTTTGGTGAAATCA
Found at i:34871558 original size:59 final size:58
Alignment explanation
Indices: 34871296--34871660 Score: 421
Period size: 58 Copynumber: 6.3 Consensus size: 58
34871286 ACCCGGAGGC
* * * * *
34871296 AAAATGGTAA-TTTCGGTGAAA-TCGAGGTTAAAAATAGAATTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATTAG-GGTTAAAAATGGAATTTTAGAAGTTCGGGGGT
* * * *
34871353 AAAATGGTAATTTTTGGTGAAATCAGGGTTGAAAATGGAATTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTAGAAGTTCGGGGGT
* * ** *
34871411 AAAATGGTAAATTTTAGTGAAATTAGGGTTAAAAATTAAATTTTAGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTAGAAGTTCGGGGGT
* * * *
34871469 AAAATGGTAATTTTGGGTAAAATTAGGGTTAAAAATGGAATTTTAGAAGGATCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTAGAA-GTTCGGGGGT
* * * * *
34871528 AAAATAGTAATTTTTGATGAAA-TCGAGGTTAAAAATGGTATTTTAGAAAGTTCGCGGGT
1 AAAATGGTAATTTTTGGTGAAATTAG-GGTTAAAAATGGAATTTTAG-AAGTTCGGGGGT
* * *
34871587 AAAATGGTAATTTTCGGTAAAATTAGGGTTAAAAATGGAATTTTAAAAGGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTAGAA-GTTCGGGGGT
*
34871646 AAAATGGTATTTTTT
1 AAAATGGTAATTTTT
34871661 TAAAATTTTA
Statistics
Matches: 262, Mismatches: 39, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
57 10 0.04
58 135 0.52
59 113 0.43
60 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTAGAAGTTCGGGGGT
Found at i:34871954 original size:162 final size:161
Alignment explanation
Indices: 34871761--34872101 Score: 538
Period size: 162 Copynumber: 2.1 Consensus size: 161
34871751 AGGCATCCAT
* * * *
34871761 CAGTCAAGGGATTAAATTGTAAATCTTGAAAAATTCTTGGGCCAATTTTATAATTAAATAAAAGT
1 CAGTCAAAGGATTAAATTATAAACCTTGAAAAATTCTTGAGCCAATTTTATAATTAAATAAAAGT
* * * *
34871826 TAATTTAAGGATTAAATTAAGACAAATTAGAAATGTCAAGGACTAGATGCATAAATAAGCCAAAA
66 TAATTTAAGGATTAAATTAAAACAAATAAAAAATGTCAAGGACTAAATGCA-AAATAAGCCAAAA
*
34871891 AATGACACGTGGCAGCCTCTGGTGCAGTTAAA
130 AATGACACGTGGCAGCCTCTGGTGCAGTCAAA
* * *
34871923 CAGTTAAAGGATTAATTTATAAACCTTGAAAAATTCTTGAGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAAGGATTAAATTATAAACCTTGAAAAATTCTTGAGCCAATTTTATAATTAAATAAAAGT
* * *
34871988 TGATTTAAGGATTAAATTAAAACAAATAAAAAATGTCAGGGACTAAATGTAAAATAAGCCAAAAA
66 TAATTTAAGGATTAAATTAAAACAAATAAAAAATGTCAAGGACTAAATGCAAAATAAGCCAAAAA
34872053 ATGACACGTGGCAGCCTCTGGTGCAGTCAAA
131 ATGACACGTGGCAGCCTCTGGTGCAGTCAAA
34872084 CAGTCAAAGGATTAAATT
1 CAGTCAAAGGATTAAATT
34872102 GAAAACTAAT
Statistics
Matches: 162, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
161 60 0.37
162 102 0.63
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.28
Consensus pattern (161 bp):
CAGTCAAAGGATTAAATTATAAACCTTGAAAAATTCTTGAGCCAATTTTATAATTAAATAAAAGT
TAATTTAAGGATTAAATTAAAACAAATAAAAAATGTCAAGGACTAAATGCAAAATAAGCCAAAAA
ATGACACGTGGCAGCCTCTGGTGCAGTCAAA
Found at i:34872659 original size:16 final size:16
Alignment explanation
Indices: 34872638--34872668 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34872628 TTGGTCTTTC
34872638 AAAACCCAGATCTGGG
1 AAAACCCAGATCTGGG
34872654 AAAACCCAGATCTGG
1 AAAACCCAGATCTGG
34872669 AAATATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.13
Consensus pattern (16 bp):
AAAACCCAGATCTGGG
Found at i:34873674 original size:17 final size:17
Alignment explanation
Indices: 34873656--34873759 Score: 119
Period size: 17 Copynumber: 6.4 Consensus size: 17
34873646 TAAATATTAT
34873656 TTTAAA-TTAAATTAAA
1 TTTAAATTTAAATTAAA
*
34873672 TTTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
34873689 TTTAAA--TAAA-TAAA
1 TTTAAATTTAAATTAAA
34873703 TTTAAATTTAAGA-TAAA
1 TTTAAATTTAA-ATTAAA
*
34873720 TTTAAATTTAAATAAAA
1 TTTAAATTTAAATTAAA
* *
34873737 TTTAAAATTAATTTAAA
1 TTTAAATTTAAATTAAA
*
34873754 CTTAAA
1 TTTAAA
34873760 AATCAAAATC
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
14 10 0.13
15 4 0.05
16 10 0.13
17 53 0.69
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:34873678 original size:6 final size:6
Alignment explanation
Indices: 34873656--34873759 Score: 87
Period size: 6 Copynumber: 18.0 Consensus size: 6
34873646 TAAATATTAT
* *
34873656 TTTAAA -TTAAA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TAAATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* *
34873703 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA -TAAAA TTTAAA ATT-AA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
34873748 TTTAAA CTTAAA
1 TTTAAA TTTAAA
34873760 AATCAAAATC
Statistics
Matches: 80, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
4 1 0.01
5 25 0.31
6 48 0.60
7 1 0.01
8 5 0.06
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:34873678 original size:11 final size:11
Alignment explanation
Indices: 34873656--34873759 Score: 86
Period size: 11 Copynumber: 9.0 Consensus size: 11
34873646 TAAATATTAT
34873656 TTTAAATTAAA
1 TTTAAATTAAA
34873667 -TTAAATTTAAA
1 TTTAAA-TTAAA
*
34873678 TTTAAAATAAA
1 TTTAAATTAAA
34873689 TTTAAATAAATAAA
1 TTTAAAT---TAAA
*
34873703 TTTAAATTTAA
1 TTTAAATTAAA
**
34873714 GATAAATTTAAA
1 TTTAAA-TTAAA
*
34873726 TTTAAATAAAA
1 TTTAAATTAAA
34873737 TTTAAAATT-AA
1 TTT-AAATTAAA
34873748 TTTAAACTTAAA
1 TTTAAA-TTAAA
34873760 AATCAAAATC
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
10 8 0.11
11 36 0.49
12 19 0.26
14 11 0.15
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:34873708 original size:37 final size:37
Alignment explanation
Indices: 34873658--34873752 Score: 99
Period size: 37 Copynumber: 2.5 Consensus size: 37
34873648 AATATTATTT
34873658 TAAATTAAATTAAATTTAA-ATTTAAA-ATAAATTTAAA
1 TAAATTAAATTAAATTTAAGA--TAAATATAAATTTAAA
*
34873695 TAAA-TAAATTTAAATTTAAGATAAATTTAAATTTAAA
1 TAAATTAAA-TTAAATTTAAGATAAATATAAATTTAAA
34873732 TAAAATTTAAAATT-AATTTAA
1 T-AAA-TT-AAATTAAATTTAA
34873753 ACTTAAAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
36 8 0.16
37 25 0.50
38 4 0.08
39 7 0.14
40 3 0.06
41 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (37 bp):
TAAATTAAATTAAATTTAAGATAAATATAAATTTAAA
Found at i:34873760 original size:17 final size:16
Alignment explanation
Indices: 34873645--34873760 Score: 75
Period size: 17 Copynumber: 7.4 Consensus size: 16
34873635 TTTATTAATT
*
34873645 TTAAATATTATTTTAAA
1 TTAAA-ATTAATTTAAA
34873662 TT-AAATTAAATTTAAA
1 TTAAAATT-AATTTAAA
*
34873678 TTTAAAATAAATTTAAA
1 -TTAAAATTAATTTAAA
*
34873695 -T-AAATAAATTTAAA
1 TTAAAATTAATTTAAA
* *
34873709 TTTAAGATAAATTTAAA
1 -TTAAAATTAATTTAAA
* *
34873726 TTTAAA-TAA---AAT
1 TTAAAATTAATTTAAA
34873738 TTAAAATTAATTTAAA
1 TTAAAATTAATTTAAA
34873754 CTTAAAA
1 -TTAAAA
34873761 ATCAAAATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
12 7 0.09
13 3 0.04
14 13 0.16
15 6 0.08
16 16 0.20
17 30 0.38
18 4 0.05
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
TTAAAATTAATTTAAA
Found at i:34874344 original size:75 final size:76
Alignment explanation
Indices: 34874022--34874761 Score: 1068
Period size: 76 Copynumber: 10.1 Consensus size: 76
34874012 TCGAGGCTTC
*
34874022 ATCTTGCTCTTA-TTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGTG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
*
34874086 GGTAGGAAATG
66 GATAGGAAATG
* *
34874097 A-CGTTGCTCTTACTTCAATTTCAGAGATGACGACTTGTTATCCAACTCTACTTCAATTTCAAGA
1 ATC-TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
34874161 GGATAGGAAATG
65 GGATAGGAAATG
34874173 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
34874238 GATAGGAAATG
66 GATAGGAAATG
* *
34874249 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
34874313 GATAGGAAATG
66 GATAGGAAATG
* *
34874324 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATGCAACTCTACTTCAATTTCAAGCG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
34874389 GATAGGAAATG
66 GATAGGAAATG
*
34874400 A-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCAATTTTAAGA
1 ATC-TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
34874463 GGATAGGAAATG
65 GGATAGGAAATG
* *
34874475 ATTTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTC-A-A-
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
34874536 G--AGG--ATG
66 GATAGGAAATG
* *
34874543 ACCTTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
*
34874607 GAT--G--ACG
66 GATAGGAAATG
* * *
34874614 ---TTGCTCTTACCTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
*
34874676 GAT--G--ACG
66 GATAGGAAATG
* * *
34874683 ---TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACCCTACTTCAATTTCAAGCG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
*
34874745 GATGGGAAATG
66 GATAGGAAATG
34874756 ATCTTG
1 ATCTTG
34874762 TTTGGTCTGA
Statistics
Matches: 618, Mismatches: 28, Indels: 37
0.90 0.04 0.05
Matches are distributed among these distances:
68 97 0.16
69 91 0.15
70 4 0.01
71 5 0.01
72 1 0.00
73 3 0.00
74 2 0.00
75 168 0.27
76 246 0.40
77 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
GATAGGAAATG
Found at i:34874392 original size:151 final size:150
Alignment explanation
Indices: 34874022--34874761 Score: 1092
Period size: 151 Copynumber: 5.0 Consensus size: 150
34874012 TCGAGGCTTC
*
34874022 ATCTTGCTCTTA-TTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGTG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCG
* * * *
34874086 GGTAGGAAATGACGTTGCTCTTACTTCAATTTCAGAGATGACGACTTGTTATCCAACTCTACTTC
66 GATAGGAAATGAC-TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTC
34874151 AATTTCAAGAGGATAGGAAATG
129 AATTTCAAGAGGATAGGAAATG
*
34874173 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCG
*
34874238 GATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTTTACTTCA
66 GATAGGAAATGA-CTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCA
34874303 ATTTCAAGAGGATAGGAAATG
130 ATTTCAAGAGGATAGGAAATG
*
34874324 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATGCAACTCTACTTCAATTTCAAGCG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCG
*
34874389 GATAGGAAATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCA
66 GATAGGAAATGAC-TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCA
*
34874454 ATTTTAAGAGGATAGGAAATG
130 ATTTCAAGAGGATAGGAAATG
* *
34874475 ATTTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAA---
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCG
*
34874536 G--AGG--ATGACCTTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCA
66 GATAGGAAATGA-CTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCA
*
34874597 ATTTCAAGAGGAT--G--ACG
130 ATTTCAAGAGGATAGGAAATG
* *
34874614 ---TTGCTCTTACCTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCG
* *
34874676 GAT--G--ACG--TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACCCTACTTCA
66 GATAGGAAATGACTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCA
* *
34874735 ATTTCAAGCGGATGGGAAATG
130 ATTTCAAGAGGATAGGAAATG
34874756 ATCTTG
1 ATCTTG
34874762 TTTGGTCTGA
Statistics
Matches: 548, Mismatches: 23, Indels: 42
0.89 0.04 0.07
Matches are distributed among these distances:
136 39 0.07
137 57 0.10
138 22 0.04
139 2 0.00
140 5 0.01
141 1 0.00
142 2 0.00
143 66 0.12
144 1 0.00
145 6 0.01
147 1 0.00
150 19 0.03
151 227 0.41
152 99 0.18
153 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (150 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCG
GATAGGAAATGACTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAA
TTTCAAGAGGATAGGAAATG
Found at i:34874587 original size:68 final size:69
Alignment explanation
Indices: 34874252--34874748 Score: 660
Period size: 75 Copynumber: 7.0 Consensus size: 69
34874242 GGAAATGATC
*
34874252 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTTTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
*
34874316 AGGAAATG
66 --G--ACG
* *
34874324 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATGCAACTCTACTTCAATTTCAAGCG
1 ---TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAA---
34874389 GATAGGAAATGACG
60 G--AGG--ATGACG
* *
34874403 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCAATTTTAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
*
34874467 AGGAAATG
66 --G--ACG
34874475 ATTTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAG
1 ---TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAG
*
34874539 GATGACC
63 GATGACG
*
34874546 TTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
34874610 GACG
66 GACG
* *
34874614 TTGCTCTTACCTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
34874679 GACG
66 GACG
* *
34874683 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACCCTACTTCAATTTCAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
34874748 G
66 G
34874749 GGAAATGATC
Statistics
Matches: 388, Mismatches: 18, Indels: 38
0.87 0.04 0.09
Matches are distributed among these distances:
68 106 0.27
69 91 0.23
70 4 0.01
71 1 0.00
72 3 0.01
73 1 0.00
75 117 0.30
76 56 0.14
79 3 0.01
81 4 0.01
83 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (69 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
GACG
Found at i:34882647 original size:24 final size:27
Alignment explanation
Indices: 34882597--34882647 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 27
34882587 TATGTTAACA
* *
34882597 GTATGCAAGATATGATGCAAAATGCAT
1 GTATGCAAGATACGATGCAAAAGGCAT
34882624 GTATGCAA-ATACGA-G-AAAAGGCAT
1 GTATGCAAGATACGATGCAAAAGGCAT
34882648 TGATTCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 8 0.36
25 1 0.05
26 5 0.23
27 8 0.36
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.22
Consensus pattern (27 bp):
GTATGCAAGATACGATGCAAAAGGCAT
Found at i:34886572 original size:15 final size:16
Alignment explanation
Indices: 34886545--34886578 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
34886535 ATTAGATACG
34886545 AAATAATATAATAAGC
1 AAATAATATAATAAGC
*
34886561 AAATAA-ATAATATGC
1 AAATAATATAATAAGC
34886576 AAA
1 AAA
34886579 ATATAAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (16 bp):
AAATAATATAATAAGC
Found at i:34886755 original size:29 final size:29
Alignment explanation
Indices: 34886722--34886811 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 29
34886712 TAAAAAATAG
34886722 AATTTTTGAGAGTTCGGGGGTAATATGGT
1 AATTTTTGAGAGTTCGGGGGTAATATGGT
* * *
34886751 AA-TTTTGATGAAATT-GGGGTTAAAAATGGT
1 AATTTTTGA-G-AGTTCGGGGGT-AATATGGT
* * *
34886781 -ATTTTAGAAAGTTCGAGGGTAATATGGT
1 AATTTTTGAGAGTTCGGGGGTAATATGGT
34886809 AAT
1 AAT
34886812 CTTCGATAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
28 16 0.35
29 15 0.33
30 15 0.33
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (29 bp):
AATTTTTGAGAGTTCGGGGGTAATATGGT
Found at i:34886830 original size:59 final size:59
Alignment explanation
Indices: 34886683--34887165 Score: 544
Period size: 58 Copynumber: 8.3 Consensus size: 59
34886673 CAATATTCGA
* * * * * *
34886683 TAAAATGGTAA-TTTTGGTGAAGTTGGGGTTAAAAAATAGAATTTTTGAGAGTTCGGGGG
1 TAAAATGGTAATTTTTGATGAAATCGGGGTT-AAAAATGGAATTTTAGAAAGTTCGGGGG
* * * *
34886742 TAATATGGTAA-TTTTGATGAAATTGGGGTTAAAAATGGTATTTTAGAAAGTTCGAGGG
1 TAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGG
* * * * * **
34886800 TAATATGGTAATCTTCGATAAAATCGGGGTTAAAAATAGAATTTT-GAAAGTTCAAGGG
1 TAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGG
* * *** * *
34886858 TAAAACGGTAATTTTTGGTGAAATTAAGGTTAAAAATGGAATTTT-GGAAGTTCAGGGG
1 TAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGG
* * * * *
34886916 TAAAATGGTAAATTTTGGTTAAATCAGGGTTAAAAATGAAATTTTAG-AAGTTCGGGGG
1 TAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGG
* * * * *
34886974 TAAAATGGTAATTTTAGGTGAAACCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGAGG
1 TAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGG
* ** * *
34887033 TAAAATGGTAATTTTCGATGAAATTAGGGTTAAAAATGGTATTTTAGAAAGTTTGGGGG
1 TAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGG
* * *
34887092 TAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATAGAATTTTAGAAGGTTCGGGGG
1 TAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGG
34887151 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
34887166 CTAAAATTTT
Statistics
Matches: 362, Mismatches: 59, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
58 182 0.50
59 180 0.50
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (59 bp):
TAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGG
Found at i:34886902 original size:29 final size:29
Alignment explanation
Indices: 34886870--34887077 Score: 92
Period size: 31 Copynumber: 7.1 Consensus size: 29
34886860 AAACGGTAAT
*
34886870 TTTTGGTGAAATTAAGGTTAAAAATGGAA
1 TTTTGGTGAAATTAGGGTTAAAAATGGAA
* *
34886899 TTTT-G-GAAGTTCAGGGGT-AAAATGGTAAA
1 TTTTGGTGAAATT-AGGGTTAAAAATGG--AA
* * *
34886928 TTTTGGTTAAATCAGGGTTAAAAATGAAA
1 TTTTGGTGAAATTAGGGTTAAAAATGGAA
* * * *
34886957 TTTT--AGAAGTTCGGGGGT-AAAATGGTAA
1 TTTTGGTGAAATT-AGGGTTAAAAATGG-AA
***
34886985 TTTTAGGTGAAACCGGGGTTAAAAATGGAA
1 TTTT-GGTGAAATTAGGGTTAAAAATGGAA
* * * *
34887015 TTTT--AGAAGGTTCGGAGGT-AAAATGGTAA
1 TTTTGGTGAA-ATTAGG-GTTAAAAATGG-AA
* *
34887044 TTTTCGATGAAATTAGGGTTAAAAATGGTA
1 TTTT-GGTGAAATTAGGGTTAAAAATGGAA
34887074 TTTT
1 TTTT
34887078 AGAAAGTTTG
Statistics
Matches: 129, Mismatches: 31, Indels: 37
0.65 0.16 0.19
Matches are distributed among these distances:
27 24 0.19
28 24 0.19
29 24 0.19
30 24 0.19
31 30 0.23
32 3 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
TTTTGGTGAAATTAGGGTTAAAAATGGAA
Found at i:34887105 original size:29 final size:29
Alignment explanation
Indices: 34886683--34887165 Score: 186
Period size: 29 Copynumber: 16.5 Consensus size: 29
34886673 CAATATTCGA
* * *
34886683 TAAAATGGTAATTTTGGTGAAGTT-GGGGT
1 TAAAATGGTAATTTTAG-AAAGTTCGGGGG
* * *
34886712 TAAAAAATAG-AATTTTTGAGAGTTCGGGGG
1 T--AAAATGGTAATTTTAGAAAGTTCGGGGG
* *
34886742 TAATATGGTAATTTTGATGAAA-TT-GGGGT
1 TAAAATGGTAATTTT-A-GAAAGTTCGGGGG
*
34886771 TAAAAATGGT-ATTTTAGAAAGTTCGAGGG
1 T-AAAATGGTAATTTTAGAAAGTTCGGGGG
* * * ** *
34886800 TAATATGGTAATCTTCGATAAAATCGGGGT
1 TAAAATGGTAATTTTAGA-AAGTTCGGGGG
* **
34886830 TAAAAATAG-AATTTT-GAAAGTTCAAGGG
1 T-AAAATGGTAATTTTAGAAAGTTCGGGGG
* * ** *
34886858 TAAAACGGTAATTTTTGGTGAAA-TT-AAGGT
1 TAAAATGGTAA-TTTT--AGAAAGTTCGGGGG
* *
34886888 TAAAAATGG-AATTTT-GGAAGTTCAGGGG
1 T-AAAATGGTAATTTTAGAAAGTTCGGGGG
* * *
34886916 TAAAATGGTAAATTTTGGTTAAA--TCAGGGT
1 TAAAATGGT-AATTTTAG--AAAGTTCGGGGG
*
34886946 TAAAAAT-GAAATTTTAG-AAGTTCGGGGG
1 T-AAAATGGTAATTTTAGAAAGTTCGGGGG
* *
34886974 TAAAATGGTAATTTTAGGTGAAA--CCGGGGT
1 TAAAATGGTAATTTTA---GAAAGTTCGGGGG
* *
34887004 TAAAAATGG-AATTTTAGAAGGTTCGGAGG
1 T-AAAATGGTAATTTTAGAAAGTTCGGGGG
* *
34887033 TAAAATGGTAATTTTCGATGAAA-TT-AGGGT
1 TAAAATGGTAATTTT--A-GAAAGTTCGGGGG
*
34887063 TAAAAATGGT-ATTTTAGAAAGTTTGGGGG
1 T-AAAATGGTAATTTTAGAAAGTTCGGGGG
* *
34887092 TAAAATGGTAATTTTTGATGAAA--TCGAGGT
1 TAAAATGGTAA-TTTT-A-GAAAGTTCGGGGG
* *
34887122 TAAAAATAG-AATTTTAGAAGGTTCGGGGG
1 T-AAAATGGTAATTTTAGAAAGTTCGGGGG
34887151 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
34887166 CTAAAATTTT
Statistics
Matches: 341, Mismatches: 62, Indels: 102
0.68 0.12 0.20
Matches are distributed among these distances:
26 5 0.01
27 33 0.10
28 67 0.20
29 86 0.25
30 82 0.24
31 53 0.16
32 15 0.04
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (29 bp):
TAAAATGGTAATTTTAGAAAGTTCGGGGG
Found at i:34887440 original size:162 final size:161
Alignment explanation
Indices: 34887267--34887613 Score: 532
Period size: 162 Copynumber: 2.1 Consensus size: 161
34887257 AGGCATCCAG
*
34887267 CAGTCAAGGGATTAAATTGTAAATCTTGAAAAATTCTTGAGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAGGGATTAAATTGTAAACCTTGAAAAATTCTTGAGCCAATTTTGTAATTAAATAAAAGT
* *** * *
34887332 TGATTTAAGGATTAAATTAAAACAAATTTGAAATGTTAGGGACTAGATGCATAAATAAGCCAAAA
66 TGATCTAAGGATTAAATTAAAACAAATCAAAAATGTCAGGGACTAAATGCA-AAATAAGCCAAAA
*
34887397 AATGACACGTGGCAACCTCTGGTGCAGTCAAA
130 AATGACACATGGCAACCTCTGGTGCAGTCAAA
* * *
34887429 CAGTCAAGGGATTAATTTATAAACCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAGGGATTAAATTGTAAACCTTGAAAAATTCTTGAGCCAATTTTGTAATTAAATAAAAGT
*
34887494 TGATCTAAGGATTAAATTAAAACAAATCAAAAATGTCAGGGACTAAATGTAAAATAAGCCAAAAA
66 TGATCTAAGGATTAAATTAAAACAAATCAAAAATGTCAGGGACTAAATGCAAAATAAGCCAAAAA
* *
34887559 ATGACACATGGCAGCCTCTGGTGTAGTCAAA
131 ATGACACATGGCAACCTCTGGTGCAGTCAAA
** *
34887590 CAGTCAAAAGATTAAATTGAAAAC
1 CAGTCAAGGGATTAAATTGTAAAC
34887614 TAATTAAAAT
Statistics
Matches: 166, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
161 61 0.37
162 105 0.63
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (161 bp):
CAGTCAAGGGATTAAATTGTAAACCTTGAAAAATTCTTGAGCCAATTTTGTAATTAAATAAAAGT
TGATCTAAGGATTAAATTAAAACAAATCAAAAATGTCAGGGACTAAATGCAAAATAAGCCAAAAA
ATGACACATGGCAACCTCTGGTGCAGTCAAA
Found at i:34889159 original size:13 final size:13
Alignment explanation
Indices: 34889137--34889251 Score: 56
Period size: 11 Copynumber: 9.7 Consensus size: 13
34889127 ACTTTTATTT
34889137 TATTAATTTTAAA
1 TATTAATTTTAAA
*
34889150 TATTATTTTTAAA
1 TATTAATTTTAAA
34889163 T-TTAA--TTAAA
1 TATTAATTTTAAA
*
34889173 T-TTAAATTTAAA
1 TATTAATTTTAAA
*
34889185 -A-TAAATTTAAA
1 TATTAATTTTAAA
* *
34889196 TAAATAAATTTAAA
1 T-ATTAATTTTAAA
**
34889210 T-TTAA-GATAAA
1 TATTAATTTTAAA
*
34889221 T-TTAAATTTAAA
1 TATTAATTTTAAA
*
34889233 TA--AAATTTAAA
1 TATTAATTTTAAA
34889244 -ATTAATTT
1 TATTAATTT
34889252 AAACTTAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
10 11 0.13
11 28 0.33
12 20 0.24
13 14 0.17
14 11 0.13
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (13 bp):
TATTAATTTTAAA
Found at i:34889166 original size:6 final size:6
Alignment explanation
Indices: 34889157--34889260 Score: 87
Period size: 6 Copynumber: 18.0 Consensus size: 6
34889147 AAATATTATT
* *
34889157 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TAAATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* *
34889204 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA -TAAAA TTTAAA ATT-AA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
34889249 TTTAAA CTTAAA
1 TTTAAA TTTAAA
34889261 AATCAAAATC
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
4 3 0.04
5 19 0.24
6 51 0.65
7 1 0.01
8 5 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:34889170 original size:16 final size:16
Alignment explanation
Indices: 34889157--34889260 Score: 104
Period size: 17 Copynumber: 6.4 Consensus size: 16
34889147 AAATATTATT
34889157 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
*
34889173 TTTAAATTTAAAATAAA
1 TTTAAATTT-AATTAAA
*
34889190 TTTAAA--TAAATAAA
1 TTTAAATTTAATTAAA
*
34889204 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-TTAAA
*
34889221 TTTAAATTTAAATAAAA
1 TTTAAATTT-AATTAAA
*
34889238 TTTAAAATTAATTTAAA
1 TTTAAATTTAA-TTAAA
*
34889255 CTTAAA
1 TTTAAA
34889261 AATCAAAATC
Statistics
Matches: 76, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.17
15 1 0.01
16 14 0.18
17 46 0.61
18 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:34889191 original size:17 final size:16
Alignment explanation
Indices: 34889157--34889248 Score: 125
Period size: 17 Copynumber: 5.7 Consensus size: 16
34889147 AAATATTATT
*
34889157 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
34889173 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
34889190 TTTAAA--TAAATAAA
1 TTTAAATTTAAATAAA
34889204 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
34889221 TTTAAATTTAAATAAAA
1 TTTAAATTTAAAT-AAA
*
34889238 TTTAAAATTAA
1 TTTAAATTTAA
34889249 TTTAAACTTA
Statistics
Matches: 69, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
14 13 0.19
15 1 0.01
16 14 0.20
17 41 0.59
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:34894463 original size:49 final size:50
Alignment explanation
Indices: 34894389--34894483 Score: 138
Period size: 49 Copynumber: 1.9 Consensus size: 50
34894379 GGCCTTGAAG
* * * *
34894389 ATATGTGGGGTGTGTTTGGAGAGTGTTTAACTTTATGCTACACTTAAGGC
1 ATATGTGGGATGTGTTTGGAAAGTGTATAACTTGATGCTACACTTAAGGC
*
34894439 ATATGTGGGATGT-TTTGGAAAGTGTATAGCTTGATGCTACACTTA
1 ATATGTGGGATGTGTTTGGAAAGTGTATAACTTGATGCTACACTTA
34894484 TGGGAGGTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 28 0.70
50 12 0.30
ACGTcount: A:0.24, C:0.09, G:0.28, T:0.38
Consensus pattern (50 bp):
ATATGTGGGATGTGTTTGGAAAGTGTATAACTTGATGCTACACTTAAGGC
Found at i:34894912 original size:18 final size:18
Alignment explanation
Indices: 34894889--34894923 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
34894879 CGCTTGGGCG
34894889 TAGAGATATCTTTCTATA
1 TAGAGATATCTTTCTATA
34894907 TAGAGATATCTTTCTAT
1 TAGAGATATCTTTCTAT
34894924 CTGTTGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
TAGAGATATCTTTCTATA
Found at i:34895580 original size:18 final size:18
Alignment explanation
Indices: 34895557--34895591 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34895547 TTTATAATTT
* *
34895557 TTATCCTTAATTAATAAA
1 TTATCCTCAACTAATAAA
34895575 TTATCCTCAACTAATAA
1 TTATCCTCAACTAATAA
34895592 TTTACCATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (18 bp):
TTATCCTCAACTAATAAA
Found at i:34896531 original size:23 final size:24
Alignment explanation
Indices: 34896496--34896541 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
34896486 ATTTGTTGAT
*
34896496 TTTTAAATATTTAT-TATTATATC
1 TTTTAAATATTTATAAATTATATC
* *
34896519 TTTTGAATTTTTATAAATTATAT
1 TTTTAAATATTTATAAATTATAT
34896542 GTGGACTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTAAATATTTATAAATTATATC
Found at i:34897123 original size:16 final size:16
Alignment explanation
Indices: 34897072--34897124 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
34897062 GAAACTAATT
34897072 TTTTTTTACAACA-TTCA
1 TTTTTTTA-AA-ATTTCA
*
34897089 TTTTTTATAATATTT-A
1 TTTTTT-TAAAATTTCA
34897105 TTTTTTTAAAATTTCA
1 TTTTTTTAAAATTTCA
34897121 TTTT
1 TTTT
34897125 AAATTATGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 7 0.23
16 13 0.42
17 9 0.29
18 2 0.06
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTTTAAAATTTCA
Found at i:34897823 original size:15 final size:15
Alignment explanation
Indices: 34897777--34897825 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
34897767 AAATCATTTA
34897777 TTTTAATTTAATAAT
1 TTTTAATTTAATAAT
* *
34897792 TTTTTATATTCATAAT
1 TTTTAAT-TTAATAAT
*
34897808 TTTTAATTTAAAAAT
1 TTTTAATTTAATAAT
34897823 TTT
1 TTT
34897826 AATGAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTAATTTAATAAT
Found at i:34898382 original size:23 final size:23
Alignment explanation
Indices: 34898356--34898399 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
34898346 TAAGGTCCAC
*
34898356 CGATTTCGATCGTCGGCGATCGG
1 CGATTGCGATCGTCGGCGATCGG
*
34898379 CGATTGGGATCGTCGGCGATC
1 CGATTGCGATCGTCGGCGATC
34898400 AAGCGGGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (23 bp):
CGATTGCGATCGTCGGCGATCGG
Found at i:34904358 original size:58 final size:58
Alignment explanation
Indices: 34904289--34904408 Score: 179
Period size: 58 Copynumber: 2.1 Consensus size: 58
34904279 AAAAAGAGTT
** *
34904289 GTTTATGAGTGTTATTTAGGAATAAAATTATA-TTTGATTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAAAATAAAATTATATTTTG-TTTTAAAAATATTTGAGTTTA
* *
34904347 GTTTATGAGTGTTTTTTAAAAATGAAATTATATTTTGTTTTAAAAATATTTGAGTTTA
1 GTTTATGAGTGTTATTTAAAAATAAAATTATATTTTGTTTTAAAAATATTTGAGTTTA
34904405 GTTT
1 GTTT
34904409 GTTGATGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 52 0.93
59 4 0.07
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAAAATAAAATTATATTTTGTTTTAAAAATATTTGAGTTTA
Found at i:34904422 original size:58 final size:58
Alignment explanation
Indices: 34904313--34904424 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
34904303 TTTAGGAATA
* **
34904313 AAATTATATTTGATTTTAAAAATATTTGGGTTTAGTTTATGAGTGTTTTTTAAAAATG
1 AAATTATATTTGATTTTAAAAATATTTGAGTTTAGTTTATGAGTGGGTTTTAAAAATG
*
34904371 AAATTATATTTTG-TTTTAAAAATATTTGAGTTTAGTTTGTTGA-TGGGTTTTAAA
1 AAATTATA-TTTGATTTTAAAAATATTTGAGTTTAGTTT-ATGAGTGGGTTTTAAA
34904425 TATTAGGGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 41 0.85
59 7 0.15
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (58 bp):
AAATTATATTTGATTTTAAAAATATTTGAGTTTAGTTTATGAGTGGGTTTTAAAAATG
Found at i:34915529 original size:30 final size:30
Alignment explanation
Indices: 34915495--34915584 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 30
34915485 GTAATCTCAA
*
34915495 TATAATGTTAGCTTGTGTGAGCAACTCTAT
1 TATAATGTCAGCTTGTGTGAGCAACTCTAT
* *
34915525 TATAATGTCAACTTGTGTGAACAAC-CT-T
1 TATAATGTCAGCTTGTGTGAGCAACTCTAT
*
34915553 GATATACTGTCAGCTTGTGTGAGCAACT-TAT
1 --TATAATGTCAGCTTGTGTGAGCAACTCTAT
34915584 T
1 T
34915585 CTCGTGTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
28 1 0.02
29 3 0.06
30 45 0.90
31 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (30 bp):
TATAATGTCAGCTTGTGTGAGCAACTCTAT
Found at i:34918372 original size:22 final size:22
Alignment explanation
Indices: 34918346--34918400 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
34918336 CTAAATTTTA
34918346 AAATTTAAAAAATAAAAAGATT
1 AAATTTAAAAAATAAAAAGATT
* **
34918368 AAATTCTTAAAAATAAAATTATT
1 AAATT-TAAAAAATAAAAAGATT
34918391 AAATGTTAAA
1 AAAT-TTAAA
34918401 TTTTTTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 21 0.78
24 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATTTAAAAAATAAAAAGATT
Found at i:34929611 original size:5 final size:5
Alignment explanation
Indices: 34929603--34929636 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
34929593 AATGGAAGTA
34929603 GATGG GATGG GATGG GATGG GATGG GATGG GATG
1 GATGG GATGG GATGG GATGG GATGG GATGG GATG
34929637 TTCAGTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.59, T:0.21
Consensus pattern (5 bp):
GATGG
Found at i:34937282 original size:19 final size:17
Alignment explanation
Indices: 34937258--34937305 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
34937248 AAAGCACCAA
*
34937258 CCTTTCTTTCTTTTCTTTT
1 CCTTTC-TTCTTTT-TATT
34937277 CCTTTCTT-TTTTTATT
1 CCTTTCTTCTTTTTATT
34937293 CCTTTCTTCTTTT
1 CCTTTCTTCTTTT
34937306 ATGGTCGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 11 0.41
17 8 0.30
18 2 0.07
19 6 0.22
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (17 bp):
CCTTTCTTCTTTTTATT
Found at i:34937294 original size:16 final size:16
Alignment explanation
Indices: 34937263--34937307 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
34937253 ACCAACCTTT
*
34937263 CTTTCTTTTCTT-TTC
1 CTTTCTTTTTTTATTC
34937278 CTTTCTTTTTTTATTC
1 CTTTCTTTTTTTATTC
*
34937294 CTTTCTTCTTTTAT
1 CTTTCTTTTTTTAT
34937308 GGTCGGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.73
Consensus pattern (16 bp):
CTTTCTTTTTTTATTC
Found at i:34937682 original size:17 final size:17
Alignment explanation
Indices: 34937660--34937693 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
34937650 TTAACATTGG
34937660 ATTGGGAATATT-ATTTA
1 ATTGGGAA-ATTAATTTA
34937677 ATTGGGAAATTAATTTA
1 ATTGGGAAATTAATTTA
34937694 TTATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (17 bp):
ATTGGGAAATTAATTTA
Found at i:34942073 original size:15 final size:15
Alignment explanation
Indices: 34942053--34942090 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
34942043 ATATAATGAT
34942053 ATATATGTGAGAAAA
1 ATATATGTGAGAAAA
* *
34942068 ATATATGTGTGAAAT
1 ATATATGTGAGAAAA
34942083 AT-TATGTG
1 ATATATGTG
34942091 GTTAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (15 bp):
ATATATGTGAGAAAA
Found at i:34942408 original size:41 final size:41
Alignment explanation
Indices: 34942356--34942460 Score: 110
Period size: 38 Copynumber: 2.7 Consensus size: 41
34942346 TACTTCGACC
** *
34942356 TAGAGTCGATGAGACACTGGGTGTCATTATTTTACTTCGGA
1 TAGAGTCGATGAGACACTGGGTGTCACCACTTTACTTCGGA
* ** *
34942397 TAGATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGC
1 TAGAGTCGATGAGACACTGGGTGTCACCACTTTACTTCGGA
*
34942435 TAG-GCCGATGAGACACTGGGTGTCAC
1 TAGAGTCGATGAGACACTGGGTGTCAC
34942461 TTTATTGCTT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
37 10 0.20
38 17 0.34
39 4 0.08
40 4 0.08
41 15 0.30
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.30
Consensus pattern (41 bp):
TAGAGTCGATGAGACACTGGGTGTCACCACTTTACTTCGGA
Found at i:34944929 original size:4 final size:4
Alignment explanation
Indices: 34944922--34944959 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
34944912 CATGTTTACG
34944922 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
34944960 TTTAATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:34946404 original size:27 final size:29
Alignment explanation
Indices: 34946355--34946409 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
34946345 CTTAATTTTT
34946355 TATTTTATAAAAATTAATATTAA-AATTA
1 TATTTTATAAAAATTAATATTAACAATTA
*
34946383 TATTTT-TAAAAA-TAGTACTTAACAATT
1 TATTTTATAAAAATTAATA-TTAACAATT
34946410 TTCTTTTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 10 0.42
28 10 0.42
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (29 bp):
TATTTTATAAAAATTAATATTAACAATTA
Found at i:34946830 original size:25 final size:26
Alignment explanation
Indices: 34946802--34946861 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
34946792 TATATATAAG
34946802 CTTATAATAATTATAAAA-ACAAAAA
1 CTTATAATAATTATAAAATACAAAAA
*
34946827 CTTATAA-ATATTATAAAATATAAAAA
1 CTTATAATA-ATTATAAAATACAAAAA
*
34946853 ATT-TAATAA
1 CTTATAATAA
34946862 ATTCTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 1 0.03
25 20 0.67
26 9 0.30
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (26 bp):
CTTATAATAATTATAAAATACAAAAA
Found at i:34946862 original size:28 final size:28
Alignment explanation
Indices: 34946822--34946880 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
34946812 TTATAAAAAC
34946822 AAAAACTTATAAATAT-T-ATAAAATATA
1 AAAAACTTATAAAT-TCTAATAAAATATA
* *
34946849 AAAAATTTAATAAATTCTAATAAATTATA
1 AAAAACTT-ATAAATTCTAATAAAATATA
34946878 AAA
1 AAA
34946881 TTATAAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 7 0.26
29 12 0.44
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (28 bp):
AAAAACTTATAAATTCTAATAAAATATA
Found at i:34946927 original size:30 final size:28
Alignment explanation
Indices: 34946892--34946970 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 28
34946882 TATAAAGTTA
*
34946892 ATAAAACATATTTAAAATATTTAGAACATT
1 ATAAAACATA-TTAAAATATTTA-AAAATT
* *
34946922 ATAAAAACATATAAAAATTCTTTAAAAATT
1 AT-AAAACATATTAAAA-TATTTAAAAATT
*
34946952 ATAAAA-TTATTAAAATATT
1 ATAAAACATATTAAAATATT
34946971 ACAATTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
27 3 0.07
28 7 0.17
29 4 0.10
30 14 0.34
31 13 0.32
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (28 bp):
ATAAAACATATTAAAATATTTAAAAATT
Found at i:34946956 original size:9 final size:9
Alignment explanation
Indices: 34946803--34946967 Score: 69
Period size: 9 Copynumber: 18.1 Consensus size: 9
34946793 ATATATAAGC
*
34946803 TTATAATAA
1 TTATAAAAA
34946812 TTATAAAAA
1 TTATAAAAA
* *
34946821 -CA-AAAAC
1 TTATAAAAA
*
34946828 TTATAAATA
1 TTATAAAAA
34946837 TTAT-AAAA
1 TTATAAAAA
34946845 -TATAAAAAA
1 TTAT-AAAAA
34946854 TT-TAATAAA
1 TTATAA-AAA
*
34946863 TTCTAATAAA
1 TTATAA-AAA
34946873 TTAT-AAAA
1 TTATAAAAA
*
34946881 TTAT-AAAG
1 TTATAAAAA
34946889 TTAATAAAACA
1 TT-ATAAAA-A
*
34946900 TATTTAAAATA
1 T-TATAAAA-A
*
34946911 TT-TAGAACA
1 TTATA-AAAA
34946920 TTATAAAAA
1 TTATAAAAA
*
34946929 CATATAAAAA
1 -TTATAAAAA
*
34946939 TTCTTTAAAAA
1 -T-TATAAAAA
34946950 TTAT-AAAA
1 TTATAAAAA
*
34946958 TTATTAAAA
1 TTATAAAAA
34946967 T
1 T
34946968 ATTACAATTA
Statistics
Matches: 121, Mismatches: 19, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
7 7 0.06
8 27 0.22
9 43 0.36
10 28 0.23
11 15 0.12
12 1 0.01
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (9 bp):
TTATAAAAA
Found at i:34948057 original size:9 final size:9
Alignment explanation
Indices: 34948031--34948388 Score: 82
Period size: 9 Copynumber: 38.7 Consensus size: 9
34948021 TCTATTAGAT
34948031 TTTTTATAA
1 TTTTTATAA
34948040 TTTTATATAA
1 TTTT-TATAA
*
34948050 TATTTATAA
1 TTTTTATAA
* *
34948059 GTTTTATGA
1 TTTTTATAA
*
34948068 TTTTTATAG
1 TTTTTATAA
34948077 TTTTTATAA
1 TTTTTATAA
*
34948086 GTTTATATGAA
1 -TTTTTAT-AA
**
34948097 -TTTTAGCA
1 TTTTTATAA
*
34948105 TTTTAAT-A
1 TTTTTATAA
* *
34948113 -TTTAATTA
1 TTTTTATAA
34948121 TTTTTAT-A
1 TTTTTATAA
*
34948129 TTTTTATGA
1 TTTTTATAA
*
34948138 TTTTTAATGA
1 TTTTT-ATAA
*
34948148 TTTGTAATAA
1 TTT-TTATAA
*
34948158 TTTTTATAGGGTT
1 TTTTTATA----A
34948171 TTTTTATAA
1 TTTTTATAA
* *
34948180 CTTTTATACG
1 TTTTTATA-A
34948190 TTTTTATAAA
1 TTTTTAT-AA
**
34948200 AGTTTA-AA
1 TTTTTATAA
*
34948208 TATTTTAAACA
1 T-TTTTATA-A
34948219 TGTTTTTATTAA
1 --TTTTTA-TAA
34948231 TTTTGTAT--
1 TTTT-TATAA
*
34948239 TTTTTATCA
1 TTTTTATAA
* * *
34948248 TTGATTAGAT
1 TT-TTTATAA
34948258 TTTTTAT-A
1 TTTTTATAA
34948266 TTTTTA-AA
1 TTTTTATAA
*
34948274 TATTTATAA
1 TTTTTATAA
34948283 GTTTTTAT--
1 -TTTTTATAA
34948291 TTATTTAT--
1 TT-TTTATAA
*
34948299 TTATTATAA
1 TTTTTATAA
34948308 TTTTTATAA
1 TTTTTATAA
*
34948317 GTTTATATAA
1 -TTTTTATAA
*
34948327 -ATTT-TAA
1 TTTTTATAA
*
34948334 TATTTAATAA
1 T-TTTTATAA
*
34948344 TATTTAT-A
1 TTTTTATAA
*
34948352 TTTTATCTAA
1 TTTT-TATAA
**
34948362 TATTTTAATTT
1 T-TTTT-ATAA
34948373 TATTTTATAA
1 T-TTTTATAA
34948383 TTTTTA
1 TTTTTA
34948389 ATCACTTTTA
Statistics
Matches: 256, Mismatches: 54, Indels: 78
0.66 0.14 0.20
Matches are distributed among these distances:
7 18 0.07
8 42 0.16
9 91 0.36
10 72 0.28
11 17 0.07
12 6 0.02
13 10 0.04
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:34948057 original size:11 final size:10
Alignment explanation
Indices: 34947950--34948101 Score: 57
Period size: 10 Copynumber: 15.5 Consensus size: 10
34947940 TTTTATAAGT
*
34947950 TTTTATAAAA
1 TTTTATATAA
* *
34947960 TTTAAAATAA
1 TTTTATATAA
*
34947970 TTTAAGTAT-A
1 TTTTA-TATAA
34947980 TTTTAT-TAA
1 TTTTATATAA
*
34947989 TTTTATATAGT
1 TTTTATATA-A
*
34948000 TTTTAAATAA
1 TTTTATATAA
** * *
34948010 AATAATACAA
1 TTTTATATAA
* *
34948020 ATCTAT-TAGA
1 TTTTATATA-A
*
34948030 TTTTTTATAA
1 TTTTATATAA
34948040 TTTTATATAA
1 TTTTATATAA
*
34948050 TATT-TATAA
1 TTTTATATAA
* *
34948059 GTTT-TATGA
1 TTTTATATAA
*
34948068 TTTT-TATAG
1 TTTTATATAA
34948077 TTTT-TATAA
1 TTTTATATAA
*
34948086 GTTTATATGAA
1 TTTTATAT-AA
34948097 TTTTA
1 TTTTA
34948102 GCATTTTAAT
Statistics
Matches: 103, Mismatches: 31, Indels: 15
0.69 0.21 0.10
Matches are distributed among these distances:
8 1 0.01
9 37 0.36
10 47 0.46
11 18 0.17
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.54
Consensus pattern (10 bp):
TTTTATATAA
Found at i:34948287 original size:26 final size:25
Alignment explanation
Indices: 34948258--34948315 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
34948248 TTGATTAGAT
34948258 TTTTTATATT-TTTAAATATTTATAA
1 TTTTTATATTATTTAAATA-TTATAA
**
34948283 GTTTTTAT-TTATTTATTTATTATAA
1 -TTTTTATATTATTTAAATATTATAA
34948308 TTTTTATA
1 TTTTTATA
34948316 AGTTTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 7 0.25
25 8 0.29
26 13 0.46
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTTATATTATTTAAATATTATAA
Found at i:34948893 original size:17 final size:19
Alignment explanation
Indices: 34948867--34948919 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
34948857 TTTTTCAATA
34948867 AAAATGATTAAAAAATAT-G
1 AAAAT-ATTAAAAAATATAG
*
34948886 AAAA-ATTATAAAAAAATAG
1 AAAATATTA-AAAAATATAG
*
34948905 AAAATATTATAAAAT
1 AAAATATTAAAAAAT
34948920 TATTACAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 4 0.14
18 7 0.25
19 13 0.46
20 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (19 bp):
AAAATATTAAAAAATATAG
Found at i:34948898 original size:9 final size:9
Alignment explanation
Indices: 34948864--34949120 Score: 72
Period size: 10 Copynumber: 28.0 Consensus size: 9
34948854 ATATTTTTCA
*
34948864 ATAAAAATG
1 ATAAAAATT
*
34948873 ATTAAAAAAT
1 A-TAAAAATT
34948883 ATGAAAAATT
1 AT-AAAAATT
*
34948893 ATAAAAAAAT
1 AT-AAAAATT
*
34948903 AGAAAATATT
1 ATAAAA-ATT
34948913 AT-AAAATT
1 ATAAAAATT
*
34948921 ATTACAAA-T
1 A-TAAAAATT
34948930 A-AAAATATT
1 ATAAAA-ATT
*
34948939 TTAAAAA-T
1 ATAAAAATT
*
34948947 A-AAATATT
1 ATAAAAATT
34948955 ATAAAAA-T
1 ATAAAAATT
*
34948963 A-CAAAA-T
1 ATAAAAATT
34948970 ATAAAAATCT
1 ATAAAAAT-T
* *
34948980 A-ATATATT
1 ATAAAAATT
*
34948988 CTAATAAATT
1 ATAA-AAATT
*
34948998 ATAAAAAAT
1 ATAAAAATT
*
34949007 AT-AAAATCA
1 ATAAAAAT-T
34949016 ATAAACATATT
1 ATAAA-A-ATT
*
34949027 -TAAAATTTT
1 ATAAAA-ATT
*
34949036 ATTTAAACA-T
1 A--TAAAAATT
*
34949046 ATTAAAATT
1 ATAAAAATT
*
34949055 CTATAAAATT
1 ATA-AAAATT
*
34949065 CATAAAAAAT
1 -ATAAAAATT
*
34949075 ATTAAAACTT
1 A-TAAAAATT
*
34949085 ATAAAACTT
1 ATAAAAATT
34949094 AT-AAAATT
1 ATAAAAATT
*
34949102 ATAAAAAATC
1 AT-AAAAATT
34949112 ATAAAAATT
1 ATAAAAATT
34949121 GAAATTTACC
Statistics
Matches: 180, Mismatches: 40, Indels: 56
0.65 0.14 0.20
Matches are distributed among these distances:
7 13 0.07
8 30 0.17
9 54 0.30
10 74 0.41
11 3 0.02
12 6 0.03
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:34948970 original size:18 final size:17
Alignment explanation
Indices: 34948926--34948971 Score: 67
Period size: 16 Copynumber: 2.7 Consensus size: 17
34948916 AAATTATTAC
*
34948926 AAATAAAAATATTTTAA
1 AAATAAAAATATTATAA
34948943 AAAT-AAAATATTATAA
1 AAATAAAAATATTATAA
34948959 AAATACAAAATAT
1 AAATA-AAAATAT
34948972 AAAAATCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 15 0.58
17 4 0.15
18 7 0.27
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAAAAATATTATAA
Found at i:34948972 original size:15 final size:16
Alignment explanation
Indices: 34948913--34948977 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
34948903 AGAAAATATT
* *
34948913 ATAAAATTATTACAAAT
1 ATAAAA-TATTATAAAA
*
34948930 A-AAAATATTTTAAAA
1 ATAAAATATTATAAAA
34948945 ATAAAATATTATAAAA
1 ATAAAATATTATAAAA
34948961 ATACAAA-A-TATAAAA
1 ATA-AAATATTATAAAA
34948976 AT
1 AT
34948978 CTAATATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
15 17 0.40
16 21 0.50
17 4 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAATATTATAAAA
Found at i:34948986 original size:15 final size:15
Alignment explanation
Indices: 34948940--34948986 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
34948930 AAAAATATTT
*
34948940 TAAAAATAAAATATTA
1 TAAAAATACAATA-TA
*
34948956 TAAAAATACAAAATA
1 TAAAAATACAATATA
34948971 TAAAAAT-CTAATATA
1 TAAAAATAC-AATATA
34948986 T
1 T
34948987 TCTAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 1 0.04
15 15 0.56
16 11 0.41
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAATACAATATA
Found at i:34949080 original size:19 final size:18
Alignment explanation
Indices: 34949058--34949120 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
34949048 TAAAATTCTA
34949058 TAAAATTCATAAAAAATAT
1 TAAAATT-ATAAAAAATAT
**
34949077 TAAAACTTATAAAACTTA-
1 TAAAA-TTATAAAAAATAT
34949095 TAAAATTATAAAAAATCAT
1 TAAAATTATAAAAAAT-AT
*
34949114 AAAAATT
1 TAAAATT
34949121 GAAATTTACC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
17 9 0.25
18 6 0.17
19 19 0.53
20 2 0.06
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAATTATAAAAAATAT
Found at i:34949105 original size:8 final size:8
Alignment explanation
Indices: 34949056--34949107 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 8
34949046 ATTAAAATTC
34949056 TATAAAAT
1 TATAAAAT
*
34949064 TCATAAAAAA
1 T-AT-AAAAT
34949074 TATTAAAACT
1 TA-TAAAA-T
34949084 TATAAAACT
1 TATAAAA-T
34949093 TATAAAAT
1 TATAAAAT
34949101 TATAAAA
1 TATAAAA
34949108 AATCATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 9 0.24
9 21 0.55
10 8 0.21
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.33
Consensus pattern (8 bp):
TATAAAAT
Found at i:34949323 original size:31 final size:31
Alignment explanation
Indices: 34949288--34949346 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
34949278 GTCACTAATG
34949288 TTTTAGATCATTTCTATTTTGGTCACTCACT
1 TTTTAGATCATTTCTATTTTGGTCACTCACT
34949319 TTTTAGATCATTTCTATTTTGGTCACTC
1 TTTTAGATCATTTCTATTTTGGTCACTC
34949347 TCAGTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.53
Consensus pattern (31 bp):
TTTTAGATCATTTCTATTTTGGTCACTCACT
Found at i:34962391 original size:30 final size:30
Alignment explanation
Indices: 34962353--34962419 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
34962343 TAGGGTTTTG
**
34962353 ATTT-TTTACCAAAATAAAATGTAAAAAAT
1 ATTTATTTACCAAAATAAAATACAAAAAAT
* * *
34962382 ATTTATTTACTAAAATAATATACAAAAATT
1 ATTTATTTACCAAAATAAAATACAAAAAAT
34962412 ATTTATTT
1 ATTTATTT
34962420 TATTTGATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (30 bp):
ATTTATTTACCAAAATAAAATACAAAAAAT
Found at i:34962422 original size:35 final size:36
Alignment explanation
Indices: 34962383--34962455 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
34962373 GTAAAAAATA
* *
34962383 TTTATTT-ACTAAAATAATA-TACAAAAATTATTTAT
1 TTTATTTGACTAAAATAATATTA-AAAAAGTATTAAT
* *
34962418 TTTATTTGATTAAAGTAATATTAAAAAAGTATTAAT
1 TTTATTTGACTAAAATAATATTAAAAAAGTATTAAT
34962454 TT
1 TT
34962456 AATAAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 7 0.22
36 23 0.72
37 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTATTTGACTAAAATAATATTAAAAAAGTATTAAT
Found at i:34963283 original size:24 final size:23
Alignment explanation
Indices: 34963238--34963306 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 23
34963228 GTGGAACTTG
*
34963238 TAGAAAATGAAATCCAATTCCAA
1 TAGAAAATGAAATCCAACTCCAA
34963261 TAGAAAATGAAGATCCAACTCCAA
1 TAGAAAATGAA-ATCCAACTCCAA
34963285 TAGAAAATGAAAATCCAACTCC
1 TAGAAAATG-AAATCCAACTCC
34963307 GTGTATGGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
23 11 0.26
24 30 0.70
25 2 0.05
ACGTcount: A:0.51, C:0.20, G:0.10, T:0.19
Consensus pattern (23 bp):
TAGAAAATGAAATCCAACTCCAA
Found at i:34971418 original size:7 final size:7
Alignment explanation
Indices: 34971408--34971460 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
34971398 TGGTTTCTAA
*
34971408 TTTAGGG
1 TTTAAGG
34971415 TTTAAGG
1 TTTAAGG
34971422 TTT-AGAG
1 TTTAAG-G
*
34971429 TTTAAAG
1 TTTAAGG
34971436 TTTAAGG
1 TTTAAGG
*
34971443 TTTAAGA
1 TTTAAGG
*
34971450 TTTAGGG
1 TTTAAGG
34971457 TTTA
1 TTTA
34971461 TAAATATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
6 2 0.05
7 35 0.92
8 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (7 bp):
TTTAAGG
Found at i:34971425 original size:14 final size:14
Alignment explanation
Indices: 34971408--34971460 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
34971398 TGGTTTCTAA
34971408 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
* *
34971422 TTTAGAGTTTAAAG
1 TTTAGGGTTTAAGG
* *
34971436 TTTAAGGTTTAAGA
1 TTTAGGGTTTAAGG
34971450 TTTAGGGTTTA
1 TTTAGGGTTTA
34971461 TAAATATGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:34971432 original size:21 final size:21
Alignment explanation
Indices: 34971407--34971460 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
34971397 ATGGTTTCTA
34971407 ATTTAGGGTTTAAGGTTT-AG
1 ATTTAGGGTTTAAGGTTTAAG
**
34971427 AGTTTAAAGTTTAAGGTTTAAG
1 A-TTTAGGGTTTAAGGTTTAAG
34971449 ATTTAGGGTTTA
1 ATTTAGGGTTTA
34971461 TAAATATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.86
22 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (21 bp):
ATTTAGGGTTTAAGGTTTAAG
Found at i:34971789 original size:45 final size:45
Alignment explanation
Indices: 34971725--34971815 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
34971715 AGGAGGAATA
* *
34971725 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGGGGCTCGTCAAACTGAAGCTGATATCCTTGGCTT
*
34971770 GAGTATTGCGGGGGCTCGTCAAACTGAAGCTGATATCTTTGGCTT
1 GAGTATTGCGGGGGCTCGTCAAACTGAAGCTGATATCCTTGGCTT
34971815 G
1 G
34971816 TTGAGCTAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.31
Consensus pattern (45 bp):
GAGTATTGCGGGGGCTCGTCAAACTGAAGCTGATATCCTTGGCTT
Found at i:34973738 original size:16 final size:16
Alignment explanation
Indices: 34973717--34973765 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
34973707 GGATGGAGAT
34973717 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
*
34973733 ATTATTTT-TTATATT-
1 ATTATTTTGGTA-ATTA
34973748 A-TATTTTGGTAATTA
1 ATTATTTTGGTAATTA
34973763 ATT
1 ATT
34973766 TAGAGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:34974107 original size:21 final size:21
Alignment explanation
Indices: 34974082--34974122 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
34974072 TTACTTACTA
34974082 TTACTAACAAAATAAAATTAC
1 TTACTAACAAAATAAAATTAC
*
34974103 TTACTAACAAAATTAAATTA
1 TTACTAACAAAATAAAATTA
34974123 AATTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (21 bp):
TTACTAACAAAATAAAATTAC
Found at i:34974423 original size:13 final size:13
Alignment explanation
Indices: 34974405--34974433 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
34974395 ACAAATTAAA
34974405 AAATTTTAAAAAT
1 AAATTTTAAAAAT
34974418 AAA-TTTAAAAAT
1 AAATTTTAAAAAT
34974430 AAAT
1 AAAT
34974434 ACACTACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:34974448 original size:4 final size:4
Alignment explanation
Indices: 34974441--34974516 Score: 57
Period size: 4 Copynumber: 18.0 Consensus size: 4
34974431 AATACACTAC
* *
34974441 CTTT CTTT CCTTCT CCTT CTTCT CCTT CTTT CTTT CTTT CTTT CCTTT
1 CTTT CTTT -CTT-T CTTT CTT-T CTTT CTTT CTTT CTTT CTTT -CTTT
*
34974489 CCTTT -TCT CTTTT CTTT CTTT -TTT CTTT
1 -CTTT CTTT C-TTT CTTT CTTT CTTT CTTT
34974517 GTTCTACCGT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
3 5 0.08
4 33 0.56
5 20 0.34
6 1 0.02
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:34974477 original size:17 final size:17
Alignment explanation
Indices: 34974441--34974514 Score: 50
Period size: 17 Copynumber: 4.5 Consensus size: 17
34974431 AATACACTAC
34974441 CTTTCTT-TCCTTC--T
1 CTTTCTTCTCCTTCTTT
*
34974455 CCTTCTTCTCCTTCTTT
1 CTTTCTTCTCCTTCTTT
*
34974472 CTTTCTT-TCTTTCCTTT
1 CTTTCTTCTCCTT-CTTT
* *
34974489 CCTT-TTCTCTTTTCTTT
1 CTTTCTTCTC-CTTCTTT
*
34974506 CTTTTTTCT
1 CTTTCTTCT
34974515 TTGTTCTACC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
14 6 0.12
15 6 0.12
16 6 0.12
17 23 0.48
18 7 0.15
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTCTTCTCCTTCTTT
Found at i:34974488 original size:9 final size:8
Alignment explanation
Indices: 34974441--34974516 Score: 57
Period size: 9 Copynumber: 9.0 Consensus size: 8
34974431 AATACACTAC
34974441 CTTTCTTT
1 CTTTCTTT
*
34974449 CCTTCTCCTT
1 -CTT-TCTTT
*
34974459 CTTCTCCTT
1 CTT-TCTTT
34974468 CTTTCTTT
1 CTTTCTTT
34974476 CTTTCTTT
1 CTTTCTTT
34974484 CCTTTCCTTT
1 -CTTT-CTTT
*
34974494 -TCTCTTTT
1 CTTTC-TTT
34974502 CTTTCTTT
1 CTTTCTTT
34974510 -TTTCTTT
1 CTTTCTTT
34974517 GTTCTACCGT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
7 8 0.14
8 20 0.34
9 22 0.38
10 8 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (8 bp):
CTTTCTTT
Found at i:34977525 original size:39 final size:39
Alignment explanation
Indices: 34977463--34977636 Score: 104
Period size: 39 Copynumber: 4.5 Consensus size: 39
34977453 CATTGAAAAT
* * * *
34977463 GCAATGATACTATAAGCAGTGCAATACTATACTAAACTA
1 GCAATGACACTGTAAACATTGCAATACTATACTAAACTA
* ** * * *
34977502 GCAATGACACTGCAAACATTGCAATGGTACACTGAACTG
1 GCAATGACACTGTAAACATTGCAATACTATACTAAACTA
* * * * * *
34977541 GCAGTGATACTTTAAACACTT-CAATGCAATACTAAA-TT
1 GCAATGACACTGTAAACA-TTGCAATACTATACTAAACTA
* * *
34977579 GACAATGACACTGTAAACACTGCAATA-TAGCACCAAACT-
1 G-CAATGACACTGTAAACATTGCAATACTA-TACTAAACTA
*
34977618 GACAGTGACACTGTAAACA
1 G-CAATGACACTGTAAACA
34977637 CCGTAGTGTT
Statistics
Matches: 102, Mismatches: 28, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
38 4 0.04
39 95 0.93
40 3 0.03
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (39 bp):
GCAATGACACTGTAAACATTGCAATACTATACTAAACTA
Found at i:34978215 original size:69 final size:67
Alignment explanation
Indices: 34978085--34978216 Score: 183
Period size: 69 Copynumber: 1.9 Consensus size: 67
34978075 ATAAACAATA
* * * * *
34978085 TAATGGTTTTGCCTTTTAACTTAATAAGTAAACATTTATTAAAACGACGTAATTTTGCCTTTTAA
1 TAATGGTTTCGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACGTAATTTTACCTTTTAA
34978150 CT
66 CT
* *
34978152 TAATGGTTTCGACTTTTAACTTTAAAAAGGTAAACATTTATCAAAATGACGTAGTTTTACCTTTT
1 TAATGGTTTCGACTTTTAAC-TTAAAAA-GTAAACATTTATCAAAACGACGTAATTTTACCTTTT
34978217 CTTATTCGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 18 0.32
68 6 0.11
69 32 0.57
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (67 bp):
TAATGGTTTCGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACGTAATTTTACCTTTTAA
CT
Found at i:34983409 original size:6 final size:6
Alignment explanation
Indices: 34983398--34983432 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
34983388 ACACCTGAAT
*
34983398 GGAAAA GGAAAA GGAAAA GGAAAA GGAAAA AGAAA
1 GGAAAA GGAAAA GGAAAA GGAAAA GGAAAA GGAAA
34983433 TCATTGTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
GGAAAA
Found at i:35000572 original size:24 final size:24
Alignment explanation
Indices: 35000511--35000573 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
35000501 TAGAGTAATA
* *
35000511 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
35000535 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
35000559 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
35000574 GATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:35002558 original size:24 final size:24
Alignment explanation
Indices: 35002497--35002559 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
35002487 TAGAGTAATA
* * *
35002497 AGAGTTTGACTCAAACGAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
35002521 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
35002545 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
35002560 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:35009783 original size:2 final size:2
Alignment explanation
Indices: 35009771--35009802 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
35009761 TTAATAGATA
*
35009771 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35009803 TTTGATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:35012268 original size:11 final size:11
Alignment explanation
Indices: 35012252--35012299 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
35012242 TTTTTTTATT
35012252 AAAAATTATAA
1 AAAAATTATAA
35012263 AAAAATTATATA
1 AAAAATTATA-A
*
35012275 AAAATATTATTA
1 AAAA-ATTATAA
*
35012287 ATAAA-TATAA
1 AAAAATTATAA
35012297 AAA
1 AAA
35012300 TATAGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 6 0.19
11 11 0.35
12 9 0.29
13 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:35014937 original size:26 final size:26
Alignment explanation
Indices: 35014891--35014941 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
35014881 TAAATTCGTA
**
35014891 CTATATTCAAATAGGTGTAGCCAGAC
1 CTATATTCAAATAGGACTAGCCAGAC
*
35014917 CTATATTCAAATTGGACTAGCCAGA
1 CTATATTCAAATAGGACTAGCCAGA
35014942 ATCTCTCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (26 bp):
CTATATTCAAATAGGACTAGCCAGAC
Found at i:35020623 original size:18 final size:17
Alignment explanation
Indices: 35020600--35020645 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
35020590 CTAATTAAAA
*
35020600 TTAATTTAATTATTTTT
1 TTAATTTAATTATTATT
*
35020617 CTTAATTAAATTATTATT
1 -TTAATTTAATTATTATT
*
35020635 TTAATCTAATT
1 TTAATTTAATT
35020646 TTAATTTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAATTTAATTATTATT
Found at i:35039150 original size:22 final size:22
Alignment explanation
Indices: 35039111--35039152 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35039101 ATTTTCATAA
* * *
35039111 AGAGAAATTGATAGAAAAATCT
1 AGAGAAATGGAGAAAAAAATCT
35039133 AGAGAAATGGAGAAAAAAAT
1 AGAGAAATGGAGAAAAAAAT
35039153 GATGAAAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.17
Consensus pattern (22 bp):
AGAGAAATGGAGAAAAAAATCT
Found at i:35040683 original size:18 final size:18
Alignment explanation
Indices: 35040660--35040696 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35040650 TTTGTGAACA
35040660 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
35040678 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
35040696 A
1 A
35040697 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:35046606 original size:6 final size:6
Alignment explanation
Indices: 35046599--35046643 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
35046589 TGATCAAAAC
* * * *
35046599 TGAAAC TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
35046644 TATGAATTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.47, C:0.02, G:0.29, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:35049785 original size:2 final size:2
Alignment explanation
Indices: 35049778--35049803 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35049768 TTAGAATTTC
35049778 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
35049804 TCATGTGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35056683 original size:20 final size:20
Alignment explanation
Indices: 35056658--35056714 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
35056648 TGGACAATGG
35056658 CTGGTATTGCTCGATGCTCC
1 CTGGTATTGCTCGATGCTCC
* * *
35056678 CTGGTACTGCTCAATGCTTC
1 CTGGTATTGCTCGATGCTCC
* *
35056698 CTGATGTTGCTCGATGC
1 CTGGTATTGCTCGATGC
35056715 ATGCTGGTGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.28, G:0.25, T:0.35
Consensus pattern (20 bp):
CTGGTATTGCTCGATGCTCC
Found at i:35060221 original size:58 final size:58
Alignment explanation
Indices: 35060146--35060255 Score: 177
Period size: 58 Copynumber: 1.9 Consensus size: 58
35060136 AACATAGTTT
* * *
35060146 TTTTTTTTTTACTAAGAGAAAGGAGTAGGAATTA-CCCGGACATTAAATCCGAACATAG
1 TTTTTTTTTTAATAAGAGAAAGGAGTAGGAATTATCCAGG-CAGTAAATCCGAACATAG
35060204 TTTTTTTTTTAATAAGAGAAAGGAGTAGGAATTATCCAGGCAGTAAATCCGA
1 TTTTTTTTTTAATAAGAGAAAGGAGTAGGAATTATCCAGGCAGTAAATCCGA
35060256 GACTTCTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
58 44 0.92
59 4 0.08
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (58 bp):
TTTTTTTTTTAATAAGAGAAAGGAGTAGGAATTATCCAGGCAGTAAATCCGAACATAG
Found at i:35061308 original size:15 final size:14
Alignment explanation
Indices: 35061269--35061317 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
35061259 TATATTTACA
*
35061269 TTTAAAATTTAATT
1 TTTATAATTTAATT
*
35061283 TTTATATTTTAATT
1 TTTATAATTTAATT
35061297 TGTTATAATTTAATT
1 T-TTATAATTTAATT
35061312 CTTTAT
1 -TTTAT
35061318 TTTTATCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.43
15 16 0.53
16 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTATAATTTAATT
Found at i:35061480 original size:21 final size:21
Alignment explanation
Indices: 35061451--35061498 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
35061441 GTTTTAATTG
* *
35061451 AAATAAATTTATCA-ATTATTT
1 AAATTAATTAATCATATTA-TT
*
35061472 AAATTAATTAATGATATTATT
1 AAATTAATTAATCATATTATT
35061493 AAATTA
1 AAATTA
35061499 TAATAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AAATTAATTAATCATATTATT
Found at i:35061512 original size:22 final size:21
Alignment explanation
Indices: 35061464--35061524 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
35061454 TAAATTTATC
* *
35061464 AATTATTTAAATTAATTAATGA
1 AATTA-TTAAATTAAATAATTA
*
35061486 TATTATTAAATTATAATAATTA
1 AATTATTAAATTA-AATAATTA
35061508 AATTATATCAAATTAAA
1 AATTAT-T-AAATTAAA
35061525 ATATAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 8 0.25
22 15 0.47
23 3 0.09
24 6 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTATTAAATTAAATAATTA
Found at i:35063414 original size:41 final size:41
Alignment explanation
Indices: 35063367--35063452 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
35063357 AAGGTAAAGT
* * * *
35063367 ATTAGCGGCCCTTATGGGAAAGGGCCGCTAAAGATTAGAGC
1 ATTAGCGGCCCTTATGGAAAAGCGCCACTAAAGATCAGAGC
* * *
35063408 ATTAGCGGCGCTTGTGGAAAAGCGCCACTAAAGGTCAGAGC
1 ATTAGCGGCCCTTATGGAAAAGCGCCACTAAAGATCAGAGC
35063449 ATTA
1 ATTA
35063453 ACGACGCTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCCCTTATGGAAAAGCGCCACTAAAGATCAGAGC
Found at i:35063471 original size:41 final size:41
Alignment explanation
Indices: 35063381--35063494 Score: 120
Period size: 41 Copynumber: 2.8 Consensus size: 41
35063371 GCGGCCCTTA
* * * * * *
35063381 TGGGAAAGGGCCGCTAAAGATTAGAGCATTAGCGGCGCTTG
1 TGGGAAAGCGCCGCTAAAGGTCAGAGCATTAACGACGCTAG
* *
35063422 TGGAAAAGCGCCACTAAAGGTCAGAGCATTAACGACGCTAG
1 TGGGAAAGCGCCGCTAAAGGTCAGAGCATTAACGACGCTAG
** *
35063463 TGGGAAAGCATCGCTAAAAGGTCAAAGCATTA
1 TGGGAAAGCGCCGCT-AAAGGTCAGAGCATTA
35063495 GCGGCACTTA
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
41 44 0.75
42 15 0.25
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (41 bp):
TGGGAAAGCGCCGCTAAAGGTCAGAGCATTAACGACGCTAG
Found at i:35067615 original size:43 final size:42
Alignment explanation
Indices: 35067559--35067716 Score: 183
Period size: 43 Copynumber: 3.7 Consensus size: 42
35067549 TGTTAGTGGC
*
35067559 GTTTGTG-GAAAAGCGCCGTAAAAGACCATGTTCTTTAGCTGT
1 GTTTGTGAGAAAAGCGCCGT-AAAGACCATGTTCTTTAGCGGT
* * *
35067601 GTTTGTGAGAAAAGCACCGCTAAAGATCATGTTCTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCG-TAAAGACCATGTTCTTTAGCGGT
* * *
35067644 ATTTGTGATAAAAGCGCCACTAAAGACCATGTTCTTTAGCGGT
1 GTTTGTGAGAAAAGCGCC-GTAAAGACCATGTTCTTTAGCGGT
* * *
35067687 GTTTGTGTGAAAAGTGTCGCTAAAGACCAT
1 GTTTGTGAGAAAAGCGCCG-TAAAGACCAT
35067717 CAGCTAAAGA
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
42 7 0.07
43 88 0.92
44 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
GTTTGTGAGAAAAGCGCCGTAAAGACCATGTTCTTTAGCGGT
Found at i:35067784 original size:47 final size:46
Alignment explanation
Indices: 35067722--35067858 Score: 147
Period size: 47 Copynumber: 3.0 Consensus size: 46
35067712 ACCATCAGCT
* *
35067722 AAAGAACATGGTCTTTAGTGGTGTTTGTAGGAAAAGCGTCGCTAAAG
1 AAAGAACATGGTCTTTAGCGGTGTTTGT-GGAAAAGCGCCGCTAAAG
*** *
35067769 AAAGAACATGGTCTTTAGCGACATTTGTGGAGAAGCGCCGCT----
1 AAAGAACATGGTCTTTAGCGGTGTTTGTGGAAAAGCGCCGCTAAAG
* * *
35067811 AAAGAACATAGTCTTTAACGGTGTTTGTTGAAAAAGCGCCGCTAAAG
1 AAAGAACATGGTCTTTAGCGGTGTTTG-TGGAAAAGCGCCGCTAAAG
35067858 A
1 A
35067859 CCATGTTCTA
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
42 22 0.31
43 13 0.18
46 12 0.17
47 25 0.35
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.26
Consensus pattern (46 bp):
AAAGAACATGGTCTTTAGCGGTGTTTGTGGAAAAGCGCCGCTAAAG
Found at i:35072945 original size:13 final size:13
Alignment explanation
Indices: 35072927--35072951 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35072917 AATATAAATC
35072927 AATAAAAAAATTT
1 AATAAAAAAATTT
35072940 AATAAAAAAATT
1 AATAAAAAAATT
35072952 AATCAATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAAAAAATTT
Found at i:35073626 original size:24 final size:25
Alignment explanation
Indices: 35073585--35073632 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
35073575 TTAAACAAAT
35073585 ATTTATTTGGTTTAATTTTTTATTA
1 ATTTATTTGGTTTAATTTTTTATTA
* *
35073610 ATTTGTTT-GTTTGATTTTTTATT
1 ATTTATTTGGTTTAATTTTTTATT
35073633 TTTTCGTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (25 bp):
ATTTATTTGGTTTAATTTTTTATTA
Found at i:35081736 original size:81 final size:81
Alignment explanation
Indices: 35081601--35081768 Score: 336
Period size: 81 Copynumber: 2.1 Consensus size: 81
35081591 GGTTAGGAAG
35081601 CAGTTTATAAAGACTTTGAGTCTAAAAGTCTTGTTTATGGTGTGTCTATTGGTAATCACTGTTTT
1 CAGTTTATAAAGACTTTGAGTCTAAAAGTCTTGTTTATGGTGTGTCTATTGGTAATCACTGTTTT
35081666 TCTTTTTCATCAAATT
66 TCTTTTTCATCAAATT
35081682 CAGTTTATAAAGACTTTGAGTCTAAAAGTCTTGTTTATGGTGTGTCTATTGGTAATCACTGTTTT
1 CAGTTTATAAAGACTTTGAGTCTAAAAGTCTTGTTTATGGTGTGTCTATTGGTAATCACTGTTTT
35081747 TCTTTTTCATCAAATT
66 TCTTTTTCATCAAATT
35081763 CAGTTT
1 CAGTTT
35081769 TTTTTGTTTT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 87 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.47
Consensus pattern (81 bp):
CAGTTTATAAAGACTTTGAGTCTAAAAGTCTTGTTTATGGTGTGTCTATTGGTAATCACTGTTTT
TCTTTTTCATCAAATT
Found at i:35084960 original size:46 final size:46
Alignment explanation
Indices: 35084893--35084986 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
35084883 CTAATTTGAG
35084893 CACCAATCCTATCTGAAAAACTTTGGTTTTAACACAACAGCTCAAC
1 CACCAATCCTATCTGAAAAACTTTGGTTTTAACACAACAGCTCAAC
35084939 CACCAATCCTATCTGAAAAACTTTGGTTTTAACACAACAGCTCAAC
1 CACCAATCCTATCTGAAAAACTTTGGTTTTAACACAACAGCTCAAC
35084985 CA
1 CA
35084987 GATGGCCCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.26
Consensus pattern (46 bp):
CACCAATCCTATCTGAAAAACTTTGGTTTTAACACAACAGCTCAAC
Found at i:35090401 original size:15 final size:16
Alignment explanation
Indices: 35090381--35090413 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35090371 ATGTCCAACC
35090381 AAAATTA-ATATATTA
1 AAAATTAGATATATTA
*
35090396 AAAATTAGATATTTTA
1 AAAATTAGATATATTA
35090412 AA
1 AA
35090414 CCAATCGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAATTAGATATATTA
Found at i:35090530 original size:28 final size:28
Alignment explanation
Indices: 35090484--35090544 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 28
35090474 ACACTTTTAT
35090484 TTTTTTTTTTAAAGTAACATCTCTAATAC
1 TTTTTTTTTTAAAG-AACATCTCTAATAC
35090513 TTTTTTTTTTAATA-AACATCTCTAATAC
1 TTTTTTTTTTAA-AGAACATCTCTAATAC
35090541 TTTT
1 TTTT
35090545 AAATTAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 18 0.58
29 12 0.39
30 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTTTTTTTTAAAGAACATCTCTAATAC
Found at i:35093579 original size:29 final size:29
Alignment explanation
Indices: 35093546--35093605 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
35093536 ATCTCTTGGT
*
35093546 AAAAAAAATTTTGACCT-TTAAAAATTAA
1 AAAAAAAATTTGGACCTCTTAAAAATTAA
* * *
35093574 AAAAAATATTTGGGCCTCTTAGAAATTAA
1 AAAAAAAATTTGGACCTCTTAAAAATTAA
35093603 AAA
1 AAA
35093606 CACACAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.30
Consensus pattern (29 bp):
AAAAAAAATTTGGACCTCTTAAAAATTAA
Found at i:35093584 original size:28 final size:28
Alignment explanation
Indices: 35093546--35093605 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
35093536 ATCTCTTGGT
*
35093546 AAAAAAAATTTTGACCT-TTAAAAATTA
1 AAAAAAAATTTGGACCTCTTAAAAATTA
* *
35093573 AAAAAAATATTTGGGCCTCTTAGAAATTA
1 AAAAAAA-ATTTGGACCTCTTAAAAATTA
35093602 AAAA
1 AAAA
35093606 CACACAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 7 0.25
28 8 0.29
29 13 0.46
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.30
Consensus pattern (28 bp):
AAAAAAAATTTGGACCTCTTAAAAATTA
Found at i:35101202 original size:54 final size:54
Alignment explanation
Indices: 35101143--35101252 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
35101133 AACTTAATTT
35101143 GAAGTTTCATATATTACATATACGAGGCTAGATGACGACATGTATGAATAGAAA
1 GAAGTTTCATATATTACATATACGAGGCTAGATGACGACATGTATGAATAGAAA
*
35101197 GAAGTTTCATATATTACATATACGAGGTTAGATGACGACATGTATGAATAGAAA
1 GAAGTTTCATATATTACATATACGAGGCTAGATGACGACATGTATGAATAGAAA
35101251 GA
1 GA
35101253 GATAAATAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (54 bp):
GAAGTTTCATATATTACATATACGAGGCTAGATGACGACATGTATGAATAGAAA
Done.