Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 93 of 161
Found at i:29526870 original size:15 final size:15
Alignment explanation
Indices: 29526850--29526879 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29526840 AATCGCTTGA
29526850 ACATGCTTTGTGAAT
1 ACATGCTTTGTGAAT
29526865 ACATGCTTTGTGAAT
1 ACATGCTTTGTGAAT
29526880 GCAACACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
ACATGCTTTGTGAAT
Found at i:29527212 original size:88 final size:90
Alignment explanation
Indices: 29526997--29527212 Score: 233
Period size: 90 Copynumber: 2.4 Consensus size: 90
29526987 ACCAAAAATT
* * * * * * *
29526997 TTGCAGGTTAATACATTGCCAAATGGTTGTGAATACACAACATATTTGCAAATAAGAGCTTCTAG
1 TTGCAGATTAATACACTGCCAGATGGTTGTGAATACACAACATATTCGCAAATAAGAACTGCCAG
* *
29527062 ATATTGGATGGATGAACCAACGATG
66 AAAGTGGATGGATGAACCAACGATG
* * * *
29527087 TTGCAGGTTAATACACTACTAGATGGTTGTGAGTACACAACATATTCG-AAGATAAGAACTGCCA
1 TTGCAGATTAATACACTGCCAGATGGTTGTGAATACACAACATATTCGCAA-ATAAGAACTGCCA
* *
29527151 -AAAGTGGGTGGATGAACC-AC-CTG
65 GAAAGTGGATGGATGAACCAACGATG
* *
29527174 TTTTCAGATTTATACACTGCCAGATGGTTGTGAATACAC
1 -TTGCAGATTAATACACTGCCAGATGGTTGTGAATACAC
29527213 CATAGGGTTG
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
87 2 0.02
88 34 0.32
89 17 0.16
90 52 0.50
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (90 bp):
TTGCAGATTAATACACTGCCAGATGGTTGTGAATACACAACATATTCGCAAATAAGAACTGCCAG
AAAGTGGATGGATGAACCAACGATG
Found at i:29529477 original size:21 final size:21
Alignment explanation
Indices: 29529461--29529514 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
29529451 ATGAGGGTCT
*
29529461 ACACTCCCATGTGGAGGCTAC
1 ACACGCCCATGTGGAGGCTAC
* *
29529482 ACACGCCCATGTGAAGGCCAC
1 ACACGCCCATGTGGAGGCTAC
29529503 ACACGCCCATGT
1 ACACGCCCATGT
29529515 AAACAGCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.37, G:0.22, T:0.15
Consensus pattern (21 bp):
ACACGCCCATGTGGAGGCTAC
Found at i:29533873 original size:20 final size:19
Alignment explanation
Indices: 29533832--29533873 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 19
29533822 GTCAAAATTA
29533832 TTCTAAGTGTTTAAAGCATT
1 TTCTAAGTGTTTAAAG-ATT
29533852 TTCTAAGCTGTTTGAAAG-TT
1 TTCTAAG-TGTTT-AAAGATT
29533872 TT
1 TT
29533874 GAAATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 11 0.55
21 5 0.25
22 4 0.20
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.48
Consensus pattern (19 bp):
TTCTAAGTGTTTAAAGATT
Found at i:29544242 original size:17 final size:17
Alignment explanation
Indices: 29544220--29544252 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29544210 TTATACTACA
29544220 AAATATTTATTATTAAT
1 AAATATTTATTATTAAT
*
29544237 AAATATTTTTTATTAA
1 AAATATTTATTATTAA
29544253 AACATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATATTTATTATTAAT
Found at i:29544322 original size:16 final size:16
Alignment explanation
Indices: 29544291--29544327 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
29544281 ATTTGAAGAA
29544291 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
29544307 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
29544323 TATTA
1 TATTA
29544328 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:29544336 original size:18 final size:19
Alignment explanation
Indices: 29544313--29544348 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29544303 TTATTATTTT
*
29544313 TAAAATTTAT-TATTAAAA
1 TAAAATTGATATATTAAAA
29544331 TAAAATTGATATATTAAA
1 TAAAATTGATATATTAAA
29544349 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAATTGATATATTAAAA
Found at i:29544381 original size:31 final size:30
Alignment explanation
Indices: 29544312--29544388 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
29544302 ATTATTATTT
29544312 TTAAAATTTATTATTAAAATAAAATTGATA
1 TTAAAATTTATTATTAAAATAAAATTGATA
*
29544342 TATTAAA-TTATTTATTAAAATAATGAATT-ATA
1 T-TAAAATTTA-TTATTAAAATAA--AATTGATA
29544374 TTAAAATTTTATTAT
1 TTAAAA-TTTATTAT
29544389 ATGATTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 4 0.10
31 20 0.51
32 8 0.21
33 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
TTAAAATTTATTATTAAAATAAAATTGATA
Found at i:29544485 original size:17 final size:18
Alignment explanation
Indices: 29544458--29544491 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29544448 TATATTAATA
*
29544458 TTTTAATAAATTTAAATG
1 TTTTAATAAATATAAATG
29544476 TTTTAA-AAATATAAAT
1 TTTTAATAAATATAAAT
29544492 AAAAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTTAATAAATATAAATG
Found at i:29550403 original size:21 final size:21
Alignment explanation
Indices: 29550377--29550417 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29550367 AGACGAGCAA
* *
29550377 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
29550398 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
29550418 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:29556524 original size:23 final size:23
Alignment explanation
Indices: 29556498--29556547 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
29556488 TTAATATTTA
29556498 TATTTGACTATTT-TATATATGTT
1 TATTT-ACTATTTGTATATATGTT
* * *
29556521 TATTTATTGTTTGTATATTTGTT
1 TATTTACTATTTGTATATATGTT
29556544 TATT
1 TATT
29556548 ATTCATGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.66
Consensus pattern (23 bp):
TATTTACTATTTGTATATATGTT
Found at i:29560825 original size:40 final size:40
Alignment explanation
Indices: 29560704--29560843 Score: 151
Period size: 40 Copynumber: 3.5 Consensus size: 40
29560694 AACTTTGAGT
* * *
29560704 CGATGAGACACTAGGTGTCAAATTATTACTTCGGATATATT
1 CGATGAGACATTGGGTGTCAAATTATTACTTCGGAT-TATC
* * * *
29560745 CGATGAGGCATTGTGTGTC-AA-T-TTACTTCGGTTTAGC
1 CGATGAGACATTGGGTGTCAAATTATTACTTCGGATTATC
*
29560782 CGATGAGACATTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACATTGGGTGTCAAATTATTACTTCGGATTATC
* * *
29560822 CGATGAGGCAGTGGGTGCCAAA
1 CGATGAGACATTGGGTGTCAAA
29560844 CTGGATTGTA
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
37 19 0.23
38 12 0.15
39 2 0.02
40 33 0.41
41 15 0.19
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (40 bp):
CGATGAGACATTGGGTGTCAAATTATTACTTCGGATTATC
Found at i:29571578 original size:27 final size:27
Alignment explanation
Indices: 29571548--29571608 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
29571538 TCATATTGCG
29571548 CCACAAAAAAGTTCCTTTCATAATTCA
1 CCACAAAAAAGTTCCTTTCATAATTCA
** * * *
29571575 CCACAAAGGATTTTCTTTCATATTTCA
1 CCACAAAAAAGTTCCTTTCATAATTCA
29571602 CCACAAA
1 CCACAAA
29571609 GGGTTTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (27 bp):
CCACAAAAAAGTTCCTTTCATAATTCA
Found at i:29571620 original size:27 final size:27
Alignment explanation
Indices: 29571563--29571620 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
29571553 AAAAAGTTCC
**
29571563 TTTCATAATTCACCACAAAGGATTTTC
1 TTTCATAATTCACCACAAAGGATTTAA
* *
29571590 TTTCATATTTCACCACAAAGGGTTTAA
1 TTTCATAATTCACCACAAAGGATTTAA
29571617 TTTC
1 TTTC
29571621 CTTATGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (27 bp):
TTTCATAATTCACCACAAAGGATTTAA
Found at i:29586506 original size:23 final size:23
Alignment explanation
Indices: 29586463--29586509 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29586453 TTTAGTAATA
*
29586463 AATATTTTATAGAATAAAATATG
1 AATATTTTATAAAATAAAATATG
*
29586486 AATATTTTATTAAAAT-TAATATG
1 AATATTTTA-TAAAATAAAATATG
29586509 A
1 A
29586510 GTTTTTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
AATATTTTATAAAATAAAATATG
Found at i:29593606 original size:3 final size:3
Alignment explanation
Indices: 29593598--29593629 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29593588 CTGTTGAACT
29593598 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29593630 TTTGGTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29593840 original size:44 final size:43
Alignment explanation
Indices: 29593775--29594272 Score: 249
Period size: 44 Copynumber: 11.5 Consensus size: 43
29593765 CAAGTAGCCT
*
29593775 CACTGCAACTTCA-GGAGGATAAGACTTGTTTACTTAGTCTGCTC
1 CACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTC
* * * *
29593819 CACTGCAACTTCAGGGAGATAAGACTAGATGC--GATCTGCT-
1 CACTGCAACTTCAGGGAGATAAGACTTGTTACTTAATCTGCTC
* * * ** *
29593859 CTCTACAACTTCAGAGAGATAAGATCCAAGATT--TTAATCCGCTC
1 CACTGCAACTTCAGGGAGATAAGA--CTTG-TTACTTAATCTGCTC
* * * * * * *
29593903 CCCTGAAACTTCAGGGAAATAGGA-TTATTGGCTTTAACCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTTGTT-AC-TTAATCTGCTC
* ** * *
29593947 CACTGCAACTTCGGGGAGATAAGGTTTGTCATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGTTA-CTT-AATCTGCTC
* *
29593991 TCACTGCAACTTCA-GGAGGATAAGACCTGCTTACTTAGTCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTC
* * **
29594036 CACTGCAACTTCAGGGAGTTAAGACTAG--A-TGGGATCTGC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGTTACT-TAATCTGCTC
* * ** **
29594076 CTCTGCAACTTCAGAGAGATAAGATCCAAGATT--TTAATCCACTC
1 CACTGCAACTTCAGGGAGATAAGA--CTTG-TTACTTAATCTGCTC
* * * * * *
29594120 CACTACAACTTCAGGGAAATAGGA-TTATTGGATTTAACCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTTGTT--ACTTAATCTGCTC
* ** *
29594164 CACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGTTA-CTT-AATCTGCTC
*
29594208 TCGCTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAATCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTC
29594253 CACTGCAACTTCAGGGAGAT
1 CACTGCAACTTCAGGGAGAT
29594273 GAGATTATTG
Statistics
Matches: 337, Mismatches: 79, Indels: 76
0.68 0.16 0.15
Matches are distributed among these distances:
40 48 0.14
41 12 0.04
42 6 0.02
43 14 0.04
44 179 0.53
45 75 0.22
46 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (43 bp):
CACTGCAACTTCAGGGAGATAAGACTTGTTACTTAATCTGCTC
Found at i:29594146 original size:217 final size:217
Alignment explanation
Indices: 29593771--29594272 Score: 862
Period size: 217 Copynumber: 2.3 Consensus size: 217
29593761 TCTTCAAGTA
*
29593771 GCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
1 GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
* *
29593836 GATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCGC
66 GATAAGACTAGATGCGATCTGCCCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCAC
* * *
29593901 TCCCCTGAAACTTCAGGGAAATAGGATTATTGGCTTTAACCTGCTCCACTGCAACTTCGGGGAGA
131 TCCACTGAAACTTCAGGGAAATAGGATTATTGGATTTAACCTGCTCCACTGCAACTTCAGGGAGA
* *
29593966 TAAGGTTTGTCATCTTCAGTCT
196 TAAGATTTGCCATCTTCAGTCT
*
29593988 GCCTCACTGCAACTTCAGGAGGATAAGACCTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
1 GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
* * *
29594053 GTTAAGACTAGATGGGATCTGCCCTCTGCAACTTCAGAGAGATAAGATCCAAGATTTTAATCCAC
66 GATAAGACTAGATGCGATCTGCCCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCAC
29594118 TCCACT-ACAACTTCAGGGAAATAGGATTATTGGATTTAACCTGCTCCACTGCAACTTCAGGGAG
131 TCCACTGA-AACTTCAGGGAAATAGGATTATTGGATTTAACCTGCTCCACTGCAACTTCAGGGAG
29594182 ATAAGATTTGCCATCTTCAGTCT
195 ATAAGATTTGCCATCTTCAGTCT
* *
29594205 GCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTACTTAATCTGCTCCACTGCAACTTCAGGGA
1 GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
29594270 GAT
66 GAT
29594273 GAGATTATTG
Statistics
Matches: 268, Mismatches: 16, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
216 1 0.00
217 267 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (217 bp):
GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
GATAAGACTAGATGCGATCTGCCCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCAC
TCCACTGAAACTTCAGGGAAATAGGATTATTGGATTTAACCTGCTCCACTGCAACTTCAGGGAGA
TAAGATTTGCCATCTTCAGTCT
Found at i:29607762 original size:3 final size:3
Alignment explanation
Indices: 29607754--29607779 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29607744 CTGTTGAACT
29607754 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
29607780 GGTGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29608222 original size:22 final size:24
Alignment explanation
Indices: 29608183--29608226 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
29608173 TTTGATTCGT
29608183 TTTTTTAGTTTATAATATATTAAA
1 TTTTTTAGTTTATAATATATTAAA
*
29608207 TTTTTTA-TTT-TTATATATTA
1 TTTTTTAGTTTATAATATATTA
29608227 TATATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 3 0.16
24 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTTTAGTTTATAATATATTAAA
Found at i:29617147 original size:21 final size:22
Alignment explanation
Indices: 29617114--29617156 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
29617104 CAAATTTCAG
*
29617114 AAATTGATATTT-ATTTTTTAA
1 AAATTGATATTTAATTATTTAA
* *
29617135 AAATTTATTTTTAATTATTTAA
1 AAATTGATATTTAATTATTTAA
29617157 TTTAAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AAATTGATATTTAATTATTTAA
Found at i:29620654 original size:94 final size:94
Alignment explanation
Indices: 29620520--29620707 Score: 252
Period size: 94 Copynumber: 2.0 Consensus size: 94
29620510 TATTTTTAAG
* * * *
29620520 GCTCGTTGATTTACGATCACAGTCTAAGTTCATTGATTTACAATTATGAACAAGTTT-TCCTGAG
1 GCTCGGTGATTTACAATCACAGCCTAAGTTCATTGATTTACAATCATGAACAA-TTTCTCCTGAG
29620584 TTTGCTGACTTACAATCACAACTCCAAATA
65 TTTGCTGACTTACAATCACAACTCCAAATA
* * * *
29620614 GCTCGGTGATTTACAATCACAGCCTAAGTTTATTGATTTACGATCATGAATAATTTCTCTTGAGT
1 GCTCGGTGATTTACAATCACAGCCTAAGTTCATTGATTTACAATCATGAACAATTTCTCCTGAGT
* * **
29620679 TTGTTGATTTATTATCACAACTCCAAATA
66 TTGCTGACTTACAATCACAACTCCAAATA
29620708 ACTCACTAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
93 3 0.04
94 78 0.96
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (94 bp):
GCTCGGTGATTTACAATCACAGCCTAAGTTCATTGATTTACAATCATGAACAATTTCTCCTGAGT
TTGCTGACTTACAATCACAACTCCAAATA
Found at i:29620696 original size:63 final size:63
Alignment explanation
Indices: 29620620--29620892 Score: 212
Period size: 63 Copynumber: 4.3 Consensus size: 63
29620610 AATAGCTCGG
* * * * *
29620620 TGATTTACAATCACAGCCTAAGTTTATTGATTTACGATCATGAATAATTTCTCTTGAGTTTGT
1 TGATTTACGATCACAACCTAAATTCATTAATTTACGATCATGAATAATTTCTCTTGAGTTTGT
** * * * * * * *
29620683 TGATTTATTATCACAACTCCAAATAACTCACTAATTTACGATCAT-AGTTGATAT-TATTAAGGC
1 TGATTTACGATCACAAC-CTAAAT---TCATTAATTTACGATCATGA-ATAATTTCTCTTGA-G-
29620746 TTT-T
59 TTTGT
* * * * * * *
29620750 TGATTTACGATCACAACCTAAGTTCATTGATTAACGATCATGAACAATTTCTCCTGAGTTCGC
1 TGATTTACGATCACAACCTAAATTCATTAATTTACGATCATGAATAATTTCTCTTGAGTTTGT
* *
29620813 TGATTTACGATCACAACCTAAATTCATTAATTTACGATCATGAATAATATT-TCCTGAGTTAGT
1 TGATTTACGATCACAACCTAAATTCATTAATTTACGATCATGAATAAT-TTCTCTTGAGTTTGT
* * *
29620876 GGATTCACAATCACAAC
1 TGATTTACGATCACAAC
29620893 TTAGGTACGA
Statistics
Matches: 161, Mismatches: 38, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
62 2 0.01
63 101 0.63
64 10 0.06
66 9 0.06
67 36 0.22
68 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (63 bp):
TGATTTACGATCACAACCTAAATTCATTAATTTACGATCATGAATAATTTCTCTTGAGTTTGT
Found at i:29620779 original size:27 final size:27
Alignment explanation
Indices: 29620749--29620852 Score: 73
Period size: 27 Copynumber: 3.5 Consensus size: 27
29620739 TTAAGGCTTT
29620749 TTGATTTACGATCACAACCTAAGTTCA
1 TTGATTTACGATCACAACCTAAGTTCA
* * *
29620776 TTGATTAACGATCATGAACAATTTCTCCTGAGTTCG
1 TTGATTTACGATC----ACAA-----CCTAAGTTCA
* *
29620812 CTGATTTACGATCACAACCTAAATTCA
1 TTGATTTACGATCACAACCTAAGTTCA
*
29620839 TTAATTTACGATCA
1 TTGATTTACGATCA
29620853 TGAATAATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
27 31 0.53
31 4 0.07
32 4 0.07
36 19 0.33
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (27 bp):
TTGATTTACGATCACAACCTAAGTTCA
Found at i:29620799 original size:130 final size:126
Alignment explanation
Indices: 29620620--29620853 Score: 324
Period size: 130 Copynumber: 1.8 Consensus size: 126
29620610 AATAGCTCGG
* * * * * * *
29620620 TGATTTACAATCACAGCCTAAGTTTATTGATTTACGATCATGAATAATTTCTCTTGAGTTTGTTG
1 TGATTTACAATCACAACCTAAGTTCATTGATTAACGATCATGAACAATTTCTCCTGAGTTCGCTG
**
29620685 ATTTATTATCACAACTCCAAATAACTCACTAATTTACGATCATAGTTGATATTATTAAGGCTTTT
66 ATTTACGATCACAAC-CCAAAT---TCACTAATTTACGATCATAGTTGATATTATTAAGGCTTTT
*
29620750 TGATTTACGATCACAACCTAAGTTCATTGATTAACGATCATGAACAATTTCTCCTGAGTTCGCTG
1 TGATTTACAATCACAACCTAAGTTCATTGATTAACGATCATGAACAATTTCTCCTGAGTTCGCTG
* *
29620815 ATTTACGATCACAACCTAAATTCATTAATTTACGATCAT
66 ATTTACGATCACAACCCAAATTCACTAATTTACGATCAT
29620854 GAATAATATT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
126 17 0.18
129 5 0.05
130 70 0.76
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (126 bp):
TGATTTACAATCACAACCTAAGTTCATTGATTAACGATCATGAACAATTTCTCCTGAGTTCGCTG
ATTTACGATCACAACCCAAATTCACTAATTTACGATCATAGTTGATATTATTAAGGCTTTT
Found at i:29628478 original size:16 final size:16
Alignment explanation
Indices: 29628459--29628492 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29628449 TGAAATGAAT
*
29628459 ATGTGTAAATATGATA
1 ATGTGAAAATATGATA
29628475 ATGTGAAAATATGATA
1 ATGTGAAAATATGATA
29628491 AT
1 AT
29628493 TGGATATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (16 bp):
ATGTGAAAATATGATA
Found at i:29632705 original size:83 final size:85
Alignment explanation
Indices: 29632604--29632771 Score: 286
Period size: 85 Copynumber: 2.0 Consensus size: 85
29632594 AAGGGGATGT
*
29632604 GGATGAAGGGAGCTCTACATGTAGCAACAGA-G-GTGAGTTTAAGGCTAGCAATGGAGAAAAGAG
1 GGATGAAGGGAGCTCTACATGTAGCAACAGAGGTGTGAGTTTAAGGCTAACAATGGAGAAAAGAG
29632667 GAACTGGTAAGTCTCTTTAC
66 GAACTGGTAAGTCTCTTTAC
**
29632687 GGATGAAGGGAGCTCTACATGTAGCAGTAGAGGTGTGAGTTTAAGGCTAACAATGGAGAAAAGAG
1 GGATGAAGGGAGCTCTACATGTAGCAACAGAGGTGTGAGTTTAAGGCTAACAATGGAGAAAAGAG
*
29632752 GAACTGGTAAGTTTCTTTAC
66 GAACTGGTAAGTCTCTTTAC
29632772 CTCCCTCTAT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
83 29 0.37
84 1 0.01
85 49 0.62
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.23
Consensus pattern (85 bp):
GGATGAAGGGAGCTCTACATGTAGCAACAGAGGTGTGAGTTTAAGGCTAACAATGGAGAAAAGAG
GAACTGGTAAGTCTCTTTAC
Found at i:29643806 original size:62 final size:57
Alignment explanation
Indices: 29643719--29643831 Score: 138
Period size: 62 Copynumber: 1.9 Consensus size: 57
29643709 TATATATACA
*
29643719 TTTTTTATAATATATATATACACACACTTTTCCA-AATTATTATAAATATATTTTCTGCAT
1 TTTTTTATAATACATATATACACACA-TTTT-CATAA-T-TTATAAATATATTTTCTGCAT
* *
29643779 TTTTCTTATATATACATATATATACACATTTTCATAATTTATTAATATATTTT
1 TTTT-TTATA-ATACATATATACACACATTTTCATAATTTATAAATATATTTT
29643832 ACTTGTATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
59 14 0.30
60 7 0.15
61 11 0.23
62 15 0.32
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.51
Consensus pattern (57 bp):
TTTTTTATAATACATATATACACACATTTTCATAATTTATAAATATATTTTCTGCAT
Found at i:29644000 original size:19 final size:20
Alignment explanation
Indices: 29643965--29644009 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
29643955 TCATGTTTAT
29643965 ATATTTTATATAATATATAC
1 ATATTTTATATAATATATAC
* *
29643985 ATATTTTGTAAATATATATAC
1 ATATTTTATATA-ATATATAC
29644006 ATAT
1 ATAT
29644010 AATTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
ATATTTTATATAATATATAC
Found at i:29649149 original size:41 final size:41
Alignment explanation
Indices: 29649104--29649205 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
29649094 GCTTAGCGCT
*
29649104 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTAAATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
* * *
29649145 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
29649186 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
29649206 TACTGAATCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
40 3 0.05
41 53 0.95
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
Found at i:29653833 original size:73 final size:73
Alignment explanation
Indices: 29653741--29653886 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
29653731 TGGCATGGTA
*
29653741 TGAAATGAGACATTTCTGACTTTGTTTCGAAATGTTTAATTTGTCAGCAAGTTAAAGCCGAGCAT
1 TGAAACGAGACATTTCTGACTTTGTTTCGAAATGTTTAATTTGTCAGCAAGTTAAAGCCGAGCAT
29653806 AAGGTACC
66 AAGGTACC
29653814 TGAAACGAGACATTTCTGACTTTGTTTCGAAATGTTTAATTTGTCAGCAAGTTAAAGCCGAGCAT
1 TGAAACGAGACATTTCTGACTTTGTTTCGAAATGTTTAATTTGTCAGCAAGTTAAAGCCGAGCAT
*
29653879 CAGGTACC
66 AAGGTACC
29653887 ATCTGGGTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (73 bp):
TGAAACGAGACATTTCTGACTTTGTTTCGAAATGTTTAATTTGTCAGCAAGTTAAAGCCGAGCAT
AAGGTACC
Found at i:29655287 original size:15 final size:15
Alignment explanation
Indices: 29655258--29655301 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
29655248 AAAGATGTGA
29655258 AAAAATG-AAAA-GG
1 AAAAATGAAAAATGG
29655271 AAAAATGAAAAATGG
1 AAAAATGAAAAATGG
29655286 AAAAA-GTAAAAATGG
1 AAAAATG-AAAAATGG
29655301 A
1 A
29655302 GAGGCTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.25
14 5 0.18
15 16 0.57
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.11
Consensus pattern (15 bp):
AAAAATGAAAAATGG
Found at i:29656670 original size:88 final size:88
Alignment explanation
Indices: 29656561--29656872 Score: 498
Period size: 88 Copynumber: 3.5 Consensus size: 88
29656551 CTGAAGATAG
* *
29656561 CAGATCTTGCCTTCCTATACTGACAGAGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGCA
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGCA
*
29656626 GTAGTGAAGTAGGTTGAAAATGA
66 GTAGTGGAGTAGGTTGAAAATGA
*
29656649 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGTA
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGCA
29656714 GTAGTGGAGTAGGTTGAAAATGA
66 GTAGTGGAGTAGGTTGAAAATGA
* *
29656737 CAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTATCTCCCTGGGCA
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGCA
* * *
29656802 ATAGTGGAGTAGGTTAAAAATAA
66 GTAGTGGAGTAGGTTGAAAATGA
* * * * *
29656825 CAAATCTTGCCTTCTTGTACTGGCAGCGAAGTAGATCGAAGACACCAG
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAG
29656873 TCTTATCACC
Statistics
Matches: 208, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 208 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGCA
GTAGTGGAGTAGGTTGAAAATGA
Found at i:29656965 original size:50 final size:50
Alignment explanation
Indices: 29656900--29657049 Score: 165
Period size: 50 Copynumber: 3.0 Consensus size: 50
29656890 CGCAATTAAA
*
29656900 AAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAG
1 AAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAG
* * *** * * * * * ** *
29656950 CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAA
1 AAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAG
*
29657000 AAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGTGGTGCAGTGGAG
1 AAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAG
29657050 TGGACTTGAG
Statistics
Matches: 72, Mismatches: 28, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (50 bp):
AAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAG
Found at i:29657197 original size:50 final size:49
Alignment explanation
Indices: 29657143--29657390 Score: 149
Period size: 50 Copynumber: 5.0 Consensus size: 49
29657133 CCCTGGCGGT
*
29657143 GTAATGGAGCAGATTGAAGTCATAACGGCAGATCTGGTTTCGCCGACAGC
1 GTAATGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTC-CCGACAGC
** ** * *** * * *
29657193 GTAATTAAAAAGATTGAA-TCCACAATGGCAGATCTTACTTCCCTGGCGGT
1 GTAATGGAGCAGATTGAAGT-CACAACGGCAGATCTGGTTTCCC-GACAGC
* * *
29657243 GCAGA-GGAGCAGATTGAAGTCACAACGGTAAATCTGGTTTCCCCGACAGC
1 GTA-ATGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTT-CCCGACAGC
* ** ** * * *** * * * *
29657293 GCAATTAAAAAGGTTGAAGCCACAACGGCAGATCTTACTTCCTTGGCGGT
1 GTAATGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCC-CGACAGC
*
29657343 GTAATGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACA
1 GTAATGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTT-CCCGACA
29657391 ACGCAATTAA
Statistics
Matches: 135, Mismatches: 55, Indels: 16
0.66 0.27 0.08
Matches are distributed among these distances:
49 6 0.04
50 122 0.90
51 7 0.05
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (49 bp):
GTAATGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCGACAGC
Found at i:29657235 original size:100 final size:100
Alignment explanation
Indices: 29656885--29657426 Score: 607
Period size: 100 Copynumber: 5.4 Consensus size: 100
29656875 TTATCACCTT
* *
29656885 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAG
1 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAG
29656950 CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
66 CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
* *
29656985 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGTGGTGCAGTGGAG
1 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAG
** * * * **
29657050 TGGACTTG-AG--A-TA--GCAAAT-T-TTATTCTTTC
66 CAGA-TTGAAGTCACAACGGCAGATCTGGT-TTC-CCC
* ** *** * * *
29657080 GAGCAGACTGAAGACCCAAATCCTATCTCAAGCCACAACGGCAGATCTTAATTCCCTGGCGGTGT
1 GA-CAG-C-GCA-A-TTAAA-AAGAT-TGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* *
29657145 AATGGAGCAGATTGAAGTCATAACGGCAGATCTGGTTTCGCC
59 AATGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
* * *
29657187 GACAGCGTAATTAAAAAGATTGAATCCACAATGGCAGATCTTACTTCCCTGGCGGTGCAGA-GGA
1 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCA-ATGGA
* *
29657251 GCAGATTGAAGTCACAACGGTAAATCTGGTTTCCCC
65 GCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
* * *
29657287 GACAGCGCAATTAAAAAGGTTGAAGCCACAACGGCAGATCTTACTTCCTTGGCGGTGTAATGGAG
1 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAG
*
29657352 CAGATTGAAGTCACAACGGCGGATCTGGTTTCCCC
66 CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
* * *
29657387 GACAACGCAATTAAAAAAGATTAAAGCCACAACAGCAGAT
1 GACAGCGCAATT-AAAAAGATTGAAGCCACAACGGCAGAT
29657427 TTTTACCTCC
Statistics
Matches: 366, Mismatches: 55, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
93 1 0.00
94 4 0.01
95 8 0.02
96 3 0.01
97 2 0.01
98 3 0.01
99 2 0.01
100 239 0.65
101 35 0.10
102 47 0.13
103 1 0.00
104 3 0.01
105 2 0.01
106 3 0.01
107 8 0.02
108 4 0.01
109 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (100 bp):
GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAG
CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
Found at i:29657486 original size:102 final size:100
Alignment explanation
Indices: 29657109--29657492 Score: 304
Period size: 100 Copynumber: 3.8 Consensus size: 100
29657099 ATCCTATCTC
* ** * * * * * * * *
29657109 AAGCCACAACGGCAGATCTTAATTCCCTGGCGGTGTAATGGAGCAGATTGAAGTCATAACGGCAG
1 AAGCCACAACAGCAGATCTTACCTCCTTAGCGGTGCAATGGAACAGATGGAAGTCACAACAGCGG
* * * * *
29657174 ATCTGGTTTCGCCGACAGCGTAATTAAAAAGATTG
66 ATCTGCTTTCCCCGACAACGCAATTAAAAAGATTA
* ** * * * * * * **
29657209 AATCCACAATGGCAGATCTTACTTCCCTGGCGGTGCAGA-GGAGCAGATTGAAGTCACAACGGTA
1 AAGCCACAACAGCAGATCTTACCTCCTTAGCGGTGCA-ATGGAACAGATGGAAGTCACAACAGCG
* * * * *
29657273 AATCTGGTTTCCCCGACAGCGCAATTAAAAAGGTTG
65 GATCTGCTTTCCCCGACAACGCAATTAAAAAGATTA
* * * * * * *
29657309 AAGCCACAACGGCAGATCTTACTTCCTTGGCGGTGTAATGGAGCAGATTGAAGTCACAACGGCGG
1 AAGCCACAACAGCAGATCTTACCTCCTTAGCGGTGCAATGGAACAGATGGAAGTCACAACAGCGG
*
29657374 ATCTGGTTTCCCCGACAACGCAATTAAAAAAGATTA
66 ATCTGCTTTCCCCGACAACGCAATT-AAAAAGATTA
* * * *
29657410 AAGCCACAACAGCAGATTTTTACCTCCTTAGCGGTGCAGTTGAACAGATGGAAG-CTACAACAGT
1 AAGCCACAACAGCAGA-TCTTACCTCCTTAGCGGTGCAATGGAACAGATGGAAGTC-ACAACAGC
* *
29657474 GGATCTTCTTTCCTCGACA
64 GGATCTGCTTTCCCCGACA
29657493 TTGTAATTGG
Statistics
Matches: 245, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
99 1 0.00
100 168 0.69
101 25 0.10
102 51 0.21
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (100 bp):
AAGCCACAACAGCAGATCTTACCTCCTTAGCGGTGCAATGGAACAGATGGAAGTCACAACAGCGG
ATCTGCTTTCCCCGACAACGCAATTAAAAAGATTA
Found at i:29659237 original size:62 final size:58
Alignment explanation
Indices: 29659166--29659280 Score: 142
Period size: 62 Copynumber: 1.9 Consensus size: 58
29659156 ATATATATAC
*
29659166 TTTTTTTATAAATATATATATACACACACTTTTCCA-AATTATTATAAATATATTTTCTGCA
1 TTTTTTTATAAATACATATATACACACA-TTTT-CATAA-T-TTATAAATATATTTTCTGCA
* * *
29659227 TTTTTCTTATATATACATATATATACACATTTTCATAATTTATTAATATATTTT
1 TTTTT-TTATAAATACATATATACACACATTTTCATAATTTATAAATATATTTT
29659281 ACTTGTATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 14 0.29
60 3 0.06
61 11 0.23
62 20 0.42
ACGTcount: A:0.37, C:0.11, G:0.01, T:0.51
Consensus pattern (58 bp):
TTTTTTTATAAATACATATATACACACATTTTCATAATTTATAAATATATTTTCTGCA
Found at i:29659421 original size:10 final size:9
Alignment explanation
Indices: 29659398--29659434 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
29659388 TTTTCCCGTA
29659398 TTATATAAT
1 TTATATAAT
*
29659407 TTATATATGT
1 TTATATA-AT
29659417 TTATATAAT
1 TTATATAAT
29659426 TTATATAAT
1 TTATATAAT
29659435 ATATTCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
TTATATAAT
Found at i:29659473 original size:21 final size:22
Alignment explanation
Indices: 29659419--29659474 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
29659409 ATATATGTTT
* *
29659419 ATATAATTTATATAATATATTC
1 ATATAATTTAAATAATATATAC
*
29659441 ATAT-TTTGTAAAT-ATATATAC
1 ATATAATT-TAAATAATATATAC
29659462 ATATAATTTAAAT
1 ATATAATTTAAAT
29659475 TAAAATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATAATTTAAATAATATATAC
Found at i:29661812 original size:19 final size:21
Alignment explanation
Indices: 29661774--29661813 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
29661764 CTTGTTTTGA
*
29661774 TTAAATAAATTATTTAAAATT
1 TTAAATAAATTATATAAAATT
29661795 TTAAA-AAA-TATATAAAATT
1 TTAAATAAATTATATAAAATT
29661814 GATTAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAATAAATTATATAAAATT
Found at i:29663864 original size:124 final size:125
Alignment explanation
Indices: 29663638--29663908 Score: 383
Period size: 124 Copynumber: 2.2 Consensus size: 125
29663628 TTATTTCGAG
* * **
29663638 TTGACGTTTCT-GGTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCAGAGAAGAAATTGT
1 TTGACGTTTCTAAG-CAAATAGTATAAAATCACTGATACCAGGATGCTATCAGAGAAGAAATTGT
*
29663702 GAAATCGTGCCCTCGTGGACGCCATTTCGGCACAGTTGGTCATGTCA-GAAATAA-T-TTTT
65 GAAATCGCGCCCTCGTGGACGCCATTTCGGCACAGTTGGTCATGT-AGGAAATAATTATTTT
*
29663761 TTGACGTTTTCTAAGCAAATAGTATAAAATTACTGATACCAGGATGCTAT-ATGAGAAGAAATTG
1 TTGACG-TTTCTAAGCAAATAGTATAAAATCACTGATACCAGGATGCTATCA-GAGAAGAAATTG
*
29663825 TGAAATCGCGCCCTCGTGGACGCGATTTC-GCTACAGTTGGTCATGTAGGAAATAATTATTTT
64 TGAAATCGCGCCCTCGTGGACGCCATTTCGGC-ACAGTTGGTCATGTAGGAAATAATTATTTT
*
29663887 TTGACGTTTCTGAGCAAATAGT
1 TTGACGTTTCTAAGCAAATAGT
29663909 GTCAAATCGT
Statistics
Matches: 133, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
123 10 0.08
124 96 0.72
125 17 0.13
126 10 0.08
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (125 bp):
TTGACGTTTCTAAGCAAATAGTATAAAATCACTGATACCAGGATGCTATCAGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCCATTTCGGCACAGTTGGTCATGTAGGAAATAATTATTTT
Found at i:29667029 original size:29 final size:29
Alignment explanation
Indices: 29666996--29667248 Score: 470
Period size: 29 Copynumber: 8.7 Consensus size: 29
29666986 TATCAAATTA
29666996 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
29667025 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
29667054 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
29667083 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
29667112 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
29667141 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
29667170 GGTTAGGGTTTTTAATCAAATTAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
29667199 GGTTAAGGTTTTTAATCAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
29667228 GGTTAGGGTTTTTAATTAAAT
1 GGTTAGGGTTTTTAATTAAAT
29667249 CAAATAATAT
Statistics
Matches: 218, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 218 1.00
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.44
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:29667399 original size:29 final size:29
Alignment explanation
Indices: 29667347--29667439 Score: 170
Period size: 29 Copynumber: 3.2 Consensus size: 29
29667337 ATACGGTANC
*
29667347 AAATTAGGTTAGGGTTAGAGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
29667376 AAATTAGGTTA-GGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
29667404 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
29667433 AAATTAG
1 AAATTAG
29667440 NNNNNNNNNN
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
28 27 0.44
29 35 0.56
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:29669773 original size:14 final size:15
Alignment explanation
Indices: 29669756--29669789 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29669746 AATATTTATC
29669756 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
29669770 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
29669785 TAAAA
1 TAAAA
29669790 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:29669922 original size:28 final size:28
Alignment explanation
Indices: 29669887--29669943 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
29669877 TTGAAAATAT
* *
29669887 TAAAAATA-TTAAAATTATTTTTAAAAAA
1 TAAAAATATTTAAAAGT-TTCTTAAAAAA
29669915 TAAAAATATTTAAAAGTTTCTTAAAAAA
1 TAAAAATATTTAAAAGTTTCTTAAAAAA
29669943 T
1 T
29669944 GAAATTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
TAAAAATATTTAAAAGTTTCTTAAAAAA
Found at i:29669924 original size:19 final size:21
Alignment explanation
Indices: 29669886--29669925 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
29669876 GTTGAAAATA
*
29669886 TTAAAAATATTAAAATTATTT
1 TTAAAAATATTAAAAATATTT
29669907 TTAAAAA-A-TAAAAATATTT
1 TTAAAAATATTAAAAATATTT
29669926 AAAAGTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAAATATTAAAAATATTT
Found at i:29670021 original size:21 final size:21
Alignment explanation
Indices: 29669977--29670025 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
29669967 TAATATGGAG
*
29669977 TTGAGAGATTTTTTGAAGGAAAT
1 TTGAG-GA-TTTTGGAAGGAAAT
29670000 TGTGAGGATTTTGGAAGG-AAT
1 T-TGAGGATTTTGGAAGGAAAT
29670021 TTGAG
1 TTGAG
29670026 AGTTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 9 0.38
23 3 0.12
24 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.37
Consensus pattern (21 bp):
TTGAGGATTTTGGAAGGAAAT
Found at i:29670052 original size:52 final size:52
Alignment explanation
Indices: 29669980--29670079 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
29669970 TATGGAGTTG
* * * *
29669980 AGAGATTTTTTGAAGGAAATTGTGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAGTTTA
*
29670032 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTTGAAGGAATTTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAG
29670080 AATTTTTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAGTTTA
Found at i:29670057 original size:22 final size:22
Alignment explanation
Indices: 29670032--29670100 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
29670022 TGAGAGTTTA
*
29670032 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
*
29670054 AGAGAATTTTTGAAGGAATTTG
1 AGAGAATTTTTGAAGGAAATTG
*
29670076 AGAGAATTTTTGAATGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
29670098 AGA
1 AGA
29670101 TGGGATTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.32
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGAAATTG
Found at i:29674872 original size:25 final size:25
Alignment explanation
Indices: 29674843--29674910 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
29674833 CGGTAAACAA
* *
29674843 TAAGCTGTTCCGAGCTGAATAAGGG
1 TAAGCTCTTCCGAGCTGAATAACGG
* *
29674868 TAAGCTCTTTCGAGCTGCATAACGG
1 TAAGCTCTTCCGAGCTGAATAACGG
* *
29674893 TAAGCTCATACGAGCTGA
1 TAAGCTCTTCCGAGCTGA
29674911 TTATTGATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (25 bp):
TAAGCTCTTCCGAGCTGAATAACGG
Found at i:29681528 original size:58 final size:58
Alignment explanation
Indices: 29681438--29681558 Score: 233
Period size: 58 Copynumber: 2.1 Consensus size: 58
29681428 TTACATTGTG
*
29681438 TAATAAAGTAGAGATAATCACTTAGTTCAACTAGTAAGAACATGGATTTTCATCTAAT
1 TAATAAAGTAGAGATAATCACTTAGTTCAACTAGTAAGAACATGAATTTTCATCTAAT
29681496 TAATAAAGTAGAGATAATCACTTAGTTCAACTAGTAAGAACATGAATTTTCATCTAAT
1 TAATAAAGTAGAGATAATCACTTAGTTCAACTAGTAAGAACATGAATTTTCATCTAAT
29681554 TAATA
1 TAATA
29681559 CATGAACCTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (58 bp):
TAATAAAGTAGAGATAATCACTTAGTTCAACTAGTAAGAACATGAATTTTCATCTAAT
Found at i:29682158 original size:16 final size:16
Alignment explanation
Indices: 29682115--29682167 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
29682105 TTACCCTATA
29682115 AAAAATAAT-AATTTT
1 AAAAATAATAAATTTT
* *
29682130 AGTATATAA-AAATTTT
1 A-AAAATAATAAATTTT
29682146 AAAAATAATAAA--TT
1 AAAAATAATAAATTTT
29682160 AAAAATAA
1 AAAAATAA
29682168 CCAAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 10 0.32
15 6 0.19
16 15 0.48
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAAATAATAAATTTT
Found at i:29682164 original size:15 final size:15
Alignment explanation
Indices: 29682144--29682178 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
29682134 TATAAAAATT
*
29682144 TTAAAAATAA-TAAA
1 TTAAAAATAACCAAA
29682158 TTAAAAATAACCAAA
1 TTAAAAATAACCAAA
29682173 TTAAAA
1 TTAAAA
29682179 TAGTCAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TTAAAAATAACCAAA
Found at i:29684719 original size:29 final size:29
Alignment explanation
Indices: 29684686--29684758 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
29684676 AAATTGCATT
*
29684686 ATTATATTAATTATGTTAT-AAAAATAATA
1 ATTATATTAATTAT-ATATGAAAAATAATA
**
29684715 ATTATATTAATTATATATGTTAAATAATA
1 ATTATATTAATTATATATGAAAAATAATA
*
29684744 ATTATA-TATTTATAT
1 ATTATATTAATTATAT
29684759 TAAATCACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 11 0.28
29 28 0.72
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
ATTATATTAATTATATATGAAAAATAATA
Found at i:29685325 original size:12 final size:12
Alignment explanation
Indices: 29685310--29685343 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29685300 CTTAGGCTTT
29685310 ATAATAATAACA
1 ATAATAATAACA
* *
29685322 ATAACAACAACA
1 ATAATAATAACA
29685334 ATAATAATAA
1 ATAATAATAA
29685344 GAGTACTATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (12 bp):
ATAATAATAACA
Found at i:29686747 original size:56 final size:54
Alignment explanation
Indices: 29686677--29686799 Score: 131
Period size: 56 Copynumber: 2.2 Consensus size: 54
29686667 AAAGGGGTTT
29686677 TTTA-CAAAATTATTATAAAAAAATAAAAATAACCAAAATATTATAACTTTTTTTTA
1 TTTACCAAAA-TATTATAAAAAAATAAAAATAACCAAAATATTATAA--TTTTTTTA
**** *** * *
29686733 TTTACCAAAATATTATAAATTTTTTTTATTTACCAAAATATTATAATTTTTTTA
1 TTTACCAAAATATTATAAAAAAATAAAAATAACCAAAATATTATAATTTTTTTA
29686787 TTTACCAAAATAT
1 TTTACCAAAATAT
29686800 ACCAAAAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
54 21 0.37
56 31 0.54
57 5 0.09
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (54 bp):
TTTACCAAAATATTATAAAAAAATAAAAATAACCAAAATATTATAATTTTTTTA
Found at i:29686782 original size:26 final size:27
Alignment explanation
Indices: 29686708--29686799 Score: 159
Period size: 28 Copynumber: 3.4 Consensus size: 27
29686698 AATAAAAATA
29686708 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAA-TTTTTTTTATTT
29686736 ACCAAAATATTATAAATTTTTTTTATTT
1 ACCAAAATATTAT-AATTTTTTTTATTT
29686764 ACCAAAATATTATAA-TTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTTATTT
29686790 ACCAAAATAT
1 ACCAAAATAT
29686800 ACCAAAAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
26 21 0.33
27 2 0.03
28 38 0.60
29 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (27 bp):
ACCAAAATATTATAATTTTTTTTATTT
Found at i:29687141 original size:19 final size:19
Alignment explanation
Indices: 29687117--29687183 Score: 82
Period size: 19 Copynumber: 3.6 Consensus size: 19
29687107 ATAGATAAAA
*
29687117 TATTTTAATTTAACAACTC
1 TATTTTAATTTAATAACTC
* *
29687136 TATTTTAATGTAATAA-AC
1 TATTTTAATTTAATAACTC
* *
29687154 TATTCTCATTTAATAACTC
1 TATTTTAATTTAATAACTC
29687173 TATTTTAATTT
1 TATTTTAATTT
29687184 TAAAAAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.51
Consensus pattern (19 bp):
TATTTTAATTTAATAACTC
Found at i:29687360 original size:82 final size:82
Alignment explanation
Indices: 29687267--29687431 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
29687257 AAAAGGAAAA
*
29687267 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATGTTCTTAATAGACTTATAA
1 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
29687332 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
29687349 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
29687414 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
29687431 A
1 A
29687432 TTTTAATTAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.39
Consensus pattern (82 bp):
AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
CATAAACATGTTAGACT
Found at i:29687539 original size:18 final size:19
Alignment explanation
Indices: 29687500--29687558 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
29687490 ATTTTATATT
29687500 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
29687519 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
29687537 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
29687556 TTA
1 TTA
29687559 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:29688172 original size:27 final size:27
Alignment explanation
Indices: 29688133--29688191 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
29688123 TTTTAGTCCT
29688133 TTGGCACCATTGGTGCCGCCAATCTCA
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * * *
29688160 TTGGCACCTTTGGTGCCTCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
29688187 TTGGC
1 TTGGC
29688192 CTGATCAGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.29, G:0.25, T:0.31
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:29688271 original size:27 final size:28
Alignment explanation
Indices: 29688241--29688305 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
29688231 TTTTTTTGGT
*
29688241 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
29688268 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
29688296 ATATTTTGGT
1 ATATTTTGGT
29688306 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.42
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:29689873 original size:54 final size:54
Alignment explanation
Indices: 29689756--29689879 Score: 158
Period size: 54 Copynumber: 2.3 Consensus size: 54
29689746 AAGCTTTAAG
* * * * *
29689756 TCAGTGAGTTACACGGCCTAGCACACGGCCTGGCACATGGGCATGTGTGACAAC
1 TCAGTGAGTTACACGACCTAGCACACGACCTGGAACACGGGCATGTGGGACAAC
* * * *
29689810 TCAGAGAGTTACACGACCTAGCACACGACCTGGAACACGGGCTTGTGGGGCTAC
1 TCAGTGAGTTACACGACCTAGCACACGACCTGGAACACGGGCATGTGGGACAAC
*
29689864 TTAGTGAGTTACACGA
1 TCAGTGAGTTACACGA
29689880 GTGAGGACAC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (54 bp):
TCAGTGAGTTACACGACCTAGCACACGACCTGGAACACGGGCATGTGGGACAAC
Found at i:29693521 original size:16 final size:16
Alignment explanation
Indices: 29693482--29693521 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29693472 CTTACTCCTT
*
29693482 CCCAATTGAAACCCAG
1 CCCAATTTAAACCCAG
*
29693498 CCCAATTTAAATCCAG
1 CCCAATTTAAACCCAG
29693514 CCCAATTT
1 CCCAATTT
29693522 TTTCTTAGGC
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:0.35, C:0.35, G:0.07, T:0.23
Consensus pattern (16 bp):
CCCAATTTAAACCCAG
Found at i:29694673 original size:9 final size:9
Alignment explanation
Indices: 29694642--29694723 Score: 74
Period size: 9 Copynumber: 8.7 Consensus size: 9
29694632 TGTAGTGATT
29694642 TAATTTGGG
1 TAATTTGGG
*
29694651 TAATTCGGG
1 TAATTTGGG
*
29694660 CAATTTGGG
1 TAATTTGGG
*
29694669 TAATTTTCGGA
1 TAA-TTT-GGG
*
29694680 TAATTCGGG
1 TAATTTGGG
*
29694689 TAATTTGAG
1 TAATTTGGG
29694698 TAATTTTCGGG
1 TAA-TTT-GGG
*
29694709 TAATTCGGG
1 TAATTTGGG
29694718 TAATTT
1 TAATTT
29694724 TTAACAAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
9 37 0.65
10 10 0.18
11 10 0.18
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.41
Consensus pattern (9 bp):
TAATTTGGG
Found at i:29694684 original size:20 final size:20
Alignment explanation
Indices: 29694642--29694694 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
29694632 TGTAGTGATT
*
29694642 TAATTTGGGTAA--TTCGGG
1 TAATTTGGGTAATTTTCGGA
*
29694660 CAATTTGGGTAATTTTCGGA
1 TAATTTGGGTAATTTTCGGA
*
29694680 TAATTCGGGTAATTT
1 TAATTTGGGTAATTT
29694695 GAGTAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 11 0.38
20 18 0.62
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.42
Consensus pattern (20 bp):
TAATTTGGGTAATTTTCGGA
Found at i:29694685 original size:29 final size:29
Alignment explanation
Indices: 29694651--29694723 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
29694641 TTAATTTGGG
* *
29694651 TAATTCGGGCAATTTGGGTAATTTTCGGA
1 TAATTCGGGTAATTTGAGTAATTTTCGGA
*
29694680 TAATTCGGGTAATTTGAGTAATTTTCGGG
1 TAATTCGGGTAATTTGAGTAATTTTCGGA
29694709 TAATTCGGGTAATTT
1 TAATTCGGGTAATTT
29694724 TTAACAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (29 bp):
TAATTCGGGTAATTTGAGTAATTTTCGGA
Found at i:29694706 original size:20 final size:20
Alignment explanation
Indices: 29694683--29694724 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
29694673 TTTCGGATAA
*
29694683 TTCGGGTAATTTGAGTAATT
1 TTCGGGTAATTCGAGTAATT
*
29694703 TTCGGGTAATTCGGGTAATT
1 TTCGGGTAATTCGAGTAATT
29694723 TT
1 TT
29694725 TAACAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.45
Consensus pattern (20 bp):
TTCGGGTAATTCGAGTAATT
Found at i:29699204 original size:21 final size:21
Alignment explanation
Indices: 29699165--29699384 Score: 135
Period size: 21 Copynumber: 10.5 Consensus size: 21
29699155 AAGCCTGAAG
*
29699165 GCTGAACAG-AA-TACATAAGT
1 GCTGAACAGAAACT-CATAAGA
* * *
29699185 GCTAAACAGAAACCCATAAGG
1 GCTGAACAGAAACTCATAAGA
* * *
29699206 GTTGAACGGAAGCTCATAAGA
1 GCTGAACAGAAACTCATAAGA
29699227 GCTGAAC-GAAAGCTCATAAGA
1 GCTGAACAGAAA-CTCATAAGA
** *
29699248 GCTGAATGGAAGCTCATAAGA
1 GCTGAACAGAAACTCATAAGA
* *
29699269 GCTGAACAGAAACCCATAAGG
1 GCTGAACAGAAACTCATAAGA
* * * *
29699290 GTTAAACAGAAGCTCGTAAGA
1 GCTGAACAGAAACTCATAAGA
* * *
29699311 GCTGAACAGAAACCCATCAGG
1 GCTGAACAGAAACTCATAAGA
* * * *
29699332 GTTAAATAGAAGCTCA-ATAGA
1 GCTGAACAGAAACTCATA-AGA
*
29699353 GCTGAAC-GAAAACTCATATGA
1 GCTGAACAG-AAACTCATAAGA
* *
29699374 GTTAAACAGAA
1 GCTGAACAGAA
29699385 GCTTGTGAGA
Statistics
Matches: 147, Mismatches: 45, Indels: 15
0.71 0.22 0.07
Matches are distributed among these distances:
20 12 0.08
21 130 0.88
22 5 0.03
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (21 bp):
GCTGAACAGAAACTCATAAGA
Found at i:29699344 original size:84 final size:84
Alignment explanation
Indices: 29699178--29699405 Score: 255
Period size: 84 Copynumber: 2.7 Consensus size: 84
29699168 GAACAGAATA
* * * * * *
29699178 CATAAGTGCTAAACAGAAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTGAACGAAAGCTCA
1 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACGAAAGCCCA
* *
29699243 TAAGAGCTGAATGGAAGCT
66 TAAGAGCTAAATAGAAGCT
29699262 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACAGAAA-CCC
1 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAAC-GAAAGCCC
* * *
29699326 ATCAGGGTTAAATAGAAGCT
65 ATAAGAGCTAAATAGAAGCT
* * * * * *
29699346 CA-ATAGAGCTGAAC-GAAAACTCATATGAGTTAAACAGAAGCTTGTGAGAGCTAAACGAAA
1 CATA-AGAGCTGAACAG-AAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACGAAA
29699406 AGTAAACATG
Statistics
Matches: 124, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
83 6 0.05
84 114 0.92
85 4 0.03
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (84 bp):
CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACGAAAGCCCA
TAAGAGCTAAATAGAAGCT
Found at i:29699378 original size:42 final size:42
Alignment explanation
Indices: 29699178--29699387 Score: 219
Period size: 42 Copynumber: 5.0 Consensus size: 42
29699168 GAACAGAATA
* * * * *
29699178 CATAAGTGCTAAACAGAAACCCATAAGGGTTGAACGGAAGCT
1 CATAAGAGCTGAACAGAAACCCATAAGAGTTAAACAGAAGCT
* * * **
29699220 CATAAGAGCTGAAC-GAAAGCTCATAAGAGCTGAATGGAAGCT
1 CATAAGAGCTGAACAGAAA-CCCATAAGAGTTAAACAGAAGCT
*
29699262 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCT
1 CATAAGAGCTGAACAGAAACCCATAAGAGTTAAACAGAAGCT
* * * *
29699304 CGTAAGAGCTGAACAGAAACCCATCAGGGTTAAATAGAAGCT
1 CATAAGAGCTGAACAGAAACCCATAAGAGTTAAACAGAAGCT
* *
29699346 CA-ATAGAGCTGAAC-GAAAACTCATATGAGTTAAACAGAAGCT
1 CATA-AGAGCTGAACAG-AAACCCATAAGAGTTAAACAGAAGCT
29699388 TGTGAGAGCT
Statistics
Matches: 143, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 6 0.04
42 133 0.93
43 4 0.03
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (42 bp):
CATAAGAGCTGAACAGAAACCCATAAGAGTTAAACAGAAGCT
Found at i:29701515 original size:24 final size:25
Alignment explanation
Indices: 29701461--29701517 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
29701451 ATAAATTATT
* * *
29701461 AATATTAATTACTTAGAAATATTTA
1 AATATTAATTAATTACAAATATTAA
*
29701486 AA-ATTAATTAATT-CATATATTAA
1 AATATTAATTAATTACAAATATTAA
29701509 AATATTAAT
1 AATATTAAT
29701518 AATAAGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.33
24 16 0.59
25 2 0.07
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AATATTAATTAATTACAAATATTAA
Found at i:29702037 original size:11 final size:11
Alignment explanation
Indices: 29702021--29702045 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29702011 TGTAAGAATA
29702021 AAAATATTGAT
1 AAAATATTGAT
29702032 AAAATATTGAT
1 AAAATATTGAT
29702043 AAA
1 AAA
29702046 GATTTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (11 bp):
AAAATATTGAT
Found at i:29706373 original size:12 final size:12
Alignment explanation
Indices: 29706356--29706382 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29706346 CGAAAACAGG
29706356 CTTTTAGCGGCA
1 CTTTTAGCGGCA
29706368 CTTTTAGCGGCA
1 CTTTTAGCGGCA
29706380 CTT
1 CTT
29706383 GGAAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (12 bp):
CTTTTAGCGGCA
Found at i:29706583 original size:41 final size:41
Alignment explanation
Indices: 29706517--29706597 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
29706507 CTTACCTTTT
* *
29706517 GGGGCTTTAGCGGCGATTTTAAAAAAGTGCCGCTAATGCTC
1 GGGGCTTTAGAGGCGATTTTAAAAAAGCGCCGCTAATGCTC
* *
29706558 GGGGCTTTAGAGGCGTTTTTGAAAAAGCGCCGCTAATGCT
1 GGGGCTTTAGAGGCGATTTTAAAAAAGCGCCGCTAATGCT
29706598 GGAGGATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (41 bp):
GGGGCTTTAGAGGCGATTTTAAAAAAGCGCCGCTAATGCTC
Found at i:29707401 original size:15 final size:15
Alignment explanation
Indices: 29707381--29707410 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29707371 GGGGATTTAA
29707381 AGTTTAGGGGTTAGG
1 AGTTTAGGGGTTAGG
29707396 AGTTTAGGGGTTAGG
1 AGTTTAGGGGTTAGG
29707411 CATATTATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (15 bp):
AGTTTAGGGGTTAGG
Found at i:29707640 original size:7 final size:7
Alignment explanation
Indices: 29707628--29707657 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
29707618 ATAGATTTAG
29707628 GGATTAT
1 GGATTAT
29707635 GGATTAT
1 GGATTAT
*
29707642 GGATTAG
1 GGATTAT
29707649 GGATTAT
1 GGATTAT
29707656 GG
1 GG
29707658 TTTAAGGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (7 bp):
GGATTAT
Found at i:29707818 original size:302 final size:302
Alignment explanation
Indices: 29707099--29708180 Score: 1646
Period size: 302 Copynumber: 3.6 Consensus size: 302
29707089 ATGGATCTAT
* * * * * * * * * *
29707099 GGGTTAGACGTTAGGGGTTAAAAGTTAAGGATTTAAGGTTTAGGAATTTAGGGGTCGAGTTAAGA
1 GGGTTAGACGATAGCGGTTAAGAGTTAGGGATTCAAAGTTTAGGGATTCAAGGGTCGAGTTAAGG
*
29707164 TTTTGGGTGTTTAGATTAA--ATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAA
66 TTTT--GAGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAA
* * * *
29707227 AAGAGATAATAATAAATTTGTTTAGGGTTTTTGGTTTAGGGTATTTGATTTATTTAAGATTTAAA
129 AAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAG
** * * * *
29707292 GCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATAGGTGTAGGGATTATGGA-T-T-G--
194 GCATGTTTAAGAGTGCATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATGGATTATGGAT
* * *
29707352 --GGGATTATGGTTTAATGG-TGGGGATTTAAAGTTTAGGGGTTAG
259 TAGGGATTATGGTTTAAGGGCT-GAGATTTAAGGTTTA-GGGTTAG
* * * * * ** * *
29707395 GAGTT------TAGGGGTTAGGCATATTATGGG-TTAAAAG-TTAGGGATT-TGGGGTCGGGTCA
1 GGGTTAGACGATAGCGGTTAAG-A-GTTA-GGGATTCAAAGTTTAGGGATTCAAGGGTCGAGTTA
* *
29707451 GGGTTTTGGGTTTAGATTAATTA-TTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTA
63 AGGTTTTGAGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTA
29707515 AAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAA
128 AAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAA
29707580 GGCATGTTTAAGAGTGCATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATGGATTATGGA
193 GGCATGTTTAAGAGTGCATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATGGATTATGGA
29707645 TTAGGGATTATGGTTTAAGGGCTGAGATTTAAGGTTTAGGGTTAG
258 TTAGGGATTATGGTTTAAGGGCTGAGATTTAAGGTTTAGGGTTAG
29707690 GGGTTAGACGATAGCGGTTAAGAGTTAGGGATTCAAAGTTTAGGGATTCAAGGGTCGAGTTAAGG
1 GGGTTAGACGATAGCGGTTAAGAGTTAGGGATTCAAAGTTTAGGGATTCAAGGGTCGAGTTAAGG
29707755 TTTTGAGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAA
66 TTTTGAGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAA
29707820 GAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGC
131 GAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGC
29707885 ATGTTTAAGAGTGCATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATGGATTATGGATTA
196 ATGTTTAAGAGTGCATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATGGATTATGGATTA
29707950 GGGATTATGGTTTAAGGGCTGAGATTTAAGGTTTAGGGTTAG
261 GGGATTATGGTTTAAGGGCTGAGATTTAAGGTTTAGGGTTAG
29707992 GGGTTAGACGATAGCGGTTAAGAGTTAGGGATTCAAAGTTTAGGGATTCAAGGGTCGAGTTAAGG
1 GGGTTAGACGATAGCGGTTAAGAGTTAGGGATTCAAAGTTTAGGGATTCAAGGGTCGAGTTAAGG
29708057 TTTTGAGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAA
66 TTTTGAGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAA
29708122 GAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATT
131 GAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATT
29708181 AAGTTTTTTT
Statistics
Matches: 725, Mismatches: 38, Indels: 40
0.90 0.05 0.05
Matches are distributed among these distances:
288 12 0.02
289 154 0.21
290 26 0.04
291 10 0.01
292 9 0.01
293 2 0.00
295 11 0.02
296 34 0.05
297 1 0.00
298 3 0.00
299 9 0.01
300 10 0.01
301 39 0.05
302 405 0.56
ACGTcount: A:0.30, C:0.03, G:0.26, T:0.42
Consensus pattern (302 bp):
GGGTTAGACGATAGCGGTTAAGAGTTAGGGATTCAAAGTTTAGGGATTCAAGGGTCGAGTTAAGG
TTTTGAGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAA
GAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGC
ATGTTTAAGAGTGCATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATGGATTATGGATTA
GGGATTATGGTTTAAGGGCTGAGATTTAAGGTTTAGGGTTAG
Found at i:29707942 original size:7 final size:7
Alignment explanation
Indices: 29707930--29707959 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
29707920 ATAGATTTAG
29707930 GGATTAT
1 GGATTAT
29707937 GGATTAT
1 GGATTAT
*
29707944 GGATTAG
1 GGATTAT
29707951 GGATTAT
1 GGATTAT
29707958 GG
1 GG
29707960 TTTAAGGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (7 bp):
GGATTAT
Found at i:29708254 original size:12 final size:12
Alignment explanation
Indices: 29708237--29708263 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29708227 CGAAAACAGG
29708237 CTTTTAGCGGCA
1 CTTTTAGCGGCA
29708249 CTTTTAGCGGCA
1 CTTTTAGCGGCA
29708261 CTT
1 CTT
29708264 GGAAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (12 bp):
CTTTTAGCGGCA
Found at i:29708464 original size:41 final size:41
Alignment explanation
Indices: 29708398--29708478 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
29708388 CTTACCTTTT
* *
29708398 GGGGCTTTAGCGGCGATTTTAAAAAAGTGCCGCTAATGCTC
1 GGGGCTTTAGAGGCGATTTTAAAAAAGCGCCGCTAATGCTC
* *
29708439 GGGGCTTTAGAGGCGTTTTTGAAAAAGCGCCGCTAATGCT
1 GGGGCTTTAGAGGCGATTTTAAAAAAGCGCCGCTAATGCT
29708479 GGAGGATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (41 bp):
GGGGCTTTAGAGGCGATTTTAAAAAAGCGCCGCTAATGCTC
Found at i:29709282 original size:15 final size:15
Alignment explanation
Indices: 29709262--29709291 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29709252 GGGGATTTAA
29709262 AGTTTAGGGGTTAGG
1 AGTTTAGGGGTTAGG
29709277 AGTTTAGGGGTTAGG
1 AGTTTAGGGGTTAGG
29709292 CATATTATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (15 bp):
AGTTTAGGGGTTAGG
Found at i:29709406 original size:289 final size:293
Alignment explanation
Indices: 29708995--29709715 Score: 906
Period size: 289 Copynumber: 2.4 Consensus size: 293
29708985 AGACGTTAGG
* * * * * * * * *
29708995 GGTTAA-AAGTTAAGGATTTAAGGTTTAGGAATTTAGGGGTCGAGTTAAGATTTTGGGTGTTTAG
1 GGTTAAGAA-TTAGGGATTAAAAGTTTAGGGATTCAAGGGTCGAGTCAAGGTTTT--GAGTTTAG
*
29709059 ATTAAAT-TTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAA
63 ATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAA
* * * * * *
29709123 ATTTGTTTAGGGTTTTTGGTTTAGGGTATTTGATTTATTTAAGATTTAAAGCCGGTTTAGGAGTT
128 ATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAAGCAGGTTTAAGAGTG
* *
29709188 CATATTTTAAGGTTTAGGGAGTATAGGTGTAGGGATTATGGA-T-T-G-GGGATTATGGTTTAAT
193 CATATTTTAAGGTTTAGGGAGTATAGATGTAGGGATTATGGATTATGGAGGGATTATGGTTTAAG
* *
29709249 GG-TGGGGATTTAAAGTTTAGGGGTTAGGAGTT-TAGG
258 GGCT-GAGATTTAAAGTTTA-GGGTTAGGAGTTATAGC
* ** * * *
29709285 GGTTAGGCATATTATGGG-TTAAAAG-TTAGGGATT-TGGGGTCGGGTCAGGGTTTTGGGTTTAG
1 GGTTAAG-A-ATTA-GGGATTAAAAGTTTAGGGATTCAAGGGTCGAGTCAAGGTTTTGAGTTTAG
29709347 ATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAA
63 ATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAA
* *
29709412 ATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCATGTTTAAGAGTG
128 ATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAAGCAGGTTTAAGAGTG
*
29709477 CATATTTTAAGGTTTAGGGAGTATAGATTTAGGGATTATGGATTATGGATTAGGGATTATGGTTT
193 CATATTTTAAGGTTTAGGGAGTATAGATGTAGGGATTATGGATTATGG---AGGGATTATGGTTT
* *
29709542 AAGGGCTGAGATTTAAGGTTTAGGGTTAGGGGTTAGACGATAGC
255 AAGGGCTGAGATTTAAAGTTTAGGGTTAGGAGTT-----ATAGC
* * *
29709586 GGTTAAGAGTTAGGGATTCAAAGTTTAGGGATTCAAGGGTCGAGTTAAGGTTTTGAGTTTAGATT
1 GGTTAAGAATTAGGGATTAAAAGTTTAGGGATTCAAGGGTCGAGTCAAGGTTTTGAGTTTAGATT
29709651 AATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAAAT
66 AATTA-TTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAAAT
29709716 CAAATATATT
Statistics
Matches: 372, Mismatches: 36, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
288 13 0.03
289 154 0.41
290 21 0.06
291 9 0.02
292 10 0.03
293 3 0.01
295 11 0.03
296 30 0.08
297 1 0.00
298 3 0.01
299 9 0.02
300 10 0.03
301 39 0.10
302 59 0.16
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (293 bp):
GGTTAAGAATTAGGGATTAAAAGTTTAGGGATTCAAGGGTCGAGTCAAGGTTTTGAGTTTAGATT
AATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAAATT
TGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAAGCAGGTTTAAGAGTGCAT
ATTTTAAGGTTTAGGGAGTATAGATGTAGGGATTATGGATTATGGAGGGATTATGGTTTAAGGGC
TGAGATTTAAAGTTTAGGGTTAGGAGTTATAGC
Found at i:29709521 original size:7 final size:7
Alignment explanation
Indices: 29709509--29709538 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
29709499 ATAGATTTAG
29709509 GGATTAT
1 GGATTAT
29709516 GGATTAT
1 GGATTAT
*
29709523 GGATTAG
1 GGATTAT
29709530 GGATTAT
1 GGATTAT
29709537 GG
1 GG
29709539 TTTAAGGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (7 bp):
GGATTAT
Found at i:29713906 original size:43 final size:43
Alignment explanation
Indices: 29713821--29713911 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
29713811 CTTTGAGTTC
* * * * *
29713821 ATTA-CAAGATTTCCTTGATTAAGTAAGTGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATGATATCTTTT
* *
29713863 ATTACCAAGATTTACTTGATTAAGAAAATGCATGGTATTTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATGATATCTTTT
29713906 ATTACC
1 ATTACC
29713912 TTGCAATGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 4 0.10
43 37 0.90
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATGATATCTTTT
Found at i:29714323 original size:43 final size:43
Alignment explanation
Indices: 29714262--29714571 Score: 329
Period size: 43 Copynumber: 7.3 Consensus size: 43
29714252 TAATTTTTTT
* * * * * *
29714262 TAAAGGTTATG-TTTTTAGCGGCGTTTTTGCGAGAAGCGCTGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGAGAAAAGCGCCGC
* * *
29714304 TAAAGGCCACGATCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGAGAAAAGCGCCGC
* * * * *
29714347 TAAAGGTCAAGATCTTTAGCGGTGTTTGTGATAAAAGTGCTGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGAGAAAAGCGCCGC
* * * *
29714390 GAAAGGTCAAGATATTTAGCGGCGTTTGTGATAAAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGAGAAAAGCGCCGC
* * *
29714433 TAAAGGTCATAATCTTTAGCGGTGTTCGTGAGAAAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGAGAAAAGCGCCGC
* * * * *
29714476 TAAAGGTCATGTTCTTTAGCAGCGTTCGTGGGAAAAGCACCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGAGAAAAGCGCCGC
* *
29714519 TGAAGGTCATGTTCTTTAGCGGCGTTT-TCGA-AAAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGT-GAGAAAAGCGCCGC
*
29714561 TAAAGATCATG
1 TAAAGGTCATG
29714572 TTCTATTGTG
Statistics
Matches: 227, Mismatches: 39, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
42 28 0.12
43 199 0.88
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (43 bp):
TAAAGGTCATGATCTTTAGCGGCGTTTGTGAGAAAAGCGCCGC
Found at i:29722803 original size:20 final size:20
Alignment explanation
Indices: 29722759--29722796 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29722749 ATAGATTGCA
*
29722759 GTTAAAAATTTAATAAATAG
1 GTTAAAAAGTTAATAAATAG
29722779 GTTAAAAAGTTAATAAAT
1 GTTAAAAAGTTAATAAAT
29722797 TTTTTAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (20 bp):
GTTAAAAAGTTAATAAATAG
Found at i:29724279 original size:16 final size:15
Alignment explanation
Indices: 29724254--29724283 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29724244 GTACGATGTA
29724254 TCCCCCCATTATGCG
1 TCCCCCCATTATGCG
29724269 TCCCACCCATTATGC
1 TCCC-CCCATTATGC
29724284 ATCTTCTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.47, G:0.10, T:0.27
Consensus pattern (15 bp):
TCCCCCCATTATGCG
Found at i:29728693 original size:20 final size:19
Alignment explanation
Indices: 29728642--29728699 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
29728632 AACTTTATCT
29728642 CTAAAAAATATTATAAAAAA
1 CTAAAAAATA-TATAAAAAA
* *
29728662 CTAAAGAATATATAATAAA
1 CTAAAAAATATATAAAAAA
29728681 CTTAAAAAATATA-AAAAAA
1 C-TAAAAAATATATAAAAAA
29728700 AATCAAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (19 bp):
CTAAAAAATATATAAAAAA
Found at i:29729434 original size:20 final size:19
Alignment explanation
Indices: 29729411--29729464 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
29729401 AAAGCATTTA
*
29729411 AAAATTTTA-AAAAGTTATT
1 AAAATTATATAAAA-TTATT
29729430 GAAAATTATATAAAATTATT
1 -AAAATTATATAAAATTATT
* *
29729450 AAAATGATAAAAAAT
1 AAAATTATATAAAAT
29729465 ATAAAAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.43
20 13 0.43
21 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (19 bp):
AAAATTATATAAAATTATT
Found at i:29729454 original size:9 final size:10
Alignment explanation
Indices: 29729294--29729453 Score: 76
Period size: 10 Copynumber: 16.5 Consensus size: 10
29729284 GATTTAAGCC
29729294 TAAAAATTAT
1 TAAAAATTAT
29729304 TAAAATATT-T
1 TAAAA-ATTAT
29729314 ATAAAAA-T-T
1 -TAAAAATTAT
*
29729323 TAGAAAATCA-
1 TA-AAAATTAT
*
29729333 TAAAAAATA-
1 TAAAAATTAT
* *
29729342 TATAATTTAT
1 TAAAAATTAT
29729352 T-AAAA-TAT
1 TAAAAATTAT
29729360 TATAAAATTA-
1 TA-AAAATTAT
29729370 TAAAATATTA-
1 TAAAA-ATTAT
29729380 TAAAAA-T-T
1 TAAAAATTAT
*
29729388 TAGAAATTAT
1 TAAAAATTAT
* **
29729398 AAAAAAGCATT
1 TAAAAATTA-T
29729409 TAAAAATT-T
1 TAAAAATTAT
29729418 TAAAAAGTTAT
1 TAAAAA-TTAT
*
29729429 TGAAAATTA-
1 TAAAAATTAT
29729438 TATAAAATTAT
1 TA-AAAATTAT
29729449 TAAAA
1 TAAAA
29729454 TGATAAAAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
8 12 0.11
9 32 0.28
10 46 0.40
11 24 0.21
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:29729462 original size:9 final size:9
Alignment explanation
Indices: 29729294--29729471 Score: 112
Period size: 9 Copynumber: 18.7 Consensus size: 9
29729284 GATTTAAGCC
29729294 TAAAAATTA
1 TAAAAATTA
29729303 TTAAAATATTTA
1 -TAAAA-A-TTA
29729315 TAAAAATT-
1 TAAAAATTA
*
29729323 TAGAAAATCA
1 TA-AAAATTA
*
29729333 TAAAAAATA
1 TAAAAATTA
* *
29729342 TATAATTTA
1 TAAAAATTA
29729351 TTAAAATATTA
1 -TAAAA-ATTA
29729362 T-AAAATTA
1 TAAAAATTA
29729370 TAAAATATTA
1 TAAAA-ATTA
29729380 TAAAAATT-
1 TAAAAATTA
*
29729388 TAGAAATTA
1 TAAAAATTA
29729397 TAAAAAAGCATT-
1 T--AAAA--ATTA
*
29729409 TAAAAATTT
1 TAAAAATTA
29729418 TAAAAAGTTA
1 TAAAAA-TTA
*
29729428 TTGAAAATTA
1 -TAAAAATTA
29729438 TATAAAATTA
1 TA-AAAATTA
* *
29729448 TTAAAATGA
1 TAAAAATTA
*
29729457 TAAAAAATA
1 TAAAAATTA
29729466 TAAAAA
1 TAAAAA
29729472 AGATTATAAT
Statistics
Matches: 133, Mismatches: 18, Indels: 35
0.72 0.10 0.19
Matches are distributed among these distances:
8 17 0.13
9 53 0.40
10 39 0.29
11 17 0.13
12 4 0.03
13 3 0.02
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:29729463 original size:19 final size:20
Alignment explanation
Indices: 29729418--29729464 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
29729408 TTAAAAATTT
* *
29729418 TAAAAAGTTATTGAAAATTA
1 TAAAAAATTATTGAAAATGA
*
29729438 TATAAAATTATT-AAAATGA
1 TAAAAAATTATTGAAAATGA
29729457 TAAAAAAT
1 TAAAAAAT
29729465 ATAAAAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (20 bp):
TAAAAAATTATTGAAAATGA
Found at i:29740465 original size:40 final size:40
Alignment explanation
Indices: 29740382--29740644 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
29740372 TTGAATGCTG
* * * * * *
29740382 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
29740422 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
29740462 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
29740502 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
29740542 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
29740582 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
29740621 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29740645 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:29740664 original size:79 final size:80
Alignment explanation
Indices: 29740421--29740679 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
29740411 AAGTGAATAT
* * * * * *
29740421 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
29740485 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
29740501 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
29740566 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
29740581 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
29740645 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
29740660 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
29740680 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:29759001 original size:292 final size:290
Alignment explanation
Indices: 29758477--29759064 Score: 814
Period size: 292 Copynumber: 2.0 Consensus size: 290
29758467 TCAACAGCCG
*
29758477 ACAACATCTCCCTCAAAGACTTCCTCGCCCACCTTTGTTCAGACTCTTCTCTTGACATCCCAACG
1 ACAACATCTCCCTCAAAGACTTCCTCACCCACCTTTGTTCAGACTCTTCTCTTGACATCCCAACG
* * *
29758542 GTGCCTTCGAACCAACAGCTCGGATACTTCTTGGTTCGAACTCTAGCTCTGGTACCACTTGTCAC
66 GTGCCTTCGAACCAACAGCTCGAATACTACTTGGTTCAAACTCTAGCTCTGGTACCACTTGTCAC
* * * * * *
29758607 GGGGCTGGACCTTTCGTCTCGCGATCCGTGCGGCCTTAGGCGATTCGCTCGTCCAAACTCGCCCA
131 GGGGATAGACCTTTCGTCTCGCAATCCGTACGGCCTTAGGCAATCCGCTCGTCCAAACTCGCCCA
* * * *
29758672 AGTCAGCCTTTACTCGAATGAGGATTCCTTAAGAACTCCTCCAAGGCACCAACTCGTACAGCGGA
196 AGTCAGCCTTAACTCAAAAGAGGATTCCTTAAGAACTCCTCCAAGGCACCAACTCATACAGCGGA
29758737 AGCAAACTTATGCCAAAAGAAGCT-TATAAAGA
261 AGC-AA-TTATGCCAAAAGAAGCTATA-AAAGA
*
29758769 ACAACATCTCCCTCAAAGACTTCCTCACCCACCTTTGTTCAGACTCTTCTTTTGACATCCCAACG
1 ACAACATCTCCCTCAAAGACTTCCTCACCCACCTTTGTTCAGACTCTTCTCTTGACATCCCAACG
29758834 GTGCCTTCGAACC-A-A-CTCGAATA-TCACTTGGTTCAAAAC-CT-GCTC-GGATACCACTTGT
66 GTGCCTTCGAACCAACAGCTCGAATACT-ACTTGGTTC-AAACTCTAGCTCTGG-TACCACTTGT
*
29758892 CACGGGGATAGACCTTTCGTCTCGCAATCCGTACGGCCTTAGGCAATCCGTTCGTCCAAACTCGC
128 CACGGGGATAGACCTTTCGTCTCGCAATCCGTACGGCCTTAGGCAATCCGCTCGTCCAAACTCGC
* * * * *
29758957 CCAAGTCAGCCTTAACTCCCAAAAGAGAGGATTCTTTTAGAACTCCTCCAAGGCATCAATTTATA
193 CCAAGTCAGCCTTAACT--C-AAA-AGAGGATTCCTTAAGAACTCCTCCAAGGCACCAACTCATA
* * *
29759022 TAGCGGAAGCGATTGTGCCAAAAGAAGCTATAAAAGA
254 CAGCGGAAGCAATTATGCCAAAAGAAGCTATAAAAGA
29759059 ACAACA
1 ACAACA
29759065 GAAAGCCAAA
Statistics
Matches: 264, Mismatches: 24, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
287 2 0.01
288 89 0.34
289 17 0.06
290 32 0.12
291 6 0.02
292 118 0.45
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (290 bp):
ACAACATCTCCCTCAAAGACTTCCTCACCCACCTTTGTTCAGACTCTTCTCTTGACATCCCAACG
GTGCCTTCGAACCAACAGCTCGAATACTACTTGGTTCAAACTCTAGCTCTGGTACCACTTGTCAC
GGGGATAGACCTTTCGTCTCGCAATCCGTACGGCCTTAGGCAATCCGCTCGTCCAAACTCGCCCA
AGTCAGCCTTAACTCAAAAGAGGATTCCTTAAGAACTCCTCCAAGGCACCAACTCATACAGCGGA
AGCAATTATGCCAAAAGAAGCTATAAAAGA
Found at i:29760577 original size:10 final size:10
Alignment explanation
Indices: 29760549--29760582 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
29760539 AATAATTTTT
29760549 TTATTAAAAA
1 TTATTAAAAA
*
29760559 GTATCTAAAAA
1 TTAT-TAAAAA
29760570 TTATTAAAAA
1 TTATTAAAAA
29760580 TTA
1 TTA
29760583 CAAAGATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:29760607 original size:20 final size:21
Alignment explanation
Indices: 29760569--29760608 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
29760559 GTATCTAAAA
* *
29760569 ATTATTAAAAATTACAAAGAT
1 ATTATTAAAAAATAAAAAGAT
29760590 ATTA-TAAAAAATAAAAAGA
1 ATTATTAAAAAATAAAAAGA
29760609 AAATATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (21 bp):
ATTATTAAAAAATAAAAAGAT
Found at i:29760766 original size:29 final size:30
Alignment explanation
Indices: 29760731--29760789 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
29760721 TATGAGTTAA
29760731 TGTGCAATTGT-ATACAT-AAACTTTGATTT
1 TGTGCAATT-TCATACATAAAACTTTGATTT
*
29760760 TGTGCAATTTCATACATAAAATTTTGATTT
1 TGTGCAATTTCATACATAAAACTTTGATTT
29760790 GATCCAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 15 0.56
30 11 0.41
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (30 bp):
TGTGCAATTTCATACATAAAACTTTGATTT
Found at i:29760798 original size:30 final size:29
Alignment explanation
Indices: 29760742--29760798 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
29760732 GTGCAATTGT
*
29760742 ATACATAAACTTTGATTTTGTGCAATTTC
1 ATACATAAACTTTGATTTTGTCCAATTTC
*
29760771 ATACATAAAATTTTGA-TTTGATCCAATT
1 ATACAT-AAACTTTGATTTTG-TCCAATT
29760799 CTTGTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (29 bp):
ATACATAAACTTTGATTTTGTCCAATTTC
Found at i:29770680 original size:17 final size:17
Alignment explanation
Indices: 29770644--29770682 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
29770634 TTTTATAATG
*
29770644 GATTGGAAGTTTGTTAA
1 GATTGGAAGTTTGTCAA
29770661 GATTGGAAG-TTGTCAGA
1 GATTGGAAGTTTGTCA-A
29770678 GATTG
1 GATTG
29770683 CATCACATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.28, C:0.03, G:0.33, T:0.36
Consensus pattern (17 bp):
GATTGGAAGTTTGTCAA
Found at i:29775106 original size:81 final size:81
Alignment explanation
Indices: 29775005--29775275 Score: 228
Period size: 81 Copynumber: 3.3 Consensus size: 81
29774995 TCCTTGGCGA
* * * * * *
29775005 CAGTTTT-CAAAGCTTGTTCACTATCTTTCTTTACTGGTTCAACTTCTTGTGATGGTGGCTTTGC
1 CAGTTTTGC-AAGCTTCTTCACTATCTTTCTTTAATGGTGCAACTTCTTGTGAAGCTGGCTTGGC
** *
29775069 TTCA-GAATCTTTTATTT
65 TTCAGGAA-CTTCGACTT
* * *
29775086 CAGTTTTGCAAGCTTCTTCACTATCTTTCTTCAATGGTGGAACTTCTTGTGAAGCTGGGTTGGCT
1 CAGTTTTGCAAGCTTCTTCACTATCTTTCTTTAATGGTGCAACTTCTTGTGAAGCTGGCTTGGCT
29775151 TCAGGAACTTCGACTT
66 TCAGGAACTTCGACTT
* * * * ** *
29775167 CATTTTTGGAAGCTTCTTCACTCTCTTTCTTTAAAGGTGGGGAC-TCTTGTGACAG-TGGCTTTG
1 CAGTTTTGCAAGCTTCTTCACTATCTTTCTTTAATGGT-GCAACTTCTTGTGA-AGCTGGCTTGG
* * **
29775230 CTT-TGGAATTTTCGGTTT
64 CTTCAGGAA-CTTCGACTT
***
29775248 CAGTTTTTTTAGCTTCTTCACTATCTTT
1 CAGTTTTGCAAGCTTCTTCACTATCTTT
29775276 GCTTGATGGA
Statistics
Matches: 156, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
80 4 0.03
81 142 0.91
82 10 0.06
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (81 bp):
CAGTTTTGCAAGCTTCTTCACTATCTTTCTTTAATGGTGCAACTTCTTGTGAAGCTGGCTTGGCT
TCAGGAACTTCGACTT
Found at i:29777093 original size:18 final size:18
Alignment explanation
Indices: 29777038--29777143 Score: 86
Period size: 18 Copynumber: 5.9 Consensus size: 18
29777028 CTACATCACC
* * *
29777038 TGCAGGTGGCTCTGTACT
1 TGCAGGTGGATCCGTAGT
* * * *
29777056 TGTAGGCGGATCAGTTGT
1 TGCAGGTGGATCCGTAGT
*
29777074 TGTAGGTGGATCCGTAGT
1 TGCAGGTGGATCCGTAGT
*
29777092 TGCAGGTGGATCCATAGT
1 TGCAGGTGGATCCGTAGT
* * *
29777110 TGCAGGTGCATCTGTACT
1 TGCAGGTGGATCCGTAGT
* *
29777128 TGCAGGAGGACCCGTA
1 TGCAGGTGGATCCGTA
29777144 CTTGGCGATG
Statistics
Matches: 69, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 69 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (18 bp):
TGCAGGTGGATCCGTAGT
Found at i:29779859 original size:64 final size:64
Alignment explanation
Indices: 29779753--29779885 Score: 248
Period size: 64 Copynumber: 2.1 Consensus size: 64
29779743 ATCGAACTCT
* *
29779753 ACTTGAGAGATGCGAGATTTTTGAACGTGGCCCTTATGGGTGAGGGGTGTAAATTGAACCCCAC
1 ACTTGAGAGATGCGAGATTTTTGAACGTGGCCCTTATAGGTGAGGGGTGTAAATTGAACCACAC
29779817 ACTTGAGAGATGCGAGATTTTTGAACGTGGCCCTTATAGGTGAGGGGTGTAAATTGAACCACAC
1 ACTTGAGAGATGCGAGATTTTTGAACGTGGCCCTTATAGGTGAGGGGTGTAAATTGAACCACAC
29779881 ACTTG
1 ACTTG
29779886 TAAGCGCGTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (64 bp):
ACTTGAGAGATGCGAGATTTTTGAACGTGGCCCTTATAGGTGAGGGGTGTAAATTGAACCACAC
Found at i:29780669 original size:24 final size:24
Alignment explanation
Indices: 29780642--29780688 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
29780632 TTTTTTAAAT
*
29780642 TTGAATTATATAA-TATTAGTATAG
1 TTGAATTATA-AATTAATAGTATAG
*
29780666 TTGACTTATAAATTAATAGTATA
1 TTGAATTATAAATTAATAGTATA
29780689 TATAACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (24 bp):
TTGAATTATAAATTAATAGTATAG
Found at i:29782065 original size:17 final size:17
Alignment explanation
Indices: 29782023--29782059 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
29782013 CTAAAAGTTC
*
29782023 AAAAATAATGCATTGAA
1 AAAAATAATGCACTGAA
29782040 AAAAATAATGCACTGAA
1 AAAAATAATGCACTGAA
29782057 AAA
1 AAA
29782060 TCTAATCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.08, G:0.11, T:0.19
Consensus pattern (17 bp):
AAAAATAATGCACTGAA
Found at i:29782310 original size:21 final size:22
Alignment explanation
Indices: 29782277--29782336 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
29782267 TTTACATCTC
29782277 AAAAAAT-TATAAAAAAAAC-T
1 AAAAAATATATAAAAAAAACTT
* *
29782297 AAAGAGTATATAAAAATAAACTT
1 AAAAAATATATAAAAA-AAACTT
29782320 AAAAAATATATAAAAAA
1 AAAAAATATATAAAAAA
29782337 CCCTTAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.15
21 8 0.24
22 5 0.15
23 15 0.45
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (22 bp):
AAAAAATATATAAAAAAAACTT
Found at i:29784906 original size:16 final size:16
Alignment explanation
Indices: 29784887--29784917 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29784877 ATATTAATCT
29784887 AATACTAATATAATAG
1 AATACTAATATAATAG
*
29784903 AATACTAATCTAATA
1 AATACTAATATAATA
29784918 CCAATAGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.32
Consensus pattern (16 bp):
AATACTAATATAATAG
Found at i:29784906 original size:27 final size:27
Alignment explanation
Indices: 29784876--29784940 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
29784866 ATCACTAACA
* * *
29784876 AATATTAATCTAATACTAATATAATAG
1 AATACTAATCTAATACCAATAGAATAG
29784903 AATACTAATCTAATACCAATAGAATAG
1 AATACTAATCTAATACCAATAGAATAG
29784930 AAAATACTAAT
1 --AATACTAAT
29784941 AGAATAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 24 0.73
29 9 0.27
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.31
Consensus pattern (27 bp):
AATACTAATCTAATACCAATAGAATAG
Found at i:29784941 original size:18 final size:18
Alignment explanation
Indices: 29784914--29784950 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29784904 ATACTAATCT
29784914 AATACCAATAGAATAGAA
1 AATACCAATAGAATAGAA
*
29784932 AATACTAATAGAATAGAA
1 AATACCAATAGAATAGAA
29784950 A
1 A
29784951 GAAAGAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.08, G:0.11, T:0.19
Consensus pattern (18 bp):
AATACCAATAGAATAGAA
Found at i:29790541 original size:39 final size:39
Alignment explanation
Indices: 29790487--29790567 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
29790477 CTAACTATTT
*
29790487 AACTAAATTTCTAAAATCTTGTTACAGTATTTTTAGAAC
1 AACTAAATTTCTAAAATCTTGTTACAGTATTTTCAGAAC
29790526 AACTAAATTTCTAAAATCTTGTTACAGTATTTTCAGAAC
1 AACTAAATTTCTAAAATCTTGTTACAGTATTTTCAGAAC
29790565 AAC
1 AAC
29790568 CATATTAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (39 bp):
AACTAAATTTCTAAAATCTTGTTACAGTATTTTCAGAAC
Found at i:29791079 original size:25 final size:25
Alignment explanation
Indices: 29791031--29791079 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
29791021 TCAATTTATT
* *
29791031 TCATAAACAATAAATATCCCTTAAC
1 TCATAAACAATAAATAGCCATTAAC
* *
29791056 TCATAATCACTAAATAGCCATTAA
1 TCATAAACAATAAATAGCCATTAA
29791080 TATGACTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (25 bp):
TCATAAACAATAAATAGCCATTAAC
Found at i:29792288 original size:22 final size:22
Alignment explanation
Indices: 29792263--29792305 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29792253 TATATATTAA
29792263 CTTTTAGTTGAATCTTTTCTTC
1 CTTTTAGTTGAATCTTTTCTTC
* **
29792285 CTTTTATTTTTATCTTTTCTT
1 CTTTTAGTTGAATCTTTTCTT
29792306 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (22 bp):
CTTTTAGTTGAATCTTTTCTTC
Found at i:29792382 original size:25 final size:24
Alignment explanation
Indices: 29792354--29792401 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
29792344 AAAATGACAA
* *
29792354 TTAATTAATTTCATTTAAAAATTAT
1 TTAATGAA-TTCATCTAAAAATTAT
*
29792379 TTAATGAATTCATCTCAAAATTA
1 TTAATGAATTCATCTAAAAATTA
29792402 ATATATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (24 bp):
TTAATGAATTCATCTAAAAATTAT
Found at i:29792703 original size:29 final size:29
Alignment explanation
Indices: 29792670--29792748 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 29
29792660 ATTAGCGTGA
*
29792670 TTCTGTTTTGATCACTCATGTTTA-AAAAT
1 TTCTGTTTT-ATCACTCATGTTGACAAAAT
*
29792699 TTCTGTTTTAGTCACTAATGTTGACAAAAT
1 TTCTGTTTTA-TCACTCATGTTGACAAAAT
* *
29792729 TTAATGTTTTAATCGCTCAT
1 TT-CTGTTTT-ATCACTCAT
29792749 CCGTTAAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
28 1 0.02
29 20 0.49
30 7 0.17
31 12 0.29
32 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (29 bp):
TTCTGTTTTATCACTCATGTTGACAAAAT
Found at i:29793019 original size:20 final size:20
Alignment explanation
Indices: 29792963--29793011 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
29792953 TCATTTTTCA
**
29792963 ATAAAAATACATCA-AATTTT
1 ATAAAAATACAT-ATAAAATT
29792983 ATAAAAATACATATAAAATT
1 ATAAAAATACATATAAAATT
29793003 ATAAAAATA
1 ATAAAAATA
29793012 TTTATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAAATACATATAAAATT
Found at i:29793746 original size:7 final size:7
Alignment explanation
Indices: 29793736--29793766 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
29793726 TTTTAAATTT
29793736 TTTTAAA
1 TTTTAAA
29793743 TTTTAAA
1 TTTTAAA
29793750 TTTTAAA
1 TTTTAAA
29793757 TTTTAAA
1 TTTTAAA
29793764 TTT
1 TTT
29793767 AATTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTTAAA
Found at i:29795324 original size:13 final size:13
Alignment explanation
Indices: 29795306--29795348 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
29795296 TAGATTTTTC
29795306 CTAAATATTATCA
1 CTAAATATTATCA
*
29795319 CTAAATA--AT-T
1 CTAAATATTATCA
29795329 CTAAATATTATCA
1 CTAAATATTATCA
29795342 CTAAATA
1 CTAAATA
29795349 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:29795336 original size:23 final size:23
Alignment explanation
Indices: 29795306--29795357 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
29795296 TAGATTTTTC
29795306 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
29795329 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
29795352 CAAAAT
1 CTAAAT
29795358 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Done.