Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold293
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: 1704560
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 7 of 12
Found at i:914126 original size:24 final size:23
Alignment explanation
Indices: 914099--914144 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
914089 ATTTGAATAA
*
914099 TAAAATATTAAAAATTTAAAATTT
1 TAAAATATGAAAAA-TTAAAATTT
*
914123 TAAAATATGAATAATTAAAATT
1 TAAAATATGAAAAATTAAAATT
914145 CAATTAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAAATATGAAAAATTAAAATTT
Found at i:915119 original size:28 final size:28
Alignment explanation
Indices: 915075--915133 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
915065 ACGGTATGAT
*
915075 ACGATTACAACACGAATAACATGAAAAC
1 ACGATTACAACACGAATAACACGAAAAC
* * *
915103 ACGATTA-AGACATGAATTATACGAAAAC
1 ACGATTACA-ACACGAATAACACGAAAAC
915131 ACG
1 ACG
915134 CTCAGGACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.17
Consensus pattern (28 bp):
ACGATTACAACACGAATAACACGAAAAC
Found at i:918561 original size:14 final size:14
Alignment explanation
Indices: 918542--918572 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
918532 AGAAATGTTG
*
918542 AAATTTATATAATA
1 AAATTTAAATAATA
918556 AAATTTAAATAATA
1 AAATTTAAATAATA
918570 AAA
1 AAA
918573 AAAATTATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATTTAAATAATA
Found at i:919743 original size:11 final size:11
Alignment explanation
Indices: 919727--919751 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
919717 ATACCACTAA
919727 TTAATCGTGTC
1 TTAATCGTGTC
919738 TTAATCGTGTC
1 TTAATCGTGTC
919749 TTA
1 TTA
919752 TGCGTGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (11 bp):
TTAATCGTGTC
Found at i:922781 original size:12 final size:13
Alignment explanation
Indices: 922714--922790 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 13
922704 TATATATATT
922714 TATTTTTTA--AA
1 TATTTTTTATTAA
922725 TATGTTTTTCATTTAA
1 TAT-TTTTT-A-TTAA
* *
922741 TATTTAATAATTAAA
1 TATTT-TTTATT-AA
922756 TATATTTTTATTAA
1 TAT-TTTTTATTAA
*
922770 -ATTTTTTGTTAA
1 TATTTTTTATTAA
922782 TATTTTTTA
1 TATTTTTTA
922791 AAAAATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
11 3 0.06
12 14 0.27
13 10 0.20
14 4 0.08
15 12 0.24
16 8 0.16
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (13 bp):
TATTTTTTATTAA
Found at i:922892 original size:20 final size:21
Alignment explanation
Indices: 922862--922909 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
922852 AATCATTATT
922862 ATTATTATTAC-AAAATATATA
1 ATTATTATTACTAAAATATA-A
922883 ATTA-TATTACTAAAATATAA
1 ATTATTATTACTAAAATATAA
922903 ATT-TTAT
1 ATTATTAT
922910 AATAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTATTACTAAAATATAA
Found at i:923638 original size:18 final size:18
Alignment explanation
Indices: 923615--923650 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
923605 TTTATTAAAA
923615 ATATAATTAAAAATTAAT
1 ATATAATTAAAAATTAAT
* *
923633 ATATAATTTATAATTAAT
1 ATATAATTAAAAATTAAT
923651 TAAAGTTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATTAAAAATTAAT
Found at i:924420 original size:2 final size:2
Alignment explanation
Indices: 924413--924458 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
924403 TCTCGATCAA
924413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
924455 -T AT A
1 AT AT A
924459 ATCAAAGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:925656 original size:2 final size:2
Alignment explanation
Indices: 925649--925677 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
925639 TTGTATAATA
925649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
925678 GGGTTTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:925940 original size:14 final size:15
Alignment explanation
Indices: 925923--925955 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
925913 TGTTATATAA
925923 ATTTTTATT-TATTT
1 ATTTTTATTATATTT
925937 ATTTTTATTATATTT
1 ATTTTTATTATATTT
925952 -TTTT
1 ATTTT
925956 ATCGTATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTTATTATATTT
Found at i:926901 original size:15 final size:17
Alignment explanation
Indices: 926863--926902 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
926853 TTAAAAATAA
926863 ATTA-TTTTTAGTTTAG
1 ATTATTTTTTAGTTTAG
926879 ATTATTTTTTA-TTTA-
1 ATTATTTTTTAGTTTAG
*
926894 ATTCTTTTT
1 ATTATTTTT
926903 AAATTTGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 8 0.36
16 8 0.36
17 6 0.27
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (17 bp):
ATTATTTTTTAGTTTAG
Found at i:927467 original size:5 final size:5
Alignment explanation
Indices: 927457--927487 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
927447 ATACCATGCC
927457 CATTT CATTT CATTT CATTT CATTT CATTT C
1 CATTT CATTT CATTT CATTT CATTT CATTT C
927488 TTTGTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (5 bp):
CATTT
Found at i:930440 original size:3 final size:3
Alignment explanation
Indices: 930432--930471 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
930422 AATTGCTTCA
930432 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
930472 TATGAAATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:930855 original size:17 final size:18
Alignment explanation
Indices: 930834--930879 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
930824 AATATAGTAA
930834 ATATTTAATAAA-AATAT
1 ATATTTAATAAATAATAT
*
930851 GTATTTAACTAAATAATAT
1 ATATTTAA-TAAATAATAT
*
930870 ATCTTTAATA
1 ATATTTAATA
930880 TAGATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.29
18 6 0.25
19 11 0.46
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATATTTAATAAATAATAT
Found at i:932043 original size:11 final size:11
Alignment explanation
Indices: 932027--932092 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 11
932017 ACATGAATAA
932027 TTATATTTATT
1 TTATATTTATT
*
932038 TTATATTTATA
1 TTATATTTATT
932049 TTAT-TATT-TT
1 TTATAT-TTATT
932059 TTATCATATTATT
1 TTAT-AT-TTATT
*
932072 TTATA-ATATT
1 TTATATTTATT
932082 TTA-A-TTATT
1 TTATATTTATT
932091 TT
1 TT
932093 TTCATATGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
9 7 0.15
10 13 0.28
11 16 0.34
12 5 0.11
13 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATTTATT
Found at i:932070 original size:23 final size:21
Alignment explanation
Indices: 932034--932084 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
932024 TAATTATATT
*
932034 TATTTTATATTTATATTATTA
1 TATTTTATATTTATATTATAA
* *
932055 TTTTTTATCATATTATTTTATAA
1 TATTTTAT-AT-TTATATTATAA
932078 TATTTTA
1 TATTTTA
932085 ATTATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 7 0.29
22 2 0.08
23 15 0.62
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTATATTTATATTATAA
Found at i:932075 original size:13 final size:12
Alignment explanation
Indices: 932027--932084 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 12
932017 ACATGAATAA
932027 TTATAT-TTATT
1 TTATATATTATT
*
932038 TTATAT-TTATA
1 TTATATATTATT
932049 TTAT-TATT-TT
1 TTATATATTATT
932059 TTATCATATTATT
1 TTAT-ATATTATT
932072 TTATA-A-TATT
1 TTATATATTATT
932082 TTA
1 TTA
932085 ATTATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
10 13 0.32
11 17 0.41
12 5 0.12
13 6 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATATTATT
Found at i:936283 original size:169 final size:169
Alignment explanation
Indices: 936004--936344 Score: 682
Period size: 169 Copynumber: 2.0 Consensus size: 169
935994 AATCTAGAGA
936004 AAGAAATTTGAAGTCCAAAAGCTTGCCCTGAAATAATTTATTACAATCTATTCAAGATGGAAATT
1 AAGAAATTTGAAGTCCAAAAGCTTGCCCTGAAATAATTTATTACAATCTATTCAAGATGGAAATT
936069 TATCAATTGTTTAAAATAAGTATCAAATGGTTGACTTAGCTCTATTGTTATCAAGGGCACAAGGT
66 TATCAATTGTTTAAAATAAGTATCAAATGGTTGACTTAGCTCTATTGTTATCAAGGGCACAAGGT
936134 GCACTCTGGGCACTAGAACCCTTATATTGCCTAAGGAGC
131 GCACTCTGGGCACTAGAACCCTTATATTGCCTAAGGAGC
936173 AAGAAATTTGAAGTCCAAAAGCTTGCCCTGAAATAATTTATTACAATCTATTCAAGATGGAAATT
1 AAGAAATTTGAAGTCCAAAAGCTTGCCCTGAAATAATTTATTACAATCTATTCAAGATGGAAATT
936238 TATCAATTGTTTAAAATAAGTATCAAATGGTTGACTTAGCTCTATTGTTATCAAGGGCACAAGGT
66 TATCAATTGTTTAAAATAAGTATCAAATGGTTGACTTAGCTCTATTGTTATCAAGGGCACAAGGT
936303 GCACTCTGGGCACTAGAACCCTTATATTGCCTAAGGAGC
131 GCACTCTGGGCACTAGAACCCTTATATTGCCTAAGGAGC
936342 AAG
1 AAG
936345 GCGCAAAAAG
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 172 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (169 bp):
AAGAAATTTGAAGTCCAAAAGCTTGCCCTGAAATAATTTATTACAATCTATTCAAGATGGAAATT
TATCAATTGTTTAAAATAAGTATCAAATGGTTGACTTAGCTCTATTGTTATCAAGGGCACAAGGT
GCACTCTGGGCACTAGAACCCTTATATTGCCTAAGGAGC
Found at i:940353 original size:25 final size:26
Alignment explanation
Indices: 940325--940378 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
940315 TTGTGTACCT
* *
940325 ATTTTTAAG-AGATAGTTTTAAGTAA
1 ATTTTAAAGTAGATAATTTTAAGTAA
940350 A-TTTAAAGTAGATAATTTTAAGTAA
1 ATTTTAAAGTAGATAATTTTAAGTAA
940375 ATTT
1 ATTT
940379 AGAGTTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 17 0.68
26 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (26 bp):
ATTTTAAAGTAGATAATTTTAAGTAA
Found at i:941674 original size:2 final size:2
Alignment explanation
Indices: 941667--941693 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
941657 TTATACATAC
941667 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
941694 CATTATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:943262 original size:20 final size:19
Alignment explanation
Indices: 943233--943270 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
943223 TTAAGATCTG
943233 TATTTAATTTTATTAAATTT
1 TATTTAATTTT-TTAAATTT
*
943253 TATTTTATTTTTTAAATT
1 TATTTAATTTTTTAAATT
943271 AAATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTAATTTTTTAAATTT
Found at i:943566 original size:21 final size:22
Alignment explanation
Indices: 943529--943572 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
943519 TCTTTATATC
*
943529 TATAAATTTTTATTATTTTAAA
1 TATAAATTTTTATTATTATAAA
*
943551 TATATATTTTTA-TATTATAAA
1 TATAAATTTTTATTATTATAAA
943572 T
1 T
943573 TTTTACAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATAAATTTTTATTATTATAAA
Found at i:943639 original size:12 final size:13
Alignment explanation
Indices: 943621--943658 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
943611 AAATTTATTA
943621 AACCATATTTTTT
1 AACCATATTTTTT
943634 -ACCATATTTTTT
1 AACCATATTTTTT
*
943646 AAACATATTTTTT
1 AACCATATTTTTT
943659 TTAACTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (13 bp):
AACCATATTTTTT
Found at i:943652 original size:13 final size:13
Alignment explanation
Indices: 943613--943658 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
943603 AATACTTAAA
*
943613 ATTTATTAAACCAT
1 ATTTTTTAAA-CAT
*
943627 ATTTTTT-ACCAT
1 ATTTTTTAAACAT
943639 ATTTTTTAAACAT
1 ATTTTTTAAACAT
943652 ATTTTTT
1 ATTTTTT
943659 TTAACTCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.36
13 12 0.43
14 6 0.21
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTTTTAAACAT
Found at i:944296 original size:11 final size:11
Alignment explanation
Indices: 944264--944304 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
944254 AACTTAAAAA
*
944264 AATATATATA-
1 AATATAAATAT
*
944274 AATTTAAA-AT
1 AATATAAATAT
944284 AATATAAATAT
1 AATATAAATAT
944295 AATATAAATA
1 AATATAAATA
944305 CATAAATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
9 1 0.04
10 13 0.50
11 12 0.46
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAAATAT
Found at i:944301 original size:16 final size:16
Alignment explanation
Indices: 944264--944301 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
944254 AACTTAAAAA
*
944264 AATAT-ATATAAATTT
1 AATATAATATAAATAT
*
944279 AAAATAATATAAATAT
1 AATATAATATAAATAT
944295 AATATAA
1 AATATAA
944302 ATACATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATAATATAAATAT
Found at i:945063 original size:21 final size:20
Alignment explanation
Indices: 945033--945073 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
945023 TATTATTATT
945033 CAATA-TTTTTAATTACAATA
1 CAATATTTTTTAATT-CAATA
945053 CAATAATTTTTTAATTCAATA
1 CAAT-ATTTTTTAATTCAATA
945074 ATGAAGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 9 0.47
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
CAATATTTTTTAATTCAATA
Found at i:945372 original size:3 final size:3
Alignment explanation
Indices: 945366--945390 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
945356 TATTCAAAAG
945366 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
945391 CTATAACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:945504 original size:23 final size:26
Alignment explanation
Indices: 945478--945528 Score: 81
Period size: 23 Copynumber: 2.1 Consensus size: 26
945468 AAATTGAATT
945478 ATACTAAATA-T-TTTTTTT-AAATA
1 ATACTAAATATTATTTTTTTAAAATA
945501 ATACTAAATATTATTTTTTTAAAATA
1 ATACTAAATATTATTTTTTTAAAATA
945527 AT
1 AT
945529 TTTTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 10 0.40
24 1 0.04
25 7 0.28
26 7 0.28
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
ATACTAAATATTATTTTTTTAAAATA
Found at i:945682 original size:25 final size:25
Alignment explanation
Indices: 945654--945733 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
945644 TTAAAACATG
945654 ACAAACACAAAATAGCATGAATAGT
1 ACAAACACAAAATAGCATGAATAGT
* * ** * * *
945679 ACAAAAATATGATA--ATTAAAACAT
1 ACAAACACAAAATAGCATGAATA-GT
945703 GACAAACACAAAATAGCATGAATAGT
1 -ACAAACACAAAATAGCATGAATAGT
945729 ACAAA
1 ACAAA
945734 AATATGTAAA
Statistics
Matches: 37, Mismatches: 14, Indels: 8
0.63 0.24 0.14
Matches are distributed among these distances:
23 5 0.14
24 1 0.03
25 25 0.68
26 1 0.03
27 5 0.14
ACGTcount: A:0.59, C:0.14, G:0.10, T:0.17
Consensus pattern (25 bp):
ACAAACACAAAATAGCATGAATAGT
Found at i:945696 original size:50 final size:50
Alignment explanation
Indices: 945640--945739 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
945630 ATATGAAAAA
945640 ATAATTAAAACATGACAAACACAAAATAGCATGAATAGTACAAAAATATG
1 ATAATTAAAACATGACAAACACAAAATAGCATGAATAGTACAAAAATATG
945690 ATAATTAAAACATGACAAACACAAAATAGCATGAATAGTACAAAAATATG
1 ATAATTAAAACATGACAAACACAAAATAGCATGAATAGTACAAAAATATG
945740 TAAATATATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.58, C:0.12, G:0.10, T:0.20
Consensus pattern (50 bp):
ATAATTAAAACATGACAAACACAAAATAGCATGAATAGTACAAAAATATG
Found at i:946317 original size:14 final size:13
Alignment explanation
Indices: 946284--946313 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
946274 CGACATAAAC
*
946284 ATAACATAAAAAA
1 ATAATATAAAAAA
946297 ATAATATAAAAAA
1 ATAATATAAAAAA
946310 ATAA
1 ATAA
946314 ATATGATACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAATATAAAAAA
Found at i:948401 original size:34 final size:34
Alignment explanation
Indices: 948355--948419 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
948345 AAAGTGATTG
* *
948355 AGAAGTTCTATCTTAGCCTTTGAAAAAATAGGAA
1 AGAAGTTCTATCTTAACCTTCGAAAAAATAGGAA
* *
948389 AGAAGTTTTATCTTAACCTTCGAAAAGATAG
1 AGAAGTTCTATCTTAACCTTCGAAAAAATAG
948420 TATTATAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (34 bp):
AGAAGTTCTATCTTAACCTTCGAAAAAATAGGAA
Found at i:948592 original size:17 final size:17
Alignment explanation
Indices: 948570--948604 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
948560 TCTTACCCTT
948570 ACTCTCTTTATTATTCG
1 ACTCTCTTTATTATTCG
948587 ACTCTCTTTATTATTCG
1 ACTCTCTTTATTATTCG
948604 A
1 A
948605 TTTGTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.06, T:0.51
Consensus pattern (17 bp):
ACTCTCTTTATTATTCG
Found at i:951487 original size:17 final size:16
Alignment explanation
Indices: 951465--951504 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
951455 ATAAGGTTAA
* *
951465 AATAGTAATTTTCTAT
1 AATAGTAATATTATAT
951481 GAATAGTAATATTATAT
1 -AATAGTAATATTATAT
951498 AATAGTA
1 AATAGTA
951505 TAATTAGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (16 bp):
AATAGTAATATTATAT
Found at i:951571 original size:21 final size:21
Alignment explanation
Indices: 951547--951588 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
951537 AAATCTGATG
*
951547 ATAATGTATTAAATATAAAAA
1 ATAATATATTAAATATAAAAA
* *
951568 ATAATATTTTAAATATCAAAA
1 ATAATATATTAAATATAAAAA
951589 TTTATATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAATATATTAAATATAAAAA
Found at i:951598 original size:20 final size:21
Alignment explanation
Indices: 951555--951597 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
951545 TGATAATGTA
951555 TTAAATATAAAAAATAATATT
1 TTAAATATAAAAAATAATATT
* * *
951576 TTAAATATCAAAATTTATATT
1 TTAAATATAAAAAATAATATT
951597 T
1 T
951598 ATCTTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAATATAAAAAATAATATT
Found at i:958952 original size:198 final size:198
Alignment explanation
Indices: 958614--959010 Score: 591
Period size: 198 Copynumber: 2.0 Consensus size: 198
958604 TTACTGTTTG
* ** *
958614 TAATAATATTAAAAATATTATTTTTATATTAATATTTATGCATTTTTATAATTAAACTTAAATAA
1 TAATAATATTAAAAATATTATTTTTATATTAATATCTATAAATTTCTATAATTAAACTTAAATAA
*
958679 AAAAAATTTATTATTAAAATAGCAAATCGAGACAGGCTGTGCCTGCTTGAATTTATGAAAACCTT
66 AAAAAATTTATTATTAAAATAGCAAATAGAGACAGGCTGTGCCTGCTTGAATTTATGAAAACCTT
* *
958744 GTCCAAGGCCTGACTTGTACAGGCCGAGCCTT-CTGGGCCAGGCAGGTAGCCCGACAATGTACAG
131 GTCCAAGGCCTGACTTGTACAGGCCG-GCCTTCCTGAGCCAGGCAGGAAGCCCGACAATGTACAG
958808 GTCT
195 GTCT
*
958812 TAATAATATT-AAAATATTATTTTTATATTAATATCTATAAATTTCTATAATTAAATTTAAATAA
1 TAATAATATTAAAAATATTATTTTTATATTAATATCTATAAATTTCTATAATTAAACTTAAATAA
** * * ** * *
958876 AAACATTTTTGTTATTAAAATAGTAAATAGAGATGGGTTGTGCCTGCTTGAATTTATTAAAACCT
66 AAA-AAATTTATTATTAAAATAGCAAATAGAGACAGGCTGTGCCTGCTTGAATTTATGAAAACCT
** *
958941 TGTCCAAGGCCTGACTTGTATGGGCCGGGCTTCCTGAGCCAGGCAGGAAGCCCGACAATGTACAG
130 TGTCCAAGGCCTGACTTGTACAGGCCGGCCTTCCTGAGCCAGGCAGGAAGCCCGACAATGTACAG
959006 GTCT
195 GTCT
959010 T
1 T
959011 CATGACATCT
Statistics
Matches: 178, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
197 56 0.31
198 122 0.69
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (198 bp):
TAATAATATTAAAAATATTATTTTTATATTAATATCTATAAATTTCTATAATTAAACTTAAATAA
AAAAAATTTATTATTAAAATAGCAAATAGAGACAGGCTGTGCCTGCTTGAATTTATGAAAACCTT
GTCCAAGGCCTGACTTGTACAGGCCGGCCTTCCTGAGCCAGGCAGGAAGCCCGACAATGTACAGG
TCT
Found at i:963796 original size:12 final size:12
Alignment explanation
Indices: 963776--963919 Score: 83
Period size: 12 Copynumber: 11.3 Consensus size: 12
963766 GTTGCATACA
*
963776 ACACACACACAC
1 ACACGCACACAC
963788 ACACGCACACAC
1 ACACGCACACAC
* *
963800 ACAGGCACACGC
1 ACACGCACACAC
* *
963812 GCACGTGCACGCAC
1 ACAC--GCACACAC
*
963826 GCACGCACGTACAC
1 ACACGCAC--ACAC
*
963840 A-AGCCCACACAC
1 ACA-CGCACACAC
*
963852 GCACGCATGCACATGC
1 ACACGCA--CACA--C
* **
963868 ACATGCACATGC
1 ACACGCACACAC
963880 ACACGCACACAC
1 ACACGCACACAC
*
963892 ACACACACACAC
1 ACACGCACACAC
*
963904 ACACACACACAC
1 ACACGCACACAC
963916 ACAC
1 ACAC
963920 ACATATATAT
Statistics
Matches: 102, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
12 71 0.70
13 2 0.02
14 23 0.23
16 6 0.06
ACGTcount: A:0.38, C:0.45, G:0.13, T:0.04
Consensus pattern (12 bp):
ACACGCACACAC
Found at i:963868 original size:6 final size:6
Alignment explanation
Indices: 963857--963888 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
963847 CACACGCACG
*
963857 CATGCA CATGCA CATGCA CATGCA CACGCA CA
1 CATGCA CATGCA CATGCA CATGCA CATGCA CA
963889 CACACACACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.38, G:0.16, T:0.12
Consensus pattern (6 bp):
CATGCA
Found at i:963892 original size:2 final size:2
Alignment explanation
Indices: 963879--963922 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
963869 CATGCACATG
*
963879 CA CA CG CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
963921 CA
1 CA
963923 TATATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.50, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:965360 original size:39 final size:41
Alignment explanation
Indices: 965305--965385 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 41
965295 ATTGACAATA
*
965305 AAACTGGGAAACACTGTC-AGATAATCAATGCCAATGGATC
1 AAACTGGGAAACACTGTCAAAATAATCAATGCCAATGGATC
965345 AAACT-GGAAACACTGTCAAAATAATCAATGCCAATGGATC
1 AAACTGGGAAACACTGTCAAAATAATCAATGCCAATGGATC
965385 A
1 A
965386 GTAGTCACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 12 0.31
40 27 0.69
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (41 bp):
AAACTGGGAAACACTGTCAAAATAATCAATGCCAATGGATC
Found at i:973526 original size:24 final size:25
Alignment explanation
Indices: 973499--973551 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
973489 TAATAGATTA
973499 AATTAATTAAAATATATTT-AATTC
1 AATTAATTAAAATATATTTAAATTC
* * *
973523 AATTAATTTATATATTTTTAAATTC
1 AATTAATTAAAATATATTTAAATTC
973548 AATT
1 AATT
973552 TTATTAATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
AATTAATTAAAATATATTTAAATTC
Found at i:974577 original size:14 final size:14
Alignment explanation
Indices: 974545--974575 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
974535 ATATTAAAAG
974545 ATTTAATTATTTTT
1 ATTTAATTATTTTT
974559 ATTTAATTA-TTTT
1 ATTTAATTATTTTT
974572 ATTT
1 ATTT
974576 TATATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTAATTATTTTT
Found at i:975614 original size:17 final size:18
Alignment explanation
Indices: 975574--975615 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
975564 TTATTTTTTA
* *
975574 ATATAAATTATAAAATTT
1 ATATTAATTATAAAATAT
*
975592 AAATTAATTA-AAAATAT
1 ATATTAATTATAAAATAT
975609 ATATTAA
1 ATATTAA
975616 CATTTTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATTAATTATAAAATAT
Found at i:976398 original size:24 final size:23
Alignment explanation
Indices: 976368--976421 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
976358 ATGATATACT
976368 AACAATATCTATAAATAAAAAAATA
1 AACAATAT-T-TAAATAAAAAAATA
* *
976393 AA-AATATTTATATTAAAAAATA
1 AACAATATTTAAATAAAAAAATA
976415 AACAATA
1 AACAATA
976422 AATATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 14 0.54
23 5 0.19
24 5 0.19
25 2 0.08
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (23 bp):
AACAATATTTAAATAAAAAAATA
Found at i:976415 original size:30 final size:28
Alignment explanation
Indices: 976380--976441 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
976370 CAATATCTAT
976380 AAATAAAAAAATAAAAATATTTATATTAAA
1 AAATAAAAAAATAAAAAT-TTTATA-TAAA
* * *
976410 AAAT-AAACAATAAATATTTTTTATAAA
1 AAATAAAAAAATAAAAATTTTATATAAA
976437 AAATA
1 AAATA
976442 TATAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 8 0.29
28 5 0.18
29 11 0.39
30 4 0.14
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (28 bp):
AAATAAAAAAATAAAAATTTTATATAAA
Found at i:976769 original size:15 final size:16
Alignment explanation
Indices: 976744--976776 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
976734 GATAATTTAT
976744 ATTTAATATATTAATA
1 ATTTAATATATTAATA
*
976760 ATTT-ATATATTTATA
1 ATTTAATATATTAATA
976775 AT
1 AT
976777 GAATTAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTAATATATTAATA
Found at i:978049 original size:21 final size:20
Alignment explanation
Indices: 978015--978058 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
978005 TAATTTTTTT
*
978015 AATATTAATAAAAATAATAA
1 AATATTAATAAAAATAAAAA
*
978035 AATATATATTAAAAATAAAAA
1 AATAT-TAATAAAAATAAAAA
978056 AAT
1 AAT
978059 TAGATGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AATATTAATAAAAATAAAAA
Found at i:979626 original size:22 final size:23
Alignment explanation
Indices: 979558--979630 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
979548 CTTAGATTTG
*
979558 ATCATTTTTATAT-TTATATTTAT
1 ATCA-TTTTATATCATATATTTAT
*
979581 AT-ATTTTATATGATATATTGTAT
1 ATCATTTTATATCATATATT-TAT
979604 ATCATTATTAT-TCATA-ATTTAT
1 ATCATT-TTATATCATATATTTAT
979626 ATCAT
1 ATCAT
979631 ATCGATTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
21 8 0.18
22 15 0.34
23 10 0.23
24 7 0.16
25 4 0.09
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (23 bp):
ATCATTTTATATCATATATTTAT
Found at i:993247 original size:40 final size:40
Alignment explanation
Indices: 993192--993271 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
993182 GTAGAGTGTT
993192 AGACTCTTAATTTTAGTGATTAGGGATCAAATACTAGCAA
1 AGACTCTTAATTTTAGTGATTAGGGATCAAATACTAGCAA
993232 AGACTCTTAATTTTAGTGATTAGGGATCAAATACTAGCAA
1 AGACTCTTAATTTTAGTGATTAGGGATCAAATACTAGCAA
993272 CACCAACTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (40 bp):
AGACTCTTAATTTTAGTGATTAGGGATCAAATACTAGCAA
Found at i:993455 original size:66 final size:66
Alignment explanation
Indices: 993349--993482 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
993339 TCAAAAGGGT
*
993349 TTGGCGCTTTGGTTGTCTGGAGCTAAGGTGCATGCCTTAAAAACACTATTGAAACCACTCCTTAA
1 TTGGCGCTTTGGTTGTCTGGAGCTAAGATGCATGCCTTAAAAACACTATTGAAACCACTCCTTAA
993414 C
66 C
993415 TTGGCGCTTTGGTTGTCTGGAGCTAAGATGCATGCCTTAAAAACACTATTGAAACCACTCCTTAA
1 TTGGCGCTTTGGTTGTCTGGAGCTAAGATGCATGCCTTAAAAACACTATTGAAACCACTCCTTAA
993480 C
66 C
993481 TT
1 TT
993483 CTATATTATG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (66 bp):
TTGGCGCTTTGGTTGTCTGGAGCTAAGATGCATGCCTTAAAAACACTATTGAAACCACTCCTTAA
C
Found at i:996543 original size:19 final size:19
Alignment explanation
Indices: 996495--996546 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
996485 ATTAAAATTT
996495 ATATAATT-TAA-ATTATTA
1 ATATAATTATAATATT-TTA
*
996513 ATAT-A-CATAATATTTTA
1 ATATAATTATAATATTTTA
996530 ATATAATTATAATATTT
1 ATATAATTATAATATTT
996547 AAAAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 11 0.39
18 8 0.29
19 9 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATAATTATAATATTTTA
Found at i:999294 original size:32 final size:31
Alignment explanation
Indices: 999254--999313 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
999244 AATTTACCTA
999254 AAACTGAAATGA-ATTAAAACTAAAATGAATC
1 AAACTGAAATGATA-TAAAACTAAAATGAATC
999285 AAACTTGAAATGATATAAAACTAAAATGA
1 AAAC-TGAAATGATATAAAACTAAAATGA
999314 TTTAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 4 0.15
32 22 0.81
33 1 0.04
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.23
Consensus pattern (31 bp):
AAACTGAAATGATATAAAACTAAAATGAATC
Found at i:999312 original size:48 final size:48
Alignment explanation
Indices: 999252--999343 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
999242 TCAATTTACC
*
999252 TAAAACTGAAATGAATTAAAACTAAAATGAATC-AAACTTGAAATGATA
1 TAAAACTAAAATGAATTAAAACTAAAATG-ATCTAAACTTGAAATGATA
* *
999300 TAAAACTAAAATGATTTAAAATTAAAATGATCTAAACTTGAAAT
1 TAAAACTAAAATGAATTAAAACTAAAATGATCTAAACTTGAAAT
999344 TAAAACGACT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 3 0.08
48 37 0.93
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (48 bp):
TAAAACTAAAATGAATTAAAACTAAAATGATCTAAACTTGAAATGATA
Found at i:999328 original size:32 final size:32
Alignment explanation
Indices: 999260--999335 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
999250 CCTAAAACTG
* *
999260 AAATGA-ATTAAAACTAAAATGAATCAAACTTG
1 AAATGATA-TAAAACTAAAATGAATCAAAATTA
* *
999292 AAATGATATAAAACTAAAATGATTTAAAATTA
1 AAATGATATAAAACTAAAATGAATCAAAATTA
*
999324 AAATGATCTAAA
1 AAATGATATAAA
999336 CTTGAAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 37 0.97
33 1 0.03
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.28
Consensus pattern (32 bp):
AAATGATATAAAACTAAAATGAATCAAAATTA
Found at i:999330 original size:16 final size:16
Alignment explanation
Indices: 999252--999335 Score: 80
Period size: 16 Copynumber: 5.2 Consensus size: 16
999242 TCAATTTACC
* *
999252 TAAAACTGAAATGAAT
1 TAAAACTAAAATGATT
*
999268 TAAAACTAAAATGA-A
1 TAAAACTAAAATGATT
* * *
999283 TCAAACTTGAAATGATA
1 TAAAAC-TAAAATGATT
999300 TAAAACTAAAATGATT
1 TAAAACTAAAATGATT
* *
999316 TAAAATTAAAATGATC
1 TAAAACTAAAATGATT
999332 TAAA
1 TAAA
999336 CTTGAAATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
15 5 0.09
16 46 0.81
17 6 0.11
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.27
Consensus pattern (16 bp):
TAAAACTAAAATGATT
Found at i:999343 original size:16 final size:16
Alignment explanation
Indices: 999270--999343 Score: 64
Period size: 16 Copynumber: 4.7 Consensus size: 16
999260 AAATGAATTA
999270 AAAC-TAAAATGAATC-
1 AAACTTAAAATG-ATCT
* *
999285 AAACTTGAAATGATAT
1 AAACTTAAAATGATCT
*
999301 AAAAC-TAAAATGATTT
1 -AAACTTAAAATGATCT
*
999317 AAAATTAAAATGATCT
1 AAACTTAAAATGATCT
*
999333 AAACTTGAAAT
1 AAACTTAAAAT
999344 TAAAACGACT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
15 9 0.19
16 34 0.72
17 4 0.09
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28
Consensus pattern (16 bp):
AAACTTAAAATGATCT
Found at i:999571 original size:14 final size:13
Alignment explanation
Indices: 999538--999571 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
999528 TTTTTTAGCT
999538 AAAAAATTAAAAA
1 AAAAAATTAAAAA
999551 AATAAAATCTAAAAA
1 AA-AAAAT-TAAAAA
999566 AAAAAA
1 AAAAAA
999572 AGGTGCCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 9 0.47
15 8 0.42
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATTAAAAA
Found at i:999572 original size:15 final size:14
Alignment explanation
Indices: 999538--999572 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
999528 TTTTTTAGCT
999538 AAAAAATTAAAAAA
1 AAAAAATTAAAAAA
*
999552 ATAAAATCTAAAAAA
1 AAAAAAT-TAAAAAA
999567 AAAAAA
1 AAAAAA
999573 GGTGCCACGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAATTAAAAAA
Found at i:1000663 original size:10 final size:10
Alignment explanation
Indices: 1000633--1000671 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1000623 CCAAAAAAAA
1000633 TTATATATAT
1 TTATATATAT
*
1000643 ATATATATAT
1 TTATATATAT
*
1000653 TTATTTATAT
1 TTATATATAT
1000663 TTGATATAT
1 TT-ATATAT
1000672 TAATAGGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 19 0.79
11 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
TTATATATAT
Found at i:1001399 original size:29 final size:30
Alignment explanation
Indices: 1001342--1001399 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
1001332 ATGAGTAACT
* * *
1001342 TAATTTATTAATAATAAAATTTTAGTGACA
1 TAATTTAATAATAATAAAATGTTAATGACA
*
1001372 TAATTTAATAA-AATTAAATGTTAATGAC
1 TAATTTAATAATAATAAAATGTTAATGAC
1001400 TCACATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (30 bp):
TAATTTAATAATAATAAAATGTTAATGACA
Found at i:1002603 original size:22 final size:22
Alignment explanation
Indices: 1002562--1002604 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1002552 AAATTTTAAA
*
1002562 ATATTTTTATATTAATATTTAT
1 ATATTTTTAAATTAATATTTAT
1002584 ATATTTTTAAAATTAA-ATTTA
1 ATATTTTT-AAATTAATATTTA
1002605 AATAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTAAATTAATATTTAT
Found at i:1005928 original size:18 final size:18
Alignment explanation
Indices: 1005836--1005929 Score: 54
Period size: 18 Copynumber: 5.3 Consensus size: 18
1005826 CAATTAAATC
* *
1005836 TATTTATTATTAAGATAT-
1 TATTT-TTATTAAAATTTA
*
1005854 TATTTTTACGTTAATATTTA
1 TATTTTTA--TTAAAATTTA
* *
1005874 TATATTT-TTATAATTTA
1 TATTTTTATTAAAATTTA
* *
1005891 -A-TTTAATTAAAA-ATA
1 TATTTTTATTAAAATTTA
1005906 TTATTTTTATTAAAATTTA
1 -TATTTTTATTAAAATTTA
1005925 TATTT
1 TATTT
1005930 AATATATTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
15 4 0.07
16 6 0.11
17 12 0.21
18 20 0.35
19 9 0.16
20 6 0.11
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (18 bp):
TATTTTTATTAAAATTTA
Found at i:1006058 original size:25 final size:25
Alignment explanation
Indices: 1006016--1006064 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1006006 TATTTTTAAA
*
1006016 AATTTTTAATAAAAATATATAATTT
1 AATTTTTAATAAAAATATAAAATTT
*
1006041 AATTTATTAAT-AATATATAAAATT
1 AATTT-TTAATAAAAATATAAAATT
1006065 ATATATTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTTTTAATAAAAATATAAAATTT
Found at i:1010415 original size:13 final size:13
Alignment explanation
Indices: 1010397--1010424 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1010387 GAACATACTG
1010397 AAAACTAAACCTC
1 AAAACTAAACCTC
1010410 AAAACTAAACCTC
1 AAAACTAAACCTC
1010423 AA
1 AA
1010425 CTTACCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAACTAAACCTC
Found at i:1015997 original size:2 final size:2
Alignment explanation
Indices: 1015938--1015978 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1015928 ATGCAGAACC
1015938 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1015979 CCTTTCAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1017508 original size:6 final size:6
Alignment explanation
Indices: 1017481--1017534 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
1017471 ATGCATGCAC
*
1017481 GAAGGG G-AGGG G-AGGA GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
1017527 GAAGGG GA
1 GAAGGG GA
1017535 TCTTCTACCA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
5 9 0.20
6 36 0.80
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:1019111 original size:145 final size:145
Alignment explanation
Indices: 1018842--1019133 Score: 494
Period size: 145 Copynumber: 2.0 Consensus size: 145
1018832 GCAGCTGCAA
* * * *
1018842 TTAATCAAAATCAGAAAAATGGGCATAAGAAATATGACAATGAGAAAAGTTTAAGCAGCTTCTCT
1 TTAATCAAAATCAGAAAAATAGGCAAAAGAAATATGAAAATGAGAAAAATTTAAGCAGCTTCTCT
* * **
1018907 CCTGAAGTGCAAAATTAACTCCTAAAAGAAGCTAGGGTCTTTCACAATCAATATGTAACTTCTCT
66 CCTGAAGTGCAAAATCAACTCCTAAAAGAAGCTAGGGTCCTTCACAATCAATACATAACTTCTCT
1018972 AGGAAAACTTGTAAC
131 AGGAAAACTTGTAAC
*
1018987 TTAATCAAAATGAGAAAAATAGGCAAAAGAAATATGAAAATGAGAAAAATTTAAGCAGCTTCTCT
1 TTAATCAAAATCAGAAAAATAGGCAAAAGAAATATGAAAATGAGAAAAATTTAAGCAGCTTCTCT
*
1019052 CCTGAAGTGCAAAATCAACTCCTAAAAGAAGTTAGGGTCCTTCACAATCAATACATAACTTCTCT
66 CCTGAAGTGCAAAATCAACTCCTAAAAGAAGCTAGGGTCCTTCACAATCAATACATAACTTCTCT
1019117 AGGAAAACTTGTAAC
131 AGGAAAACTTGTAAC
1019132 TT
1 TT
1019134 CCAACAAAAG
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
145 137 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (145 bp):
TTAATCAAAATCAGAAAAATAGGCAAAAGAAATATGAAAATGAGAAAAATTTAAGCAGCTTCTCT
CCTGAAGTGCAAAATCAACTCCTAAAAGAAGCTAGGGTCCTTCACAATCAATACATAACTTCTCT
AGGAAAACTTGTAAC
Found at i:1025259 original size:18 final size:17
Alignment explanation
Indices: 1025232--1025267 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1025222 GTCCCTAATT
1025232 ATTTAATTTTTTATTAAA
1 ATTTAATTTTTT-TTAAA
*
1025250 ATTTATTTTTTTTTAAA
1 ATTTAATTTTTTTTAAA
1025267 A
1 A
1025268 AAACAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTAATTTTTTTTAAA
Found at i:1025268 original size:18 final size:18
Alignment explanation
Indices: 1025232--1025267 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1025222 GTCCCTAATT
1025232 ATTTAATTTTTTATTAAA
1 ATTTAATTTTTTATTAAA
*
1025250 ATTT-ATTTTTTTTTAAA
1 ATTTAATTTTTTATTAAA
1025267 A
1 A
1025268 AAACAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTAATTTTTTATTAAA
Found at i:1027345 original size:6 final size:6
Alignment explanation
Indices: 1027334--1027363 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1027324 CACTTTTGGT
*
1027334 TCTATA TCTATA TCTATA TCTATA TATATA
1 TCTATA TCTATA TCTATA TCTATA TCTATA
1027364 AAATCTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTATA
Found at i:1028549 original size:20 final size:21
Alignment explanation
Indices: 1028511--1028569 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
1028501 TTTTATTAAA
* *
1028511 TAATTTAAGAAATAATATTTTT
1 TAATTTAA-TAATAATATTATT
*
1028533 TATTTTAATAA-AATATTATT
1 TAATTTAATAATAATATTATT
*
1028553 TAATTTATTAATAATAT
1 TAATTTAATAATAATAT
1028570 ATAAATTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 17 0.55
21 7 0.23
22 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TAATTTAATAATAATATTATT
Found at i:1028776 original size:2 final size:2
Alignment explanation
Indices: 1028769--1028806 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1028759 GCAGCCCTCC
1028769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1028807 TTAGATTCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1028981 original size:25 final size:24
Alignment explanation
Indices: 1028953--1028999 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
1028943 ATATTTTATT
1028953 AAAATTTAATTTAAAATATAAATAA
1 AAAATTTAATTTAAAAT-TAAATAA
*
1028978 AAAATTTTATTTAAAATTAAAT
1 AAAATTTAATTTAAAATTAAAT
1029000 TTGATCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATTTAATTTAAAATTAAATAA
Found at i:1029043 original size:20 final size:23
Alignment explanation
Indices: 1029004--1029060 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 23
1028994 TTAAATTTGA
1029004 TCATATAAAATTATCATTTAAAC
1 TCATATAAAATTATCATTTAAAC
*
1029027 TCATAT-AAA-TA-CATTTAAAT
1 TCATATAAAATTATCATTTAAAC
*
1029047 TTATATATAAATTA
1 TCATATA-AAATTA
1029061 ATTTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 13 0.45
21 2 0.07
22 6 0.21
23 8 0.28
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
TCATATAAAATTATCATTTAAAC
Found at i:1033704 original size:8 final size:8
Alignment explanation
Indices: 1033686--1033732 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
1033676 TTTTATTAAT
1033686 TATATAAA
1 TATATAAA
1033694 TATA-AATA
1 TATATAA-A
1033702 TATTATAAA
1 TA-TATAAA
* *
1033711 TTTTTAAA
1 TATATAAA
1033719 TATATAAA
1 TATATAAA
1033727 TATATA
1 TATATA
1033733 TTAATTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
7 2 0.06
8 24 0.75
9 4 0.12
10 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TATATAAA
Found at i:1033736 original size:19 final size:19
Alignment explanation
Indices: 1033679--1033759 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 19
1033669 TTAAATTTTT
*
1033679 TATTAATTATATAAATATA
1 TATTAAATATATAAATATA
* *
1033698 -AATATAT-TATAAAT-T-
1 TATTAAATATATAAATATA
1033713 T-TTAAATATATAAATATA
1 TATTAAATATATAAATATA
* *
1033731 TATTAATTATATTAATA-A
1 TATTAAATATATAAATATA
1033749 TATTTAAATAT
1 TA-TTAAATAT
1033760 GTTACATCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
15 4 0.08
16 8 0.17
17 8 0.17
18 8 0.17
19 20 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTAAATATATAAATATA
Found at i:1034020 original size:2 final size:2
Alignment explanation
Indices: 1034015--1034054 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1034005 AAAACAGTTT
*
1034015 TA TA TA TA TA TA TA TA TA -A TA TA AA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1034055 TTTTTCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1037853 original size:16 final size:16
Alignment explanation
Indices: 1037832--1037890 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
1037822 AGACAGTGAT
1037832 GAAGAAAAGAAGAAGA
1 GAAGAAAAGAAGAAGA
1037848 GAAGAAAAGATA-AAGA
1 GAAGAAAAGA-AGAAGA
* *
1037864 GAACAAAGAGGAAGAAAA
1 GAAGAAA-A-GAAGAAGA
*
1037882 TAAGAAAAG
1 GAAGAAAAG
1037891 CGATGGCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 21 0.60
17 4 0.11
18 10 0.29
ACGTcount: A:0.68, C:0.02, G:0.27, T:0.03
Consensus pattern (16 bp):
GAAGAAAAGAAGAAGA
Found at i:1040434 original size:23 final size:23
Alignment explanation
Indices: 1040391--1040434 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1040381 ATAACCATAT
* *
1040391 AATAATTTATTTTTATTTTATAA
1 AATAATTTATTTTAATATTATAA
1040414 AATAATTT-TTTATAATATTAT
1 AATAATTTATTT-TAATATTAT
1040435 TTTATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATAATTTATTTTAATATTATAA
Found at i:1040550 original size:23 final size:23
Alignment explanation
Indices: 1040503--1040550 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1040493 TATAATTATT
* *
1040503 TTAAAAGATTTATATTTTATTTA
1 TTAAAAGATTTAAATTTTATATA
1040526 TTAAAA-ATTTAAATTTTATAATA
1 TTAAAAGATTTAAATTTTAT-ATA
1040549 TT
1 TT
1040551 TTATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTAAAAGATTTAAATTTTATATA
Found at i:1040570 original size:30 final size:30
Alignment explanation
Indices: 1040534--1040590 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1040524 TATTAAAAAT
* *
1040534 TTAAATTTTATAATAT-TTTATTTTATTGAG
1 TTAAATTAT-TAATATAATTATTTTATTGAG
1040564 TTAAATTATTAATATAATTATTTTATT
1 TTAAATTATTAATATAATTATTTTATT
1040591 TTATTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (30 bp):
TTAAATTATTAATATAATTATTTTATTGAG
Found at i:1042386 original size:22 final size:21
Alignment explanation
Indices: 1042348--1042392 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1042338 ACAATAATTC
*
1042348 AATCAATAAAATTATAAAATA
1 AATCAATAAAATCATAAAATA
*
1042369 AATCAAATATAATCATAAAATA
1 AATC-AATAAAATCATAAAATA
1042391 AA
1 AA
1042393 AATTAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (21 bp):
AATCAATAAAATCATAAAATA
Found at i:1042599 original size:22 final size:22
Alignment explanation
Indices: 1042567--1042608 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
1042557 CTAGTTTGTC
1042567 AAATTCTAATAATATTTTTAAAA
1 AAATTCTAATAAT-TTTTTAAAA
1042590 AAATT-TAATAATTTTTTAA
1 AAATTCTAATAATTTTTTAA
1042609 GAGAAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 7 0.37
23 5 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATTCTAATAATTTTTTAAAA
Found at i:1043700 original size:16 final size:16
Alignment explanation
Indices: 1043661--1043692 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1043651 TTTTATTAAT
1043661 ATAAATAA-T-AAATA
1 ATAAATAATTAAAATA
1043675 ATAAATAATTAAAATA
1 ATAAATAATTAAAATA
1043691 AT
1 AT
1043693 TAAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAATAATTAAAATA
Found at i:1045808 original size:23 final size:23
Alignment explanation
Indices: 1045768--1045815 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
1045758 TGTATCTGAT
*
1045768 AAAATTAAATAATTATAACTTAAA
1 AAAATTAAAT-ATTATAACCTAAA
1045792 AAAATTAAAT-TTAATAACCTAAA
1 AAAATTAAATATT-ATAACCTAAA
1045815 A
1 A
1045816 TATAAGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 2 0.09
23 10 0.45
24 10 0.45
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATTAAATATTATAACCTAAA
Found at i:1047690 original size:18 final size:16
Alignment explanation
Indices: 1047667--1047701 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1047657 TAAGAAATTT
1047667 TAAATAAAATTATTAAAA
1 TAAATAAAA--ATTAAAA
1047685 TAAATAAAAATTAAAA
1 TAAATAAAAATTAAAA
1047701 T
1 T
1047702 TTATTTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAATAAAAATTAAAA
Found at i:1050404 original size:3 final size:3
Alignment explanation
Indices: 1050396--1050427 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1050386 TGTCAAGTTT
1050396 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1050428 GCAGGAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1051342 original size:34 final size:33
Alignment explanation
Indices: 1051303--1051421 Score: 136
Period size: 34 Copynumber: 3.5 Consensus size: 33
1051293 CCAAGGGAAG
*
1051303 AAGCTTTATAGGTTTAGTATCTTAACCAATAAGA
1 AAGCTTTATAGGTTGAGTATCTTAACCAATAA-A
* *
1051337 AAGCTTTATATGTTGAGT-TTTTCAACCAAGTAAA
1 AAGCTTTATAGGTTGAGTATCTT-AACCAA-TAAA
*
1051371 AAGGTTTTATAGGTTGAGTATC--AACCAATAAA
1 AA-GCTTTATAGGTTGAGTATCTTAACCAATAAA
1051403 GAAGCTTTATAGGTTGAGT
1 -AAGCTTTATAGGTTGAGT
1051422 TTGTCAACCA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
32 19 0.26
33 11 0.15
34 25 0.34
35 17 0.23
36 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (33 bp):
AAGCTTTATAGGTTGAGTATCTTAACCAATAAA
Found at i:1051361 original size:69 final size:67
Alignment explanation
Indices: 1051279--1051432 Score: 204
Period size: 69 Copynumber: 2.3 Consensus size: 67
1051269 GGATATAGCA
* *
1051279 GTTGAGTTTTTCAACCAAGGGAAGAA-GCTTTATAGGTTTAGTATCTTAACCAAT-AAGAAAGCT
1 GTTGAGTTTTTCAACCAA-GGAAAAAGGCTTTATAGGTTGAGTATC--AACCAATAAAG-AAGCT
*
1051342 TTATAT
62 TTATAG
* *
1051348 GTTGAGTTTTTCAACCAAGTAAAAAGGTTTTATAGGTTGAGTATCAACCAATAAAGAAGCTTTAT
1 GTTGAGTTTTTCAACCAAGGAAAAAGGCTTTATAGGTTGAGTATCAACCAATAAAGAAGCTTTAT
1051413 AG
66 AG
*
1051415 GTTGAGTTTGTCAACCAA
1 GTTGAGTTTTTCAACCAA
1051433 AAAAACTCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
67 34 0.44
68 8 0.10
69 35 0.45
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (67 bp):
GTTGAGTTTTTCAACCAAGGAAAAAGGCTTTATAGGTTGAGTATCAACCAATAAAGAAGCTTTAT
AG
Found at i:1051431 original size:67 final size:68
Alignment explanation
Indices: 1051279--1051432 Score: 206
Period size: 67 Copynumber: 2.3 Consensus size: 68
1051269 GGATATAGCA
* *
1051279 GTTGAGTTTTTCAACCAAGGGAAGAAGCTTTATAGGTTTAGTATCTTAACCAATAAGAAAGCTTT
1 GTTGAGTTTTTCAACCAAGGGAAAAAGCTTTATAGGTTGAGTATC-TAACCAATAAGAAAGCTTT
*
1051344 ATAT
65 ATAG
* *
1051348 GTTGAGTTTTTCAACCAA-GTAAAAAGGTTTTATAGGTTGAGTATC-AACCAATAA-AGAAGCTT
1 GTTGAGTTTTTCAACCAAGGGAAAAA-GCTTTATAGGTTGAGTATCTAACCAATAAGA-AAGCTT
1051410 TATAG
64 TATAG
*
1051415 GTTGAGTTTGTCAACCAA
1 GTTGAGTTTTTCAACCAA
1051433 AAAAACTCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
66 1 0.01
67 36 0.47
68 5 0.06
69 35 0.45
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (68 bp):
GTTGAGTTTTTCAACCAAGGGAAAAAGCTTTATAGGTTGAGTATCTAACCAATAAGAAAGCTTTA
TAG
Found at i:1052261 original size:35 final size:36
Alignment explanation
Indices: 1052141--1052297 Score: 128
Period size: 35 Copynumber: 4.4 Consensus size: 36
1052131 CGCTTTTGTT
1052141 ATACTCAACCTATAGAA-CTTCTTTTC-TTAGTTGAA
1 ATACTCAACCTATA-AAGCTTCTTTTCGTTAGTTGAA
** * * * *
1052176 ACGCTCAACCTATAAAGTTTGTTTTCCCGTTAATTGAG
1 ATACTCAACCTATAAAGCTTCTTTT--CGTTAGTTGAA
* * * *
1052214 ATATTCAACCTATGAAGCTTCCTTTC-TTGGTTGAA
1 ATACTCAACCTATAAAGCTTCTTTTCGTTAGTTGAA
* *
1052249 ATACTCAACCTATAAAGC-T-TTTTCTTTGGTTGACA
1 ATACTCAACCTATAAAGCTTCTTTTCGTTAGTTGA-A
1052284 A-ACTCAACCTATAA
1 ATACTCAACCTATAA
1052298 TGGGTTTTCC
Statistics
Matches: 97, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
33 4 0.04
34 24 0.25
35 42 0.43
36 1 0.01
37 1 0.01
38 25 0.26
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (36 bp):
ATACTCAACCTATAAAGCTTCTTTTCGTTAGTTGAA
Found at i:1056601 original size:55 final size:54
Alignment explanation
Indices: 1056513--1056621 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 54
1056503 TGTACAATAT
* * *
1056513 TCTCTATCTGCATACTTGTTATGGCCTTCTATCTACTTAATATGTTATCTTCTG
1 TCTCTATCTGCATACTTGTTATGACCTTATATCTACTTAATACGTTATCTTCTG
1056567 TCTCTATCTGTCATACTTGTTATGACCTTATATCTACTTAATACGTTATCTTCTG
1 TCTCTATCTG-CATACTTGTTATGACCTTATATCTACTTAATACGTTATCTTCTG
1056622 GATAAACCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 10 0.20
55 41 0.80
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.48
Consensus pattern (54 bp):
TCTCTATCTGCATACTTGTTATGACCTTATATCTACTTAATACGTTATCTTCTG
Found at i:1058731 original size:12 final size:12
Alignment explanation
Indices: 1058688--1058731 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1058678 AATTTTTAAA
*
1058688 AATATATTATTT
1 AATAAATTATTT
*
1058700 AATATAATAATTT
1 AATA-AATTATTT
*
1058713 AAAAAATTATTT
1 AATAAATTATTT
1058725 AATAAAT
1 AATAAAT
1058732 ATAGTCAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AATAAATTATTT
Found at i:1058764 original size:5 final size:5
Alignment explanation
Indices: 1058748--1058873 Score: 79
Period size: 5 Copynumber: 25.8 Consensus size: 5
1058738 AATTATTAAA
* *
1058748 ATAAT ATAAAT ATAAT ATAAGA ATAAA ATAA- AT-AT ATAAT ATAAT A-AA-
1 ATAAT AT-AAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * *
1058796 ATAAT ATAAAT ATAAT ATAAA ATAAT A-ATT TTAAT ATAAT AT-AT AATAAA
1 ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT
* *
1058846 ATAAT A-AAA ATAA- AAACAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATA-AT ATAAT ATAA
1058874 AATATAACAT
Statistics
Matches: 96, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
3 2 0.02
4 17 0.18
5 60 0.62
6 17 0.18
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.33
Consensus pattern (5 bp):
ATAAT
Found at i:1058784 original size:24 final size:24
Alignment explanation
Indices: 1058747--1058885 Score: 130
Period size: 24 Copynumber: 5.9 Consensus size: 24
1058737 CAATTATTAA
1058747 AATAATATAAATATAATATAAGAAT
1 AATAATATAAATATAATATAA-AAT
1058772 AA-AATA-AATATATAATATAATAA-
1 AATAATATAA-ATATAATATAA-AAT
1058795 AATAATATAAATATAATATAAAAT
1 AATAATATAAATATAATATAAAAT
* * *
1058819 AATAATTTTAATATAATATATAAT
1 AATAATATAAATATAATATAAAAT
* *
1058843 AA-AATAATAAAAATAA-A-AACAT
1 AATAAT-ATAAATATAATATAAAAT
*
1058865 -ATAATATAAAATATAACATAA
1 AATAATAT-AAATATAATATAA
1058886 CGATAAAAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
21 3 0.03
22 13 0.14
23 11 0.12
24 64 0.67
25 4 0.04
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (24 bp):
AATAATATAAATATAATATAAAAT
Found at i:1058801 original size:48 final size:48
Alignment explanation
Indices: 1058724--1058857 Score: 166
Period size: 48 Copynumber: 2.7 Consensus size: 48
1058714 AAAAATTATT
*
1058724 TAATAAATATAGTCAAT-TATTAAAATAATATAAATATAATATAAGAATAA
1 TAATAAATATA-T-AATATAATAAAATAATATAAATATAATATAA-AATAA
1058774 -AATAAATATATAATATAATAAAATAATATAAATATAATATAAAATAA
1 TAATAAATATATAATATAATAAAATAATATAAATATAATATAAAATAA
* *
1058821 TAATTTTAATATA-ATATATAATAAAATAATAAAAATA
1 TAA--TAAATATATA-ATATAATAAAATAATATAAATA
1058858 AAAACATATA
Statistics
Matches: 76, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
47 8 0.11
48 29 0.38
49 11 0.14
50 28 0.37
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (48 bp):
TAATAAATATATAATATAATAAAATAATATAAATATAATATAAAATAA
Found at i:1058866 original size:29 final size:28
Alignment explanation
Indices: 1058744--1058877 Score: 84
Period size: 29 Copynumber: 4.8 Consensus size: 28
1058734 AGTCAATTAT
* *
1058744 TAAAATAATATA-AATATAAT-ATAAGAA
1 TAAAA-AATATATAATAAAATAATAAAAA
*
1058771 TAAAATAA-ATAT-ATAATATAAT-AAAA
1 TAAAA-AATATATAATAAAATAATAAAAA
***
1058797 TAATATAAATATA-ATATAAAATAATAATTT
1 TAA-A-AAATATATA-ATAAAATAATAAAAA
*
1058827 TAATATAATATATAATAAAATAATAAAAA
1 TAA-AAAATATATAATAAAATAATAAAAA
1058856 TAAAAACATATA-ATATAAAATA
1 TAAAAA-ATATATA-ATAAAATA
1058878 TAACATAACG
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
26 14 0.17
27 13 0.15
28 7 0.08
29 43 0.51
30 7 0.08
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (28 bp):
TAAAAAATATATAATAAAATAATAAAAA
Found at i:1059038 original size:2 final size:2
Alignment explanation
Indices: 1059031--1059067 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1059021 ACTTGACCAA
1059031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1059068 AAAGTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1059107 original size:29 final size:29
Alignment explanation
Indices: 1059074--1059131 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1059064 TATAAAAGTA
* *
1059074 AAAATAATAATGTTTTGATAAATT-ATTTT
1 AAAATAATAATATTTTAAT-AATTAATTTT
1059103 AAAATAATAATATTTTAATAATTAATTTT
1 AAAATAATAATATTTTAATAATTAATTTT
1059132 GTAAACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (29 bp):
AAAATAATAATATTTTAATAATTAATTTT
Found at i:1059648 original size:21 final size:21
Alignment explanation
Indices: 1059624--1059671 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1059614 GTACTTGAAT
1059624 TATAATATA-ACGTAATTAAAA
1 TATAATATATA-GTAATTAAAA
*
1059645 TATAATTTTATAGTAATTAAAA
1 TATAA-TATATAGTAATTAAAA
1059667 -ATAAT
1 TATAAT
1059672 TTTAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 9 0.38
22 13 0.54
23 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (21 bp):
TATAATATATAGTAATTAAAA
Found at i:1059672 original size:21 final size:22
Alignment explanation
Indices: 1059635--1059675 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1059625 ATAATATAAC
1059635 GTAATTAAAATATAATTTTATA
1 GTAATTAAAATATAATTTTATA
1059657 GTAATTAAAA-ATAATTTTA
1 GTAATTAAAATATAATTTTA
1059676 AAATTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
GTAATTAAAATATAATTTTATA
Found at i:1059683 original size:22 final size:22
Alignment explanation
Indices: 1059635--1059686 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1059625 ATAATATAAC
*
1059635 GTAATTAAAATATAATTTTATA
1 GTAATTAAAATATAATTTTAAA
1059657 GTAATTAAAA-ATAATTTTAAAA
1 GTAATTAAAATATAATTTT-AAA
*
1059679 TTAATTAA
1 GTAATTAA
1059687 CTTTTCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
GTAATTAAAATATAATTTTAAA
Found at i:1062112 original size:16 final size:16
Alignment explanation
Indices: 1062077--1062155 Score: 65
Period size: 16 Copynumber: 5.0 Consensus size: 16
1062067 ATTTCGAAGT
* *
1062077 TTTTAAAATTAAGATCA
1 TTTTAAATTTAA-ATTA
1062094 TTTTAAATTTAAATTA
1 TTTTAAATTTAAATTA
* * *
1062110 TTTTGAGTTGAAATTA
1 TTTTAAATTTAAATTA
1062126 TTTTAAATTTTAAA--A
1 TTTTAAA-TTTAAATTA
*
1062141 TTTTTAA-TTAAATTA
1 TTTTAAATTTAAATTA
1062156 AATTTTAATT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
13 5 0.10
15 8 0.16
16 21 0.42
17 16 0.32
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:1062739 original size:2 final size:2
Alignment explanation
Indices: 1062732--1062758 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1062722 ACTGAAAGAA
1062732 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1062759 GAACAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1074471 original size:236 final size:234
Alignment explanation
Indices: 1074053--1074516 Score: 630
Period size: 236 Copynumber: 2.0 Consensus size: 234
1074043 TGCCAGACAA
* * * *
1074053 AAAGTTTGAATCAAACTCAAGAAACAACTATTAAACAAATTACATGATTTAACTAGAAATGTTAT
1 AAAGTTTGAATCAAACTCAAGAAACAACGATGAAACAAATGACATGATTTAACTAGAAATGTGAT
** * ** *
1074118 TCACACGATATGGAAAACAAGGAAAGGTGAAAACTTTCATCAAATAAGGGTGAAAATACTTTCTA
66 TCACACGATACAGAAAACAAAGAAAGGTGAAAACTTTCATCAAATAAAAGTGAAAACACTTTCTA
* *
1074183 TTTTTAGCAAACACTAATAATCTTTTTCATGATTCAATGAAGGAATTGTACTAAAACATAAAGCC
131 TTTTTAGCAAACACTAATAATCCTTTTCATGATTCAATGAAGGAACTGTACTAAAACATAAAGCC
*
1074248 TCAAAAGAGA-TAAATAAGATGTTTAACAAGATCAACAG
196 TCAAAAGAGATTAAATAAGATGTTCAACAAGATCAACAG
* *
1074286 AAAGCTTT-AATCAAACTCAAGAAACAACGATGAAACAAATGATATGATTTAATTAGAAATGTGA
1 AAAG-TTTGAATCAAACTCAAGAAACAACGATGAAACAAATGACATGATTTAACTAGAAATGTGA
* * * * *
1074350 TTCACGCTATACAGAAAAGCACGAAGAAAGGTGAAAGCTTTCATCCAATAAAAGTGCAAACACTT
65 TTCACACGATACAGAAAA-CA--AAGAAAGGTGAAAACTTTCATCAAATAAAAGTGAAAACACTT
* * * *
1074415 TCTATTTTTAGCAAACGA-TGATAA-CCTTTTCATGATTCATTTGAATGACCTGTACTAAAACAT
127 TCTATTTTTAGCAAAC-ACTAATAATCCTTTTCATGATTCA-ATGAAGGAACTGTACTAAAACAT
1074478 AAAGCCTCAAAAGAGATTAAATAAGATGTTCAACAAGAT
190 AAAGCCTCAAAAGAGATTAAATAAGATGTTCAACAAGAT
1074517 AGAATACAAC
Statistics
Matches: 200, Mismatches: 24, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
233 68 0.34
234 5 0.03
235 14 0.07
236 91 0.46
237 22 0.11
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (234 bp):
AAAGTTTGAATCAAACTCAAGAAACAACGATGAAACAAATGACATGATTTAACTAGAAATGTGAT
TCACACGATACAGAAAACAAAGAAAGGTGAAAACTTTCATCAAATAAAAGTGAAAACACTTTCTA
TTTTTAGCAAACACTAATAATCCTTTTCATGATTCAATGAAGGAACTGTACTAAAACATAAAGCC
TCAAAAGAGATTAAATAAGATGTTCAACAAGATCAACAG
Found at i:1076310 original size:27 final size:28
Alignment explanation
Indices: 1076280--1076334 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1076270 AACTTGGTCC
*
1076280 CTTGTCCTAATT-AGCCTTGTGGTTATG
1 CTTGTCATAATTAAGCCTTGTGGTTATG
*
1076307 CTTGTCATAATTAAGCCTTGTTGTTATG
1 CTTGTCATAATTAAGCCTTGTGGTTATG
1076335 GCCTCACAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.45
Consensus pattern (28 bp):
CTTGTCATAATTAAGCCTTGTGGTTATG
Found at i:1080571 original size:13 final size:13
Alignment explanation
Indices: 1080553--1080599 Score: 67
Period size: 13 Copynumber: 3.4 Consensus size: 13
1080543 GCTGATTTTT
1080553 AAATAAATTATTA
1 AAATAAATTATTA
1080566 AAATAATATTTATTTA
1 AAATAA-A-TTA-TTA
1080582 AAATAAATTATTA
1 AAATAAATTATTA
1080595 AAATA
1 AAATA
1080600 TTATTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 14 0.45
14 4 0.13
15 4 0.13
16 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATAAATTATTA
Found at i:1080610 original size:29 final size:29
Alignment explanation
Indices: 1080547--1080611 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
1080537 AGTATTGCTG
*
1080547 ATTTTTAAATAAATTATTAAAATAATATT
1 ATTTTAAAATAAATTATTAAAATAATATT
*
1080576 -TATTTAAAATAAATTATTAAAATATTATT
1 AT-TTTAAAATAAATTATTAAAATAATATT
1080605 ATTTTAA
1 ATTTTAA
1080612 TTTACTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 30 0.94
30 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTTAAAATAAATTATTAAAATAATATT
Found at i:1081524 original size:9 final size:9
Alignment explanation
Indices: 1081457--1081524 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
1081447 ATTTGATTTG
1081457 ATTTATAATT
1 ATTTAT-ATT
*
1081467 TTTTA-ATT
1 ATTTATATT
*
1081475 ATATTATAGT
1 AT-TTATATT
*
1081485 ATTTTTATT
1 ATTTATATT
1081494 -TTTATA-T
1 ATTTATATT
*
1081501 ATTTTATATA
1 A-TTTATATT
1081511 ATTTATATT
1 ATTTATATT
1081520 ATTTA
1 ATTTA
1081525 AAGATTATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
7 1 0.02
8 9 0.20
9 26 0.58
10 9 0.20
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (9 bp):
ATTTATATT
Found at i:1081599 original size:11 final size:11
Alignment explanation
Indices: 1081544--1081604 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 11
1081534 TATAATATAT
*
1081544 TATAATAAAAA
1 TATATTAAAAA
1081555 TAT-TTAAAAA
1 TATATTAAAAA
*
1081565 -ATATTAAATTATT
1 TATATTAAA--A-A
1081578 TATATTTAAAAA
1 TATA-TTAAAAA
1081590 TATATTAAAAA
1 TATATTAAAAA
1081601 TATA
1 TATA
1081605 AAAAATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
9 2 0.05
10 11 0.27
11 14 0.34
12 5 0.12
13 1 0.02
14 3 0.07
15 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATATTAAAAA
Found at i:1082461 original size:23 final size:19
Alignment explanation
Indices: 1082445--1082484 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1082435 TAATTATAGC
1082445 ATAATA-AAATATATAATT
1 ATAATATAAATATATAATT
1082463 ATAATATAAATATATAAATT
1 ATAATATAAATATAT-AATT
1082483 AT
1 AT
1082485 CAAATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATATAAATATATAATT
Found at i:1082770 original size:16 final size:17
Alignment explanation
Indices: 1082741--1082772 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1082731 CTAAGACATG
1082741 TAAAAAATATAATTATT
1 TAAAAAATATAATTATT
1082758 TAAAAAATA-AATTAT
1 TAAAAAATATAATTAT
1082773 ATCAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAATATAATTATT
Found at i:1083015 original size:20 final size:19
Alignment explanation
Indices: 1082988--1083055 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 19
1082978 TATTTAAATT
1082988 ATTTT-ATAT-TTATATAA
1 ATTTTAATATATTATATAA
1083005 ATTTTAATATATTA-AT-A
1 ATTTTAATATATTATATAA
1083022 A--TT--TATATTATATAA
1 ATTTTAATATATTATATAA
*
1083037 ATTTTAAAATATTTATATA
1 ATTTTAATATA-TTATATA
1083056 TTTATTTTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
13 7 0.17
14 2 0.05
15 4 0.10
17 9 0.22
18 6 0.15
19 6 0.15
20 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTAATATATTATATAA
Found at i:1083036 original size:32 final size:34
Alignment explanation
Indices: 1082990--1083060 Score: 110
Period size: 32 Copynumber: 2.1 Consensus size: 34
1082980 TTTAAATTAT
*
1082990 TTTATATTTATATAAATTTTAATATATTAATA-A
1 TTTATATTTATATAAATTTTAAAATATTAATATA
*
1083023 TTTATA-TTATATAAATTTTAAAATATTTATATA
1 TTTATATTTATATAAATTTTAAAATATTAATATA
1083056 TTTAT
1 TTTAT
1083061 TTTGTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 23 0.66
33 12 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TTTATATTTATATAAATTTTAAAATATTAATATA
Found at i:1083261 original size:12 final size:12
Alignment explanation
Indices: 1083244--1083269 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1083234 TTTGTTGCTC
1083244 ATTTGGATAGGG
1 ATTTGGATAGGG
1083256 ATTTGGATAGGG
1 ATTTGGATAGGG
1083268 AT
1 AT
1083270 GAAATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (12 bp):
ATTTGGATAGGG
Found at i:1089663 original size:24 final size:25
Alignment explanation
Indices: 1089635--1089704 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
1089625 AATAAAAATT
*
1089635 AGCCACCAATTTTGACAAAC-AATA
1 AGCCACCAATTTTGACAAACGAAAA
*
1089659 AGCCA-TAATTTTTGACAAACGAAAA
1 AGCCACCAA-TTTTGACAAACGAAAA
*
1089684 AGAACCACCATTTTTGACAAA
1 AG--CCACCAATTTTGACAAA
1089705 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 16 0.43
25 5 0.14
27 13 0.35
28 1 0.03
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAACGAAAA
Found at i:1089704 original size:27 final size:26
Alignment explanation
Indices: 1089637--1089733 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 26
1089627 TAAAAATTAG
* *
1089637 CCACCAATTTTGACAAACAATAAG--
1 CCACCATTTTTGACAAACAAAAAGAA
**
1089661 CCATAATTTTTGACAAACGAAAAAGAA
1 CCACCATTTTTGACAAAC-AAAAAGAA
* *
1089688 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAG-AA
*
1089715 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
1089734 CAAATGGTGG
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
24 15 0.25
25 5 0.08
26 5 0.08
27 34 0.58
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (26 bp):
CCACCATTTTTGACAAACAAAAAGAA
Found at i:1091657 original size:21 final size:22
Alignment explanation
Indices: 1091619--1091664 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1091609 ATCTGTTGAA
* **
1091619 ACTCTACCTGTTTTGGAGTA-T
1 ACTCCACCTGTTGCGGAGTACT
1091640 ACTCCACCTGTTGCGGAGTACT
1 ACTCCACCTGTTGCGGAGTACT
1091662 ACT
1 ACT
1091665 TATCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.35
Consensus pattern (22 bp):
ACTCCACCTGTTGCGGAGTACT
Done.