Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 3 of 210
Found at i:1003530 original size:19 final size:18
Alignment explanation
Indices: 1003506--1003554 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
1003496 AATCATAAAA
*
1003506 AATTATAAAATGGTCATTT
1 AATTATAAAAT-GTCATAT
1003525 AATTATTAATAATGTCATAT
1 AATTA-TAA-AATGTCATAT
1003545 AATTATAAAA
1 AATTATAAAA
1003555 AATTATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 8 0.30
20 14 0.52
21 3 0.11
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (18 bp):
AATTATAAAATGTCATAT
Found at i:1003571 original size:11 final size:11
Alignment explanation
Indices: 1003543--1003571 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1003533 ATAATGTCAT
1003543 ATAATTATAAA
1 ATAATTATAAA
1003554 A-AATTATAAA
1 ATAATTATAAA
1003564 ATAATTAT
1 ATAATTAT
1003572 TTAACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAATTATAAA
Found at i:1011617 original size:42 final size:42
Alignment explanation
Indices: 1011570--1011655 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
1011560 GAATTTCGAC
1011570 TTCATTTTGTCTTTCATTTCATCTCCGACTTTACAATCAGAT
1 TTCATTTTGTCTTTCATTTCATCTCCGACTTTACAATCAGAT
1011612 TTCATTTTGTCTTTCATTTCATCTCCGACTTTACAATCAGAT
1 TTCATTTTGTCTTTCATTTCATCTCCGACTTTACAATCAGAT
1011654 TT
1 TT
1011656 ATGGTGAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49
Consensus pattern (42 bp):
TTCATTTTGTCTTTCATTTCATCTCCGACTTTACAATCAGAT
Found at i:1014626 original size:31 final size:31
Alignment explanation
Indices: 1014591--1014656 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
1014581 AACAATCTAG
* *
1014591 TGACTTAAATAAAAACTTTCGAATAGTTCAA
1 TGACTTAAATAAAAAATTTCGAATAATTCAA
*
1014622 TGACTTAAATAAAAAATTTTGAATAATTCAA
1 TGACTTAAATAAAAAATTTCGAATAATTCAA
1014653 TGAC
1 TGAC
1014657 CATTTTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAAATTTCGAATAATTCAA
Found at i:1024202 original size:27 final size:26
Alignment explanation
Indices: 1024154--1024204 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1024144 TAGAATTAAT
*
1024154 TTGTTATTCATCATTTGCTTTGTATA
1 TTGTTAATCATCATTTGCTTTGTATA
1024180 TTGTTAATCAATCATATTG-TTTGTA
1 TTGTTAATC-ATCAT-TTGCTTTGTA
1024205 AGAATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.55
Consensus pattern (26 bp):
TTGTTAATCATCATTTGCTTTGTATA
Found at i:1033138 original size:13 final size:13
Alignment explanation
Indices: 1033120--1033165 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1033110 AAATTTTAAT
1033120 TAAATTGATGTCA
1 TAAATTGATGTCA
1033133 TAAATTGATGTC-
1 TAAATTGATGTCA
*
1033145 -AAA-TAATTGTCA
1 TAAATTGA-TGTCA
1033157 TAAATTGAT
1 TAAATTGAT
1033166 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
10 2 0.07
11 7 0.26
13 16 0.59
14 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (13 bp):
TAAATTGATGTCA
Found at i:1037862 original size:27 final size:27
Alignment explanation
Indices: 1037827--1037878 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1037817 TCATGTATGC
* *
1037827 ATATGAACCGCAATTTAAGTTTCATTT
1 ATATAAACCACAATTTAAGTTTCATTT
1037854 ATATAAACCACAATTTAAGTTTCAT
1 ATATAAACCACAATTTAAGTTTCAT
1037879 GTGTATAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (27 bp):
ATATAAACCACAATTTAAGTTTCATTT
Found at i:1037885 original size:27 final size:27
Alignment explanation
Indices: 1037827--1037886 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1037817 TCATGTATGC
* * *
1037827 ATATGAACCGCAATTTAAGTTTCATTT
1 ATATAAACCACAATTTAAGTTTCATGT
1037854 ATATAAACCACAATTTAAGTTTCATGT
1 ATATAAACCACAATTTAAGTTTCATGT
*
1037881 GTATAA
1 ATATAA
1037887 TCGTACCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (27 bp):
ATATAAACCACAATTTAAGTTTCATGT
Found at i:1038986 original size:61 final size:61
Alignment explanation
Indices: 1038882--1039072 Score: 244
Period size: 60 Copynumber: 3.1 Consensus size: 61
1038872 ATAAATATAG
* * * * *
1038882 GTACTAAATTGAACCTAAAAAGAAGCTTAGGTACCAAATTAGAAAAAATATGTCAAGTTCAG
1 GTACCAAATTGAGCC-AAAAAAAAGTTTAGGTACCAAATTAGAAAAAATATGTCAAGTTCAA
* * *
1038944 GTACCAAATTG-GGCACAAAAAAAGTTTAGGTATCAAATTAG-AAAAATGTGTCAAGTTCAA
1 GTACCAAATTGAGCCA-AAAAAAAGTTTAGGTACCAAATTAGAAAAAATATGTCAAGTTCAA
* *
1039004 GTACCAAATTGAGCCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAA-ATGTCAAATTTAA
1 GTACCAAATTGAGCCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAATATGTCAAGTTCAA
*
1039064 GTATCAAAT
1 GTACCAAAT
1039073 ATTATATTAA
Statistics
Matches: 112, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
60 71 0.63
61 31 0.28
62 10 0.09
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.25
Consensus pattern (61 bp):
GTACCAAATTGAGCCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAATATGTCAAGTTCAA
Found at i:1042286 original size:17 final size:17
Alignment explanation
Indices: 1042260--1042304 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1042250 CGAAATTTTA
*
1042260 AAATTAAAATTGATTAT
1 AAATTAAAATTAATTAT
*
1042277 AAATTTAAATTAATTATT
1 AAATTAAAATTAATTA-T
*
1042295 TAATTAAAAT
1 AAATTAAAAT
1042305 ATTCTACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AAATTAAAATTAATTAT
Found at i:1055419 original size:31 final size:31
Alignment explanation
Indices: 1055364--1055426 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1055354 GACAAAAAAA
* *
1055364 AATTCAAGCCCCATTGTGAAAACAATTGCCT
1 AATTCAAGCCCCATTATGAAAACAATTACCT
* **
1055395 AATTCAAGCCCTATTATGGGAACAATTACCT
1 AATTCAAGCCCCATTATGAAAACAATTACCT
1055426 A
1 A
1055427 GTTTGGGGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (31 bp):
AATTCAAGCCCCATTATGAAAACAATTACCT
Found at i:1055419 original size:90 final size:90
Alignment explanation
Indices: 1055305--1055474 Score: 218
Period size: 90 Copynumber: 1.9 Consensus size: 90
1055295 AAAACCCTAA
* *
1055305 AATTCAAACCCTAGTATGAGAACAATT-CTCAAGTTCAATGACTAGCTTGGACAAAAAAAAATTC
1 AATTCAAACCCTAGTATGAGAACAATTAC-CAAGTTCAAGGACTACCTTGGAC-AAAAAAAATTC
*
1055369 AAGCCCCATTGT-GAAAACAATTGCCT
64 AAGCCCCAATGTAGAAAACAATTGCCT
* * * * ***
1055395 AATTCAAGCCCTATTATGGGAACAATTACCTAGTTTGGGGACTACCTTGGACAAAAAAAATTCAA
1 AATTCAAACCCTAGTATGAGAACAATTACCAAGTTCAAGGACTACCTTGGACAAAAAAAATTCAA
1055460 GCCCCAATGTAGAAA
66 GCCCCAATGTAGAAA
1055475 TTGTTACCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
89 22 0.32
90 45 0.66
91 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (90 bp):
AATTCAAACCCTAGTATGAGAACAATTACCAAGTTCAAGGACTACCTTGGACAAAAAAAATTCAA
GCCCCAATGTAGAAAACAATTGCCT
Found at i:1062644 original size:16 final size:16
Alignment explanation
Indices: 1062604--1062644 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1062594 TTTAATTCAA
1062604 AATTATAA-TTAAAAT
1 AATTATAATTTAAAAT
*
1062619 AATCTA-AATTTGAAAT
1 AAT-TATAATTTAAAAT
1062635 AATTATAATT
1 AATTATAATT
1062645 CAACATCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
AATTATAATTTAAAAT
Found at i:1064196 original size:16 final size:16
Alignment explanation
Indices: 1064175--1064217 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1064165 GTGTGCATTA
1064175 TAAAATTAAAATATAT
1 TAAAATTAAAATATAT
*
1064191 TAAAATATTAAA-ATAT
1 TAAAAT-TAAAATATAT
1064207 TAAAA-TAAAAT
1 TAAAATTAAAAT
1064218 TTTGATTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 4 0.17
16 15 0.65
17 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATTAAAATATAT
Found at i:1064198 original size:8 final size:8
Alignment explanation
Indices: 1064187--1064213 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1064177 AAATTAAAAT
1064187 ATATTAAA
1 ATATTAAA
1064195 ATATTAAA
1 ATATTAAA
1064203 ATATTAAA
1 ATATTAAA
1064211 ATA
1 ATA
1064214 AAATTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATTAAA
Found at i:1065365 original size:16 final size:16
Alignment explanation
Indices: 1065344--1065377 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1065334 TCTCAAACCT
1065344 AAATAA-TTCGAACTCA
1 AAATAATTTC-AACTCA
1065360 AAATAATTTCAACTCA
1 AAATAATTTCAACTCA
1065376 AA
1 AA
1065378 TGACTTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATAATTTCAACTCA
Found at i:1066154 original size:22 final size:21
Alignment explanation
Indices: 1066106--1066154 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1066096 ATAAAATCTT
*
1066106 ATATATGCATATACATATATA
1 ATATATGCATATACATACATA
* *
1066127 AGTATATGCATGTATATACATA
1 A-TATATGCATATACATACATA
1066149 CATATA
1 -ATATA
1066155 ATGTTTTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.91
23 1 0.04
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (21 bp):
ATATATGCATATACATACATA
Found at i:1067099 original size:21 final size:19
Alignment explanation
Indices: 1067065--1067132 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
1067055 AAAAATTAAC
*
1067065 TAAATACCATTAAAAATAATA
1 TAAATA-CAATAAAAAT-ATA
1067086 TAAACTACAATAAATAATATA
1 TAAA-TACAATAAA-AATATA
* *
1067107 TAATATATAATAAAATTATA
1 TAA-ATACAATAAAAATATA
1067127 TAAATA
1 TAAATA
1067133 ATATTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.07
20 8 0.20
21 24 0.59
22 6 0.15
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAATACAATAAAAATATA
Found at i:1067132 original size:14 final size:16
Alignment explanation
Indices: 1067095--1067136 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1067085 ATAAACTACA
1067095 ATAAATAATATATAAT
1 ATAAATAATATATAAT
*
1067111 ATATAATAA-A-ATTAT
1 ATA-AATAATATATAAT
1067126 ATAAATAATAT
1 ATAAATAATAT
1067137 TTTTTTTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
14 5 0.23
15 8 0.36
16 4 0.18
17 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAATAATATATAAT
Found at i:1069421 original size:15 final size:15
Alignment explanation
Indices: 1069403--1069453 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1069393 AAAAAAATTT
1069403 AAATTTTAAAATATA
1 AAATTTTAAAATATA
*
1069418 AAA-TATAAAGATAT-
1 AAATTTTAAA-ATATA
1069432 AAATTATTAAAATTATA
1 AAATT-TTAAAA-TATA
1069449 AAATT
1 AAATT
1069454 ATGTTTTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.28
15 9 0.31
16 7 0.24
17 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
AAATTTTAAAATATA
Found at i:1069431 original size:8 final size:7
Alignment explanation
Indices: 1069409--1069452 Score: 52
Period size: 8 Copynumber: 5.9 Consensus size: 7
1069399 ATTTAAATTT
1069409 TAAAATA
1 TAAAATA
1069416 TAAAATA
1 TAAAATA
1069423 TAAAGATA
1 TAAA-ATA
*
1069431 TAAATTA
1 TAAAATA
1069438 TTAAAATTA
1 -TAAAA-TA
1069447 TAAAAT
1 TAAAAT
1069453 TATGTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 14 0.44
8 16 0.50
9 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (7 bp):
TAAAATA
Found at i:1069453 original size:8 final size:8
Alignment explanation
Indices: 1069403--1069455 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
1069393 AAAAAAATTT
*
1069403 AAATTTTA
1 AAATTATA
1069411 AAA-TATA
1 AAATTATA
1069418 AAA-TATA
1 AAATTATA
1069425 AAGA-TAT-
1 AA-ATTATA
1069432 AAATTATTA
1 AAATTA-TA
1069441 AAATTATA
1 AAATTATA
1069449 AAATTAT
1 AAATTAT
1069456 GTTTTTACGA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
6 1 0.03
7 16 0.40
8 17 0.43
9 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (8 bp):
AAATTATA
Found at i:1070583 original size:25 final size:24
Alignment explanation
Indices: 1070547--1070594 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1070537 ACAGCAACTT
*
1070547 CAAAAAATAAAACAATTAATAAAC
1 CAAAAAATAAAACAATAAATAAAC
* *
1070571 CAAAAACTAAAAATAATAAATAAA
1 CAAAAAAT-AAAACAATAAATAAA
1070595 TAATCAGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (24 bp):
CAAAAAATAAAACAATAAATAAAC
Found at i:1070877 original size:2 final size:2
Alignment explanation
Indices: 1070870--1070900 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1070860 ATTAGTAAGT
1070870 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 T
1070901 TATTTTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1073300 original size:75 final size:75
Alignment explanation
Indices: 1073188--1074232 Score: 1016
Period size: 75 Copynumber: 14.0 Consensus size: 75
1073178 AACCAAACAC
* * * * ** * * ** * * *
1073188 CTAAATTTCCCGAACCTGAACCCCGAGCTATATCTTGTGAACCCACTGCAATTGACGTTTTTGGT
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
1073253 AAACAGGCTT
66 AAACAGGCTT
* * ** ** *
1073263 CTAAATTTCCCGAGCCTGAACCTCAAGTGATGCCTTGTGAACCTGGTGGAATCAACATGTTTGGT
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
*
1073328 AAGC-GGCCTT
66 AAACAGG-CTT
* *
1073338 CTAAATTTCCTGAACCTGAAACTCAA-CCGATGACTTGTGAACCTACTGGAATCAACATGTTTGG
1 CTAAATTTCCTGAACCTGAACCTCAAGCC-ATGCCTTGTGAACCTACTGGAATCAACATGTTTGG
1073402 GAAACAGGCTT
65 GAAACAGGCTT
* * * * * *
1073413 CTAAATTTGCTGAACCTGAACCTCAAGGCATGCCTTGTGAACCTGCTGAAATCCACATGTTCGGG
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
*
1073478 AAGCAGGCTT
66 AAACAGGCTT
* * * * * * *
1073488 CTAAATTTGCTGAACCTGAACCACAAGGCATGCCTTGTGAACCTGCTGAAATCCACATGTTCGGG
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
*
1073553 AAGCAGGCTT
66 AAACAGGCTT
* * * * * * ** *
1073563 CTAAATTTGCTGAACCTGAACCTCGAGCCATACCTTGTGAACCCATTGGAATCGATGTGTTTGGA
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
1073628 AAACAGGCTT
66 AAACAGGCTT
* * *
1073638 CTAAATTTCCCGAACCTGAACCTCTAGCCATGCAC-TGTGAACCTGCTGGAATCAACATGTTT-G
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGC-CTTGTGAACCTACTGGAATCAACATGTTTGG
*
1073701 GAAAGCATGCTT
65 GAAA-CAGGCTT
* * *
1073713 CTAAATTTCCTGAACCTGAAACTCAACCCATGCAC-TGTGAACCAACTGGAATCAACATGTTT-G
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGC-CTTGTGAACCTACTGGAATCAACATGTTTGG
1073776 GAAAGCAGGCTT
65 GAAA-CAGGCTT
* * *
1073788 CTAAATTTCCTGAACCTGAAACTCAACCCATGCAC-TGTGAACCAACTGGAATCAACAT-TTTCG
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGC-CTTGTGAACCTACTGGAATCAACATGTTT-G
*
1073851 GGAAACAGGCTA
64 GGAAACAGGCTT
* * * * * *
1073863 CTAAATTTCCTGAACCCGAACCTCAAGCTATGCCTTGTGGACCAACAGGAATCAACATG-TTCGG
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
* *
1073927 AAAGCAGCCAT
66 AAA-CAGGCTT
*
1073938 CTAAATTTCCTG-A-C----CCTCAAGCCATGCCTTGTGAATCC-ACTGGAATCAACAAT-TTCG
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAA-CCTACTGGAATCAAC-ATGTTTG
*
1073995 GGAAGCAGGCTT
64 GGAAACAGGCTT
* * * **
1074007 CTAAATTTCCCGAACCTGAACTTCGAA-CCATGTCTTGTGAACCTACCAGAATCAACAT-TTTCG
1 CTAAATTTCCTGAACCTGAACCTC-AAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTT-G
*
1074070 GGAAACAAGCTT
64 GGAAACAGGCTT
* * * * * *
1074082 CTAAATTTCCTGAACCTGAACCTCAAACTATACCTTGTGAACCCACTGGACTCAACATGTTCGGG
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
*
1074147 AAACAAGCTT
66 AAACAGGCTT
* * * * * *
1074157 CTAAGTTTCTTGAACCAGAACAC-CAAGCCATACCATGTGAACCTACTGGACTCAACAT-TTTCG
1 CTAAATTTCCTGAACCTGAAC-CTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTT-G
*
1074220 GTAAACAGGCTT
64 GGAAACAGGCTT
1074232 C
1 C
1074233 ATCTAGGCAA
Statistics
Matches: 827, Mismatches: 116, Indels: 54
0.83 0.12 0.05
Matches are distributed among these distances:
69 46 0.06
70 10 0.01
71 1 0.00
73 1 0.00
74 26 0.03
75 729 0.88
76 14 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (75 bp):
CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAACATGTTTGGG
AAACAGGCTT
Found at i:1075267 original size:9 final size:9
Alignment explanation
Indices: 1075253--1075283 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1075243 GTTAAACGAA
1075253 TCGAGTTAT
1 TCGAGTTAT
*
1075262 TCGAGTTAA
1 TCGAGTTAT
1075271 TCGAGTTAT
1 TCGAGTTAT
1075280 TCGA
1 TCGA
1075284 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:1075355 original size:9 final size:9
Alignment explanation
Indices: 1075338--1075374 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1075328 TGAGTTTTCG
1075338 AATTCGAAT
1 AATTCGAAT
*
1075347 AACTCGAAT
1 AATTCGAAT
1075356 AATTCGAAT
1 AATTCGAAT
1075365 AATTCGAAT
1 AATTCGAAT
1075374 A
1 A
1075375 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1084138 original size:9 final size:9
Alignment explanation
Indices: 1084109--1084145 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1084099 TGAGTTTTCA
1084109 AATTCGAAT
1 AATTCGAAT
*
1084118 AACTCGAAT
1 AATTCGAAT
1084127 AATTCGAAT
1 AATTCGAAT
*
1084136 AATTCAAAT
1 AATTCGAAT
1084145 A
1 A
1084146 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1084253 original size:5 final size:5
Alignment explanation
Indices: 1084243--1084267 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1084233 TCAACTTTTA
1084243 CTCCC CTCCC CTCCC CTCCC CTCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC
1084268 AACCCCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCC
Found at i:1100096 original size:27 final size:25
Alignment explanation
Indices: 1100028--1100104 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 25
1100018 TATTGTAAAT
*
1100028 TTTTAAAATTTTATAATTAAAATGTA
1 TTTT-AAATTTCATAATTAAAATGTA
*
1100054 ATTTAAATTATACATAATTACTAAAT-TA
1 TTTTAAATT-T-CATAATTA--AAATGTA
*
1100082 TTTTAAAGTTTCATAATAAAAAT
1 TTTTAAA-TTTCATAATTAAAAT
1100105 ATTATATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
25 9 0.21
26 4 0.10
27 14 0.33
28 9 0.21
29 6 0.14
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTAAATTTCATAATTAAAATGTA
Found at i:1108711 original size:6 final size:6
Alignment explanation
Indices: 1108690--1108724 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1108680 TAGTTTCTAG
* *
1108690 TTCGGA TTCAGT TTCGGT TTCGGT TTCGGT TTCGG
1 TTCGGT TTCGGT TTCGGT TTCGGT TTCGGT TTCGG
1108725 AGTCTTCGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.06, C:0.17, G:0.31, T:0.46
Consensus pattern (6 bp):
TTCGGT
Found at i:1117065 original size:26 final size:27
Alignment explanation
Indices: 1117011--1117066 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1117001 GTCAACAAAT
* *
1117011 AATTTAAAATTTATAAAAATATTTAAA
1 AATTCAAAATTCATAAAAATATTTAAA
1117038 AATTCAAAATTCA-AAAAATATTATAAA
1 AATTCAAAATTCATAAAAATATT-TAAA
1117065 AA
1 AA
1117067 AATTCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (27 bp):
AATTCAAAATTCATAAAAATATTTAAA
Found at i:1117069 original size:22 final size:21
Alignment explanation
Indices: 1117043--1117088 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
1117033 TTAAAAATTC
1117043 AAAATTCA-AAAAATATTATAAA
1 AAAATTCATAAAAA-ATTA-AAA
1117065 AAAATTCATAAAAAATTAAAA
1 AAAATTCATAAAAAATTAAAA
1117086 AAA
1 AAA
1117089 TATAATATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.26
22 12 0.52
23 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATTCATAAAAAATTAAAA
Found at i:1126568 original size:4 final size:4
Alignment explanation
Indices: 1126559--1126626 Score: 136
Period size: 4 Copynumber: 17.0 Consensus size: 4
1126549 GAAATTGAAT
1126559 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1126607 TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA
1126627 GATCATAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 64 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:1127436 original size:22 final size:22
Alignment explanation
Indices: 1127408--1127538 Score: 190
Period size: 22 Copynumber: 6.0 Consensus size: 22
1127398 TTTATTGTTC
*
1127408 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
1127430 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
1127452 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
1127474 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
1127496 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
1127518 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
1127539 GCTTCAAGCT
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 98 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:1127860 original size:6 final size:7
Alignment explanation
Indices: 1127845--1127870 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1127835 GGATAATTAG
1127845 AAAATAA
1 AAAATAA
1127852 AAAATAA
1 AAAATAA
1127859 AAAATAA
1 AAAATAA
1127866 AAAAT
1 AAAAT
1127871 TAATTCAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:1129719 original size:10 final size:11
Alignment explanation
Indices: 1129706--1129734 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1129696 AGTATTTTAA
1129706 TTTGTTTTG-T
1 TTTGTTTTGTT
1129716 TTTGTTTTGTT
1 TTTGTTTTGTT
1129727 TTTGTTTT
1 TTTGTTTT
1129735 TGTTCCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (11 bp):
TTTGTTTTGTT
Found at i:1135069 original size:12 final size:12
Alignment explanation
Indices: 1135052--1135085 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1135042 CAGTCCGCCC
1135052 ATATTAATTTTT
1 ATATTAATTTTT
*
1135064 ATATTATTTTTT
1 ATATTAATTTTT
1135076 ATA-TAATTTT
1 ATATTAATTTT
1135086 AAAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:1135201 original size:30 final size:30
Alignment explanation
Indices: 1135157--1135219 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1135147 ACTTAACAAG
1135157 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
1135187 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
1135217 CAA
1 CAA
1135220 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:1137259 original size:29 final size:27
Alignment explanation
Indices: 1137193--1137259 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 27
1137183 AAATTTAAGG
1137193 TGTATAATTGCACAAAATCAAAGTTCA
1 TGTATAATTGCACAAAATCAAAGTTCA
*
1137220 TGTATCAAATTGCACATTATATCAAAGTTCA
1 TGTAT--AATTGCACA--AAATCAAAGTTCA
1137251 TGTATAATT
1 TGTATAATT
1137260 ATGATATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 5 0.14
29 13 0.37
31 17 0.49
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (27 bp):
TGTATAATTGCACAAAATCAAAGTTCA
Found at i:1144467 original size:100 final size:100
Alignment explanation
Indices: 1144315--1144508 Score: 235
Period size: 100 Copynumber: 1.9 Consensus size: 100
1144305 GCGACATAAC
* * * * * *
1144315 AGGATCGATGTATGTGAGGACTTATGCCGTCACACACAAATTAATACACGTAGAATAAATATTAA
1 AGGATCGATATATGTGAAGACTTATACCGTCACACACAAATAAATACACGTAGAATAAAAATGAA
* *
1144380 TTTACTAATCATTTTATATCATAACACGATACAAT
66 CTGACTAATCATTTTATATCATAACACGATACAAT
** * ***
1144415 AGGATCGATATATGTGAAGACTTATATTGTCGCACACAAATAAATGTGCGTAGAATAAAAATGAA
1 AGGATCGATATATGTGAAGACTTATACCGTCACACACAAATAAATACACGTAGAATAAAAATGAA
* * *
1144480 CTGATTAATCATTTTATGTCATGACACGA
66 CTGACTAATCATTTTATATCATAACACGA
1144509 GATGACAAGA
Statistics
Matches: 77, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
100 77 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (100 bp):
AGGATCGATATATGTGAAGACTTATACCGTCACACACAAATAAATACACGTAGAATAAAAATGAA
CTGACTAATCATTTTATATCATAACACGATACAAT
Found at i:1155504 original size:2 final size:2
Alignment explanation
Indices: 1155497--1155528 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1155487 GTAAAAATCG
1155497 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
1155529 TGCTTCTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1156616 original size:30 final size:30
Alignment explanation
Indices: 1156582--1156638 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1156572 ATATTTGGAC
1156582 TTAAATAT-TAAAAATTAAAAA-ATAAAAGAA
1 TTAAAT-TCTAAAAA-TAAAAATATAAAAGAA
1156612 TTAAATTCTAAAAATAAAAATATAAAA
1 TTAAATTCTAAAAATAAAAATATAAAA
1156639 ACATATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (30 bp):
TTAAATTCTAAAAATAAAAATATAAAAGAA
Found at i:1159554 original size:21 final size:21
Alignment explanation
Indices: 1159528--1159568 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1159518 CTTCAATTTG
1159528 GTCTAATGAGAAAAGTACCAA
1 GTCTAATGAGAAAAGTACCAA
1159549 GTCTAATGAGAAAAGTACCA
1 GTCTAATGAGAAAAGTACCA
1159569 TAGAGTTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (21 bp):
GTCTAATGAGAAAAGTACCAA
Found at i:1161789 original size:28 final size:29
Alignment explanation
Indices: 1161757--1161811 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1161747 ATTACCAACC
*
1161757 GTCATT-AACTTTAATAAAATAACAAACA
1 GTCATTAAACTTTAAAAAAATAACAAACA
1161785 GTCATTAAACTTTAAAAAAATAACAAA
1 GTCATTAAACTTTAAAAAAATAACAAA
1161812 ACAGATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (29 bp):
GTCATTAAACTTTAAAAAAATAACAAACA
Found at i:1163672 original size:228 final size:229
Alignment explanation
Indices: 1163372--1164136 Score: 1027
Period size: 228 Copynumber: 3.4 Consensus size: 229
1163362 AATCTTCGCT
* * * * * * * * * *
1163372 TTCACGTTATCAATCGTATCCGAGCTCTCCACTTCTAAAGTAATCGTCTTACCGGTCAA-AGTCT
1 TTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATCGTCTTGCCGGTCAAGAGTCT
* * * * * * * * *
1163436 TGACGAAGATCTGCATCCCACCTCG-AAGACGTAGAACCAGATGAAGAGTCGATTCCTTCTGGAT
66 TAACGAAGATCTGCATCCCACCGCGCAA-ACGAAGGACAAGGTGGAGAGTTGACTCCTTCTGGAT
* * * * * *
1163500 ATTGTAATCGGCTAAAGTCCGCCCGTCCTCGAGTTGCTTTCCGGCGAAGATGAGACGTTGCTGGT
130 GTTGTAATCGGCCAAGGTCCGGCCGTCTTCGAGTTGTTTTCCGGCGAAGATGAGACGTTGCTGGT
* *
1163565 CTGGCGGGATGCCTTCCTTGTCTTGGATTTTGGCT
195 CTGGAGGGATGCCTTCCTTGTCTTGGATTTTGGCC
* * *
1163600 TTCACGTTGTCGATCGTGTCAGAGCTCTCGACCTCGAGAGTGATCGTCTTTCCGGT-AAGCGTCT
1 TTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATCGTCTTGCCGGTCAAGAGTCT
* *
1163664 TAACGAAGATTTGCATCCCGCCGCGCAAACGAAGGACAAGGTGGAGAGTTGACTCCTTCTGGATG
66 TAACGAAGATCTGCATCCCACCGCGCAAACGAAGGACAAGGTGGAGAGTTGACTCCTTCTGGATG
* *
1163729 TTGTAGTCGGCCAAGGTACGGCCGTCTTCGAGTTGTTTTCCGGCGAAGATGAGACGTTGCTGGTC
131 TTGTAATCGGCCAAGGTCCGGCCGTCTTCGAGTTGTTTTCCGGCGAAGATGAGACGTTGCTGGTC
* * *
1163794 TGGGGGGATGCCTTCCTTGTCTTGGATCTTCGCC
196 TGGAGGGATGCCTTCCTTGTCTTGGATTTTGGCC
* * *
1163828 TTAACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATTGTCTTGCCGGTCAAG-GTTT
1 TTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATCGTCTTGCCGGTCAAGAGTCT
* * * * *
1163892 TCACGAAGATTTGCATCCCACCGCGCAAACGGAGGACGAGGTGGAGAGTTGACTCCTTTTGGATG
66 TAACGAAGATCTGCATCCCACCGCGCAAACGAAGGACAAGGTGGAGAGTTGACTCCTTCTGGATG
* * *
1163957 TTGTAATCGGCCAAGGTCCGGCCGTCTTCGAGCTGTTTTCCGGCGAAGATCAGACGCTGCTGGTC
131 TTGTAATCGGCCAAGGTCCGGCCGTCTTCGAGTTGTTTTCCGGCGAAGATGAGACGTTGCTGGTC
*
1164022 TGGAGGGATGCCTTCCTTATCTTGGATTTTGGCC
196 TGGAGGGATGCCTTCCTTGTCTTGGATTTTGGCC
* *
1164056 TTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGTGTGATCGTCTTGCCGGT-TAGAGTCT
1 TTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATCGTCTTGCCGGTCAAGAGTCT
1164120 TAACGAAGATCTGCATC
66 TAACGAAGATCTGCATC
1164137 TTGTTTGGCT
Statistics
Matches: 473, Mismatches: 60, Indels: 8
0.87 0.11 0.01
Matches are distributed among these distances:
227 4 0.01
228 464 0.98
229 5 0.01
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (229 bp):
TTCACGTTGTCGATCGTGTCGGAGCTCTCGACCTCGAGAGTGATCGTCTTGCCGGTCAAGAGTCT
TAACGAAGATCTGCATCCCACCGCGCAAACGAAGGACAAGGTGGAGAGTTGACTCCTTCTGGATG
TTGTAATCGGCCAAGGTCCGGCCGTCTTCGAGTTGTTTTCCGGCGAAGATGAGACGTTGCTGGTC
TGGAGGGATGCCTTCCTTGTCTTGGATTTTGGCC
Found at i:1176993 original size:2 final size:2
Alignment explanation
Indices: 1176986--1177014 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1176976 ATTTAGTTTA
1176986 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1177015 TTTAGTAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1179845 original size:28 final size:29
Alignment explanation
Indices: 1179812--1179871 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
1179802 CCCATTTTCT
1179812 TAATTAA-T-TTTTTTAAAATCTATTTTTA
1 TAATTAATTATTTTTTAAAAT-TATTTTTA
*
1179840 TAATTAATTATTTTTTAATATTATTTTTA
1 TAATTAATTATTTTTTAAAATTATTTTTA
1179869 TAA
1 TAA
1179872 GAAAACCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 7 0.24
29 12 0.41
30 10 0.34
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
TAATTAATTATTTTTTAAAATTATTTTTA
Found at i:1179864 original size:13 final size:13
Alignment explanation
Indices: 1179820--1179867 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
1179810 CTTAATTAAT
*
1179820 TTTTTTAAAATCTA
1 TTTTTTAATAT-TA
1179834 TTTTTATAATTAATTA
1 TTTTT-TAA-T-ATTA
1179850 TTTTTTAATATTA
1 TTTTTTAATATTA
1179863 TTTTT
1 TTTTT
1179868 ATAAGAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 9 0.30
14 6 0.20
15 6 0.20
16 7 0.23
17 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTTAATATTA
Found at i:1182868 original size:13 final size:13
Alignment explanation
Indices: 1182850--1182874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1182840 AAATTTCAAT
1182850 TTTTTATAATTTA
1 TTTTTATAATTTA
1182863 TTTTTATAATTT
1 TTTTTATAATTT
1182875 TTAAAAGATT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATAATTTA
Found at i:1188125 original size:15 final size:15
Alignment explanation
Indices: 1188105--1188136 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1188095 GTAATTTGTC
1188105 ATGGTGTTGGAGTCG
1 ATGGTGTTGGAGTCG
1188120 ATGGTGTTGGAGTCG
1 ATGGTGTTGGAGTCG
1188135 AT
1 AT
1188137 CGAATAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.44, T:0.34
Consensus pattern (15 bp):
ATGGTGTTGGAGTCG
Found at i:1192610 original size:2 final size:2
Alignment explanation
Indices: 1192603--1192627 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1192593 CTAATAAATT
1192603 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1192628 TTGGAGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1193654 original size:33 final size:33
Alignment explanation
Indices: 1193612--1193680 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1193602 CGTACCACCC
1193612 CTTCCTTATCTTCAAATATATAATAGATATTCT
1 CTTCCTTATCTTCAAATATATAATAGATATTCT
1193645 CTTCCTTATCTTCAAATATATAATAGATATTCT
1 CTTCCTTATCTTCAAATATATAATAGATATTCT
1193678 CTT
1 CTT
1193681 TACTTTGCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.03, T:0.46
Consensus pattern (33 bp):
CTTCCTTATCTTCAAATATATAATAGATATTCT
Found at i:1194400 original size:15 final size:17
Alignment explanation
Indices: 1194370--1194403 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1194360 CAATTTTGAG
1194370 TTTAATTTATTTTAGGT
1 TTTAATTTATTTTAGGT
1194387 TTTAA-TTA-TTTAGGT
1 TTTAATTTATTTTAGGT
1194402 TT
1 TT
1194404 GTAAGTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 3 0.18
17 5 0.29
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (17 bp):
TTTAATTTATTTTAGGT
Found at i:1198063 original size:32 final size:32
Alignment explanation
Indices: 1198027--1198087 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1198017 AAATAAACAC
1198027 ATAATTATTCATTT-AATA-TTATAACTATTCAA
1 ATAA-TATT-ATTTAAATAGTTATAACTATTCAA
*
1198059 ATAATATTATTTAAATAGTTATAATTATT
1 ATAATATTATTTAAATAGTTATAACTATT
1198088 TTTTAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 14 0.54
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (32 bp):
ATAATATTATTTAAATAGTTATAACTATTCAA
Found at i:1200598 original size:43 final size:43
Alignment explanation
Indices: 1200537--1200624 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
1200527 TCTCTTGATT
1200537 CAATAACAGTATTAATTGAAATTAAATCATTTGGTTCAATTAC
1 CAATAACAGTATTAATTGAAATTAAATCATTTGGTTCAATTAC
*
1200580 CAATAACAGTATTAATTGAAATTGAATCATTTGGTTCAATTAC
1 CAATAACAGTATTAATTGAAATTAAATCATTTGGTTCAATTAC
1200623 CA
1 CA
1200625 TGAACCTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.36
Consensus pattern (43 bp):
CAATAACAGTATTAATTGAAATTAAATCATTTGGTTCAATTAC
Found at i:1202225 original size:20 final size:20
Alignment explanation
Indices: 1202202--1202242 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1202192 AAAATCATAC
1202202 AAAATAGTAAAA-ATTATTAA
1 AAAATAGTAAAATA-TATTAA
*
1202222 AAAATTGTAAAATATATTAA
1 AAAATAGTAAAATATATTAA
1202242 A
1 A
1202243 TTTTGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAATAGTAAAATATATTAA
Found at i:1202253 original size:20 final size:19
Alignment explanation
Indices: 1202202--1202259 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
1202192 AAAATCATAC
*
1202202 AAAATAGTAAAAATTATTAA
1 AAAATTGTAAAAATTATT-A
1202222 AAAATTGT-AAAATATATTA
1 AAAATTGTAAAAAT-TATTA
**
1202241 AATTTTGTAAAAATTATTA
1 AAAATTGTAAAAATTATTA
1202260 TAATAAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAATTGTAAAAATTATTA
Found at i:1215316 original size:20 final size:20
Alignment explanation
Indices: 1215273--1215330 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
1215263 TTATGAAGCA
*
1215273 AAATTTAAAAT-TTTCTATAC
1 AAATTTAAAATATTT-TAAAC
*
1215293 AAATTTAAAATATTTTAAAT
1 AAATTTAAAATATTTTAAAC
*
1215313 AAATCTTTAAA-ATTTTAA
1 AAAT-TTAAAATATTTTAA
1215331 TATTATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 25 0.76
21 8 0.24
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTTAAAATATTTTAAAC
Found at i:1219517 original size:24 final size:26
Alignment explanation
Indices: 1219485--1219536 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
1219475 GCCTTGAATA
*
1219485 TTCAATTTAGTAT-C-TGAATTTTTT
1 TTCAATTTAATATACTTGAATTTTTT
*
1219509 TTCAATTTAATATACTTGAGTTTTTT
1 TTCAATTTAATATACTTGAATTTTTT
1219535 TT
1 TT
1219537 TTGTCCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.50
25 1 0.04
26 11 0.46
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.60
Consensus pattern (26 bp):
TTCAATTTAATATACTTGAATTTTTT
Found at i:1224219 original size:24 final size:23
Alignment explanation
Indices: 1224171--1224220 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
1224161 TTTATAAAAA
*
1224171 AAATTAATAAATAAAAAAATATT
1 AAATTAAAAAATAAAAAAATATT
*
1224194 AAATTAAAATAATACAAACAAT-TT
1 AAATTAAAA-AATA-AAAAAATATT
1224218 AAA
1 AAA
1224221 AAATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 9 0.39
25 6 0.26
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATTAAAAAATAAAAAAATATT
Found at i:1224387 original size:18 final size:18
Alignment explanation
Indices: 1224360--1224401 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1224350 CTTAGGCTTG
1224360 ACCCGAACCTGAACCTGA
1 ACCCGAACCTGAACCTGA
* *
1224378 ACCTGAACCTGAACCCGA
1 ACCCGAACCTGAACCTGA
1224396 ACCCGA
1 ACCCGA
1224402 CTCGACCTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.40, G:0.17, T:0.10
Consensus pattern (18 bp):
ACCCGAACCTGAACCTGA
Found at i:1224401 original size:6 final size:6
Alignment explanation
Indices: 1224364--1224398 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1224354 GGCTTGACCC
*
1224364 GAACCT GAACCT GAACCT GAACCT GAACCC GAACC
1 GAACCT GAACCT GAACCT GAACCT GAACCT GAACC
1224399 CGACTCGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.37, G:0.17, T:0.11
Consensus pattern (6 bp):
GAACCT
Found at i:1227027 original size:30 final size:31
Alignment explanation
Indices: 1226978--1227037 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1226968 TTTTGTTTAA
*
1226978 TTTGGTACCTAAACTTGACACTTTTTCTTAT
1 TTTGGTACCTAAACTTGACACTTTCTCTTAT
*
1227009 TTTGGTA-CTAATCTTGACACTTTCTCTTA
1 TTTGGTACCTAAACTTGACACTTTCTCTTA
1227038 AATTGTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.48
Consensus pattern (31 bp):
TTTGGTACCTAAACTTGACACTTTCTCTTAT
Found at i:1227452 original size:6 final size:6
Alignment explanation
Indices: 1227441--1227466 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1227431 GTAGCATAAA
1227441 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
1227467 CACCATTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:1227637 original size:60 final size:60
Alignment explanation
Indices: 1227521--1227635 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 60
1227511 AGGTATAAAA
* * * *
1227521 TTTAGGCACTAAATTAGGAAAAAATGTCAAGTTCATGTACCAAATTGGGTCCAAAAAGGG
1 TTTAGGCACCAAATTAGGAAAAAATATCAAGTTCAAGTACCAAATTGGGTCAAAAAAGGG
* *
1227581 TTTAGGTACCAAATTAGG-AAAAGTATCAAGTTCAAGTACCAAATTGGG-CAAAAAA
1 TTTAGGCACCAAATTAGGAAAAAATATCAAGTTCAAGTACCAAATTGGGTCAAAAAA
1227636 AAAAGAGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 6 0.12
59 27 0.55
60 16 0.33
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (60 bp):
TTTAGGCACCAAATTAGGAAAAAATATCAAGTTCAAGTACCAAATTGGGTCAAAAAAGGG
Found at i:1243791 original size:12 final size:12
Alignment explanation
Indices: 1243774--1243798 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1243764 GGTGTTCATT
1243774 CGGTTAACCGAC
1 CGGTTAACCGAC
1243786 CGGTTAACCGAC
1 CGGTTAACCGAC
1243798 C
1 C
1243799 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:1243973 original size:9 final size:9
Alignment explanation
Indices: 1243959--1244012 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
1243949 TTTGGTTAAA
1243959 AATTACCCG
1 AATTACCCG
1243968 AATTACCCG
1 AATTACCCG
*
1243977 AATTAACCG
1 AATTACCCG
1243986 AATTA-CCG
1 AATTACCCG
*
1243994 AAAAATACCCG
1 --AATTACCCG
1244005 AATTACCC
1 AATTACCC
1244013 AAAATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
8 3 0.08
9 29 0.74
10 4 0.10
11 3 0.08
ACGTcount: A:0.41, C:0.30, G:0.09, T:0.20
Consensus pattern (9 bp):
AATTACCCG
Found at i:1244174 original size:13 final size:13
Alignment explanation
Indices: 1244156--1244185 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1244146 TTTTAGTTTT
*
1244156 ATTGGGTTGGGTA
1 ATTGGGTTGGCTA
1244169 ATTGGGTTGGCTA
1 ATTGGGTTGGCTA
1244182 ATTG
1 ATTG
1244186 AGTTTGGGCT
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:0.17, C:0.03, G:0.40, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGCTA
Found at i:1250907 original size:18 final size:20
Alignment explanation
Indices: 1250867--1250908 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
1250857 AAAAATTACA
*
1250867 AAAACTTCAAAATAATTTTT
1 AAAACTTCAAAATAATTTAT
*
1250887 AAAA-TTCAAAA-CATTTAT
1 AAAACTTCAAAATAATTTAT
1250905 AAAA
1 AAAA
1250909 ATTTCAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 7 0.35
20 4 0.20
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAACTTCAAAATAATTTAT
Found at i:1250959 original size:12 final size:13
Alignment explanation
Indices: 1250935--1250960 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1250925 TTTTTTAAAG
1250935 AATTGTAAAAAAA
1 AATTGTAAAAAAA
1250948 AATTGTAAAAAAA
1 AATTGTAAAAAAA
1250961 TTCTAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AATTGTAAAAAAA
Found at i:1257900 original size:16 final size:16
Alignment explanation
Indices: 1257862--1257898 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1257852 TGTTCTTTTA
1257862 TTGTTTTCATTTGCTT
1 TTGTTTTCATTTGCTT
*
1257878 TTGTTTTCCTTTG-TT
1 TTGTTTTCATTTGCTT
1257893 TT-TTTT
1 TTGTTTT
1257899 TTTTTGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 4 0.20
15 4 0.20
16 12 0.60
ACGTcount: A:0.03, C:0.11, G:0.11, T:0.76
Consensus pattern (16 bp):
TTGTTTTCATTTGCTT
Found at i:1258950 original size:2 final size:2
Alignment explanation
Indices: 1258932--1258972 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1258922 ATACATTATT
* *
1258932 TA TA TA TG TA TA CA 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
1258973 GTCATATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1262553 original size:19 final size:19
Alignment explanation
Indices: 1262531--1262573 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1262521 ATTTTTTTTA
*
1262531 ATATGTTTAAAATTTTAA-T
1 ATAT-TTTAAAATATTAAGT
*
1262550 ATATTTTAATATATTAAGT
1 ATATTTTAAAATATTAAGT
1262569 ATATT
1 ATATT
1262574 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
ATATTTTAAAATATTAAGT
Found at i:1262583 original size:79 final size:80
Alignment explanation
Indices: 1262489--1262664 Score: 248
Period size: 80 Copynumber: 2.2 Consensus size: 80
1262479 TATTAAAATA
* * *
1262489 TATATTAAAATTTTAAAATTGGTTATACTTC-A-ATTTTTTTTAATATGTTTAAAATTTTAATAT
1 TATATTAAAATTTTAAAACTGGTTATAC-TCAACATTTTCTTTAATATATTTAAAATTTTAATAT
*
1262552 ATTTTAATATATTAAG
65 ATTTAAATATATTAAG
*
1262568 TATATTAAAAATTTAAAACTGGTTATACTCAACATTTTCTTTAATATATTTAAAATTTTAATATA
1 TATATTAAAATTTTAAAACTGGTTATACTCAACATTTTCTTTAATATATTTAAAATTTTAATATA
* *
1262633 TTTAAATTTTTTAAG
66 TTTAAATATATTAAG
* *
1262648 TTTTTTAAAATTTTAAA
1 TATATTAAAATTTTAAA
1262665 TATATTAAGA
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
78 2 0.02
79 27 0.32
80 56 0.66
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (80 bp):
TATATTAAAATTTTAAAACTGGTTATACTCAACATTTTCTTTAATATATTTAAAATTTTAATATA
TTTAAATATATTAAG
Found at i:1262641 original size:16 final size:17
Alignment explanation
Indices: 1262607--1262670 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 17
1262597 CAACATTTTC
1262607 TTTAATATATTTAAAAT
1 TTTAATATATTTAAAAT
*
1262624 TTTAATATATTTAAATTT
1 TTTAATATATTTAAA-AT
*
1262642 TTTAAGT-TTTTTAAAAT
1 TTTAA-TATATTTAAAAT
1262659 TTTAAATATATT
1 TTT-AATATATT
1262671 AAGAAATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 20 0.51
18 18 0.46
19 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTAATATATTTAAAAT
Found at i:1262672 original size:26 final size:27
Alignment explanation
Indices: 1262623--1262673 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
1262613 ATATTTAAAA
* * *
1262623 TTTTAATATATTTAAATTTTTTAAGTT
1 TTTTAAAATATTTAAATATATTAAGTT
1262650 TTTTAAAAT-TTTAAATATATTAAG
1 TTTTAAAATATTTAAATATATTAAG
1262674 AAATATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (27 bp):
TTTTAAAATATTTAAATATATTAAGTT
Found at i:1262905 original size:70 final size:70
Alignment explanation
Indices: 1262737--1263015 Score: 260
Period size: 70 Copynumber: 3.9 Consensus size: 70
1262727 ATATTTTAAA
* *
1262737 AAATATATTGAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTTATTT
1 AAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTTAATT
1262802 TTTTT
66 TTTTT
*
1262807 AAATATATTAAATATACTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTTAATT
1 AAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTTAATT
1262872 TTTTT
66 TTTTT
* * * * * ** * * * ***
1262877 AAGTTTTTTAAA-ATTTTAAATATATTAAAAAAACCTTTTTTGT-CTTTACCTATTAAAAATATA
1 AAATATATTAAATATATTAAA-AT-TT--TAAAA--TTGGTTATACTTAACAT-TTTTTAATATA
* *
1262940 TATTAAGTATATTT
59 T-TTAA-TTTTTTT
**
1262954 AAAT-T-TTAAATATATTAAAATTTTAAAATTAATTATACTTAACATTTTTTTAATATATTTAA
1 AAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACA-TTTTTTAATATATTTAA
1263016 AATTTTAGAA
Statistics
Matches: 167, Mismatches: 30, Indels: 24
0.76 0.14 0.11
Matches are distributed among these distances:
69 6 0.04
70 87 0.52
71 16 0.10
72 5 0.03
73 4 0.02
74 8 0.05
75 21 0.13
76 12 0.07
77 8 0.05
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (70 bp):
AAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTTAATT
TTTTT
Found at i:1262988 original size:18 final size:17
Alignment explanation
Indices: 1262942--1262980 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1262932 AAAATATATA
* *
1262942 TTAAGTATATTTAAATT
1 TTAAATATATTAAAATT
1262959 TTAAATATATTAAAATT
1 TTAAATATATTAAAATT
1262976 TTAAA
1 TTAAA
1262981 ATTAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTAAATATATTAAAATT
Found at i:1263015 original size:20 final size:21
Alignment explanation
Indices: 1262982--1263021 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1262972 AATTTTAAAA
*
1262982 TTAATTATACTTAACATTTTT
1 TTAATTATACTTAAAATTTTT
*
1263003 TTAA-TATATTTAAAATTTT
1 TTAATTATACTTAAAATTTT
1263022 AGAAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTATACTTAAAATTTTT
Found at i:1263462 original size:15 final size:15
Alignment explanation
Indices: 1263442--1263493 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1263432 ATAAATTTAT
1263442 ATTTTAATTTAATTA
1 ATTTTAATTTAATTA
*
1263457 ATTTTAATATTTA-TA
1 ATTTTAAT-TTAATTA
* *
1263472 TTTTTAAAATTAATTA
1 ATTTT-AATTTAATTA
1263488 ATTTTA
1 ATTTTA
1263494 GTTTTTAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTAATTTAATTA
Found at i:1263488 original size:31 final size:30
Alignment explanation
Indices: 1263436--1263507 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
1263426 GAAGTGATAA
*
1263436 ATTTATA-TTTTAATTTAATTAATTTTAAT
1 ATTTATATTTTTAAATTAATTAATTTTAAT
*
1263465 ATTTATATTTTTAAAATTAATTAATTTTAGT
1 ATTTATATTTTT-AAATTAATTAATTTTAAT
* *
1263496 TTTTAGATTTTT
1 ATTTATATTTTT
1263508 TTTTAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 7 0.19
30 4 0.11
31 26 0.70
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (30 bp):
ATTTATATTTTTAAATTAATTAATTTTAAT
Found at i:1268553 original size:43 final size:43
Alignment explanation
Indices: 1268503--1268587 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
1268493 TTATAAAATA
*
1268503 TTAAGTATAAGCAATTTTTAAATTTTAATATATTCAATATATG
1 TTAAGTATAAGCAATTTTAAAATTTTAATATATTCAATATATG
** *
1268546 TTAAGTATAATTAATTTTAAAATTTTAATATATTTAATATAT
1 TTAAGTATAAGCAATTTTAAAATTTTAATATATTCAATATAT
1268588 TTTTTAATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (43 bp):
TTAAGTATAAGCAATTTTAAAATTTTAATATATTCAATATATG
Found at i:1268583 original size:9 final size:9
Alignment explanation
Indices: 1268526--1268589 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
1268516 ATTTTTAAAT
1268526 TTTAATATA
1 TTTAATATA
*
1268535 TTCAATATA
1 TTTAATATA
1268544 TGTTAAGTATA
1 T-TTAA-TATA
*
1268555 ATT-A-AT-
1 TTTAATATA
*
1268561 TTTAAAAT-
1 TTTAATATA
1268569 TTTAATATA
1 TTTAATATA
1268578 TTTAATATA
1 TTTAATATA
1268587 TTT
1 TTT
1268590 TTTAATAGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
6 2 0.04
7 3 0.07
8 9 0.20
9 22 0.49
10 5 0.11
11 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (9 bp):
TTTAATATA
Found at i:1268636 original size:18 final size:18
Alignment explanation
Indices: 1268613--1268648 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1268603 GAGAAAAAGT
* *
1268613 ATTTTTAATATATTTAAA
1 ATTTTTAAAAAATTTAAA
1268631 ATTTTTAAAAAATTTAAA
1 ATTTTTAAAAAATTTAAA
1268649 TATATTAAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTTAAAAAATTTAAA
Found at i:1268660 original size:16 final size:17
Alignment explanation
Indices: 1268638--1268674 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1268628 AAAATTTTTA
*
1268638 AAAAATTTAAATATATT
1 AAAATTTTAAATATATT
*
1268655 AAAATTTTAAATATGTT
1 AAAATTTTAAATATATT
1268672 AAA
1 AAA
1268675 GAAAATGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AAAATTTTAAATATATT
Found at i:1268732 original size:19 final size:18
Alignment explanation
Indices: 1268708--1268755 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1268698 TTAAATTTTT
*
1268708 AATATACTTAATATATTAA
1 AATATA-TTAAAATATTAA
*
1268727 AATATATTAAAAT-TTTA
1 AATATATTAAAATATTAA
*
1268744 AACATATTAAAA
1 AATATATTAAAA
1268756 AAATTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 14 0.54
18 6 0.23
19 6 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATATTAAAATATTAA
Found at i:1268781 original size:79 final size:80
Alignment explanation
Indices: 1268646--1268792 Score: 242
Period size: 79 Copynumber: 1.9 Consensus size: 80
1268636 TAAAAAATTT
* * * *
1268646 AAATATATTAAAATTTTAAATATGTTAAAGAAAATGTTGAGTATAACCAATTTTAAATTTTTAAT
1 AAATATATTAAAATTTTAAACATATTAAAGAAAATGTTAAGTATAACCAATTTTAAAATTTTAAT
1268711 ATACTTAATATATTA
66 ATACTTAATATATTA
*
1268726 AAATATATTAAAATTTTAAACATATTAAA-AAAATTTTAAGTATAACCAATTTTAAAATTTTAAT
1 AAATATATTAAAATTTTAAACATATTAAAGAAAATGTTAAGTATAACCAATTTTAAAATTTTAAT
1268790 ATA
66 ATA
1268793 TTTTTTAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
79 35 0.56
80 27 0.44
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (80 bp):
AAATATATTAAAATTTTAAACATATTAAAGAAAATGTTAAGTATAACCAATTTTAAAATTTTAAT
ATACTTAATATATTA
Found at i:1272045 original size:20 final size:21
Alignment explanation
Indices: 1272007--1272048 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1271997 TATCACCTGA
1272007 AATTTTTAAATGATATTTTAT
1 AATTTTTAAATGATATTTTAT
* *
1272028 AATTTTTTAAT-ATTTTTTAT
1 AATTTTTAAATGATATTTTAT
1272048 A
1 A
1272049 TGTTTAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
AATTTTTAAATGATATTTTAT
Found at i:1272054 original size:18 final size:16
Alignment explanation
Indices: 1272021--1272080 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 16
1272011 TTTAAATGAT
* *
1272021 ATTTTATAATTTTTTA
1 ATTTTTTAATATTTTA
*
1272037 ATATTTTTTATATGTTTA
1 AT-TTTTTAATAT-TTTA
1272055 GATTTTATTAATATTTTA
1 -ATTTT-TTAATATTTTA
1272073 ATTTTTTA
1 ATTTTTTA
1272081 GGAGATGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 5 0.14
17 12 0.33
18 11 0.31
19 8 0.22
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTTTTAATATTTTA
Found at i:1277333 original size:20 final size:21
Alignment explanation
Indices: 1277297--1277335 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1277287 TCCTCCTAAA
*
1277297 TTTTAAATTTTCACTTTATGT
1 TTTTAAATTATCACTTTATGT
1277318 TTTTAAATTATC-CTTTAT
1 TTTTAAATTATCACTTTAT
1277336 TAAATGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.26, C:0.10, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTTAAATTATCACTTTATGT
Found at i:1279071 original size:10 final size:10
Alignment explanation
Indices: 1279026--1279078 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
1279016 TTAAATTGGT
1279026 TATA-TTTAA
1 TATATTTTAA
*
1279035 AATATTTTTAA
1 TATA-TTTTAA
*
1279046 TAT-GTTTAA
1 TATATTTTAA
1279055 -A-ATTTTAA
1 TATATTTTAA
1279063 TATATTTTAA
1 TATATTTTAA
1279073 TATATT
1 TATATT
1279079 AAGTATATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
8 6 0.17
9 9 0.26
10 13 0.37
11 7 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (10 bp):
TATATTTTAA
Found at i:1279085 original size:19 final size:18
Alignment explanation
Indices: 1279026--1279087 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
1279016 TTAAATTGGT
**
1279026 TATA-TTTAAAATATTTT
1 TATATTTTAAAATATTAA
*
1279043 TAATATGTTTAAAATTTTAA
1 T-ATAT-TTTAAAATATTAA
*
1279063 TATATTTTAATATATTAA
1 TATATTTTAAAATATTAA
1279081 GTATATT
1 -TATATT
1279088 AAAAAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
17 1 0.03
18 14 0.39
19 10 0.28
20 11 0.31
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TATATTTTAAAATATTAA
Found at i:1279106 original size:79 final size:80
Alignment explanation
Indices: 1279003--1279149 Score: 206
Period size: 79 Copynumber: 1.9 Consensus size: 80
1278993 CTATTAAAAA
** * * * * *
1279003 TATATTAAAATTTTTAAATTGGTTATATTTAAAATATT-TTTAATATGTTTAAAATTTTAATATA
1 TATATTAAAAAATTAAAATTGGTTATACTCAAAATATTCTTTAACATATTTAAAATTTTAATATA
1279067 TTTTAATATATTAAG
66 TTTTAATATATTAAG
* *
1279082 TATATTAAAAAATTAAAATTGGTTATACTCAACATTTTCTTTAACATATTTAAAATTTTAATATA
1 TATATTAAAAAATTAAAATTGGTTATACTCAAAATATTCTTTAACATATTTAAAATTTTAATATA
1279147 TTT
66 TTT
1279150 AAAAAAATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
79 31 0.53
80 27 0.47
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (80 bp):
TATATTAAAAAATTAAAATTGGTTATACTCAAAATATTCTTTAACATATTTAAAATTTTAATATA
TTTTAATATATTAAG
Found at i:1279147 original size:17 final size:17
Alignment explanation
Indices: 1279121--1279153 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1279111 CAACATTTTC
1279121 TTTAACATATTTAAAAT
1 TTTAACATATTTAAAAT
*
1279138 TTTAATATATTTAAAA
1 TTTAACATATTTAAAA
1279154 AAATTTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAACATATTTAAAAT
Found at i:1283035 original size:8 final size:8
Alignment explanation
Indices: 1283022--1283048 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1283012 CAGTATAATT
1283022 AATTTTAA
1 AATTTTAA
1283030 AATTTTAA
1 AATTTTAA
1283038 AATTTTAA
1 AATTTTAA
1283046 AAT
1 AAT
1283049 ACATAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:1283185 original size:63 final size:63
Alignment explanation
Indices: 1283100--1283243 Score: 202
Period size: 63 Copynumber: 2.3 Consensus size: 63
1283090 TCTTAATATA
* ** * *
1283100 TTTAAAATTTTAA-AAAACTTAAAAAAATTAAATATATT-AAAAATTGTTAAATATATCCAAT
1 TTTAAAATTTTAATATATTTTAAAAAAATTAAATATATTAAAAAAATGTTAAATATAACCAAT
* *
1283161 TTTAATATATTTAATATATTTTAAAAAAATTAAATATATTAAAAAAATGTTAAGTATAACCAAT
1 TTTAAAAT-TTTAATATATTTTAAAAAAATTAAATATATTAAAAAAATGTTAAATATAACCAAT
1283225 TTTAAAATTTTAATATATT
1 TTTAAAATTTTAATATATT
1283244 CAATATACTT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
61 7 0.10
62 5 0.07
63 33 0.46
64 27 0.38
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (63 bp):
TTTAAAATTTTAATATATTTTAAAAAAATTAAATATATTAAAAAAATGTTAAATATAACCAAT
Found at i:1283218 original size:20 final size:18
Alignment explanation
Indices: 1283171--1283208 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1283161 TTTAATATAT
*
1283171 TTAATATATTTTAAAAAAA
1 TTAA-ATATATTAAAAAAA
1283190 TTAAATATATTAAAAAAA
1 TTAAATATATTAAAAAAA
1283208 T
1 T
1283209 GTTAAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAATATATTAAAAAAA
Found at i:1283400 original size:79 final size:81
Alignment explanation
Indices: 1283294--1283460 Score: 216
Period size: 79 Copynumber: 2.1 Consensus size: 81
1283284 TTTAGTATAT
* *
1283294 TTTTTAACAAACTTAAAAAATTTAAATATATTAAAATTTT-AA-ATATGTAAAGAAAATGTTGAG
1 TTTTTAACAAACTTAAAAAATTAAAATATATTAAAATTTTAAACATAT-TAAA-AAAATGTTAAG
1283357 TAT-A-ACCAATTTTAAA
64 TATAATACCAATTTTAAA
* * * * *
1283373 TTTTTAATATACTTAATATATTAAAATATATTAAAATTTTAAACATATTAAAAAAATTTTAAGTA
1 TTTTTAACAAACTTAAAAAATTAAAATATATTAAAATTTTAAACATATTAAAAAAATGTTAAGTA
1283438 TAATACCAATTTTAAA
66 TAATACCAATTTTAAA
*
1283454 ATTTTAA
1 TTTTTAA
1283461 AATATTTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
79 47 0.62
80 7 0.09
81 22 0.29
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (81 bp):
TTTTTAACAAACTTAAAAAATTAAAATATATTAAAATTTTAAACATATTAAAAAAATGTTAAGTA
TAATACCAATTTTAAA
Found at i:1283402 original size:19 final size:18
Alignment explanation
Indices: 1283378--1283425 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1283368 TTAAATTTTT
*
1283378 AATATACTTAATATATTAA
1 AATATA-TTAAAATATTAA
*
1283397 AATATATTAAAAT-TTTA
1 AATATATTAAAATATTAA
*
1283414 AACATATTAAAA
1 AATATATTAAAA
1283426 AAATTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 14 0.54
18 6 0.23
19 6 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATATTAAAATATTAA
Found at i:1286796 original size:22 final size:22
Alignment explanation
Indices: 1286762--1286803 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1286752 AGTTTCGATA
* *
1286762 TTCACTTTGATACTTAAATTCT
1 TTCAATTTAATACTTAAATTCT
*
1286784 TTCAATTTAATACTTGAATT
1 TTCAATTTAATACTTAAATT
1286804 TTTTTTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.50
Consensus pattern (22 bp):
TTCAATTTAATACTTAAATTCT
Found at i:1290629 original size:31 final size:31
Alignment explanation
Indices: 1290561--1290630 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1290551 TGTTAACAGC
* *
1290561 CAATAACCTAAATAAAAACTTTTAAATAGTT
1 CAATAACTTAAATAAAAACTTTTAAATAATT
* * *
1290592 CGATAACTTAAATGAAAATTTTTAAATAA-T
1 CAATAACTTAAATAAAAACTTTTAAATAATT
1290622 CTAATAACT
1 C-AATAACT
1290631 AAGTTGTAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.34
Consensus pattern (31 bp):
CAATAACTTAAATAAAAACTTTTAAATAATT
Found at i:1301029 original size:14 final size:14
Alignment explanation
Indices: 1301010--1301056 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
1301000 TAAGGTGAAA
1301010 TTTAATTTTTGTAT
1 TTTAATTTTTGTAT
*
1301024 TTTAATTTGAT-TATT
1 TTTAATTT-TTGTA-T
1301039 TTTAATTTTTAGTAT
1 TTTAATTTTT-GTAT
1301054 TTT
1 TTT
1301057 TCTTTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 11 0.41
15 14 0.52
16 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.70
Consensus pattern (14 bp):
TTTAATTTTTGTAT
Found at i:1301633 original size:22 final size:22
Alignment explanation
Indices: 1301608--1301653 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1301598 TATTTCTTAA
1301608 TTAAA-AAAATATTTATATAATT
1 TTAAATAAAATATTTA-ATAATT
**
1301630 TTAAATTTAATATTTAATAATT
1 TTAAATAAAATATTTAATAATT
1301652 TT
1 TT
1301654 TATTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATAAAATATTTAATAATT
Found at i:1301721 original size:15 final size:14
Alignment explanation
Indices: 1301694--1301723 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1301684 TAACATTTTT
1301694 TAGTATTTATATTA
1 TAGTATTTATATTA
1301708 TAGTATTATATATTA
1 TAGTATT-TATATTA
1301723 T
1 T
1301724 TATAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TAGTATTTATATTA
Found at i:1303873 original size:14 final size:14
Alignment explanation
Indices: 1303854--1303884 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1303844 TAATGTGGGA
1303854 TTTAATTTTTATAC
1 TTTAATTTTTATAC
*
1303868 TTTAATTTTTTTAC
1 TTTAATTTTTATAC
1303882 TTT
1 TTT
1303885 TATAATATTA
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:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTAATTTTTATAC
Found at i:1314704 original size:18 final size:18
Alignment explanation
Indices: 1314681--1314715 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1314671 CAATATATTA
*
1314681 TTTGAGTTATTCGAATTT
1 TTTGAGTTATTCAAATTT
1314699 TTTGAGTTATTCAAATT
1 TTTGAGTTATTCAAATT
1314716 GTAAAATTAA
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:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (18 bp):
TTTGAGTTATTCAAATTT
Found at i:1315045 original size:2 final size:2
Alignment explanation
Indices: 1315038--1315069 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1315028 ATAGTGGTTC
1315038 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
1315070 GAAACTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1318247 original size:44 final size:44
Alignment explanation
Indices: 1318185--1318368 Score: 190
Period size: 44 Copynumber: 4.1 Consensus size: 44
1318175 CTACTGTTAT
* * *
1318185 TGTTACCGATTCGACACTTTGTGTATCGAATACTGTTACCGTAT
1 TGTTACAGATTCGACACTTTGTGTGTCGAATACTGTTACCGTAC
* * * *
1318229 TATTATAGATTCGGCACTTTGTGTGTCGAATACTGTTATCGTTAC
1 TGTTACAGATTCGACACTTTGTGTGTCGAATACTGTTACCG-TAC
* * * *
1318274 TGTTACCA-ATTTGACACTTTGTATGTCGAATACTATTACTGTAC
1 TGTTA-CAGATTCGACACTTTGTGTGTCGAATACTGTTACCGTAC
* * * * *
1318318 TGTTACAGATTCGGCACTTTATCTGTTGAATACTGTTACTGTTAC
1 TGTTACAGATTCGACACTTTGTGTGTCGAATACTGTTACCG-TAC
1318363 TGTTAC
1 TGTTAC
1318369 TGTTACTATT
Statistics
Matches: 115, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
43 2 0.02
44 70 0.61
45 42 0.37
46 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.41
Consensus pattern (44 bp):
TGTTACAGATTCGACACTTTGTGTGTCGAATACTGTTACCGTAC
Found at i:1318303 original size:89 final size:89
Alignment explanation
Indices: 1318176--1318368 Score: 253
Period size: 89 Copynumber: 2.2 Consensus size: 89
1318166 ATGTGCCGAC
* * * * * *
1318176 TACTGTTATTGTTACCGATTCGACACTTTGTGTATCGAATACTGTTACCGTATTATTATAGATTC
1 TACTGTTACTGTTACCAATTCGACACTTTGTATATCGAATACTATTACCGTACTATTACAGATTC
* *
1318241 GGCACTTTGTGTGTCGAATACTGT
66 GGCACTTTATCTGTCGAATACTGT
* * * *
1318265 TA-TCGTTACTGTTACCAATTTGACACTTTGTATGTCGAATACTATTACTGTACTGTTACAGATT
1 TACT-GTTACTGTTACCAATTCGACACTTTGTATATCGAATACTATTACCGTACTATTACAGATT
*
1318329 CGGCACTTTATCTGTTGAATACTGT
65 CGGCACTTTATCTGTCGAATACTGT
1318354 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
1318369 TGTTACTATT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
88 1 0.01
89 87 0.98
90 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (89 bp):
TACTGTTACTGTTACCAATTCGACACTTTGTATATCGAATACTATTACCGTACTATTACAGATTC
GGCACTTTATCTGTCGAATACTGT
Found at i:1318359 original size:6 final size:6
Alignment explanation
Indices: 1318348--1318403 Score: 67
Period size: 6 Copynumber: 9.2 Consensus size: 6
1318338 ATCTGTTGAA
* * * *
1318348 TACTGT TACTGT TACTGT TACTGT TACTAT TACTGC TACCGT TATTGCT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T
1318397 TACTGT T
1 TACTGT T
1318404 TAGGTACTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 36 0.88
7 5 0.12
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:1321490 original size:50 final size:50
Alignment explanation
Indices: 1321415--1321605 Score: 283
Period size: 50 Copynumber: 3.8 Consensus size: 50
1321405 TTGGGTAAAT
*
1321415 AGGTCCCATGTAAGACCATGTCTGGGACACGGCATTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
*
1321465 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
** * *
1321515 AGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
** * *
1321565 AACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 -AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
1321606 TGTTATGATC
Statistics
Matches: 126, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 93 0.74
51 33 0.26
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
Found at i:1323912 original size:56 final size:56
Alignment explanation
Indices: 1323831--1323939 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 56
1323821 TGTATTTTGG
1323831 AGGAGGTGTAGTCCATATACATGGGTAAGTTACAACATTCATTAGCCTATAAATTC
1 AGGAGGTGTAGTCCATATACATGGGTAAGTTACAACATTCATTAGCCTATAAATTC
* * *
1323887 AGGATGTGTGGTCCATATACGTGGGTAAGTTACAACATTCATTAGCCTATAAA
1 AGGAGGTGTAGTCCATATACATGGGTAAGTTACAACATTCATTAGCCTATAAA
1323940 ATCCATTAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (56 bp):
AGGAGGTGTAGTCCATATACATGGGTAAGTTACAACATTCATTAGCCTATAAATTC
Found at i:1325087 original size:4 final size:4
Alignment explanation
Indices: 1325078--1325108 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1325068 GGAACTTATA
1325078 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
1325109 TCAGGTGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1328512 original size:21 final size:21
Alignment explanation
Indices: 1328433--1328540 Score: 110
Period size: 21 Copynumber: 5.1 Consensus size: 21
1328423 CCTCATCAGT
1328433 ATACGACACAT-AAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* ** * *
1328453 AAACGACACACGAGGTGTCTG
1 ATACGACACATAAAGTGCCTG
** *
1328474 ATACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
1328495 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCT--G
*
1328518 ATACGACACGTAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
1328539 AT
1 AT
1328541 GGGCAAAGCC
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.12
21 46 0.61
23 20 0.27
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:1330179 original size:23 final size:23
Alignment explanation
Indices: 1330153--1330274 Score: 226
Period size: 23 Copynumber: 5.3 Consensus size: 23
1330143 ATAAGTGCCA
*
1330153 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
1330176 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
1330199 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
*
1330222 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
1330245 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
1330268 CACTGAT
1 CACTGAT
1330275 CAATAACACT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 96 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATACGTAGCCGAAGCTAC
Found at i:1330526 original size:18 final size:17
Alignment explanation
Indices: 1330500--1330538 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1330490 ATTTTCCTTC
1330500 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
1330517 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
1330535 CACA
1 CACA
1330539 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:1331423 original size:36 final size:36
Alignment explanation
Indices: 1331376--1331466 Score: 105
Period size: 36 Copynumber: 2.5 Consensus size: 36
1331366 CTTTTCAAAT
* *
1331376 TCACATTTCAATTCAATTTCACTTTTTTACTTTCAA-
1 TCACAATTCAATTCAATTT-ACTTTTCTACTTTCAAG
*
1331412 TCACAATTCAATTCAAATTTACTTTTCTATTTTCAAG
1 TCACAATTCAATTC-AATTTACTTTTCTACTTTCAAG
*
1331449 TCA-ATATTCATTTCAATT
1 TCACA-ATTCAATTCAATT
1331467 CCACACATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
36 32 0.67
37 16 0.33
ACGTcount: A:0.31, C:0.20, G:0.01, T:0.48
Consensus pattern (36 bp):
TCACAATTCAATTCAATTTACTTTTCTACTTTCAAG
Found at i:1331538 original size:16 final size:16
Alignment explanation
Indices: 1331516--1331555 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
1331506 TTAATAATAA
1331516 TACTTACCTTA-TATT
1 TACTTACCTTATTATT
1331531 TCACTTACCTTATTATT
1 T-ACTTACCTTATTATT
1331548 TACTTACC
1 TACTTACC
1331556 ATACATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.04
16 17 0.74
17 5 0.22
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (16 bp):
TACTTACCTTATTATT
Found at i:1332645 original size:21 final size:20
Alignment explanation
Indices: 1332621--1332659 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1332611 ATCTGTAAAC
1332621 TACAAATATATATATTTTAAT
1 TACAAATATAT-TATTTTAAT
* *
1332642 TACACATGTATTATTTTA
1 TACAAATATATTATTTTA
1332660 TCACCATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (20 bp):
TACAAATATATTATTTTAAT
Done.