Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 105 of 182
Found at i:31680030 original size:20 final size:20
Alignment explanation
Indices: 31680005--31680048 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
31679995 TTCTATGTGG
31680005 ATATCTAGGCTATGGTAATA
1 ATATCTAGGCTATGGTAATA
31680025 ATATCTAGGCTATGGTAATA
1 ATATCTAGGCTATGGTAATA
31680045 ATAT
1 ATAT
31680049 TTGCCCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (20 bp):
ATATCTAGGCTATGGTAATA
Found at i:31693519 original size:20 final size:21
Alignment explanation
Indices: 31693462--31693519 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
31693452 TTCAATTTTC
* *
31693462 AATTAAAATA-AATTTAATTT
1 AATTAAAATATTATTTAATGT
*
31693482 AATAAAAATATTTTATTT-ATGT
1 AATTAAAATA--TTATTTAATGT
31693504 AATTAAAATATTATTT
1 AATTAAAATATTATTT
31693520 CAAAATTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 15 0.48
22 12 0.39
23 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AATTAAAATATTATTTAATGT
Found at i:31695372 original size:12 final size:12
Alignment explanation
Indices: 31695339--31695378 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
31695329 TATTATACCA
31695339 TATAATACTATA-
1 TATAAT-CTATAT
31695351 T-TAA-CTATAT
1 TATAATCTATAT
31695361 TATAATCTATAT
1 TATAATCTATAT
31695373 TATAAT
1 TATAAT
31695379 TTAGGCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 5 0.20
10 1 0.04
11 6 0.24
12 13 0.52
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TATAATCTATAT
Found at i:31702713 original size:30 final size:30
Alignment explanation
Indices: 31702677--31702749 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
31702667 ATGGGTTGTC
* *
31702677 ACACGGCCGTGTGAGACATACAGCCTGGTG
1 ACACGGCCGTGTGAGACACACAGCCTAGTG
31702707 ACACGGCCGTGTGAGACACACAGCCTAGTG
1 ACACGGCCGTGTGAGACACACAGCCTAGTG
*
31702737 ACATGGCCTGTGT
1 ACACGGCC-GTGT
31702750 CATTTGTGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 35 0.90
31 4 0.10
ACGTcount: A:0.23, C:0.27, G:0.32, T:0.18
Consensus pattern (30 bp):
ACACGGCCGTGTGAGACACACAGCCTAGTG
Found at i:31702899 original size:33 final size:33
Alignment explanation
Indices: 31702862--31702924 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
31702852 ACACGGGCTA
31702862 GGGTGATTCCAAACGGCCTGGCCACACGGCTTG
1 GGGTGATTCCAAACGGCCTGGCCACACGGCTTG
*
31702895 GGGTGATTCCAAATGGCCTGGCCACACGGC
1 GGGTGATTCCAAACGGCCTGGCCACACGGC
31702925 CTTGTGACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.19, C:0.30, G:0.33, T:0.17
Consensus pattern (33 bp):
GGGTGATTCCAAACGGCCTGGCCACACGGCTTG
Found at i:31705395 original size:43 final size:43
Alignment explanation
Indices: 31705347--31705432 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
31705337 TATGTGATAG
*
31705347 ATATTGAAATGGAAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGGAAAAGATGAGAAATGAATATGAGACGAGAAA
* *
31705390 ATATTGAAATGGAAAATATGAGAAATGATTATGAGACGAGAAA
1 ATATTGAAATGGAAAAGATGAGAAATGAATATGAGACGAGAAA
31705433 TGAGATATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.52, C:0.01, G:0.24, T:0.22
Consensus pattern (43 bp):
ATATTGAAATGGAAAAGATGAGAAATGAATATGAGACGAGAAA
Found at i:31705416 original size:16 final size:16
Alignment explanation
Indices: 31705352--31705416 Score: 61
Period size: 15 Copynumber: 4.4 Consensus size: 16
31705342 GATAGATATT
*
31705352 GAAATGGAAAAGATGA
1 GAAATGGAAAATATGA
31705368 GAAAT-G--AATATGA
1 GAAATGGAAAATATGA
*
31705381 G--ATGAGAAAATAT-T
1 GAAATG-GAAAATATGA
31705395 GAAATGGAAAATATGA
1 GAAATGGAAAATATGA
31705411 GAAATG
1 GAAATG
31705417 ATTATGAGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
11 2 0.05
13 8 0.21
14 1 0.03
15 14 0.36
16 14 0.36
ACGTcount: A:0.54, C:0.00, G:0.26, T:0.20
Consensus pattern (16 bp):
GAAATGGAAAATATGA
Found at i:31706949 original size:15 final size:15
Alignment explanation
Indices: 31706924--31706958 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
31706914 GACTCTATTT
*
31706924 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
31706938 TAATTAATATTAAGA
1 TAATTAATATTAAGA
31706953 TAATTA
1 TAATTA
31706959 TTAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:31708486 original size:24 final size:24
Alignment explanation
Indices: 31708454--31708500 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
31708444 CACAAGCATC
31708454 TGAAAGAGCTTCATATGGTTTGTT
1 TGAAAGAGCTTCATATGGTTTGTT
*
31708478 TGAAAGAGCTTCATATTGTTTGT
1 TGAAAGAGCTTCATATGGTTTGT
31708501 CTTAGCATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (24 bp):
TGAAAGAGCTTCATATGGTTTGTT
Found at i:31709651 original size:213 final size:213
Alignment explanation
Indices: 31709284--31709712 Score: 849
Period size: 213 Copynumber: 2.0 Consensus size: 213
31709274 TCGGTTTCCG
31709284 CAATAGCCATAAGGTTCAGGTAATTTTCTAGAAACCATGGTCAATAAGTTAGCAACTAATGTTCT
1 CAATAGCCATAAGGTTCAGGTAATTTTCTAGAAACCATGGTCAATAAGTTAGCAACTAATGTTCT
31709349 TGATTTTCGACAGCAAACTCTTAATTTCCAAAAAGAGATGAAGGATTTCCAACAGAAAACCGAAG
66 TGATTTTCGACAGCAAACTCTTAATTTCCAAAAAGAGATGAAGGATTTCCAACAGAAAACCGAAG
31709414 CGTCCATCAGAGAGTTGACCACATAGATCGGGAAATTGACCTCTCAAGGGAAGCTGCCGTCACAA
131 CGTCCATCAGAGAGTTGACCACATAGATCGGGAAATTGACCTCTCAAGGGAAGCTGCCGTCACAA
31709479 ACAGAACCAAACCCTAGA
196 ACAGAACCAAACCCTAGA
31709497 CAATAGCCATAAGGTTCAGGTAATTTTCTAGAAACCATGGTCAATAAGTTAGCAACTAATGTTCT
1 CAATAGCCATAAGGTTCAGGTAATTTTCTAGAAACCATGGTCAATAAGTTAGCAACTAATGTTCT
*
31709562 TGATTTTCGACAGCAAACTCTTAATTTCCAAGAAGAGATGAAGGATTTCCAACAGAAAACCGAAG
66 TGATTTTCGACAGCAAACTCTTAATTTCCAAAAAGAGATGAAGGATTTCCAACAGAAAACCGAAG
31709627 CGTCCATCAGAGAGTTGACCACATAGATCGGGAAATTGACCTCTCAAGGGAAGCTGCCGTCACAA
131 CGTCCATCAGAGAGTTGACCACATAGATCGGGAAATTGACCTCTCAAGGGAAGCTGCCGTCACAA
31709692 ACAGAACCAAACCCTAGA
196 ACAGAACCAAACCCTAGA
31709710 CAA
1 CAA
31709713 AATGTAAATG
Statistics
Matches: 215, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 215 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (213 bp):
CAATAGCCATAAGGTTCAGGTAATTTTCTAGAAACCATGGTCAATAAGTTAGCAACTAATGTTCT
TGATTTTCGACAGCAAACTCTTAATTTCCAAAAAGAGATGAAGGATTTCCAACAGAAAACCGAAG
CGTCCATCAGAGAGTTGACCACATAGATCGGGAAATTGACCTCTCAAGGGAAGCTGCCGTCACAA
ACAGAACCAAACCCTAGA
Found at i:31711120 original size:5 final size:6
Alignment explanation
Indices: 31711104--31711186 Score: 50
Period size: 7 Copynumber: 13.5 Consensus size: 6
31711094 AGGCAACCCA
*
31711104 ATTTTT ATTTTT ATTTTTTT ATTTATT ATTTATT ATTTTT -TTCTTT A-CTTT
1 ATTTTT ATTTTT A--TTTTT ATTT-TT ATTT-TT ATTTTT ATT-TTT ATTTTT
*
31711155 ATTTATT A-CTTT A-TTTT A-TTTT ATTATTT ATT
1 ATTT-TT ATTTTT ATTTTT ATTTTT ATT-TTT ATT
31711187 ACTTATTTGG
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
5 18 0.28
6 18 0.28
7 22 0.34
8 6 0.09
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:31711121 original size:12 final size:12
Alignment explanation
Indices: 31711104--31711186 Score: 50
Period size: 12 Copynumber: 6.8 Consensus size: 12
31711094 AGGCAACCCA
31711104 ATTTTTATTTTT
1 ATTTTTATTTTT
31711116 ATTTTTTTATTTATT
1 A--TTTTTATTT-TT
31711131 ATTTATTATTTTT
1 ATTT-TTATTTTT
*
31711144 -TTCTTTA-CTTT
1 ATT-TTTATTTTT
*
31711155 ATTTATTA-CTTT
1 ATTT-TTATTTTT
31711167 A-TTTTA-TTTT
1 ATTTTTATTTTT
31711177 ATTATTTATT
1 ATT-TTTATT
31711187 ACTTATTTGG
Statistics
Matches: 59, Mismatches: 2, Indels: 19
0.74 0.03 0.24
Matches are distributed among these distances:
10 7 0.12
11 7 0.12
12 20 0.34
13 7 0.12
14 15 0.25
15 3 0.05
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:31711130 original size:4 final size:4
Alignment explanation
Indices: 31711113--31711186 Score: 57
Period size: 4 Copynumber: 18.5 Consensus size: 4
31711103 AATTTTTATT
* * *
31711113 TTTA TTTT TTTA TTTA -TTA TTTA -TTA TTTT TTTC TTTA CTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
31711160 -TTA CTTTA TTTTA TTT- TATTA TTTA TT
1 TTTA -TTTA -TTTA TTTA T-TTA TTTA TT
31711187 ACTTATTTGG
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
3 10 0.18
4 35 0.61
5 12 0.21
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:31711158 original size:17 final size:17
Alignment explanation
Indices: 31711136--31711176 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
31711126 TTATTATTTA
*
31711136 TTATTTTTTTCTTTACT
1 TTATTTTTTACTTTACT
* *
31711153 TTATTTATTACTTTATT
1 TTATTTTTTACTTTACT
31711170 TTATTTT
1 TTATTTT
31711177 ATTATTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTTTTACTTTACT
Found at i:31712257 original size:16 final size:16
Alignment explanation
Indices: 31712223--31712262 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
31712213 TATAAATAAT
*
31712223 AAATAAATAAAAACCA
1 AAATAAATAAAAAACA
*
31712239 AAATAAATAAAAAAGA
1 AAATAAATAAAAAACA
31712255 AAA-AAATA
1 AAATAAATA
31712263 TAATTTGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.80, C:0.05, G:0.03, T:0.12
Consensus pattern (16 bp):
AAATAAATAAAAAACA
Found at i:31715794 original size:27 final size:28
Alignment explanation
Indices: 31715710--31715807 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
31715700 CATGAGATTG
* * * *
31715710 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
31715739 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
31715767 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
31715794 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
31715808 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:31715818 original size:27 final size:27
Alignment explanation
Indices: 31715738--31715820 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
31715728 TAAATTGTAC
* *
31715738 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
31715766 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
31715793 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
31715820 A
1 A
31715821 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:31715821 original size:29 final size:27
Alignment explanation
Indices: 31715710--31715821 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
31715700 CATGAGATTG
** * *
31715710 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
31715739 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
31715767 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
31715794 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
31715822 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:31717866 original size:6 final size:6
Alignment explanation
Indices: 31717842--31717909 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
31717832 TATAAATTTG
* *
31717842 AAAAAT AAAAA- AATAAAT AACAAT AAAAAT AAAAGT AAAAAT AAAAAT
1 AAAAAT AAAAAT AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
*
31717890 --AAAT AAAACAT AAAACT AAA
1 AAAAAT AAAA-AT AAAAAT AAA
31717910 TGAAATCACT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 4 0.08
5 2 0.04
6 38 0.73
7 8 0.15
ACGTcount: A:0.78, C:0.04, G:0.01, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:31717902 original size:17 final size:16
Alignment explanation
Indices: 31717850--31717910 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 16
31717840 TGAAAAATAA
*
31717850 AAAAATAAATAACAAT
1 AAAAATAAATAAAAAT
31717866 AAAAATAAAAGTAAAAAT
1 AAAAAT-AAA-TAAAAAT
31717884 AAAAATAAATAAAACAT
1 AAAAATAAATAAAA-AT
*
31717901 AAAACTAAAT
1 AAAAATAAAT
31717911 GAAATCACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
16 11 0.28
17 17 0.43
18 12 0.30
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (16 bp):
AAAAATAAATAAAAAT
Found at i:31721228 original size:20 final size:20
Alignment explanation
Indices: 31721205--31721265 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
31721195 ATTAGAATGT
* *
31721205 AAAAATTAAATTAAAAACAA
1 AAAAATAAAAATAAAAACAA
*
31721225 AAAAATAAAAAT-AAAA-AT
1 AAAAATAAAAATAAAAACAA
*
31721243 AAAAATAAAAATAAAAATAA
1 AAAAATAAAAATAAAAACAA
31721263 AAA
1 AAA
31721266 TAAAATGGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 13 0.37
19 8 0.23
20 14 0.40
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAATAAAAATAAAAACAA
Found at i:31721234 original size:6 final size:6
Alignment explanation
Indices: 31721225--31721270 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
31721215 TTAAAAACAA
31721225 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
31721271 TGGCTAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:31723318 original size:14 final size:14
Alignment explanation
Indices: 31723299--31723326 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31723289 ACCGTGTGTC
31723299 ATTAAACGACTATG
1 ATTAAACGACTATG
31723313 ATTAAACGACTATG
1 ATTAAACGACTATG
31723327 TTCATGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
ATTAAACGACTATG
Found at i:31726016 original size:35 final size:36
Alignment explanation
Indices: 31725954--31726026 Score: 121
Period size: 35 Copynumber: 2.0 Consensus size: 36
31725944 TAAAACTTCC
31725954 TTTGTTTTACAATTAAAAATCCTATTTAAGTAATATT
1 TTTGTTTTACAATT-AAAATCCTATTTAAGTAATATT
*
31725991 TTTGTTTTACAATT-AAATCCTATTTAATTAATATT
1 TTTGTTTTACAATTAAAATCCTATTTAAGTAATATT
31726026 T
1 T
31726027 AATTACTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 21 0.60
37 14 0.40
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (36 bp):
TTTGTTTTACAATTAAAATCCTATTTAAGTAATATT
Found at i:31728569 original size:19 final size:19
Alignment explanation
Indices: 31728547--31728583 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
31728537 TACTGTCACC
31728547 CACCGTAATCAAATTTTTG
1 CACCGTAATCAAATTTTTG
31728566 CACCGTAATCAAATTTTT
1 CACCGTAATCAAATTTTT
31728584 TATTGTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (19 bp):
CACCGTAATCAAATTTTTG
Found at i:31734830 original size:25 final size:24
Alignment explanation
Indices: 31734755--31734843 Score: 70
Period size: 26 Copynumber: 3.5 Consensus size: 24
31734745 TATACATAAG
**
31734755 TTTATAATAAATAATTTATAAAAGAAA
1 TTTA-AATAAATAATAAAT-AAA-AAA
* **
31734782 TTTAAATAAATTATATGTAAAAAA
1 TTTAAATAAATAATAAATAAAAAA
31734806 TTTCAAATAAATAATAAATATAAAAA
1 TTT-AAATAAATAATAAATA-AAAAA
*
31734832 CTTAAAATAAAT
1 -TTTAAATAAAT
31734844 GATGATAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
24 6 0.12
25 16 0.31
26 24 0.46
27 6 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
TTTAAATAAATAATAAATAAAAAA
Found at i:31736710 original size:143 final size:143
Alignment explanation
Indices: 31736329--31737124 Score: 1003
Period size: 143 Copynumber: 5.6 Consensus size: 143
31736319 CTGCACTTTA
* * * * * * * *
31736329 TAGCTTCAATCTGTTCCATTGCAATACTAGGAAAATAAGATTCGCTGTCTTCAATCTGCTTCGCT
1 TAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAGATTCGCTTTCTTCAGTCTGCTCCGCT
* * *
31736394 GCAACTTCAGGGAAATAGGGCTGGTGGCTTCAATATGCTCCACTGCAACTTCAGGAAGATAATAT
66 GCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAATAT
*
31736459 CCGCTATATTTTG
131 CCGCTATAATTTG
** * * * *
31736472 TAATTTTAATCT-ATCCACTGCAACGCCAGGGAAATAAGATTCGCTATT-TTTAGTATGCTCCGC
1 TAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAGATTCGCT-TTCTTCAGTCTGCTCCGC
* *
31736535 TGCAACTTCAGGGAGATAAGGTTGGTGGCTTCAATCTGCTCCACTGCATCTTCAGGAAGATAATA
65 TGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAATA
*
31736600 TCCGCTATATTTTG
130 TCCGCTATAATTTG
** * * * * *
31736614 TAATTTTAATCTATTCCACTGCAACGCTAGGGAAATAAGATTCGCTTTTTTTAGTCTGCTCCGCT
1 TAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAGATTCGCTTTCTTCAGTCTGCTCCGCT
* *
31736679 GCAACTTCAGGGAGATAAGGCTGGTGACTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGAT
66 GCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAATAT
31736744 CCGCTATAATTTG
131 CCGCTATAATTTG
* * *
31736757 TAGCATTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCG-TTGTCTTCAGTCTGCTCCAC
1 TAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAGATTCGCTT-TCTTCAGTCTGCTCCGC
* * * *
31736821 TGCAACTTCAAGGAGATAAGACTGGTGGCTTCAATTTGCTCCACTGCAACTTCAAGAAGATAAGT
65 TGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAA-T
*
31736886 -TCCGCCATAATTTG
129 ATCCGCTATAATTTG
* * * *
31736900 TAGCTTTAATCTGTTACACTGTAACACCAGGGAAATAAGATTTG-TTGTCTTCAGTCTACTCCGC
1 TAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAGATTCGCTT-TCTTCAGTCTGCTCCGC
* * *
31736964 TGCGACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
65 TGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAATA
* *
31737029 TCCACCATAATTTG
130 TCCGCTATAATTTG
* * * * * * *
31737043 TAGCTTTAACCTGTT-C-TTACAACACTAGGGAAATAAGATTCACTGTCTTCAGTCTGCTCCACT
1 TAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAGATTCGCTTTCTTCAGTCTGCTCCGCT
* *
31737106 GCATCTTCAAGGAGATAAG
66 GCAACTTCAGGGAGATAAG
31737125 ACTTGTAACT
Statistics
Matches: 576, Mismatches: 70, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
141 52 0.09
142 130 0.23
143 394 0.68
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (143 bp):
TAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAGATTCGCTTTCTTCAGTCTGCTCCGCT
GCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAATAT
CCGCTATAATTTG
Found at i:31736728 original size:44 final size:44
Alignment explanation
Indices: 31736668--31737027 Score: 166
Period size: 44 Copynumber: 7.7 Consensus size: 44
31736658 CTTTTTTTAG
* *
31736668 TCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGTTGACTTCAA
* *
31736712 TCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCTATAATTTGTAGCATT-AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG----GC--T--GTTG-A-C-TTCAA
* ** * ** * *
31736766 TCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGGCT-GTTGACTTCAA
* * * *
31736811 TCTGCTCCACTGCAACTTCAAGGAGATAAGACTGGTGGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGTTGACTTCAA
* * * * *
31736855 TTTGCTCCACTGCAACTTCAAGAAGATAAGTTCCGCCATAATTTGTAGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG----G-C-T--GTTG-A-CTTCAA
* * * ** * ** * *
31736909 TCTGTTACACTGTAACACCAGGGAAATAAGATTTGTTGTCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG-GCTGTTGACTTCAA
* * * *
31736954 TCTACTCCGCTGCGACTTCAGGGAGATAAGGCTAG-TGGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGGCT-GTTGACTTCAA
*
31736998 TCTGCTCCACTGCAACTTCAGGAAGATAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG
31737028 ATCCACCATA
Statistics
Matches: 229, Mismatches: 64, Indels: 46
0.68 0.19 0.14
Matches are distributed among these distances:
44 100 0.44
45 55 0.24
47 6 0.03
48 3 0.01
49 2 0.01
50 2 0.01
52 4 0.02
53 1 0.00
54 54 0.24
55 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGTTGACTTCAA
Found at i:31737293 original size:45 final size:44
Alignment explanation
Indices: 31737236--31737348 Score: 133
Period size: 44 Copynumber: 2.5 Consensus size: 44
31737226 TTGAGTCTAT
* *
31737236 TCCACTACAACTTTAGGGA-ATTAAGA-TTCGCTATCTT-AAGTCTGC
1 TCCACTACAACTTTAGGGAGA-TAAGACTT-G-TAACTTCAA-CCTGC
31737281 TCCACTACAACTTTAGGGAGATAAGACTTGTAACTTCAACCTGC
1 TCCACTACAACTTTAGGGAGATAAGACTTGTAACTTCAACCTGC
* *
31737325 TCCACTGCAACTTTAGGGGGATAA
1 TCCACTACAACTTTAGGGAGATAA
31737349 AATTAGTGGC
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
44 31 0.51
45 27 0.44
46 3 0.05
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (44 bp):
TCCACTACAACTTTAGGGAGATAAGACTTGTAACTTCAACCTGC
Found at i:31737369 original size:44 final size:44
Alignment explanation
Indices: 31737095--31737394 Score: 130
Period size: 44 Copynumber: 6.7 Consensus size: 44
31737085 CTGTCTTCAG
* * * *
31737095 TCTGCTCCACTGCATCTTCAAGGAGATAAGACTTGTAACTTTAA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGAATTGTAACTTTAA
* * * * * * *
31737139 CCTGCTCCATTGTAACTTTAGAGAGATAAG-GTT-T-ACTATGA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGAATTGTAACTTTAA
* * * * * *
31737180 TCTTCTCTACTGCAA-TTTCAGAGAGATAAGATCTGCAATTTATAACTTGAG
1 TCTGCTCCACTGCAACTTT-AGGGAGAT-A-A---G-AA-TTGTAACTTTAA
** * *
31737231 TCTATTCCACTACAACTTTAGGGA-ATTAAG-ATTCGCTATC-TTAA
1 TCTGCTCCACTGCAACTTTAGGGAGA-TAAGAATT-G-TAACTTTAA
* * *
31737275 GTCTGCTCCACTACAACTTTAGGGAGATAAGACTTGTAACTTCAA
1 -TCTGCTCCACTGCAACTTTAGGGAGATAAGAATTGTAACTTTAA
* * **
31737320 CCTGCTCCACTGCAACTTTAGGGGGATAA-AATTAGTGGCTTTAA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGAATT-GTAACTTTAA
* ** * *
31737364 TCTGCTCTACTGTGACTTCAAGGAGATAAGA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGA
31737395 TTCGCCATAA
Statistics
Matches: 187, Mismatches: 48, Indels: 41
0.68 0.17 0.15
Matches are distributed among these distances:
40 3 0.02
41 23 0.12
42 2 0.01
43 8 0.04
44 84 0.45
45 34 0.18
46 5 0.03
49 3 0.02
50 3 0.02
51 19 0.10
52 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTTAGGGAGATAAGAATTGTAACTTTAA
Found at i:31738721 original size:13 final size:14
Alignment explanation
Indices: 31738690--31738736 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
31738680 CCCAGTAGAG
* *
31738690 GTTTTTGTTTTTTT
1 GTTTTTGCTCTTTT
31738704 GTTTTTGCTCTTTT
1 GTTTTTGCTCTTTT
31738718 -TTTTTGCT-TATTT
1 GTTTTTGCTCT-TTT
31738731 GTTTTT
1 GTTTTT
31738737 TTTTTGCCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 1 0.03
13 11 0.38
14 17 0.59
ACGTcount: A:0.02, C:0.06, G:0.13, T:0.79
Consensus pattern (14 bp):
GTTTTTGCTCTTTT
Found at i:31738721 original size:19 final size:19
Alignment explanation
Indices: 31738697--31738743 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
31738687 GAGGTTTTTG
31738697 TTTTTTTG-TT-TTTGCTCTT
1 TTTTTTTGCTTATTTG-T-TT
31738716 TTTTTTTGCTTATTTGTTT
1 TTTTTTTGCTTATTTGTTT
31738735 TTTTTTTGC
1 TTTTTTTGC
31738744 CTCTCCTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 19 0.73
20 3 0.12
21 4 0.15
ACGTcount: A:0.02, C:0.09, G:0.11, T:0.79
Consensus pattern (19 bp):
TTTTTTTGCTTATTTGTTT
Found at i:31739366 original size:36 final size:38
Alignment explanation
Indices: 31739303--31739373 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 38
31739293 TATAGTATGA
*
31739303 TTATGAATGAAATGGAAAAAAATAAAAGAATATTTTGG
1 TTATGAATGAAATGGAAAAAAATAAAAGAACATTTTGG
*
31739341 TTATGATTGAAAT-G-AAAAAATAAAAGAACATTT
1 TTATGAATGAAATGGAAAAAAATAAAAGAACATTT
31739374 GCTCAGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 18 0.58
37 1 0.03
38 12 0.39
ACGTcount: A:0.54, C:0.01, G:0.15, T:0.30
Consensus pattern (38 bp):
TTATGAATGAAATGGAAAAAAATAAAAGAACATTTTGG
Found at i:31747972 original size:28 final size:27
Alignment explanation
Indices: 31747905--31747977 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
31747895 TTATTATATA
* * *
31747905 ATAAGATAAAATTTTATAATAATAAAT
1 ATAATATAAAACTTAATAATAATAAAT
*
31747932 ATCATATATAAACTTAATAATAATAAAT
1 ATAATATA-AAACTTAATAATAATAAAT
31747960 ACCTAAT-TAAAACTTAAT
1 A--TAATATAAAACTTAAT
31747978 TTAAATTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 6 0.16
28 27 0.71
29 2 0.05
30 3 0.08
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (27 bp):
ATAATATAAAACTTAATAATAATAAAT
Found at i:31748713 original size:31 final size:31
Alignment explanation
Indices: 31748678--31748739 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
31748668 ACAACCCAAC
* *
31748678 GACTTAAATAAAAACTTTTAAATAGTTTAGT
1 GACTTAAATAAAAACTTTCAAATAGCTTAGT
* * *
31748709 GACTTCAATGAACACTTTCAAATAGCTTAGT
1 GACTTAAATAAAAACTTTCAAATAGCTTAGT
31748740 AACCATTTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.35
Consensus pattern (31 bp):
GACTTAAATAAAAACTTTCAAATAGCTTAGT
Found at i:31758070 original size:19 final size:19
Alignment explanation
Indices: 31758046--31758082 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
31758036 CTCTTCTAAC
31758046 CATTTTTAATAAACAAAGA
1 CATTTTTAATAAACAAAGA
31758065 CATTTTTAATAAACAAAG
1 CATTTTTAATAAACAAAG
31758083 TCTGAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (19 bp):
CATTTTTAATAAACAAAGA
Found at i:31758134 original size:41 final size:41
Alignment explanation
Indices: 31758079--31758184 Score: 149
Period size: 41 Copynumber: 2.6 Consensus size: 41
31758069 TTTAATAAAC
* *
31758079 AAAGTCTGAAATGTTTCACCAGCGTCAAGCTTGCTAGACAT
1 AAAGTCTGAAATGTTTCACCAGCATCAAGCCTGCTAGACAT
*** *
31758120 AAAGTCTGAAATGTTTCATTGGCATCAAGCCTGCTAGACGT
1 AAAGTCTGAAATGTTTCACCAGCATCAAGCCTGCTAGACAT
*
31758161 AAAGTCTGAAATGTTTCACTAGCA
1 AAAGTCTGAAATGTTTCACCAGCA
31758185 ATAAACCTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (41 bp):
AAAGTCTGAAATGTTTCACCAGCATCAAGCCTGCTAGACAT
Found at i:31766076 original size:41 final size:41
Alignment explanation
Indices: 31766031--31766191 Score: 250
Period size: 41 Copynumber: 3.9 Consensus size: 41
31766021 ACTGGCACTT
*
31766031 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCAGCGTCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCAGCATCA
* *
31766072 AGCCTGCTAGACGTACAGTCTGAAATGTTTCACCAGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCAGCATCA
* * *
31766113 AGCCTGCTAGACATAAAGTTTGAAATGTTTCATCGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCAGCATCA
* *
31766154 AGCCTGCTAGACGTAAAGTCTGAAATGTTTCACTAGCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCAGCA
31766192 ATAAACCTGA
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCAGCATCA
Found at i:31768209 original size:321 final size:321
Alignment explanation
Indices: 31767627--31768269 Score: 1205
Period size: 321 Copynumber: 2.0 Consensus size: 321
31767617 AATCTAACTC
31767627 AACAATGGCCGAACCCTAGACAAGCTTTTATCTTTTATTCTTTCTCTAGTTTCGACCATGGAAGA
1 AACAATGGCCGAACCCTAGACAAGCTTTTATCTTTTATTCTTTCTCTAGTTTCGACCATGGAAGA
31767692 AGATGGTATGATAATGGCTTTGTTTTTCTTTTATTTGATTATAACATATATTATAATATTATTAT
66 AGATGGTATGATAATGGCTTTGTTTTTCTTTTATTTGATTATAACATATATTATAATATTATTAT
* * *
31767757 TTTAACTTTTATTTTTTACGTATAAAAACCATATAATAACACAATATGCCGGCCACTACCTTATG
131 TTTAACTTTTATTTTTAACGTATAAAAACCATATAATAAAACAATATGCCGGCCACTACCTTATA
*
31767822 ATATTGGCTAAATTTCAACATAAGGCCTCCAAATTATAAAGACAACAACAATTAGGCACATTCTT
196 ATATTGGCTAAATTTCAACATAAGGCCTCCAAATTATAAAGAAAACAACAATTAGGCACATTCTT
31767887 ATTTTAACCATCAAATTTTTATTTTATGCGATTAAGCCCTTTACTCAAATTAAGCACACAA
261 ATTTTAACCATCAAATTTTTATTTTATGCGATTAAGCCCTTTACTCAAATTAAGCACACAA
31767948 AACAATGGCCGAACCCTAGACAAGCTTTTATCTTTTATTCTTTCTCTAGTTTCGACCATGGAAGA
1 AACAATGGCCGAACCCTAGACAAGCTTTTATCTTTTATTCTTTCTCTAGTTTCGACCATGGAAGA
31768013 AGATGGTATGATAATGGCTTTGTTTTTCTTTTATTTGATTATAACATATATTATAATATTATTAT
66 AGATGGTATGATAATGGCTTTGTTTTTCTTTTATTTGATTATAACATATATTATAATATTATTAT
* ** *
31768078 TTTAACTTTTATTTTTAATGTATAAAAACCATATAATAAAACAATATGTTGTCCACTACCTTATA
131 TTTAACTTTTATTTTTAACGTATAAAAACCATATAATAAAACAATATGCCGGCCACTACCTTATA
*
31768143 ATATTGGCTAAATTTCAACATAAGGCCTCCAAATTATAAAGAAAACAACAATTAGGCACTTTCTT
196 ATATTGGCTAAATTTCAACATAAGGCCTCCAAATTATAAAGAAAACAACAATTAGGCACATTCTT
31768208 ATTTTAACCATCAAATTTTTATTTTATGCGATTAAGCCCTTTACTCAAATTAAGCACACAA
261 ATTTTAACCATCAAATTTTTATTTTATGCGATTAAGCCCTTTACTCAAATTAAGCACACAA
31768269 A
1 A
31768270 TAATAAAATT
Statistics
Matches: 313, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
321 313 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (321 bp):
AACAATGGCCGAACCCTAGACAAGCTTTTATCTTTTATTCTTTCTCTAGTTTCGACCATGGAAGA
AGATGGTATGATAATGGCTTTGTTTTTCTTTTATTTGATTATAACATATATTATAATATTATTAT
TTTAACTTTTATTTTTAACGTATAAAAACCATATAATAAAACAATATGCCGGCCACTACCTTATA
ATATTGGCTAAATTTCAACATAAGGCCTCCAAATTATAAAGAAAACAACAATTAGGCACATTCTT
ATTTTAACCATCAAATTTTTATTTTATGCGATTAAGCCCTTTACTCAAATTAAGCACACAA
Found at i:31772035 original size:16 final size:16
Alignment explanation
Indices: 31772014--31772050 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
31772004 TTGGTTCGCT
31772014 ATAATGGAATAGAGGC
1 ATAATGGAATAGAGGC
31772030 ATAATGGAATAGAGGC
1 ATAATGGAATAGAGGC
*
31772046 GTAAT
1 ATAAT
31772051 AGCAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.30, T:0.22
Consensus pattern (16 bp):
ATAATGGAATAGAGGC
Found at i:31772421 original size:18 final size:18
Alignment explanation
Indices: 31772283--31772408 Score: 75
Period size: 18 Copynumber: 6.9 Consensus size: 18
31772273 TTATTATTAA
31772283 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
31772301 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
* * *
31772319 CT-TAA--TATTAAGAAT
1 ATATAATTTAATAAAAAT
* *
31772334 ATATAA--TACTATAAA-
1 ATATAATTTAATAAAAAT
*
31772349 ATATAATTTAACATAATTATTATTAA
1 ATATAATTT-A-ATAA--A--A--AT
31772375 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
31772393 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
31772409 TTCTTAATAT
Statistics
Matches: 84, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
15 14 0.17
16 9 0.11
17 4 0.05
18 36 0.43
19 2 0.02
20 1 0.01
21 1 0.01
22 1 0.01
23 1 0.01
24 4 0.05
25 2 0.02
26 9 0.11
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:31776905 original size:12 final size:12
Alignment explanation
Indices: 31776855--31776906 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
31776845 CATCTTGCAG
*
31776855 GTTTTTGGTGCT
1 GTTTTTGGTGTT
*
31776867 -ATTTTGGTGTT
1 GTTTTTGGTGTT
*
31776878 GTTGTTGGTGTT
1 GTTTTTGGTGTT
*
31776890 GTTTTTTGTGTT
1 GTTTTTGGTGTT
31776902 GTTTT
1 GTTTT
31776907 ATTGTTGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.02, C:0.02, G:0.31, T:0.65
Consensus pattern (12 bp):
GTTTTTGGTGTT
Found at i:31776967 original size:23 final size:23
Alignment explanation
Indices: 31776941--31776986 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
31776931 ATGTTGTTCT
*
31776941 GTTGTCGTTTTTAATATTATTTG
1 GTTGTCATTTTTAATATTATTTG
*
31776964 GTTGTCATTTTTAATATTTTTTG
1 GTTGTCATTTTTAATATTATTTG
31776987 TATATTGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.63
Consensus pattern (23 bp):
GTTGTCATTTTTAATATTATTTG
Found at i:31778572 original size:59 final size:59
Alignment explanation
Indices: 31778480--31778600 Score: 226
Period size: 59 Copynumber: 2.1 Consensus size: 59
31778470 GTACAAAGAT
31778480 TTGAAGGGCTCTTATTGGTGGTCTGGAATGAAAAGGGAAATTGCTGAGCATGTCTCAAC
1 TTGAAGGGCTCTTATTGGTGGTCTGGAATGAAAAGGGAAATTGCTGAGCATGTCTCAAC
31778539 TTGAAGGGCTCTTATTGGTGGTCT-GACATGAAAAGGGAAATTGCTGAGCATGTCTCAAC
1 TTGAAGGGCTCTTATTGGTGGTCTGGA-ATGAAAAGGGAAATTGCTGAGCATGTCTCAAC
31778598 TTG
1 TTG
31778601 TTTAACTTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 2 0.03
59 59 0.97
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (59 bp):
TTGAAGGGCTCTTATTGGTGGTCTGGAATGAAAAGGGAAATTGCTGAGCATGTCTCAAC
Found at i:31794716 original size:138 final size:137
Alignment explanation
Indices: 31794414--31794713 Score: 388
Period size: 138 Copynumber: 2.2 Consensus size: 137
31794404 TTAGAGATAG
* * ** * *
31794414 CCACAAACACTCACTTTTACGGAAATTGCCATAAAGGCACTTCTTTAGATTGCGCCAAAAAAGTG
1 CCACAAAGACTCACTTATATAGAAATTACCATAAAAGCACTTCTTTAGATTGCGCCAAAAAAGTG
* * *
31794479 TTTCCTTATAGATTACCATAAATATATTCCTTACAATAAATTTTCCACAAAGGCATTCCTTTAAC
66 TCTCCTTATAGATTACCATAAAGATATTCCTTACAAT-AATTTACCACAAAGGCATTCCTTTAAC
*
31794544 ATAAACAA
130 ACAAACAA
* * * *
31794552 CCACAACGACTCACTTGTATAGAAATTACCATAAAAGCACTTCTTTAGATTGCGCCACAAAGGTG
1 CCACAAAGACTCACTTATATAGAAATTACCATAAAAGCACTTCTTTAGATTGCGCCAAAAAAGTG
* * *
31794617 TCTCCTTATAGATTACCATAAAGGTATTCCTTATCAGAT-ATTTAGCACAAAGGCTTTCCTTTAA
66 TCTCCTTATAGATTACCATAAAGATATTCCTTA-CA-ATAATTTACCACAAAGGCATTCCTTTAA
*
31794681 TACAAACAA
129 CACAAACAA
*
31794690 CCACAAAGGCTCACTTATAT-GAAA
1 CCACAAAGACTCACTTATATAGAAA
31794714 ATTTCCACAA
Statistics
Matches: 140, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
137 4 0.03
138 132 0.94
139 2 0.01
140 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (137 bp):
CCACAAAGACTCACTTATATAGAAATTACCATAAAAGCACTTCTTTAGATTGCGCCAAAAAAGTG
TCTCCTTATAGATTACCATAAAGATATTCCTTACAATAATTTACCACAAAGGCATTCCTTTAACA
CAAACAA
Found at i:31794808 original size:110 final size:112
Alignment explanation
Indices: 31794606--31794818 Score: 308
Period size: 110 Copynumber: 1.9 Consensus size: 112
31794596 TTAGATTGCG
* * *
31794606 CCACAAAGGTGTCTCCTTATAGATTACCATAAAGGTATTCCTTATCAGATATTTAGCACAAAGGC
1 CCACAAAGGCGTCTCCTTATAGATTACCATAAAGGTATTCCTTATCAGAGATTTACCACAAAGGC
* * *
31794671 TTTCCTTTAATACAAACAACCACAAAGGC-TCACTTATATGAAAATTT
66 TTTCCTTTAACAAAAACAACCAAAAAGGCGT-ACTTATATGAAAATTT
* *
31794718 CCACAAAGGCGTCTCCTTATAGATTACCATAAA-GT-TTCCTTATTAGAGATTTTCCACAAAGG-
1 CCACAAAGGCGTCTCCTTATAGATTACCATAAAGGTATTCCTTATCAGAGATTTACCACAAAGGC
31794780 TATTCCTTTAACAAAAACAACCAAAAAGGCGTACTTATA
66 T-TTCCTTTAACAAAAACAACCAAAAAGGCGTACTTATA
31794819 CGGAAATTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
109 1 0.01
110 55 0.60
111 3 0.03
112 32 0.35
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.30
Consensus pattern (112 bp):
CCACAAAGGCGTCTCCTTATAGATTACCATAAAGGTATTCCTTATCAGAGATTTACCACAAAGGC
TTTCCTTTAACAAAAACAACCAAAAAGGCGTACTTATATGAAAATTT
Found at i:31801289 original size:17 final size:17
Alignment explanation
Indices: 31801267--31801300 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31801257 ATAACGAATC
*
31801267 GGAAGCTCGTTCGAGTT
1 GGAAGCTCGTTAGAGTT
*
31801284 GGAAGCTTGTTAGAGTT
1 GGAAGCTCGTTAGAGTT
31801301 ATATCACACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.32
Consensus pattern (17 bp):
GGAAGCTCGTTAGAGTT
Found at i:31802969 original size:26 final size:26
Alignment explanation
Indices: 31802916--31802971 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
31802906 TGCTTGTAGC
31802916 AAAATTTTGACAATTTTACCCCTAGT
1 AAAATTTTGACAATTTTACCCCTAGT
* * *
31802942 AAAATTTTGACGATTTTGCCCCTGGT
1 AAAATTTTGACAATTTTACCCCTAGT
31802968 AAAA
1 AAAA
31802972 CTTCGAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (26 bp):
AAAATTTTGACAATTTTACCCCTAGT
Found at i:31805952 original size:126 final size:126
Alignment explanation
Indices: 31805717--31805989 Score: 420
Period size: 126 Copynumber: 2.2 Consensus size: 126
31805707 GCCATGCGCC
31805717 ACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAATACTTCTGCTGACAAAGCATCCTCCT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAATACTTCTGCTGACAAAGCATCCTCCT
* * * *
31805782 TAAAATGTTTTTGACACTGTTTGCTCAGAAACGTCCACTCAAAATTATTTTTTCGGGAGCT
66 TAAAACGTTTTTGACACTGTTTGCTCAGAAAAGTCCACTCAAAATTATTTTTTCAGGAGAT
* * * * *
31805843 ACTGTAGCAAAAGCGCATCCACGTGGGAGCTTTTTTCAGTACTTCTGCTGACAAAGCATCTTGCT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAATACTTCTGCTGACAAAGCATCCTCCT
* * * *
31805908 TAAAGCGTTTTTGACACTGTTTGCTCAGAAAAGTCTACTTAAAATTATTTTTTTAGGAGAT
66 TAAAACGTTTTTGACACTGTTTGCTCAGAAAAGTCCACTCAAAATTATTTTTTCAGGAGAT
*
31805969 ACTATAGCAAAAGCGCGTCCA
1 ACTGTAGCAAAAGCGCGTCCA
31805990 ACCCTAATCT
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 132 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (126 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAATACTTCTGCTGACAAAGCATCCTCCT
TAAAACGTTTTTGACACTGTTTGCTCAGAAAAGTCCACTCAAAATTATTTTTTCAGGAGAT
Found at i:31816902 original size:20 final size:20
Alignment explanation
Indices: 31816879--31816983 Score: 61
Period size: 20 Copynumber: 5.2 Consensus size: 20
31816869 ATAAATTATA
31816879 CCCTGATTGCACTTACGTGC
1 CCCTGATTGCACTTACGTGC
* * * *
31816899 CCCTGTTTGTACTTCCGTAC
1 CCCTGATTGCACTTACGTGC
*
31816919 CCCTGAATGCA--TATCGGTGC
1 CCCTGATTGCACTTA-C-GTGC
* ** * *
31816939 CCCTGGTCACACATCCGTGC
1 CCCTGATTGCACTTACGTGC
* * *
31816959 TCCTGATTACACTTTCGTGC
1 CCCTGATTGCACTTACGTGC
31816979 CCCTG
1 CCCTG
31816984 TTGTGCATCT
Statistics
Matches: 61, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 57 0.93
21 1 0.02
22 1 0.02
ACGTcount: A:0.14, C:0.36, G:0.19, T:0.30
Consensus pattern (20 bp):
CCCTGATTGCACTTACGTGC
Found at i:31820231 original size:13 final size:13
Alignment explanation
Indices: 31820215--31820239 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31820205 TAAAGAAAGC
31820215 AATTAAGATAGAT
1 AATTAAGATAGAT
31820228 AATTAAGATAGA
1 AATTAAGATAGA
31820240 AAAAAAATTA
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:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (13 bp):
AATTAAGATAGAT
Found at i:31823071 original size:32 final size:32
Alignment explanation
Indices: 31823035--31823104 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
31823025 GGGGTCATGT
31823035 TGGGATTCTGGTTAGTGCGAGGTGGTTAGTAG
1 TGGGATTCTGGTTAGTGCGAGGTGGTTAGTAG
*
31823067 TGGGATTCTGGTTAGTGGGAGGTGGTTAGTAG
1 TGGGATTCTGGTTAGTGCGAGGTGGTTAGTAG
31823099 TGGGAT
1 TGGGAT
31823105 GCTAATTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.16, C:0.04, G:0.46, T:0.34
Consensus pattern (32 bp):
TGGGATTCTGGTTAGTGCGAGGTGGTTAGTAG
Found at i:31823101 original size:17 final size:17
Alignment explanation
Indices: 31823047--31823103 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
31823037 GGATTCTGGT
*
31823047 TAGTGCGAGGTGGTTAG
1 TAGTGGGAGGTGGTTAG
**
31823064 TAGTGGGATTCTGG-T--
1 TAGTGGGA-GGTGGTTAG
31823079 TAGTGGGAGGTGGTTAG
1 TAGTGGGAGGTGGTTAG
31823096 TAGTGGGA
1 TAGTGGGA
31823104 TGCTAATTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 3 0.10
15 9 0.29
17 16 0.52
18 3 0.10
ACGTcount: A:0.18, C:0.04, G:0.47, T:0.32
Consensus pattern (17 bp):
TAGTGGGAGGTGGTTAG
Found at i:31844855 original size:9 final size:9
Alignment explanation
Indices: 31844837--31844902 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
31844827 ATTTTATTAT
31844837 TATAACATA
1 TATAACATA
*
31844846 TATAATATA
1 TATAACATA
31844855 TATAACA-A
1 TATAACATA
31844863 GT-TAACATA
1 -TATAACATA
31844872 TATAA-ATA
1 TATAACATA
* *
31844880 TATTATATA
1 TATAACATA
31844889 TAT-ACATA
1 TATAACATA
31844897 TCATAA
1 T-ATAA
31844903 ATTTTTCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
8 19 0.40
9 27 0.57
10 1 0.02
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.38
Consensus pattern (9 bp):
TATAACATA
Found at i:31849411 original size:9 final size:8
Alignment explanation
Indices: 31849381--31849409 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
31849371 CTGATATATA
31849381 TTTTTTC-
1 TTTTTTCT
31849388 TTTTTTCT
1 TTTTTTCT
31849396 TTTTTTCT
1 TTTTTTCT
31849404 TTTTTT
1 TTTTTT
31849410 TCCTTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTCT
Found at i:31850454 original size:6 final size:6
Alignment explanation
Indices: 31850453--31850498 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
31850443 TTAAAAACAA
* *
31850453 AAAAAGC AAAAGC AAAAAC AAAAAC AAAAAC -AAAAT AAAAAC AAAA
1 AAAAA-C AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
31850499 TAAAATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
5 4 0.12
6 26 0.76
7 4 0.12
ACGTcount: A:0.80, C:0.13, G:0.04, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:31850454 original size:12 final size:11
Alignment explanation
Indices: 31850420--31850534 Score: 82
Period size: 10 Copynumber: 10.9 Consensus size: 11
31850410 ACTGCAGAAT
31850420 AAAATAAAAAC
1 AAAATAAAAAC
**
31850431 AAAA-AATTA-
1 AAAATAAAAAC
*
31850440 AAATTAAAAAC
1 AAAATAAAAAC
*
31850451 -AAA-AAAAGC
1 AAAATAAAAAC
*
31850460 AAAAGCAAAAAC
1 AAAA-TAAAAAC
*
31850472 AAAAACAAAAAC
1 -AAAATAAAAAC
31850484 AAAATAAAAAC
1 AAAATAAAAAC
*
31850495 AAAAT-AAAAT
1 AAAATAAAAAC
*
31850505 AAAAT-AAAAT
1 AAAATAAAAAC
31850515 AAAATAAAAA-
1 AAAATAAAAAC
*
31850525 TAAATAAAAA
1 AAAATAAAAA
31850535 TATAAAATTA
Statistics
Matches: 86, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
9 8 0.09
10 39 0.45
11 23 0.27
12 12 0.14
13 4 0.05
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (11 bp):
AAAATAAAAAC
Found at i:31850455 original size:21 final size:20
Alignment explanation
Indices: 31850417--31850534 Score: 98
Period size: 21 Copynumber: 5.7 Consensus size: 20
31850407 TATACTGCAG
31850417 AATAAAATAAAAAC-AAAAA
1 AATAAAATAAAAACAAAAAA
*
31850436 ATTAAAATTAAAAACAAAAAA
1 AATAAAA-TAAAAACAAAAAA
** *
31850457 AGCAAAAGCAAAAACAAAAACAAA
1 AATAAAA-TAAAAAC--AAA-AAA
*
31850481 AACAAAATAAAAACAAAATAA
1 AATAAAATAAAAACAAAA-AA
31850502 AATAAAATAAAATA-AAATAAA
1 AATAAAATAAAA-ACAAA-AAA
31850523 AAT-AAATAAAAA
1 AATAAAATAAAAA
31850535 TATAAAATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
19 7 0.08
20 16 0.19
21 40 0.48
22 2 0.02
23 9 0.11
24 9 0.11
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.12
Consensus pattern (20 bp):
AATAAAATAAAAACAAAAAA
Found at i:31850487 original size:11 final size:11
Alignment explanation
Indices: 31850445--31850503 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
31850435 AATTAAAATT
31850445 AAAAAC-AAA-
1 AAAAACAAAAC
*
31850454 AAAAGCAAAAGC
1 AAAAACAAAA-C
31850466 AAAAACAAAAAC
1 AAAAAC-AAAAC
*
31850478 AAAAACAAAAT
1 AAAAACAAAAC
*
31850489 AAAAACAAAAT
1 AAAAACAAAAC
31850500 AAAA
1 AAAA
31850504 TAAAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
9 5 0.12
10 3 0.07
11 19 0.44
12 12 0.28
13 4 0.09
ACGTcount: A:0.81, C:0.12, G:0.03, T:0.03
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:31850513 original size:15 final size:14
Alignment explanation
Indices: 31850478--31850533 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 14
31850468 AAACAAAAAC
*
31850478 AAAAACAAAATAAAA
1 AAAAATAAAAT-AAA
31850493 ACAAAATAAAATAAA
1 A-AAAATAAAATAAA
31850508 ATAAAATAAAATAAA
1 A-AAAATAAAATAAA
31850523 AATAAATAAAA
1 AA-AAATAAAA
31850534 ATATAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 1 0.03
15 27 0.73
16 9 0.24
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAATAAAATAAA
Found at i:31850526 original size:6 final size:6
Alignment explanation
Indices: 31850420--31850542 Score: 55
Period size: 6 Copynumber: 20.8 Consensus size: 6
31850410 ACTGCAGAAT
* * * * * *
31850420 AAAATA AAAACAA AAAATTA AAATTA AAAACA AAAAAA GCAAAAGCA AAAACA
1 AAAATA AAAA-TA AAAA-TA AAAATA AAAATA AAAATA --AAAA-TA AAAATA
* * *
31850473 AAAACA AAAA-C AAAATA AAAA-C AAAAT- AAAAT- AAAAT- AAAAT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
31850515 AAAATA AAAAT- -AAATA AAAATA TAAAAT
1 AAAATA AAAATA AAAATA AAAATA -AAAAT
31850543 TAAATGAAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.04
5 28 0.29
6 41 0.43
7 18 0.19
8 4 0.04
9 1 0.01
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:31850664 original size:30 final size:30
Alignment explanation
Indices: 31850628--31850713 Score: 138
Period size: 30 Copynumber: 2.9 Consensus size: 30
31850618 CATGTGCCAT
31850628 GCCATGTGA-GCCACATGGCCGTGTGGCCTG
1 GCCATGT-ACGCCACATGGCCGTGTGGCCTG
*
31850658 GCCATGTACGCCACATGGCCGTGTGGCTTG
1 GCCATGTACGCCACATGGCCGTGTGGCCTG
*
31850688 GCCATGTACGCCACACGGCCGTGTGG
1 GCCATGTACGCCACATGGCCGTGTGG
31850714 ACAGGCAGTG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.14, C:0.31, G:0.35, T:0.20
Consensus pattern (30 bp):
GCCATGTACGCCACATGGCCGTGTGGCCTG
Found at i:31851111 original size:16 final size:16
Alignment explanation
Indices: 31851065--31851113 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 16
31851055 AATGTACTAA
31851065 ATTTTTTCAGATTTTGTTT
1 ATTTTTTC--ATTTT-TTT
31851084 -TTTTTT-A-TTTTTT
1 ATTTTTTCATTTTTTT
31851097 ATTTTTTCATTTTTTT
1 ATTTTTTCATTTTTTT
31851113 A
1 A
31851114 AAAATGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.11
14 9 0.33
15 2 0.07
16 7 0.26
18 6 0.22
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (16 bp):
ATTTTTTCATTTTTTT
Found at i:31855162 original size:31 final size:31
Alignment explanation
Indices: 31855127--31855187 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
31855117 GTACAAAATA
*
31855127 AATCTAGCTATAATCTCTTATTTTAATAATG
1 AATCTAGCCATAATCTCTTATTTTAATAATG
31855158 AATCTAGCCATAATCTCTTATTTTAATAAT
1 AATCTAGCCATAATCTCTTATTTTAATAAT
31855188 ATTCATTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (31 bp):
AATCTAGCCATAATCTCTTATTTTAATAATG
Found at i:31855724 original size:39 final size:39
Alignment explanation
Indices: 31855630--31855758 Score: 95
Period size: 39 Copynumber: 3.3 Consensus size: 39
31855620 AAATTAGAAA
* * *
31855630 AAAATAATAAAAAAATCATAAATTTTAT-TAAAAA--TTT
1 AAAA-AATAAAAAAATTAGAAATTTTTTATAAAAATCTTT
* *
31855667 AAAAAATTTACTAGAAATTAGAAATTTTTTATAAAAATCTTT
1 AAAAAA--TA-AAAAAATTAGAAATTTTTTATAAAAATCTTT
* * **
31855709 AAAAAATAAAAAAATTTGTAAA-ATTTTATAAAAATCATAA
1 AAAAAATAAAAAAATTAG-AAATTTTTTATAAAAATC-TTT
31855749 AAAAAATAAA
1 AAAAAATAAA
31855759 TGACCTTAGT
Statistics
Matches: 73, Mismatches: 11, Indels: 13
0.75 0.11 0.13
Matches are distributed among these distances:
36 2 0.03
37 4 0.05
38 2 0.03
39 34 0.47
40 22 0.30
42 9 0.12
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.33
Consensus pattern (39 bp):
AAAAAATAAAAAAATTAGAAATTTTTTATAAAAATCTTT
Found at i:31855741 original size:20 final size:19
Alignment explanation
Indices: 31855649--31855743 Score: 57
Period size: 20 Copynumber: 4.8 Consensus size: 19
31855639 AAAAAATCAT
*
31855649 AAATTTTATTAAAAATTTAA
1 AAATTTTA-TAAAAATTTTA
* * **
31855669 AAAATTTACTAGAAATTAGA
1 AAATTTTA-TAAAAATTTTA
*
31855689 AATTTTTTATAAAAATCTTTA
1 AA-ATTTTATAAAAAT-TTTA
** *
31855710 AAA-AATAAAAAAATTTGTA
1 AAATTTTATAAAAATTT-TA
31855729 AAATTTTATAAAAAT
1 AAATTTTATAAAAAT
31855744 CATAAAAAAA
Statistics
Matches: 54, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
18 2 0.04
19 13 0.24
20 31 0.57
21 8 0.15
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (19 bp):
AAATTTTATAAAAATTTTA
Found at i:31856171 original size:86 final size:88
Alignment explanation
Indices: 31856075--31856237 Score: 231
Period size: 89 Copynumber: 1.9 Consensus size: 88
31856065 AATTTTTAAT
** *
31856075 AAAAGAAGGGGCTTAATTG-TTTTTTTTTAAG-TTTGAAGGTCTTTTTGATGCATTTTGAAAGTT
1 AAAAGAAGGGGCTTAATTGATTTTTTTAAAAGATTTGAAGGCCTTTTTGATGCATTTTGAAAGTT
*
31856138 CAAGTACCCAAGTGAGTGTAAAA
66 CAAATACCCAAGTGAGTGTAAAA
* * *
31856161 AAAAGTAGGGGCTTAATTGACTTTTTTTAAAAGATTTGAGGGCCTTTTTTATGCATTTTGAAAGT
1 AAAAGAAGGGGCTTAATTGA-TTTTTTTAAAAGATTTGAAGGCCTTTTTGATGCATTTTGAAAGT
*
31856226 TTAAATACCCAA
65 TCAAATACCCAA
31856238 ATAAATAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
86 18 0.27
88 10 0.15
89 38 0.58
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (88 bp):
AAAAGAAGGGGCTTAATTGATTTTTTTAAAAGATTTGAAGGCCTTTTTGATGCATTTTGAAAGTT
CAAATACCCAAGTGAGTGTAAAA
Found at i:31856252 original size:89 final size:85
Alignment explanation
Indices: 31856075--31856280 Score: 216
Period size: 89 Copynumber: 2.3 Consensus size: 85
31856065 AATTTTTAAT
** *
31856075 AAAAGAAGGGGCTTAATTGTTTTTTTTTAAGTTTGAAGGTCTTTTTGATGCATTTTGAAAGTTCA
1 AAAAG-AGGGGCTTAATTGTTTTTTTAAAAGTTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCA
* * * * *
31856140 AGTACCCAAGTGAGTGTAAAA
65 AATACCCAAATAAATGAAAAA
* *
31856161 AAAAGTAGGGGCTTAATTGACTTTTTTTAAAAGATTTGAGGGCCTTTTTTATGCATTTTGAAAGT
1 AAAAG-AGGGGCTTAATTG--TTTTTTTAAAAG-TTTGAAGGCCTTTTTGATGCATTTTGAAAGT
*
31856226 TTAAATACCCAAATAAAT-AAATAA
62 TCAAATACCCAAATAAATGAAA-AA
* *
31856250 AAAAGAGGAGCTTAATTTTTATTATTTAAAA
1 AAAAGAGGGGCTTAATTGTT-TT-TTTAAAA
31856281 AAATTTGAGT
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
86 20 0.20
87 2 0.02
88 30 0.30
89 48 0.48
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (85 bp):
AAAAGAGGGGCTTAATTGTTTTTTTAAAAGTTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAA
ATACCCAAATAAATGAAAAA
Found at i:31866864 original size:14 final size:14
Alignment explanation
Indices: 31866845--31866872 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31866835 AGAATCATAG
31866845 ACCTCATCAACTGT
1 ACCTCATCAACTGT
31866859 ACCTCATCAACTGT
1 ACCTCATCAACTGT
31866873 GAGAGATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (14 bp):
ACCTCATCAACTGT
Found at i:31873480 original size:23 final size:23
Alignment explanation
Indices: 31873454--31873524 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
31873444 ATAAGTGCCA
*
31873454 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
31873477 CACTGAAATGTAGAC-ATAGCTAC
1 CACTGAAATGTAGCCGA-AGCTAC
*
31873500 CACTGAAATGTAGCTGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
31873523 CA
1 CA
31873525 TTGATCAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 40 0.95
24 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:31879003 original size:25 final size:23
Alignment explanation
Indices: 31878969--31879015 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 23
31878959 ATCAGTTACA
31878969 CCTATTAAACAAATACTTTTTTCTC
1 CCTATTAAACAAAT--TTTTTTCTC
31878994 CCTATTAAACAAATTTTTTTCT
1 CCTATTAAACAAATTTTTTTCT
31879016 TTTTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.36
25 14 0.64
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (23 bp):
CCTATTAAACAAATTTTTTTCTC
Found at i:31886479 original size:6 final size:6
Alignment explanation
Indices: 31886468--31886505 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
31886458 AAACCTAGAG
*
31886468 AAACCT AAACCT AAACCT AAACCT AAACCT AAAACT AA
1 AAACCT AAACCT AAACCT AAACCT AAACCT AAACCT AA
31886506 GCTAAAATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (6 bp):
AAACCT
Found at i:31891440 original size:94 final size:94
Alignment explanation
Indices: 31891266--31891474 Score: 258
Period size: 94 Copynumber: 2.2 Consensus size: 94
31891256 ACAAATAAAA
* * * **
31891266 TCAT-GAAAGATTATTCATGATCACAAATTAATGAATTTAGGCTGTGATCATAAATCAACGAGTT
1 TCATAGAAA-ATTGTTCATGATCACAAATCAATGAACTTAGGCTGTGATCATAAATCAACGAACT
* *
31891330 GTTTGGAGTAGTGATAGTAAATCAGCTAAC
65 GTTTGAAGTAGCGATAGTAAATCAGCTAAC
* * * **
31891360 TCATAGAAAATTGTTCATGGTCATAAATCAATGAACTTAGGTTGTGATTGTAAATCAACGAACTG
1 TCATAGAAAATTGTTCATGATCACAAATCAATGAACTTAGGCTGTGATCATAAATCAACGAACTG
* *
31891425 TTTGAAGTAGCGATAGTAAATTAGTTAAC
66 TTTGAAGTAGCGATAGTAAATCAGCTAAC
* *
31891454 TCATAGAAGATTGTTTATGAT
1 TCATAGAAAATTGTTCATGAT
31891475 TGTAACACCC
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
94 93 0.96
95 4 0.04
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (94 bp):
TCATAGAAAATTGTTCATGATCACAAATCAATGAACTTAGGCTGTGATCATAAATCAACGAACTG
TTTGAAGTAGCGATAGTAAATCAGCTAAC
Found at i:31893073 original size:55 final size:55
Alignment explanation
Indices: 31893012--31893191 Score: 299
Period size: 55 Copynumber: 3.3 Consensus size: 55
31893002 ATATTAAGTC
* * *
31893012 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
31893067 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
* *
31893122 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATATTCA-ATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAATCATACT
31893177 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31893192 GCACAATTTA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 92 0.77
56 27 0.23
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.28
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCATACT
Found at i:31893076 original size:28 final size:27
Alignment explanation
Indices: 31893012--31893191 Score: 279
Period size: 28 Copynumber: 6.6 Consensus size: 27
31893002 ATATTAAGTC
* *
31893012 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
31893039 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
31893067 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
31893094 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
31893122 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
31893150 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
31893177 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31893192 GCACAATTTA
Statistics
Matches: 143, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
27 66 0.46
28 76 0.53
29 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:31893151 original size:83 final size:82
Alignment explanation
Indices: 31893012--31893191 Score: 297
Period size: 83 Copynumber: 2.2 Consensus size: 82
31893002 ATATTAAGTC
* * *
31893012 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACTCGCACACTTA
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
31893077 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
*
31893094 CGCACACTTAGTGCTACATAATCATACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
* *
31893159 AGTGCTACATATTCAATT
65 AGTGCTACATAGTCAACT
31893177 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31893192 GCACAATTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 22 0.24
83 69 0.76
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.28
Consensus pattern (82 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:31906267 original size:3 final size:3
Alignment explanation
Indices: 31906259--31906297 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
31906249 TTATAAGTGT
31906259 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31906298 ATGAACTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31908599 original size:41 final size:41
Alignment explanation
Indices: 31908554--31908655 Score: 177
Period size: 41 Copynumber: 2.5 Consensus size: 41
31908544 TTGTCTTAAC
*
31908554 ATCTTATTACTCAGGTCCACATTGTTGAACTCCATCTTAGT
1 ATCTTATTACTCGGGTCCACATTGTTGAACTCCATCTTAGT
**
31908595 ATCTTATTACTCGGGTCCACATTGTTGAACTCTGTCTTAGT
1 ATCTTATTACTCGGGTCCACATTGTTGAACTCCATCTTAGT
31908636 ATCTTATTACTCGGGTCCAC
1 ATCTTATTACTCGGGTCCAC
31908656 CAACCGGACC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.39
Consensus pattern (41 bp):
ATCTTATTACTCGGGTCCACATTGTTGAACTCCATCTTAGT
Found at i:31908731 original size:14 final size:13
Alignment explanation
Indices: 31908695--31908740 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
31908685 CATCCGGCCT
31908695 AAAACCAAAAATA
1 AAAACCAAAAATA
*
31908708 AATAAACAAAACATA
1 AA-AACCAAAA-ATA
31908723 AAAACCAAAAAATA
1 AAAACC-AAAAATA
31908737 AAAA
1 AAAA
31908741 ATTCAAGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 17 0.61
15 9 0.32
ACGTcount: A:0.78, C:0.13, G:0.00, T:0.09
Consensus pattern (13 bp):
AAAACCAAAAATA
Found at i:31908740 original size:15 final size:15
Alignment explanation
Indices: 31908695--31908741 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
31908685 CATCCGGCCT
31908695 AAAACC-AAAAATAA
1 AAAACCAAAAAATAA
*
31908709 ATAAA-CAAAACAT-A
1 A-AAACCAAAAAATAA
31908723 AAAACCAAAAAATAA
1 AAAACCAAAAAATAA
31908738 AAAA
1 AAAA
31908742 TTCAAGTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 3 0.11
14 11 0.41
15 13 0.48
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAACCAAAAAATAA
Found at i:31909990 original size:61 final size:61
Alignment explanation
Indices: 31909894--31910008 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 61
31909884 TGTCCTAGGG
* * *
31909894 TTGGGAATATTTTCCCATTCGCCCCTGTTCTTTTTTCGCGCGTTATATTTTAGTAATTTAT
1 TTGGGAATATATTCCCATTCGCCCCTGTTCTTTTTTCACGCGTTACATTTTAGTAATTTAT
* *
31909955 TTGGGAATATATTCCTATTCGGCCCCTGTTC-TTTTTCACGTGTTACATTTTAGT
1 TTGGGAATATATTCCCATTC-GCCCCTGTTCTTTTTTCACGCGTTACATTTTAGT
31910009 CCTTAGTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
61 38 0.79
62 10 0.21
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.48
Consensus pattern (61 bp):
TTGGGAATATATTCCCATTCGCCCCTGTTCTTTTTTCACGCGTTACATTTTAGTAATTTAT
Found at i:31922771 original size:94 final size:94
Alignment explanation
Indices: 31922605--31922979 Score: 385
Period size: 94 Copynumber: 4.1 Consensus size: 94
31922595 GTAACTAACC
* * *
31922605 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTTAGATTGAAATC-ACCATAGCGAATCTTATCTC
1 ACAAATCCTACACCCCTAAAGTTGCAGTGGGTGAGATT-AAATCTACCATAGCGAATCTTATCTC
* * * *
31922669 CTTGAAGTTGCAGTGGAGAAAATTTAAGCT
65 CCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* *
31922699 ACAGATCCTACACCCCTAAAGTCGCAGTGGGATGA-ATTAAATCTACCATAGCGAATCTTATCTC
1 ACAAATCCTACACCCCTAAAGTTGCAGTGGG-TGAGATTAAATCTACCATAGCGAATCTTATCTC
* *
31922763 CCTAAAGTTACAGTGGAGCAGATTGAAGCT
65 CCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * * * * *
31922793 ACAAATCTTATC-TCCCTGAAGTTGTAGTGGAG-CAGATTAAAGCTA-C--A---AATCTTATCT
1 ACAAATCCTA-CACCCCTAAAGTTGCAGTGG-GTGAGATTAAATCTACCATAGCGAATCTTATCT
*
31922850 CCTTGAAGTTGCAGTGGAGCAGATTGAAGCGT
64 CCCTGAAGTTGCAGTGGAGCAGATTGAAGC-T
* * * * * * *
31922882 -CAAATCCTATACCTCTAAAGATGCAGTAGGTTAGATTAAATCTACCATAGCGAGTCTCATCTCC
1 ACAAATCCTACACCCCTAAAGTTGCAGTGGGTGAGATTAAATCTACCATAGCGAATCTTATCTCC
* *
31922946 CTGAAGTTGTAGTGGAGTAGATTGAAGCT
66 CTGAAGTTGCAGTGGAGCAGATTGAAGCT
31922975 ACAAA
1 ACAAA
31922980 CCTTGTCTCC
Statistics
Matches: 229, Mismatches: 37, Indels: 30
0.77 0.12 0.10
Matches are distributed among these distances:
87 1 0.00
88 68 0.30
89 2 0.01
91 2 0.01
93 8 0.03
94 144 0.63
95 4 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (94 bp):
ACAAATCCTACACCCCTAAAGTTGCAGTGGGTGAGATTAAATCTACCATAGCGAATCTTATCTCC
CTGAAGTTGCAGTGGAGCAGATTGAAGCT
Found at i:31922815 original size:44 final size:44
Alignment explanation
Indices: 31922752--31923064 Score: 281
Period size: 44 Copynumber: 7.0 Consensus size: 44
31922742 TACCATAGCG
* *
31922752 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTGAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* *
31922796 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
*
31922840 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCGT-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-TACA
* * * * ** * *
31922884 AATCCTATAC-CTCTAAAGATGCAGTAGG-TTAGATTAAATCTACCA
1 AATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGCTA-CA
* * *
31922929 TAGCGAGTCTCATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCTACA
1 -A---A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * * * *
31922978 AACCTTGTCTCCCTGAAGTAGCAGTAGAGCAGATTGAAGCTACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * * * * *
31923022 AATCTCAACTCCCTAAAGTTGCAGCGGAGAAGATTGAAACTAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
31923065 CCTTGAAGTT
Statistics
Matches: 214, Mismatches: 43, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
43 1 0.00
44 172 0.80
45 7 0.03
46 1 0.00
48 1 0.00
49 6 0.03
50 26 0.12
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
Found at i:31922922 original size:182 final size:182
Alignment explanation
Indices: 31922658--31923064 Score: 523
Period size: 182 Copynumber: 2.2 Consensus size: 182
31922648 CACCATAGCG
* * *
31922658 AATCTTATCTCCTTGAAGTTGCAGTGGAGAAAATTTAAGCTACAGATCCTACACCCCTAAAGTCG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAGCTACAAATCCTACACCCCTAAAGTCG
* *
31922723 CAGTGGGATGAATTAAATCTACCATAGCGAATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTG
66 CAGTAGGATGAATTAAATCTACCATAGCGAATCTCATCTCCCTAAAGTTACAGTGGAGCAGATTG
* * * *
31922788 AAGCTACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACA
131 AAGCTACAAACCTTATCTCCCTGAAGTAGCAGTAGAGCAGATTAAAGCTACA
* * *
31922840 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCGT-CAAATCCTATACCTCTAAAGAT
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAGC-TACAAATCCTACACCCCTAAAG-T
* * * ** *
31922904 -GCAGTAGG-TTAGATTAAATCTACCATAGCGAGTCTCATCTCCCTGAAGTTGTAGTGGAGTAGA
64 CGCAGTAGGATGA-ATTAAATCTACCATAGCGAATCTCATCTCCCTAAAGTTACAGTGGAGCAGA
* * *
31922967 TTGAAGCTACAAACCTTGTCTCCCTGAAGTAGCAGTAGAGCAGATTGAAGCTACG
128 TTGAAGCTACAAACCTTATCTCCCTGAAGTAGCAGTAGAGCAGATTAAAGCTACA
* * * * * *
31923022 AATCTCAACTCCCTAAAGTTGCAGCGGAGAAGATTGAAACTAC
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAGCTAC
31923065 CCTTGAAGTT
Statistics
Matches: 193, Mismatches: 28, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
181 3 0.02
182 188 0.97
183 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (182 bp):
AATCTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAGCTACAAATCCTACACCCCTAAAGTCG
CAGTAGGATGAATTAAATCTACCATAGCGAATCTCATCTCCCTAAAGTTACAGTGGAGCAGATTG
AAGCTACAAACCTTATCTCCCTGAAGTAGCAGTAGAGCAGATTAAAGCTACA
Found at i:31923056 original size:138 final size:138
Alignment explanation
Indices: 31922802--31923065 Score: 331
Period size: 138 Copynumber: 1.9 Consensus size: 138
31922792 TACAAATCTT
* * * *
31922802 ATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCTTGAAGTTGCAGTGG
1 ATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACAAACCTTATCTCCCTGAAGTAGCAGTAG
* **
31922867 AGCAGATTGAAGCGTCAAATCCTATACCTCTAAAGATGCAGTAGGTTAGATT-AAATCTACCATA
66 AGCAGATTGAAGCGTCAAATCCTATACCCCTAAAGATGCAGTAGGGAAGATTGAAA-CTACCATA
31922931 GCGAGTCTC
130 GCGAGTCTC
* * *
31922940 ATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAACCTTGTCTCCCTGAAGTAGCAGTAG
1 ATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACAAACCTTATCTCCCTGAAGTAGCAGTAG
* * *
31923005 AGCAGATTGAAGC-TACGAAT-CTCA-ACTCCCTAAAGTTGCAG-CGGAGAAGATTGAAACTACC
66 AGCAGATTGAAGCGT-CAAATCCT-ATAC-CCCTAAAGATGCAGTAGG-GAAGATTGAAACTACC
31923066 CTTGAAGTTG
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
137 7 0.06
138 98 0.91
139 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.26
Consensus pattern (138 bp):
ATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACAAACCTTATCTCCCTGAAGTAGCAGTAG
AGCAGATTGAAGCGTCAAATCCTATACCCCTAAAGATGCAGTAGGGAAGATTGAAACTACCATAG
CGAGTCTC
Found at i:31924683 original size:3 final size:3
Alignment explanation
Indices: 31924677--31924738 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
31924667 ATTATTATTA
31924677 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
31924725 TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TT
31924739 ATTTATCTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:31940981 original size:6 final size:6
Alignment explanation
Indices: 31940967--31940996 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
31940957 ACTGGTCCTA
*
31940967 CATGAC CATGTC CATGAC CATGAC CATGAC
1 CATGAC CATGAC CATGAC CATGAC CATGAC
31940997 TTCTATGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (6 bp):
CATGAC
Found at i:31945688 original size:6 final size:6
Alignment explanation
Indices: 31945674--31945703 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
31945664 ACTGGTCCTA
*
31945674 CATGAC CATGTC CATGAC CATGAC CATGAC
1 CATGAC CATGAC CATGAC CATGAC CATGAC
31945704 TTCTATGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (6 bp):
CATGAC
Found at i:31947093 original size:2 final size:2
Alignment explanation
Indices: 31947081--31947132 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
31947071 TTCCACCAAA
*
31947081 CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31947123 CT CT CT CT CT
1 CT CT CT CT CT
31947133 GTTTATAGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:31953560 original size:10 final size:10
Alignment explanation
Indices: 31953542--31953574 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
31953532 TGATTGTGAA
*
31953542 TTGGTATATT
1 TTGGCATATT
31953552 TTGGCATATT
1 TTGGCATATT
31953562 TTGGCATATT
1 TTGGCATATT
31953572 TTG
1 TTG
31953575 AATAGGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.18, C:0.06, G:0.21, T:0.55
Consensus pattern (10 bp):
TTGGCATATT
Found at i:31953793 original size:13 final size:13
Alignment explanation
Indices: 31953775--31953809 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
31953765 CCCAGAGAGT
31953775 TACACGGCTTGAC
1 TACACGGCTTGAC
31953788 TACACGGCTTGAC
1 TACACGGCTTGAC
*
31953801 GACACGGCT
1 TACACGGCT
31953810 GTGTGACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (13 bp):
TACACGGCTTGAC
Found at i:31958984 original size:20 final size:20
Alignment explanation
Indices: 31958956--31958995 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31958946 CACTGGTTTG
31958956 CACACGGGTGTGTGCATTTT
1 CACACGGGTGTGTGCATTTT
* *
31958976 CACATGGGTGTGTGGATTTT
1 CACACGGGTGTGTGCATTTT
31958996 TGGGGTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.38
Consensus pattern (20 bp):
CACACGGGTGTGTGCATTTT
Found at i:31969904 original size:22 final size:22
Alignment explanation
Indices: 31969877--31969927 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
31969867 CTCATATTTC
*
31969877 CTCTCAATTTCTTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
31969899 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
31969921 CTCTCAA
1 CTCTCAA
31969928 ATCCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:31969953 original size:29 final size:29
Alignment explanation
Indices: 31969921--31970007 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
31969911 TTCCAAAATT
31969921 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTCAATTTC
* **
31969950 CTCTCAATTTCC-T-TCCAA----AA-TT-
1 CTCTCAA-ATCCATATTTAATTTCAATTTC
*
31969972 CTCTCAAATCCATATTTGATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTCAATTTC
31970001 CTCTCAA
1 CTCTCAA
31970008 TTTCCTTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 18
0.63 0.10 0.27
Matches are distributed among these distances:
21 3 0.07
22 8 0.19
23 4 0.10
24 2 0.05
27 2 0.05
28 5 0.12
29 15 0.36
30 3 0.07
ACGTcount: A:0.29, C:0.28, G:0.01, T:0.43
Consensus pattern (29 bp):
CTCTCAAATCCATATTTAATTTCAATTTC
Found at i:31969962 original size:51 final size:51
Alignment explanation
Indices: 31969899--31970014 Score: 223
Period size: 51 Copynumber: 2.3 Consensus size: 51
31969889 TTCCAAAATT
31969899 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
*
31969950 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTGATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
31970001 CTCTCAATTTCCTT
1 CTCTCAATTTCCTT
31970015 TTTTAAAATA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.27, C:0.28, G:0.01, T:0.44
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:31971033 original size:383 final size:383
Alignment explanation
Indices: 31970326--31971092 Score: 1534
Period size: 383 Copynumber: 2.0 Consensus size: 383
31970316 TTTTTGGCAC
31970326 GTGGCGACGGTAGGACGGGGATGCAAGTTGTACCCGAAACTGATCAGTGCGTTCATCGAGAGGTG
1 GTGGCGACGGTAGGACGGGGATGCAAGTTGTACCCGAAACTGATCAGTGCGTTCATCGAGAGGTG
31970391 GAGACCCGAGACGCACACATTCCATCTTCCATGTGGAGAGTGCACTATCACTCTAGAAGATGTCC
66 GAGACCCGAGACGCACACATTCCATCTTCCATGTGGAGAGTGCACTATCACTCTAGAAGATGTCC
31970456 ATCTGCAATTGGGATTACCAGTGGACGAGCACCCAGTCACCGGGTCTGCCCAATCTAGCAATTGT
131 ATCTGCAATTGGGATTACCAGTGGACGAGCACCCAGTCACCGGGTCTGCCCAATCTAGCAATTGT
31970521 GAGGCGGTGTGCTACAAGCTTTTGGGCGCAATTCTGGAGAAAATGGAGGGAGGTAAGGTCGAGAT
196 GAGGCGGTGTGCTACAAGCTTTTGGGCGCAATTCTGGAGAAAATGGAGGGAGGTAAGGTCGAGAT
31970586 GGGCTGGTTACGTGACACATTCGCTGATCCGAATGAAGATTTAACCGAGATTGAAAGAATCCGAT
261 GGGCTGGTTACGTGACACATTCGCTGATCCGAATGAAGATTTAACCGAGATTGAAAGAATCCGAT
31970651 ATACTCGGGCATACATTCTTCAAATAATTGGAGGTTATCTGATGCCCGACACGTCACG
326 ATACTCGGGCATACATTCTTCAAATAATTGGAGGTTATCTGATGCCCGACACGTCACG
31970709 GTGGCGACGGTAGGACGGGGATGCAAGTTGTACCCGAAACTGATCAGTGCGTTCATCGAGAGGTG
1 GTGGCGACGGTAGGACGGGGATGCAAGTTGTACCCGAAACTGATCAGTGCGTTCATCGAGAGGTG
31970774 GAGACCCGAGACGCACACATTCCATCTTCCATGTGGAGAGTGCACTATCACTCTAGAAGATGTCC
66 GAGACCCGAGACGCACACATTCCATCTTCCATGTGGAGAGTGCACTATCACTCTAGAAGATGTCC
31970839 ATCTGCAATTGGGATTACCAGTGGACGAGCACCCAGTCACCGGGTCTGCCCAATCTAGCAATTGT
131 ATCTGCAATTGGGATTACCAGTGGACGAGCACCCAGTCACCGGGTCTGCCCAATCTAGCAATTGT
31970904 GAGGCGGTGTGCTACAAGCTTTTGGGCGCAATTCTGGAGAAAATGGAGGGAGGTAAGGTCGAGAT
196 GAGGCGGTGTGCTACAAGCTTTTGGGCGCAATTCTGGAGAAAATGGAGGGAGGTAAGGTCGAGAT
31970969 GGGCTGGTTACGTGACACATTCGCTGATCCGAATGAAGATTTAACCGAGATTGAAAGAATCCGAT
261 GGGCTGGTTACGTGACACATTCGCTGATCCGAATGAAGATTTAACCGAGATTGAAAGAATCCGAT
31971034 ATACTCGGGCATACATTCTTCAAATAATTGGAGGTTATCTGATGCCCGACACGTCACG
326 ATACTCGGGCATACATTCTTCAAATAATTGGAGGTTATCTGATGCCCGACACGTCACG
31971092 G
1 G
31971093 AGCCGCGTAC
Statistics
Matches: 384, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
383 384 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (383 bp):
GTGGCGACGGTAGGACGGGGATGCAAGTTGTACCCGAAACTGATCAGTGCGTTCATCGAGAGGTG
GAGACCCGAGACGCACACATTCCATCTTCCATGTGGAGAGTGCACTATCACTCTAGAAGATGTCC
ATCTGCAATTGGGATTACCAGTGGACGAGCACCCAGTCACCGGGTCTGCCCAATCTAGCAATTGT
GAGGCGGTGTGCTACAAGCTTTTGGGCGCAATTCTGGAGAAAATGGAGGGAGGTAAGGTCGAGAT
GGGCTGGTTACGTGACACATTCGCTGATCCGAATGAAGATTTAACCGAGATTGAAAGAATCCGAT
ATACTCGGGCATACATTCTTCAAATAATTGGAGGTTATCTGATGCCCGACACGTCACG
Found at i:31971548 original size:7 final size:7
Alignment explanation
Indices: 31971536--31971568 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
31971526 TAGTCGATTG
31971536 GTATTTA
1 GTATTTA
31971543 GTATTTA
1 GTATTTA
31971550 GTATTTA
1 GTATTTA
31971557 GTATTTA
1 GTATTTA
31971564 GTATT
1 GTATT
31971569 ATTATGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:31972250 original size:18 final size:18
Alignment explanation
Indices: 31972227--31972262 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31972217 GCGTTTCCTA
31972227 ACCCTTATATGTACCCTT
1 ACCCTTATATGTACCCTT
*
31972245 ACCCTTATATGTATCCTT
1 ACCCTTATATGTACCCTT
31972263 TTTCGAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.42
Consensus pattern (18 bp):
ACCCTTATATGTACCCTT
Found at i:31972679 original size:43 final size:43
Alignment explanation
Indices: 31972632--31972716 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
31972622 TTGTACAAAT
*
31972632 ATTTTGA-ATATTTTGATATTATTTTTATGTAAAAAAATAGAAA
1 ATTTTGAGATATTTTGATATTA-TTTGATGTAAAAAAATAGAAA
* *
31972675 ATTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAA
1 ATTTTGAGATATTTTGATATTATTTGATGTAAAAAAATAGAA
31972717 GTTTATTCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 25 0.66
44 13 0.34
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (43 bp):
ATTTTGAGATATTTTGATATTATTTGATGTAAAAAAATAGAAA
Found at i:31972765 original size:29 final size:29
Alignment explanation
Indices: 31972724--31973290 Score: 809
Period size: 29 Copynumber: 19.6 Consensus size: 29
31972714 GAAGTTTATT
* *
31972724 CCTAACCCTAACCCAATTTAATTAAAAAT
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31972753 CCTAACCCTAACCTAATTCAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31972782 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31972811 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31972840 CCTAA-CCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* * *
31972868 CATAACCCTAACCAAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31972897 CCTAACCCTAA-CTCAATTCAATT-AAAAC
1 CCTAACCCTAACCT-AATTTAATTAAAAAC
*
31972925 CCTAACCCTAACCTAATTCAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* *
31972954 CCTAACCCTAACATAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31972983 CATAACCCTAACCTAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* *
31973012 CCTAACCCTAACATAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31973041 CATAACCCTAACGC-AATTTAATTAAAAAC
1 CCTAACCCTAAC-CTAATTTAATTAAAAAC
* *
31973070 CCTAACCCTAACCCAATTCAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
** * *
31973099 CCTAACAATAACCCAATTCAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* * *
31973128 CTTAACCCTAACCCAATTCAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31973157 CCTAACCCTAACCAAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31973186 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31973215 CCTAACCCTAACCAAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31973244 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
31973273 CCTAACCCTAACCAAATT
1 CCTAACCCTAACCTAATT
31973291 ATTTCTTACA
Statistics
Matches: 491, Mismatches: 41, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
28 54 0.11
29 437 0.89
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (29 bp):
CCTAACCCTAACCTAATTTAATTAAAAAC
Found at i:31979742 original size:22 final size:24
Alignment explanation
Indices: 31979699--31979747 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
31979689 AAATAAGTTA
*
31979699 TAATTGTTTTATAGAATTTAAATAC
1 TAATTGTTTTATAGAA-TTAAAAAC
*
31979724 TAATTTTTTTATA-AA-TAAAAAC
1 TAATTGTTTTATAGAATTAAAAAC
31979746 TA
1 TA
31979748 GAACATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
24 2 0.09
25 12 0.55
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
TAATTGTTTTATAGAATTAAAAAC
Found at i:31980143 original size:17 final size:16
Alignment explanation
Indices: 31980116--31980147 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
31980106 TCAATTGTTT
31980116 TGTTGAATAGAATAAA
1 TGTTGAATAGAATAAA
31980132 TGTTGTAATAGAATAA
1 TGTTG-AATAGAATAA
31980148 GGAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
TGTTGAATAGAATAAA
Found at i:31982501 original size:51 final size:51
Alignment explanation
Indices: 31982425--31982528 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
31982415 AGGAGTAAGC
31982425 TTACAGAAAGCTTAGTAAGTTCATAGGCCCATAATAAAATCTTATCAAGAT
1 TTACAGAAAGCTTAGTAAGTTCATAGGCCCATAATAAAATCTTATCAAGAT
31982476 TTACAGAAAGCTTAGTAAGTTCATAGGCCCATAATAAAATCTTATCAAGAT
1 TTACAGAAAGCTTAGTAAGTTCATAGGCCCATAATAAAATCTTATCAAGAT
31982527 TT
1 TT
31982529 CACTAACAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (51 bp):
TTACAGAAAGCTTAGTAAGTTCATAGGCCCATAATAAAATCTTATCAAGAT
Found at i:31982807 original size:46 final size:46
Alignment explanation
Indices: 31982750--31982926 Score: 273
Period size: 46 Copynumber: 3.8 Consensus size: 46
31982740 ACAATGCTAT
* * *
31982750 AACTCAATATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* * * * * *
31982796 AACTCACTATGGCTTTCGTTACTAAAATGCCATACCTACTTCTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
31982842 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
31982888 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTAC
31982927 GTTCCACACT
Statistics
Matches: 117, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 117 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
Found at i:31989253 original size:22 final size:22
Alignment explanation
Indices: 31989209--31989682 Score: 470
Period size: 21 Copynumber: 22.3 Consensus size: 22
31989199 CAGGATAAAT
31989209 CCTAAACCCTTAACTT-AAAAC
1 CCTAAACCCTTAACTTAAAAAC
*
31989230 CCTAAACTCTTAACTTAAAAAC
1 CCTAAACCCTTAACTTAAAAAC
31989252 CCT-AACCCTTAACTT-AAAAC
1 CCTAAACCCTTAACTTAAAAAC
* * *
31989272 TCTAAACTCTTAATTTAAAAAC
1 CCTAAACCCTTAACTTAAAAAC
* *
31989294 CCT-AATCCTTAATTTAAAAAC
1 CCTAAACCCTTAACTTAAAAAC
* * *
31989315 CAT-AACCCTTAAATTTAAAAC
1 CCTAAACCCTTAACTTAAAAAC
31989336 CCTAAACCCTTAACTT-AAAAC
1 CCTAAACCCTTAACTTAAAAAC
* *
31989357 CCTTTAACCCTTAACCTAAAAAC
1 CC-TAAACCCTTAACTTAAAAAC
* *
31989380 CAT-AACCCTAAACCTT--AAAC
1 CCTAAACCCTTAA-CTTAAAAAC
* * *
31989400 CC-CAACCCTTAAATAAAAAAC
1 CCTAAACCCTTAACTTAAAAAC
* *
31989421 ACT-AACCCTTAACTTTAAAAC
1 CCTAAACCCTTAACTTAAAAAC
31989442 CCT-AACCCTTAACTTTAAAAA-
1 CCTAAACCCTTAAC-TTAAAAAC
* * *
31989463 TCTTAACTCTTAACTTAAAAAC
1 CCTAAACCCTTAACTTAAAAAC
*
31989485 CCTAAACCCTTAATTTAAAAAC
1 CCTAAACCCTTAACTTAAAAAC
* *
31989507 CCT-AACCCTAAAACCT--AAAC
1 CCTAAACCCT-TAACTTAAAAAC
*
31989527 CCT-AACCCTTAA-ATAAAAAC
1 CCTAAACCCTTAACTTAAAAAC
*
31989547 ACT-AACCCTTAACTTAAAAAC
1 CCTAAACCCTTAACTTAAAAAC
* * *
31989568 CCT-AACTCTTAACTTTAAAAT
1 CCTAAACCCTTAACTTAAAAAC
31989589 CCTAAACCCTTAACTTAAAAA-
1 CCTAAACCCTTAACTTAAAAAC
31989610 CCTAAAACCCTTAACTTAAAAAC
1 CCT-AAACCCTTAACTTAAAAAC
*
31989633 CCT-AACCTTTAACTTAAAAAC
1 CCTAAACCCTTAACTTAAAAAC
31989654 CCTAAACCCTTAACTTAAAAAC
1 CCTAAACCCTTAACTTAAAAAC
*
31989676 CATAAAC
1 CCTAAAC
31989683 TATTTGCATC
Statistics
Matches: 380, Mismatches: 51, Indels: 43
0.80 0.11 0.09
Matches are distributed among these distances:
18 1 0.00
19 3 0.01
20 48 0.13
21 183 0.48
22 136 0.36
23 9 0.02
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (22 bp):
CCTAAACCCTTAACTTAAAAAC
Found at i:31989331 original size:43 final size:42
Alignment explanation
Indices: 31989213--31989676 Score: 464
Period size: 43 Copynumber: 11.0 Consensus size: 42
31989203 ATAAATCCTA
* *
31989213 AACCCTTAACTT-AAAACCCTAAACTCTTAACTTAAAAACCCT
1 AACCCTTAACTTAAAAACCCT-AACCCTTAATTTAAAAACCCT
* *
31989255 AACCCTTAACTT-AAAACTCTAAACTCTTAATTTAAAAACCCT
1 AACCCTTAACTTAAAAACCCT-AACCCTTAATTTAAAAACCCT
* * *
31989297 AATCCTTAATTTAAAAACCATAACCCTTAAATTT-AAAACCCT
1 AACCCTTAACTTAAAAACCCTAACCCTT-AATTTAAAAACCCT
** *
31989339 AAACCCTTAACTT-AAAACCCTTTAACCCTTAACCTAAAAACCAT
1 -AACCCTTAACTTAAAAACCC--TAACCCTTAATTTAAAAACCCT
* * * * *
31989383 AACCCTAAACCTT--AAACCCCAACCCTTAAATAAAAAACACT
1 AACCCTTAA-CTTAAAAACCCTAACCCTTAATTTAAAAACCCT
* * *
31989424 AACCCTTAACTTTAAAACCCTAACCCTTAACTTTAAAAATCTT
1 AACCCTTAACTTAAAAACCCTAACCCTTAA-TTTAAAAACCCT
*
31989467 AACTCTTAACTTAAAAACCCTAAACCCTTAATTTAAAAACCCT
1 AACCCTTAACTTAAAAACCCT-AACCCTTAATTTAAAAACCCT
* * * *
31989510 AACCCTAAAACCT--AAACCCTAACCCTTAA-ATAAAAACACT
1 AACCCT-TAACTTAAAAACCCTAACCCTTAATTTAAAAACCCT
* *
31989550 AACCCTTAACTTAAAAACCCTAACTCTTAACTTT-AAAATCCT
1 AACCCTTAACTTAAAAACCCTAACCCTTAA-TTTAAAAACCCT
*
31989592 AAACCCTTAACTTAAAAA-CCTAAAACCCTTAACTTAAAAACCCT
1 -AACCCTTAACTTAAAAACCCT--AACCCTTAATTTAAAAACCCT
* *
31989636 AACCTTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACC
1 AACCCTTAACTTAAAAACCCT-AACCCTTAATTTAAAAACC
31989677 ATAAACTATT
Statistics
Matches: 355, Mismatches: 46, Indels: 41
0.80 0.10 0.09
Matches are distributed among these distances:
39 4 0.01
40 18 0.05
41 48 0.14
42 101 0.28
43 135 0.38
44 49 0.14
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (42 bp):
AACCCTTAACTTAAAAACCCTAACCCTTAATTTAAAAACCCT
Found at i:31989411 original size:127 final size:125
Alignment explanation
Indices: 31989209--31989675 Score: 562
Period size: 127 Copynumber: 3.7 Consensus size: 125
31989199 CAGGATAAAT
* *
31989209 CCTAAACCCTTAACTTAAAACCCTAAACTCTTAACTTAAAAACCCTAACCCTTAACTTAAAACTC
1 CCTAAACCCTTAACTTAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAAACTTAAAAC-C
* * * * * * *
31989274 TAAACTCTTAATTTAAAAACCCTAATCCTTAATTTAAAAACCATAACCCTTAAATTTAAAAC
65 CAAACCCTTAA-TTAAAAACACTAACCCTTAATTTAAAAACCCTAACCCTTAACTTTAAAAA
* * *
31989336 CCTAAACCCTTAACTTAAAACCCTTTAACCCTTAACCTAAAAACCATAACCCTAAACCTT-AAAC
1 CCTAAACCCTTAACTTAAAACCC-TAAACCCTTAACTTAAAAACCCTAACCCTAAA-CTTAAAAC
* *
31989400 CCCAACCCTTAAATAAAAAACACTAACCCTTAACTTT-AAAACCCTAACCCTTAACTTTAAAAA
64 CCAAACCCTT-AATTAAAAACACTAACCCTTAA-TTTAAAAACCCTAACCCTTAACTTTAAAAA
* * * * *
31989463 TCTTAACTCTTAACTTAAAAACCCTAAACCCTTAATTTAAAAACCCTAACCCTAAAACCT-AAAC
1 CCTAAACCCTTAACTT-AAAACCCTAAACCCTTAACTTAAAAACCCTAACCCT-AAACTTAAAAC
* * * * *
31989527 CCTAACCCTTAAATAAAAACACTAACCCTTAACTTAAAAACCCTAACTCTTAACTTTAAAAT
64 CCAAACCCTTAATTAAAAACACTAACCCTTAATTTAAAAACCCTAACCCTTAACTTTAAAAA
* * *
31989589 CCTAAACCCTTAACTTAAAAACCTAAAACCCTTAACTTAAAAACCCTAACCTTTAACTTAAAAAC
1 CCTAAACCCTTAACTTAAAACCCT-AAACCCTTAACTTAAAAACCCTAACCCTAAACTT-AAAAC
31989654 CCTAAACCCTTAACTTAAAAAC
64 CC-AAACCCTTAA-TTAAAAAC
31989676 CATAAACTAT
Statistics
Matches: 290, Mismatches: 38, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
125 13 0.04
126 83 0.29
127 129 0.44
128 55 0.19
129 10 0.03
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (125 bp):
CCTAAACCCTTAACTTAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAAACTTAAAACCC
AAACCCTTAATTAAAAACACTAACCCTTAATTTAAAAACCCTAACCCTTAACTTTAAAAA
Found at i:31989914 original size:127 final size:127
Alignment explanation
Indices: 31989688--31990060 Score: 590
Period size: 127 Copynumber: 3.0 Consensus size: 127
31989678 TAAACTATTT
*
31989688 GCATCCTGCTTGAAGCGTTCTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTC
1 GCATCCTGCTTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTC
*
31989753 CAGGACCTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATA
66 CAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-A
*
31989815 GCATCCTGCTTGAAGTGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTC
1 GCATCCTGCTTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTC
*
31989880 TAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAA
66 CAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAA
* * * *
31989942 GCATTCTGCTTGAAGCG-TTTTTTATACTATTTTCTTAGAAACGTCAACTCGAAATTATTT-TTC
1 GCATCCTGCTTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTC
* * * * * *
31990005 CAGGACCTACTGTAGCAAAAGCGCGTACGCGTGGGCGCGACTTCAGAAATCCTTCT
66 CAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCT
31990061 TGTCGAAACC
Statistics
Matches: 229, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
125 52 0.23
126 40 0.17
127 135 0.59
128 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (127 bp):
GCATCCTGCTTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTC
CAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAA
Found at i:31991181 original size:18 final size:16
Alignment explanation
Indices: 31991150--31991185 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
31991140 ATGCTCCTAT
31991150 ATAAATAAATATAATA
1 ATAAATAAATATAATA
31991166 ATAATATAACATATAATA
1 ATAA-ATAA-ATATAATA
31991184 AT
1 AT
31991186 GAACTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 4 0.22
18 10 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAATAAATATAATA
Found at i:31992418 original size:9 final size:9
Alignment explanation
Indices: 31992401--31992430 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
31992391 TTTTTTCTCC
31992401 AAAACCCTA
1 AAAACCCTA
*
31992410 AAAATCCTA
1 AAAACCCTA
31992419 AAAACCCTA
1 AAAACCCTA
31992428 AAA
1 AAA
31992431 TCAAAAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAACCCTA
Found at i:32004141 original size:123 final size:123
Alignment explanation
Indices: 32003905--32004320 Score: 557
Period size: 125 Copynumber: 3.3 Consensus size: 123
32003895 ATGGACGCGG
* * * *
32003905 AGAATTTGTGAAATCGTGCCCTCTTGGACACGCTTTTGCTACAGTTGGTCCTGGAAAAAATAATT
1 AGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGG-AAAAATAATT
* * * *
32003970 TTGAGTTGACGTTTCTTAGCAAATAGTATAAAATCGCTTCTACTAGGATGCTCTAAGAGA
65 TCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAC-AGGATGCTATATGAGA
* * * *
32004030 AGAATTTGTTAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GTAAAATTATTT
1 AGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAAAATAATTT
* * *
32004094 CGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATTTGAGA
66 CGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA-CAGGATGCTATATGAGA
* *
32004153 AGAATTTCTGAAATCGCG-CCATCGTGGACGCGCTTTTGCTATAGTTGGTCCTGGAAGAAATAAT
1 AGAATTTGTGAAATCGCGCCCA-CGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAA-AAATAAT
* * *
32004217 TTCGAGTTGACATTTCTGAGCAAATAGTATAAAATTGCTTCTACCAGGATGCTTTATGAGA
64 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA-CAGGATGCTATATGAGA
* * *
32004278 AGAATTTGTGAAATCGCACCCACGTGGACGTGATTTTGCTACA
1 AGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACA
32004321 ATAGCATGTT
Statistics
Matches: 253, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
122 3 0.01
123 103 0.41
124 4 0.02
125 140 0.55
126 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (123 bp):
AGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAAAATAATTT
CGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACAGGATGCTATATGAGA
Found at i:32005944 original size:40 final size:40
Alignment explanation
Indices: 32005889--32005969 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
32005879 GTGTCAAGTG
* * *
32005889 CTAGAGAGATACGTCCCAGGTGCCATCACAGACCTTGAAA
1 CTAGAAAGATACGTCCCAAGTGCCATCACAGACCTTAAAA
*
32005929 CTAGAAAGATACGTCCCAAGTGTCATCACAGACCTTAAAA
1 CTAGAAAGATACGTCCCAAGTGCCATCACAGACCTTAAAA
32005969 C
1 C
32005970 GGAACATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (40 bp):
CTAGAAAGATACGTCCCAAGTGCCATCACAGACCTTAAAA
Found at i:32007513 original size:9 final size:9
Alignment explanation
Indices: 32007495--32007526 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
32007485 ATTCTCAAAT
32007495 AATA-TCAA
1 AATATTCAA
32007503 AATATTCAA
1 AATATTCAA
32007512 AATATTCAA
1 AATATTCAA
32007521 AATATT
1 AATATT
32007527 TGTACAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (9 bp):
AATATTCAA
Found at i:32025802 original size:42 final size:42
Alignment explanation
Indices: 32025703--32025865 Score: 184
Period size: 42 Copynumber: 3.9 Consensus size: 42
32025693 TTTTACAAGA
*
32025703 TGTGTATCAGCGAAGCTCCCTACGTGAGCTTAAGTGATAAGC
1 TGTGTATCAGCGAAGCTCCCTACGTGAGCTTAAGTGATAAGT
* * ** * * * *
32025745 TGT-TATTAGCAAAGCTCTTTACGTAAGCTTAAATGTTAAAT
1 TGTGTATCAGCGAAGCTCCCTACGTGAGCTTAAGTGATAAGT
* *
32025786 TGTGTATTAGCGAAGCTCCCTATGTGAGCTTAAGTGATAAGT
1 TGTGTATCAGCGAAGCTCCCTACGTGAGCTTAAGTGATAAGT
* * * *
32025828 TGTGTATCAGTGAAGCTCCCCATGTGAGTTTAAGTGAT
1 TGTGTATCAGCGAAGCTCCCTACGTGAGCTTAAGTGAT
32025866 TGTGCTCCTC
Statistics
Matches: 99, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
41 32 0.32
42 67 0.68
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (42 bp):
TGTGTATCAGCGAAGCTCCCTACGTGAGCTTAAGTGATAAGT
Found at i:32028031 original size:26 final size:24
Alignment explanation
Indices: 32027954--32028031 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 24
32027944 TTTCTCATCC
*
32027954 CAATTTTACCGCAGTAAAATTTTGA
1 CAATTTTACC-CCGTAAAATTTTGA
** *
32027979 TGATTTTACCATCCGGTAAAGTTTTGA
1 CAATTTTACC--CC-GTAAAATTTTGA
32028006 CAATTTTACCCCTGATAAAATTTTGA
1 CAATTTTACCCC-G-TAAAATTTTGA
32028032 GAAAATTCGT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
25 11 0.27
26 11 0.27
27 19 0.46
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (24 bp):
CAATTTTACCCCGTAAAATTTTGA
Found at i:32032594 original size:12 final size:12
Alignment explanation
Indices: 32032568--32032627 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
32032558 CTTTTTCACT
*
32032568 TTCAA-TCACTA
1 TTCAATTCAATA
32032579 TTCAATTCAATA
1 TTCAATTCAATA
* * *
32032591 TTCACTTTGCCATT
1 TTCA-ATT-CAATA
*
32032605 TTCAAGTCAATA
1 TTCAATTCAATA
32032617 TTCAATTCAAT
1 TTCAATTCAAT
32032628 TCCACACATA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
11 5 0.14
12 22 0.59
13 3 0.08
14 7 0.19
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (12 bp):
TTCAATTCAATA
Found at i:32032953 original size:51 final size:50
Alignment explanation
Indices: 32032834--32033060 Score: 251
Period size: 51 Copynumber: 4.5 Consensus size: 50
32032824 CATGTAGAAT
* * *
32032834 CCTTCACATAGTACTACACACGTGATCAAG-TTTTACGGTTCACGTAGTAG
1 CCTTCACATAGTACTACACACGTGACCAAGCTTTT-CGGTACACATAGTAG
*
32032884 CCTTTACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAG
1 CCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTACACATAGTAG
* * *
32032935 CCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAG
1 CCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTACACATAGTAG
* * * * * * *
32032986 CCTTCACTTTGTACTACACATGTGACC-ATCATTTATCGATTCACGTAGTAG
1 CCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTACACATAGTAG
* *
32033037 CCTTCACACAGTACTGCACACGTG
1 CCTTCACATAGTACTACACACGTG
32033061 TTCATCGATA
Statistics
Matches: 150, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
49 2 0.01
50 27 0.18
51 117 0.78
52 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (50 bp):
CCTTCACATAGTACTACACACGTGACCAAGCTTTTCGGTACACATAGTAG
Found at i:32034488 original size:12 final size:12
Alignment explanation
Indices: 32034471--32034500 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
32034461 AACCTTTGGT
32034471 TGAAGATGACAA
1 TGAAGATGACAA
32034483 TGAAGATGACAA
1 TGAAGATGACAA
32034495 TGAAGA
1 TGAAGA
32034501 AGCAACTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.27, T:0.17
Consensus pattern (12 bp):
TGAAGATGACAA
Found at i:32037828 original size:9 final size:9
Alignment explanation
Indices: 32037804--32037847 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
32037794 CAAACAAAAC
*
32037804 TTGAGAAAA
1 TTGAGAGAA
32037813 TTGAGAGAA
1 TTGAGAGAA
*
32037822 TTGAGAGAG
1 TTGAGAGAA
*
32037831 CTGAGAGAA
1 TTGAGAGAA
*
32037840 TAGAGAGA
1 TTGAGAGA
32037848 GTTGGATTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.45, C:0.02, G:0.34, T:0.18
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:32037835 original size:18 final size:18
Alignment explanation
Indices: 32037814--32037848 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32037804 TTGAGAAAAT
*
32037814 TGAGAGAATTGAGAGAGC
1 TGAGAGAATAGAGAGAGC
32037832 TGAGAGAATAGAGAGAG
1 TGAGAGAATAGAGAGAG
32037849 TTGGATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.40, T:0.14
Consensus pattern (18 bp):
TGAGAGAATAGAGAGAGC
Done.