Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 8 of 168
Found at i:2232104 original size:20 final size:20
Alignment explanation
Indices: 2232076--2232115 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2232066 CGAAGACACT
2232076 TACAGAATACGCCACAAAGG
1 TACAGAATACGCCACAAAGG
* *
2232096 TACATAATATGCCACAAAGG
1 TACAGAATACGCCACAAAGG
2232116 CATCATAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
TACAGAATACGCCACAAAGG
Found at i:2233776 original size:49 final size:49
Alignment explanation
Indices: 2233632--2233786 Score: 159
Period size: 49 Copynumber: 3.1 Consensus size: 49
2233622 CCATGCCTCA
* *
2233632 AGACTTGCCTCATCAGCTTCAAACTTTAACTTCAAAGTTCTATGTCTCG
1 AGACTTACCTCCTCAGCTTCAAACTTTAACTTCAAAGTTCTATGTCTCG
* ** * * * *
2233681 AGACATTAACCTCC-AAGCCCCAAGACTTTAGCTTCGAAGTTTTATGTCTTG
1 AGAC-TT-ACCTCCTCAGCTTCAA-ACTTTAACTTCAAAGTTCTATGTCTCG
* * * *
2233732 GGACTTACCTCCTCATCTTCAAATTTTACCTTCAAAGTTCTATGTCTCG
1 AGACTTACCTCCTCAGCTTCAAACTTTAACTTCAAAGTTCTATGTCTCG
2233781 AGACTT
1 AGACTT
2233787 TGGAGTTATG
Statistics
Matches: 82, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
49 37 0.45
50 15 0.18
51 30 0.37
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (49 bp):
AGACTTACCTCCTCAGCTTCAAACTTTAACTTCAAAGTTCTATGTCTCG
Found at i:2236031 original size:19 final size:19
Alignment explanation
Indices: 2235988--2236031 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2235978 AATAAAGAAT
2235988 TAATTTTTTAAAAAAAGTA
1 TAATTTTTTAAAAAAAGTA
* *
2236007 -ATATTTTTTAAAATAATTA
1 TA-ATTTTTTAAAAAAAGTA
2236026 TAATTT
1 TAATTT
2236032 AGATGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 1 0.05
19 19 0.90
20 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TAATTTTTTAAAAAAAGTA
Found at i:2237489 original size:14 final size:13
Alignment explanation
Indices: 2237455--2237496 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
2237445 AACTATACGA
2237455 AAAAT-AAT-AAG
1 AAAATAAATAAAG
2237466 AAAATAAATAAAG
1 AAAATAAATAAAG
*
2237479 AAAATTAAATAAAT
1 AAAA-TAAATAAAG
2237493 AAAA
1 AAAA
2237497 AACAAGAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 5 0.19
12 3 0.11
13 7 0.26
14 12 0.44
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (13 bp):
AAAATAAATAAAG
Found at i:2240164 original size:6 final size:6
Alignment explanation
Indices: 2240153--2240178 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2240143 AAATTAAATA
2240153 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
2240179 CACCAAATCC
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:2243306 original size:12 final size:12
Alignment explanation
Indices: 2243291--2243324 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2243281 TTAGTTTAAG
2243291 GATGTGTTTTTA
1 GATGTGTTTTTA
2243303 GATGTGTTTTTA
1 GATGTGTTTTTA
*
2243315 GATGAGTTTT
1 GATGTGTTTT
2243325 CTCTCAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (12 bp):
GATGTGTTTTTA
Found at i:2244424 original size:22 final size:22
Alignment explanation
Indices: 2244367--2244438 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
2244357 ATGGGGGTAG
*
2244367 GATATGATATGATATGAAATGT
1 GATATGATATGATATGAAATAT
* * *
2244389 GTTACGACATGATATGAAATAT
1 GATATGATATGATATGAAATAT
* * *
2244411 GATATGATAAGATATGATATAA
1 GATATGATATGATATGAAATAT
2244433 GATATG
1 GATATG
2244439 CTCTTTTATG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (22 bp):
GATATGATATGATATGAAATAT
Found at i:2255191 original size:30 final size:30
Alignment explanation
Indices: 2255148--2255297 Score: 201
Period size: 30 Copynumber: 5.0 Consensus size: 30
2255138 AGGTGAATAT
* *
2255148 ATTGCTCACACAAGCTGACATTATGATAGA
1 ATTGCTTACACAAGCTGACATTATAATAGA
* *
2255178 ATTGCTTATACAAGCTGATATTATAATAGA
1 ATTGCTTACACAAGCTGACATTATAATAGA
* *
2255208 TTTGCTTACACAAGCTGACATGATAATAGA
1 ATTGCTTACACAAGCTGACATTATAATAGA
* * * *
2255238 TTTGCTCACAGAAGCTAACATTATAATAGA
1 ATTGCTTACACAAGCTGACATTATAATAGA
*
2255268 ATTGCTTATACAAGCTGACATTATAATAGA
1 ATTGCTTACACAAGCTGACATTATAATAGA
2255298 TTACCCGACC
Statistics
Matches: 103, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 103 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (30 bp):
ATTGCTTACACAAGCTGACATTATAATAGA
Found at i:2258608 original size:18 final size:18
Alignment explanation
Indices: 2258581--2258615 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2258571 AGGTATCGAG
2258581 ACCTCAATTTTATAAACC
1 ACCTCAATTTTATAAACC
*
2258599 ACCTCGATTTTATAAAC
1 ACCTCAATTTTATAAAC
2258616 TAAGCCGTAA
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:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (18 bp):
ACCTCAATTTTATAAACC
Found at i:2259791 original size:24 final size:25
Alignment explanation
Indices: 2259734--2259805 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 25
2259724 CCGTTCTATG
*
2259734 GCAAAGGATGAATTGATAGAAAAAT
1 GCAAAGGATGAATTGACAGAAAAAT
* * *
2259759 GCAATGGATGAATTGACAG-TATAT
1 GCAAAGGATGAATTGACAGAAAAAT
* *
2259783 GCAAAGGATGAGTTGACGGAAAA
1 GCAAAGGATGAATTGACAGAAAA
2259806 TGTACCCAAG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
24 19 0.51
25 18 0.49
ACGTcount: A:0.44, C:0.07, G:0.28, T:0.21
Consensus pattern (25 bp):
GCAAAGGATGAATTGACAGAAAAAT
Found at i:2260502 original size:34 final size:34
Alignment explanation
Indices: 2260462--2260528 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
2260452 ATCATGTTTG
2260462 ATATATGTGCTTGGAGTAGTTAGGCGATGGATAT
1 ATATATGTGCTTGGAGTAGTTAGGCGATGGATAT
2260496 ATATATGTGCTTGGAGTAGTTAGGCGATGGATA
1 ATATATGTGCTTGGAGTAGTTAGGCGATGGATA
2260529 GTTTATAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.34
Consensus pattern (34 bp):
ATATATGTGCTTGGAGTAGTTAGGCGATGGATAT
Found at i:2260587 original size:2 final size:2
Alignment explanation
Indices: 2260580--2260605 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2260570 GAATGTTAGG
2260580 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
2260606 GGTAATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2264595 original size:111 final size:105
Alignment explanation
Indices: 2264473--2264742 Score: 334
Period size: 110 Copynumber: 2.5 Consensus size: 105
2264463 AAAAACTTTA
*
2264473 AAATTTTTGAATTTTTTCGTATACTGGTGTCGGCCAATGACTGCCCAAAATGTAAATTTTTTTTA
1 AAATTTTTGAATTTTTTCGTATACTGGTGTCGGCCAATGAC-ACCCAAAATGTAAA-TTTTTTTA
*
2264538 CATAAAGGTGGTGCCGGCCATTGCCAGGCCACCACTAAAAAAAAT
64 CATAAAGGTGGCGCCGGCCATTGCCAGGCCACCAC---AAAAAAT
* * **
2264583 AAATTTTTTGAATTTTTTCATATACTGGTGTCGACCAATGACACGAAAAAAT-TCAAATTTTTTT
1 AAA-TTTTTGAATTTTTTCGTATACTGGTGTCGGCCAATGACAC-CCAAAATGT-AAATTTTTTT
* *
2264647 ACATAAAGGTGGCGCCGGCTATTGCCAGGCCACCACCAAAAA-
63 ACATAAAGGTGGCGCCGGCCATTGCCAGGCCACCACAAAAAAT
*
2264689 AAA--TTTGAAATTTTTT-GTATACTGGTGCCGGCCAATGACAACCCAAAATGTAAA
1 AAATTTTTG-AATTTTTTCGTATACTGGTGTCGGCCAATGAC-ACCCAAAATGTAAA
2264743 AAATATATAT
Statistics
Matches: 141, Mismatches: 13, Indels: 19
0.82 0.08 0.11
Matches are distributed among these distances:
103 32 0.23
104 11 0.08
106 3 0.02
107 5 0.04
110 46 0.33
111 44 0.31
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (105 bp):
AAATTTTTGAATTTTTTCGTATACTGGTGTCGGCCAATGACACCCAAAATGTAAATTTTTTTACA
TAAAGGTGGCGCCGGCCATTGCCAGGCCACCACAAAAAAT
Found at i:2268777 original size:21 final size:22
Alignment explanation
Indices: 2268734--2268777 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2268724 AATATCAATT
*
2268734 AATTAATTATTTCAATTAGATA
1 AATTAATTATTTCAATTAAATA
*
2268756 AATTAATT-TTTGAATTAAATA
1 AATTAATTATTTCAATTAAATA
2268777 A
1 A
2268778 TTTTTTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
AATTAATTATTTCAATTAAATA
Found at i:2271953 original size:75 final size:76
Alignment explanation
Indices: 2271830--2271972 Score: 200
Period size: 75 Copynumber: 1.9 Consensus size: 76
2271820 TCATACTTGA
* * *
2271830 TCTTCTTTGGCGTTAAGAGGGACAAGACCCCTCACCTTAGCTAATTCATC-AAAGGTATAAGACC
1 TCTTCTTTGGCGTTAAGAGGGACAAGACCCCTCACCTAAGCCAATTCATCTAAAGGGATAAGACC
2271894 TCTCACATTGG
66 TCTCACATTGG
* ** *
2271905 TCTTCTTTGGTGTTAA-AGGAGACAAGACCTTTCACCTAAGCCAATTCATCTAAGGGGATAAGAC
1 TCTTCTTTGGCGTTAAGAGG-GACAAGACCCCTCACCTAAGCCAATTCATCTAAAGGGATAAGAC
2271969 CTCT
65 CTCT
2271973 GGTATTGGCC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 3 0.05
75 41 0.69
76 15 0.25
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (76 bp):
TCTTCTTTGGCGTTAAGAGGGACAAGACCCCTCACCTAAGCCAATTCATCTAAAGGGATAAGACC
TCTCACATTGG
Found at i:2281159 original size:2 final size:2
Alignment explanation
Indices: 2281152--2281189 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2281142 GATCCTCGCC
2281152 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
2281190 CAAAATAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2287125 original size:40 final size:40
Alignment explanation
Indices: 2287081--2287157 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
2287071 GATAGTATGG
* *
2287081 ACATTGTTCCTACTGTAAAAGGATATGGGTTCGAGTGCGA
1 ACATTGTTCCTAATGTAAAAGGATATGGATTCGAGTGCGA
* *
2287121 ACATTGTTCCTAATGTAAGAGGATATGGATTTGAGTG
1 ACATTGTTCCTAATGTAAAAGGATATGGATTCGAGTG
2287158 TGTTAAAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (40 bp):
ACATTGTTCCTAATGTAAAAGGATATGGATTCGAGTGCGA
Found at i:2287317 original size:19 final size:19
Alignment explanation
Indices: 2287281--2287319 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2287271 AGTAAAATTG
*
2287281 TATTATTTTGAGGGTATTT
1 TATTATTTTGAGGATATTT
2287300 TATTATTTT-AGGAATATTT
1 TATTATTTTGAGG-ATATTT
2287319 T
1 T
2287320 TATCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (19 bp):
TATTATTTTGAGGATATTT
Found at i:2287627 original size:22 final size:24
Alignment explanation
Indices: 2287589--2287635 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
2287579 CCAGAAGGTA
*
2287589 AAAGTGGGGCCCTTTGTT-TTTTT
1 AAAGTGGGGCCCATTGTTCTTTTT
2287612 AAAGT-GGGCCCATTGTTCTTTTT
1 AAAGTGGGGCCCATTGTTCTTTTT
2287635 A
1 A
2287636 GGGATTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (24 bp):
AAAGTGGGGCCCATTGTTCTTTTT
Found at i:2293119 original size:51 final size:51
Alignment explanation
Indices: 2292988--2293175 Score: 186
Period size: 51 Copynumber: 3.7 Consensus size: 51
2292978 GAAAGTGATG
* ** * * *
2292988 GTCACGTGTGTAACACTATGTGCAGGCTACTACGTGTACC-GA-AATGATA
1 GTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTAATA
* * *
2293037 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT-TTT
1 -GTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTAATA
* * * *
2293088 GATCACGTGTGTAGTACTATGTGTAGGCTACTACT-TGTATCGGATGGTAATA
1 G-TCACATGTGTAGTACTATGTGCAGGCTACTA-TGTGTACCGGATAGTAATA
* *
2293140 GTCACATGTGTAGTACTACGTGCAGACTACTATGTG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
2293176 AACCAAACAT
Statistics
Matches: 113, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
50 37 0.33
51 71 0.63
52 5 0.04
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (51 bp):
GTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTAATA
Found at i:2293174 original size:102 final size:101
Alignment explanation
Indices: 2292989--2293175 Score: 252
Period size: 101 Copynumber: 1.8 Consensus size: 101
2292979 AAAGTGATGG
*
2292989 TCACGTGTGTAACACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAACACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCACATGTGTAGTAC
* *
2293054 TATGTGCAGGCTACTATGTGTACCGGATAGTTTTGA
66 TACGTGCAGACTACTATGTGTACCGGATAGTTTTGA
** * * * *
2293090 TCACGTGTGTAGTACTATGTGTAGGCTACTACTTGTATCG-GATGGTAATA-GTCACATGTGTAG
1 TCACGTGTGTAACACTATGTGCAGGCTACTACGTGTACCGAAAT-G--ATAGGTCACATGTGTAG
2293153 TACTACGTGCAGACTACTATGTG
63 TACTACGTGCAGACTACTATGTG
2293176 AACCAAACAT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
100 2 0.03
101 36 0.49
102 33 0.45
103 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (101 bp):
TCACGTGTGTAACACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCACATGTGTAGTAC
TACGTGCAGACTACTATGTGTACCGGATAGTTTTGA
Found at i:2293192 original size:102 final size:101
Alignment explanation
Indices: 2292989--2293192 Score: 225
Period size: 102 Copynumber: 2.0 Consensus size: 101
2292979 AAAGTGATGG
*
2292989 TCACGTGTGTAACACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAACACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCACATGTGTAGTAC
* * * ** * *
2293054 TATGTGCAGGCTACTATGTGTACCGGATAGTTTTGA
66 TACGTGCAGACTACTATGTGAACCAAACAGTATTGA
** * * * *
2293090 TCACGTGTGTAGTACTATGTGTAGGCTACTACTTGTATCG-GATGGTAATA-GTCACATGTGTAG
1 TCACGTGTGTAACACTATGTGCAGGCTACTACGTGTACCGAAAT-G--ATAGGTCACATGTGTAG
2293153 TACTACGTGCAGACTACTATGTGAACCAAACA-TCATTGA
63 TACTACGTGCAGACTACTATGTGAACCAAACAGT-ATTGA
2293192 T
1 T
2293193 TAGTAAGGTG
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
100 2 0.02
101 37 0.44
102 43 0.51
103 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAACACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCACATGTGTAGTAC
TACGTGCAGACTACTATGTGAACCAAACAGTATTGA
Found at i:2293233 original size:45 final size:45
Alignment explanation
Indices: 2293182--2293268 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
2293172 TGTGAACCAA
** * *
2293182 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACTGG
1 ACATCATCAATTAATAAGGTGGTTGCTATGTGCTGAATCCACTGG
2293227 ACATCATCAATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
1 ACATCATCAATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
2293269 CGAGTATCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (45 bp):
ACATCATCAATTAATAAGGTGGTTGCTATGTGCTGAATCCACTGG
Found at i:2296579 original size:50 final size:50
Alignment explanation
Indices: 2296525--2296718 Score: 196
Period size: 50 Copynumber: 3.9 Consensus size: 50
2296515 TATTAAGGTT
*
2296525 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
*** * * *
2296575 ATGAGAGGTCCCCCATAAGACCATGTTTGGGACATGGCATAGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
* * *
2296625 ATGAG-GACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTAC
1 ATGAGAG-GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * ** * * *
2296674 AGGAAACATCCCATGTAAGATCATGTCTAGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
2296719 TGTTATTATC
Statistics
Matches: 117, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.32
50 79 0.68
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:2296943 original size:20 final size:20
Alignment explanation
Indices: 2296918--2296956 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2296908 CATGAGTATT
2296918 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
2296938 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
2296957 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:2303359 original size:32 final size:32
Alignment explanation
Indices: 2303312--2303376 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
2303302 TTAAAGGGAG
** *
2303312 ATAGTTTGTTGTGGATATTATAGTAAGAGCTC
1 ATAGTTTGTCATGGATATTAGAGTAAGAGCTC
2303344 ATAGTTTGTCATGGATATTAGAGTAAGAGCTC
1 ATAGTTTGTCATGGATATTAGAGTAAGAGCTC
2303376 A
1 A
2303377 ATTCAAATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.37
Consensus pattern (32 bp):
ATAGTTTGTCATGGATATTAGAGTAAGAGCTC
Found at i:2313006 original size:18 final size:18
Alignment explanation
Indices: 2312964--2313008 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
2312954 TTGAATTATT
2312964 ATTTAATTAAAAATATAAA
1 ATTTAA-TAAAAATATAAA
*
2312983 AATTAATAAAAAT-TAAA
1 ATTTAATAAAAATATAAA
2313000 ACTTTAATA
1 A-TTTAATA
2313009 TATTGTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 13 0.57
19 5 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTTAATAAAAATATAAA
Found at i:2314779 original size:11 final size:11
Alignment explanation
Indices: 2314765--2314887 Score: 69
Period size: 11 Copynumber: 12.4 Consensus size: 11
2314755 TTTTTTTTAA
2314765 TTTTAAAATAT
1 TTTTAAAATAT
* *
2314776 TTTTTACATACT
1 TTTTAAAATA-T
2314788 TTTT-AAAT-T
1 TTTTAAAATAT
*
2314797 TTTT-TAA-A-
1 TTTTAAAATAT
2314805 TTTTAAAATAT
1 TTTTAAAATAT
2314816 TTTT--AA-A-
1 TTTTAAAATAT
2314823 -TTTAAAATAT
1 TTTTAAAATAT
2314833 TTTTAAAATACT
1 TTTTAAAATA-T
**
2314845 TTTTTTAAT-T
1 TTTTAAAATAT
*
2314855 TTTT----TAA
1 TTTTAAAATAT
2314862 TTTTAAAATAT
1 TTTTAAAATAT
2314873 TTTTAAAATAT
1 TTTTAAAATAT
2314884 TTTT
1 TTTT
2314888 TTTAATTTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 32
0.68 0.07 0.25
Matches are distributed among these distances:
6 4 0.05
7 4 0.05
8 7 0.08
9 12 0.14
10 6 0.07
11 41 0.47
12 13 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2314810 original size:17 final size:18
Alignment explanation
Indices: 2314755--2314879 Score: 92
Period size: 18 Copynumber: 6.6 Consensus size: 18
2314745 ATAAATATAT
*
2314755 TTTTTTTTAATTTTAAAA
1 TTTTTTTAAATTTTAAAA
*
2314773 TATTTTTTACATACTTTTTAAA
1 T-TTTTTTA-A-A-TTTTAAAA
2314795 TTTTTTTAAATTTTAAAA
1 TTTTTTTAAATTTTAAAA
*
2314813 TATTTTTAAA-TTTAAAA
1 TTTTTTTAAATTTTAAAA
* **
2314830 TATTTTTAAAATACTTTTTTTAA
1 T-TTTTT-TAA-A--TTTTAAAA
2314853 TTTTTTT-AATTTTAAAA
1 TTTTTTTAAATTTTAAAA
*
2314870 TATTTTTAAA
1 TTTTTTTAAA
2314880 ATATTTTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
17 20 0.24
18 23 0.27
19 10 0.12
20 4 0.05
21 8 0.10
22 13 0.15
23 6 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTTTAAATTTTAAAA
Found at i:2314832 original size:57 final size:57
Alignment explanation
Indices: 2314758--2314879 Score: 192
Period size: 57 Copynumber: 2.1 Consensus size: 57
2314748 AATATATTTT
* * *
2314758 TTTTTAATTTTAAAATATTTTTTACATAC-TTTTTAAATTTTTTTAAATTTTAAAATA
1 TTTTTAAATTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTT-AATTTTAAAATA
*
2314815 TTTTTAAATTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATA
1 TTTTTAAATTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATA
2314872 TTTTTAAA
1 TTTTTAAA
2314880 ATATTTTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
57 46 0.77
58 14 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (57 bp):
TTTTTAAATTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATA
Found at i:2314860 original size:40 final size:40
Alignment explanation
Indices: 2314815--2314897 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
2314805 TTTTAAAATA
2314815 TTTTTAAATTTAAAATATTTTTAAAATACTTTTTTTAATT
1 TTTTTAAATTTAAAATATTTTTAAAATACTTTTTTTAATT
* *
2314855 TTTTTAATTTTAAAATATTTTTAAAATATTTTTTTTAATT
1 TTTTTAAATTTAAAATATTTTTAAAATACTTTTTTTAATT
2314895 TTT
1 TTT
2314898 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTAAATTTAAAATATTTTTAAAATACTTTTTTTAATT
Found at i:2316925 original size:50 final size:50
Alignment explanation
Indices: 2316871--2316970 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
2316861 ACCAATGATA
2316871 CTCAAACTCAGGTTTTAGTGTCGGATATTGATATGATCTGAAAAACTATG
1 CTCAAACTCAGGTTTTAGTGTCGGATATTGATATGATCTGAAAAACTATG
2316921 CTCAAACTCAGGTTTTAGTGTCGGATATTGATATGATCTGAAAAACTATG
1 CTCAAACTCAGGTTTTAGTGTCGGATATTGATATGATCTGAAAAACTATG
2316971 TTACACGAAC
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:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (50 bp):
CTCAAACTCAGGTTTTAGTGTCGGATATTGATATGATCTGAAAAACTATG
Found at i:2319990 original size:2 final size:2
Alignment explanation
Indices: 2319983--2320023 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2319973 TATTAGTTAA
2319983 AT AT 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 AT AT A
2320024 AATGATAATC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2320327 original size:9 final size:9
Alignment explanation
Indices: 2320313--2320361 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
2320303 ATTTTTAGAT
2320313 AATTTTAAA
1 AATTTTAAA
2320322 AATTTTTAAA
1 AA-TTTTAAA
*
2320332 AATTTTTTAA
1 AA-TTTTAAA
*
2320342 AATTTTTAA
1 AATTTTAAA
2320351 AATTTTAAA
1 AATTTTAAA
2320360 AA
1 AA
2320362 ATAAATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
9 19 0.51
10 18 0.49
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTTTAAA
Found at i:2320328 original size:10 final size:10
Alignment explanation
Indices: 2320315--2320363 Score: 73
Period size: 10 Copynumber: 5.0 Consensus size: 10
2320305 TTTTAGATAA
2320315 TTTTAAAAAT
1 TTTTAAAAAT
2320325 TTTTAAAAAT
1 TTTTAAAAAT
*
2320335 TTTTTAAAAT
1 TTTTAAAAAT
2320345 TTTT-AAAAT
1 TTTTAAAAAT
*
2320354 TTTAAAAAAT
1 TTTTAAAAAT
2320364 AAATAATTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
9 8 0.22
10 28 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTTAAAAAT
Found at i:2320762 original size:20 final size:19
Alignment explanation
Indices: 2320722--2320760 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2320712 TAAAACGGAC
*
2320722 ATGAAAAGTATAAAAAGAA
1 ATGAAAAATATAAAAAGAA
2320741 ATGAAAAATATAAAAAGAA
1 ATGAAAAATATAAAAAGAA
2320760 A
1 A
2320761 ATAGATGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (19 bp):
ATGAAAAATATAAAAAGAA
Found at i:2321364 original size:22 final size:22
Alignment explanation
Indices: 2321339--2321382 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2321329 CATAACTTGC
2321339 CATTTTTTGTATTGACAATCTT
1 CATTTTTTGTATTGACAATCTT
2321361 CATTTTTTGTATTGACAATCTT
1 CATTTTTTGTATTGACAATCTT
2321383 TTGGAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (22 bp):
CATTTTTTGTATTGACAATCTT
Found at i:2325280 original size:35 final size:35
Alignment explanation
Indices: 2325241--2325348 Score: 126
Period size: 35 Copynumber: 3.1 Consensus size: 35
2325231 TAGTATAACT
*
2325241 GACAATAAATGCGCCCTGCGTTGGTCGGTAGAACC
1 GACAATAAATGCGCCCTGCGCTGGTCGGTAGAACC
** * * * *
2325276 GACAAATATGTGTGCCCAGCACTGGTCGGTATAACC
1 GAC-AATAAATGCGCCCTGCGCTGGTCGGTAGAACC
* *
2325312 GATAATAAATGCACCCTGCGCTGGTCGGTAGAACC
1 GACAATAAATGCGCCCTGCGCTGGTCGGTAGAACC
2325347 GA
1 GA
2325349 AAAACATGTG
Statistics
Matches: 57, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
35 30 0.53
36 27 0.47
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (35 bp):
GACAATAAATGCGCCCTGCGCTGGTCGGTAGAACC
Found at i:2325301 original size:71 final size:71
Alignment explanation
Indices: 2325214--2325360 Score: 213
Period size: 71 Copynumber: 2.1 Consensus size: 71
2325204 TTGACAATGA
* * * * * *
2325214 GTGTGCCTAGCACTGGTTAGTATAACTGACAATAAATGCGCCCTGCGTTGGTCGGTAGAACCGAC
1 GTGTGCCCAGCACTGGTCAGTATAACCGACAATAAATGCACCCTGCGCTGGTCGGTAGAACCGAA
*
2325279 AAATAT
66 AAACAT
* *
2325285 GTGTGCCCAGCACTGGTCGGTATAACCGATAATAAATGCACCCTGCGCTGGTCGGTAGAACCGAA
1 GTGTGCCCAGCACTGGTCAGTATAACCGACAATAAATGCACCCTGCGCTGGTCGGTAGAACCGAA
2325350 AAACAT
66 AAACAT
2325356 GTGTG
1 GTGTG
2325361 AAATCATTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (71 bp):
GTGTGCCCAGCACTGGTCAGTATAACCGACAATAAATGCACCCTGCGCTGGTCGGTAGAACCGAA
AAACAT
Found at i:2325302 original size:36 final size:35
Alignment explanation
Indices: 2325262--2325360 Score: 99
Period size: 35 Copynumber: 2.8 Consensus size: 35
2325252 CGCCCTGCGT
2325262 TGGTCGGTAGAACCGACAAATATGTGTGCCCAGCAC
1 TGGTCGGTAGAACCGA-AAATATGTGTGCCCAGCAC
* * ** ** * *
2325298 TGGTCGGTATAACCGATAATAAATGCACCCTGCGC
1 TGGTCGGTAGAACCGAAAATATGTGTGCCCAGCAC
*
2325333 TGGTCGGTAGAACCGAAAAACATGTGTG
1 TGGTCGGTAGAACCG-AAAATATGTGTG
2325361 AAATCATTTC
Statistics
Matches: 47, Mismatches: 15, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
35 26 0.55
36 21 0.45
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.21
Consensus pattern (35 bp):
TGGTCGGTAGAACCGAAAATATGTGTGCCCAGCAC
Found at i:2335741 original size:50 final size:50
Alignment explanation
Indices: 2335675--2335772 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
2335665 TACAAGCTGC
* * *
2335675 ACAAGTGGAATACGTATAGAAGTACACT-TCTTCTATTTGATATTGATTGT
1 ACAAGTAGAATACGTATAGAACTACACTCT-TTCTATTTGACATTGATTGT
* * *
2335725 ACAAGTAGAATCCGTATAGAACTTCTCTCTTTCTATTTGACATTGATT
1 ACAAGTAGAATACGTATAGAACTACACTCTTTCTATTTGACATTGATT
2335773 AGAATAAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 40 0.98
51 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (50 bp):
ACAAGTAGAATACGTATAGAACTACACTCTTTCTATTTGACATTGATTGT
Found at i:2337957 original size:2 final size:2
Alignment explanation
Indices: 2337950--2337984 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2337940 CTTATAGAAT
2337950 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2337985 ATTTGACCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2340155 original size:3 final size:3
Alignment explanation
Indices: 2340147--2340201 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
2340137 TTTAGATTTC
2340147 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2340195 TAT TAT T
1 TAT TAT T
2340202 CTTAAATTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2343542 original size:34 final size:35
Alignment explanation
Indices: 2343458--2343564 Score: 114
Period size: 34 Copynumber: 3.1 Consensus size: 35
2343448 TACTCGATAA
* *
2343458 ATTGCTACCATATTGATCTGTTATAA-CAT-ATCT
1 ATTGCTACCGTATTGATCTGTTATAAGCATGTTCT
* * *
2343491 ATTGATATCGTATTGATCTGTCATAAGCATGTTC-
1 ATTGCTACCGTATTGATCTGTTATAAGCATGTTCT
* *
2343525 CTTGCTACCGTATTGATCTATTATAAGCATG-TCAT
1 ATTGCTACCGTATTGATCTGTTATAAGCATGTTC-T
2343560 ATTGC
1 ATTGC
2343565 ACTGCATGAG
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
33 24 0.41
34 29 0.49
35 6 0.10
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (35 bp):
ATTGCTACCGTATTGATCTGTTATAAGCATGTTCT
Found at i:2348216 original size:21 final size:21
Alignment explanation
Indices: 2348191--2348237 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2348181 CTGCTCTTAT
*
2348191 TAAAAATTAGAAAAAAATTTA
1 TAAAAATAAGAAAAAAATTTA
* *
2348212 TAAAAATAATAATAAAATTTA
1 TAAAAATAAGAAAAAAATTTA
*
2348233 GAAAA
1 TAAAA
2348238 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
TAAAAATAAGAAAAAAATTTA
Found at i:2348590 original size:19 final size:19
Alignment explanation
Indices: 2348565--2348629 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
2348555 ATTTCTATAT
*
2348565 ATTTTATAATTTTTTACGA
1 ATTTTATAATTTTTTACAA
* **
2348584 TTTTTATAAAATTTTACAA
1 ATTTTATAATTTTTTACAA
* *
2348603 ATTTTAT-ATTTTTTTCTA
1 ATTTTATAATTTTTTACAA
2348621 A-TTTATAAT
1 ATTTTATAAT
2348630 AAAATTTAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
17 5 0.14
18 10 0.28
19 21 0.58
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTATAATTTTTTACAA
Found at i:2348590 original size:46 final size:49
Alignment explanation
Indices: 2348491--2348599 Score: 147
Period size: 46 Copynumber: 2.3 Consensus size: 49
2348481 TTTATAATTT
* *
2348491 TTTTTATGAAA-TTTATATTTCTTTACATTTTGTATAATTTTCTTACGA
1 TTTTTATAAAATTTTATATTTCTATACATTTTGTATAATTTTCTTACGA
* *
2348539 -CTTTATAAAATTTTATATTTCTATATA-TTT-TATAATTTT-TTACGA
1 TTTTTATAAAATTTTATATTTCTATACATTTTGTATAATTTTCTTACGA
2348584 TTTTTATAAAATTTTA
1 TTTTTATAAAATTTTA
2348600 CAAATTTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
45 6 0.11
46 23 0.43
47 11 0.20
48 14 0.26
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (49 bp):
TTTTTATAAAATTTTATATTTCTATACATTTTGTATAATTTTCTTACGA
Found at i:2348820 original size:86 final size:89
Alignment explanation
Indices: 2348725--2348898 Score: 221
Period size: 89 Copynumber: 2.0 Consensus size: 89
2348715 AATAAAAACA
* * *
2348725 GGGCTTAATTGTTTTTTTGAAAAAG-TTGGAGGGTCTTTTTGAT-GCATTTTGAAAGTTCAAGTA
1 GGGCTTAATTGCTTTTTTAAAAAAGATTGGAGGGTCTTTTTGATAACATTTTGAAAGTTCAAGTA
*
2348788 -CCTAATTGAGT-AAAAAAAAATAG
66 TCC-AAATGAGTGAAAAAAAAATAG
* * * *
2348811 GGGCTTAATTGCTTTTTTAAAAAAGATTTGAGGGTTTTTTTTATAAATATTTTGAAAGTTCAAGT
1 GGGCTTAATTGCTTTTTTAAAAAAGATTGGAGGGTCTTTTTGAT-AACATTTTGAAAGTTCAAGT
2348876 ATCCAAATGAGTGGAAAAAAAAA
65 ATCCAAATGAGT-GAAAAAAAAA
2348899 CATAAACTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
86 23 0.31
87 15 0.20
89 25 0.34
90 2 0.03
91 9 0.12
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.37
Consensus pattern (89 bp):
GGGCTTAATTGCTTTTTTAAAAAAGATTGGAGGGTCTTTTTGATAACATTTTGAAAGTTCAAGTA
TCCAAATGAGTGAAAAAAAAATAG
Found at i:2348929 original size:89 final size:90
Alignment explanation
Indices: 2348770--2348939 Score: 195
Period size: 89 Copynumber: 1.9 Consensus size: 90
2348760 TTTTTGATGC
* * *** *
2348770 ATTTTGAAAGTTCAAGTACCTAATTGAGTAAAAAAAAATAGGGGCTTAATTGCTTTTTTAAAAAA
1 ATTTTGAAAGTTCAAGTACCTAAATGAGTAAAAAAAAACAGAAACTTAATTACTTTTTTAAAAAA
*
2348835 GATTTG-AGGGTTTTTTTTATAAAT
66 GATTTGAAAGGTTTTTTTTATAAAT
* **
2348859 ATTTTGAAAGTTCAAGTATCC-AAATGAGTGGAAAAAAAAACATAAACTTAATTAC-TTTTTCGA
1 ATTTTGAAAGTTCAAGTA-CCTAAATGAGT--AAAAAAAAACAGAAACTTAATTACTTTTTTAAA
2348922 AAA-ATTTGAAAGGTTTTT
63 AAAGATTTGAAAGGTTTTT
2348940 GCAGTGTTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
89 30 0.45
90 19 0.28
91 18 0.27
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (90 bp):
ATTTTGAAAGTTCAAGTACCTAAATGAGTAAAAAAAAACAGAAACTTAATTACTTTTTTAAAAAA
GATTTGAAAGGTTTTTTTTATAAAT
Found at i:2354225 original size:43 final size:44
Alignment explanation
Indices: 2354130--2354216 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
2354120 ATACATTTGC
*
2354130 ATAAAATTTTGGGATATTGGTTGCGAAGAGAAGGAAGACTGAAT
1 ATAAAATTTTGGGATATTGGTTGCCAAGAGAAGGAAGACTGAAT
2354174 ATAAAATTTTGGGATATTGGTT-CCAAGAGAAGGAAGACTGAAT
1 ATAAAATTTTGGGATATTGGTTGCCAAGAGAAGGAAGACTGAAT
2354217 TGGCAATTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 20 0.48
44 22 0.52
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (44 bp):
ATAAAATTTTGGGATATTGGTTGCCAAGAGAAGGAAGACTGAAT
Found at i:2362795 original size:24 final size:24
Alignment explanation
Indices: 2362763--2362846 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 24
2362753 CCACAGTTCA
2362763 TATGAGCTTACCGATTTCAGCTCG
1 TATGAGCTTACCGATTTCAGCTCG
*
2362787 TGA-GAGCTTACCG-TTTCACAGCTCA
1 T-ATGAGCTTACCGATTT--CAGCTCG
*
2362812 TATGAGCTTACCAATATTCAGCTCG
1 TATGAGCTTACCGAT-TTCAGCTCG
* *
2362837 AAGGAGCTTA
1 TATGAGCTTA
2362847 TGTTTATCGC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
23 3 0.06
24 12 0.24
25 31 0.63
26 1 0.02
27 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (24 bp):
TATGAGCTTACCGATTTCAGCTCG
Found at i:2362818 original size:25 final size:26
Alignment explanation
Indices: 2362754--2362823 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
2362744 GCAGACACAC
*
2362754 CACAGTTCATATGAGCTTACCGATTT
1 CACAGCTCATATGAGCTTACCGATTT
*
2362780 --CAGCTCGTGA-GAGCTTACCG-TTT
1 CACAGCTCAT-ATGAGCTTACCGATTT
2362803 CACAGCTCATATGAGCTTACC
1 CACAGCTCATATGAGCTTACC
2362824 AATATTCAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 3 0.08
24 17 0.46
25 17 0.46
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (26 bp):
CACAGCTCATATGAGCTTACCGATTT
Found at i:2365190 original size:116 final size:116
Alignment explanation
Indices: 2365004--2365218 Score: 333
Period size: 116 Copynumber: 1.9 Consensus size: 116
2364994 ATACAAAGTA
* * *
2365004 TATTAATGTTATCCATGAATAATTTTATTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAAT
1 TATTAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAAC
2365069 GAATATACTACACTTAGGGTC-CCAGATCCAACAAGGACAACATACAAAAGG
66 GAATATACTACACTTAGGG-CACCAGATCCAACAAGGACAACATACAAAAGG
* * * *
2365120 TATTAATGTAATTCATGAATAATTTTACTAACTAGTCTGTTTGAAAAAATTATAAGTGTACAAAC
1 TATTAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAAC
* *
2365185 GAATATACTATATTTAGGGCACCAGATCCAACAA
66 GAATATACTACACTTAGGGCACCAGATCCAACAA
2365219 TCTTCAACTT
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
115 1 0.01
116 88 0.99
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (116 bp):
TATTAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAAC
GAATATACTACACTTAGGGCACCAGATCCAACAAGGACAACATACAAAAGG
Found at i:2381231 original size:28 final size:28
Alignment explanation
Indices: 2381191--2381246 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2381181 TACGGTCTAT
* *
2381191 ATCACTGATACATAGTAGCTGCTAAATG
1 ATCACTGACACATAGTACCTGCTAAATG
*
2381219 ATCACTGACACATAGTACCTTCTAAATG
1 ATCACTGACACATAGTACCTGCTAAATG
2381247 CTTACCGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (28 bp):
ATCACTGACACATAGTACCTGCTAAATG
Found at i:2390468 original size:26 final size:26
Alignment explanation
Indices: 2390428--2390484 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
2390418 TTCAATATGT
*
2390428 ATTA-AAAATAAAAATATAAATATAA
1 ATTATAAAATAAAAATATAAATAGAA
*
2390453 ATTATAAAATAAAAATATAATTAGAA
1 ATTATAAAATAAAAATATAAATAGAA
2390479 ATTATA
1 ATTATA
2390485 GAAAACTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (26 bp):
ATTATAAAATAAAAATATAAATAGAA
Found at i:2391490 original size:20 final size:20
Alignment explanation
Indices: 2391454--2391491 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2391444 GCTTTAAAAA
*
2391454 AACTCGAATTTATATTCTTT
1 AACTCGAAGTTATATTCTTT
2391474 AACTCGGAAGTTA-ATTCT
1 AACTC-GAAGTTATATTCT
2391492 ATTGTGAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
AACTCGAAGTTATATTCTTT
Found at i:2391805 original size:21 final size:21
Alignment explanation
Indices: 2391769--2391810 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2391759 CTCCAAAACA
*
2391769 AGGGAAAATGGGTTACATTTT
1 AGGGAAAATGGCTTACATTTT
* *
2391790 AGGGAAAATGTCTTACCTTTT
1 AGGGAAAATGGCTTACATTTT
2391811 CAATTTCCGT
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:0.31, C:0.10, G:0.24, T:0.36
Consensus pattern (21 bp):
AGGGAAAATGGCTTACATTTT
Found at i:2392245 original size:34 final size:35
Alignment explanation
Indices: 2392187--2392253 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
2392177 CAAACACCAG
2392187 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2392222 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
2392254 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2397248 original size:32 final size:30
Alignment explanation
Indices: 2397188--2397256 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 30
2397178 ATAATTCAAA
* *
2397188 AAAAATCTAAAATATATAAATTTAAATTTT
1 AAAAATCAAAAATATATAAAATTAAATTTT
*
2397218 AAAAATCAAAATATTATATAAAAATTAATTTTT
1 AAAAATCAAAA-A-TATAT-AAAATTAAATTTT
2397251 AGAAAA
1 A-AAAA
2397257 ATTTAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 10 0.31
31 1 0.03
32 5 0.16
33 12 0.38
34 4 0.12
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAAATCAAAAATATATAAAATTAAATTTT
Found at i:2397513 original size:21 final size:19
Alignment explanation
Indices: 2397468--2397514 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
2397458 TAGAATTTTG
2397468 ATTTTT-TGAAAAAAATTA
1 ATTTTTATGAAAAAAATTA
**
2397486 AAATTTATGAAAAGAAAATTA
1 ATTTTTATG-AAA-AAAATTA
2397507 ATTTTTAT
1 ATTTTTAT
2397515 ATAGTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 4 0.18
19 2 0.09
20 3 0.14
21 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (19 bp):
ATTTTTATGAAAAAAATTA
Found at i:2400277 original size:250 final size:253
Alignment explanation
Indices: 2399685--2400870 Score: 902
Period size: 250 Copynumber: 4.8 Consensus size: 253
2399675 CCTATCATCC
* * *
2399685 ATTTATGTCATGTTGTCACTGAAAGTTAGGCTTTGTATAAGCTGCATTTGTTAATCCGAGTTCGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTG-TAATCCGAGTTCGG
*
2399750 GTTCAGCTCTCATATAATAGA-TT-TGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGT
65 GTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGT
* * * * * *
2399813 ATTTGTAATCCGAGTTCAAGTTCAGCTCTTATATAATAGATTTATGTTATGGTGTCATTGAAAGT
130 ATTTGTAACCCAAGTTCAGGTTCAGCTCTTACATAATAGATTTATGTTATGATGTCACTGAAAGT
*** * * * * * * *
2399878 TAAGACTTTGTTTAAGCTGTATTTGTGATCCGAGTTCTGGTTTAGCCCTCGTTTGATAG
195 TAAGACTTTGCACAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATATAATAG
* * * * * *
2399937 ATTTATGTTATTGTATCGCTGAAAGTTAGACATTGTAGAAGCTGCATTTGTAATCTGAGTTCGGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * *
2400002 TTTGGCTCTCATATAATATATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGTTGTA
66 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGTA
*
2400067 TTTGTAACCCAAGTTCGGGTTCAGCTC-T-CATAATAGATTTATGTTATGATGTCACTGAAAGTT
131 TTTGTAACCCAAGTTCAGGTTCAGCTCTTACATAATAGATTTATGTTATGATGTCACTGAAAGTT
* *
2400130 -AGACTTTGCACAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCTCTCATATAATAT
196 AAGACTTTGCACAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATATAATAG
* * * *
2400187 ATTTATGTTGTGGTGTCACTGAAAGTTAGACTTTGTATAAGTTGCATTTGTAATCCAAGTTCAGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * * * * * * * *
2400252 TTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTTAGACTTTGCATGAGCTGCA
66 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGTA
* * * * * *
2400317 TTTATAACCCAAATTCAGGTTTAGC-CCT-CGT--TTGA--TA-GATT-T-ATGT---T----G-
131 TTTGTAACCCAAGTTCAGGTTCAGCTCTTACATAATAGATTTATG-TTATGATGTCACTGAAAGT
* ** * * * * * * * * *
2400365 TGA-ACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAG
195 TAAGACTTTGCACAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATATAATAG
* * * * *
2400423 ATTTATGTTATTGTGTCACTGAAAGTTAAACTTTGCATGAGCTGCATTTATAA-CCTGAGTTCGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCC-GAGTTCGG
* * * * ** * * * *
2400487 GCTTAGCTCT-ATTGTAATAGATTTAT-ATATGGTTTTGCTGAATGTTAGACTTTTTATGAGTTG
65 GTTTAGCTCTCA-TATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTG
* * * * * * **
2400550 TATTTGTAATCCGAGTTCAGGTTTAGCTCTTGA-ATTATAGATTTTATGTTACGGTGTTGCTGAA
129 TATTTGTAACCCAAGTTCAGGTTCAGCTCTT-ACATAATAGA-TTTATGTTATGATGTCACTGAA
**** * * * * * * *
2400614 AGTT-AGACTTTGTGTGAGCTGCATTTGCAATCCGATTTTTGGATT-AGCTCTTGA-ATCATAG
192 AGTTAAGACTTTGCACAAGCTGCATTTGTAATCCGA-GTTCGGGTTCAGC-CCTCATATAATAG
* * *
2400675 ATTTATGTTAT-G-G----TG-AAGTTAGACTTTGTATGAGCTGCATTTGTAATCTGAGTTTGGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * *** * * ** * * * *
2400733 TTCAGCCCTCATGCCATAGATTTGTCTTATGGTGTCACTGCCACTTGGACTTTGTATGAGCTGCA
66 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGTA
* * * * * * * * * **
2400798 TTTCTAACCTC-AGTTCGGGTTTAGCTCTCAAATCATAGGTTTATATTATGTTGTTGCTGAAAGT
131 TTTGTAACC-CAAGTTCAGGTTCAGCTCTTACATAATAGATTTATGTTATGATGTCACTGAAAGT
2400862 T-AGACTTTG
195 TAAGACTTTG
2400871 TATGTGCTGC
Statistics
Matches: 748, Mismatches: 152, Indels: 75
0.77 0.16 0.08
Matches are distributed among these distances:
235 53 0.07
236 117 0.16
237 3 0.00
239 3 0.00
241 1 0.00
242 4 0.01
243 1 0.00
244 7 0.01
245 87 0.12
246 64 0.09
247 2 0.00
248 3 0.00
249 1 0.00
250 178 0.24
251 66 0.09
252 88 0.12
253 70 0.09
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (253 bp):
ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGTA
TTTGTAACCCAAGTTCAGGTTCAGCTCTTACATAATAGATTTATGTTATGATGTCACTGAAAGTT
AAGACTTTGCACAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATATAATAG
Found at i:2400361 original size:168 final size:168
Alignment explanation
Indices: 2399666--2400883 Score: 994
Period size: 168 Copynumber: 7.4 Consensus size: 168
2399656 ATAGTCCGGT
* * ** * * *
2399666 TTTAGCTCTCCTATCATCCATTTATGTCATGTTGTCACTGAAAGTTAGGCTTTGTATAAGCTGCA
1 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
* * * * * * * *
2399731 TTTGTTAATCCGAGTTCGGGTTCAGCTCTCATATAATAGA-TT-TGTTATGGTGTCACTGAAAGT
66 TTTG-TAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGT
* * * **
2399794 TAGACTTTGTATAAGCTGTATTTGTAATCCGAGTTCAAG
130 TAGACTTTGCATGAGCTGCATTTGTAATCCGAGTTCGGG
* * * * *
2399833 TTCAGCTCTTATATAATAGATTTATGTTATGGTGTCATTGAAAGTTAAGACTTTGTTTAAGCTGT
1 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTT-AGACTTTGTATAAGCTGC
* * * * *
2399898 ATTTGTGATCCGAGTTCTGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTATCGCTGAAAGT
65 ATTTGTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGT
* * *
2399963 TAGACATTGTA-GAAGCTGCATTTGTAATCTGAGTTCGGG
130 TAGACTTTGCATG-AGCTGCATTTGTAATCCGAGTTCGGG
* * * *
2400002 TTTGGCTCTCATATAATATATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGTTGTA
1 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
* * * * * *
2400067 TTTGTAACCCAAGTTCGGGTTCAGCTCTC--ATAATAGATTTATGTTA-TGATGTCACTGAAAGT
66 TTTGTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTG-TGTCACTGAAAGT
**
2400129 TAGACTTTGCACAAGCTGCATTTGTAATCCGAGTTCGGG
130 TAGACTTTGCATGAGCTGCATTTGTAATCCGAGTTCGGG
* * * *
2400168 TTCAGCTCTCATATAATATATTTATGTTGTGGTGTCACTGAAAGTTAGACTTTGTATAAGTTGCA
1 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
*
2400233 TTTGTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTT
66 TTTGTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGTT
* * * * *
2400298 AGACTTTGCATGAGCTGCATTTATAACCCAAATTCAGG
131 AGACTTTGCATGAGCTGCATTTGTAATCCGAGTTCGGG
* * * * * *
2400336 TTTAGCCCTCGTTTGATAGATTTATG---T--TG----T----G--A-ACTTTGCATGAGCTGCA
1 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
* * *
2400385 TTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGTT
66 TTTGTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGTT
* *
2400450 AAACTTTGCATGAGCTGCATTTATAA-CCTGAGTTCGGG
131 AGACTTTGCATGAGCTGCATTTGTAATCC-GAGTTCGGG
* * * * ** * * * * *
2400488 CTTAGCTCT-ATTGTAATAGATTTAT-ATATGGTTTTGCTGAATGTTAGACTTTTTATGAGTTGT
1 TTTAGCTCTCA-TATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGC
* * * * ** **
2400551 ATTTGTAATCCGAGTTCAGGTTTAGCTCTTGAATT-ATAGATTTTATGTTACGGTGTTGCTGAAA
65 ATTTGTAATCCAAGTTCAGGTTTAGCCCTCG-TTTGATAGA-TTTATGTTATTGTGTCACTGAAA
** * * **
2400615 GTTAGACTTTGTGTGAGCTGCATTTGCAATCCGATTTTTGG
128 GTTAGACTTTGCATGAGCTGCATTTGTAATCCGAGTTCGGG
* * * *
2400656 ATTAGCTCTTGA-ATCATAGATTTATGTTAT-G-G----TG-AAGTTAGACTTTGTATGAGCTGC
1 TTTAGCTC-TCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGC
** ** * * *** * * * ** *
2400713 ATTTGTAATCTGAGTTTGGGTTCAGCCCTCATGCCATAGATTTGTCTTATGGTGTCACTGCCACT
65 ATTTGTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGT
* * * *
2400778 TGGACTTTGTATGAGCTGCATTTCTAA-CCTCAGTTCGGG
130 TAGACTTTGCATGAGCTGCATTTGTAATCC-GAGTTCGGG
* * * * * ** **
2400817 TTTAGCTCTCAAATCATAGGTTTATATTATGTTGTTGCTGAAAGTTAGACTTTGTATGTGCTGCA
1 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
2400882 TT
66 TT
2400884 CGTACTAAGA
Statistics
Matches: 854, Mismatches: 154, Indels: 85
0.78 0.14 0.08
Matches are distributed among these distances:
151 2 0.00
152 125 0.15
153 1 0.00
154 1 0.00
155 1 0.00
156 1 0.00
159 1 0.00
160 5 0.01
161 68 0.08
162 48 0.06
163 5 0.01
164 1 0.00
165 3 0.00
166 147 0.17
167 109 0.13
168 236 0.28
169 99 0.12
170 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (168 bp):
TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
TTTGTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGTT
AGACTTTGCATGAGCTGCATTTGTAATCCGAGTTCGGG
Found at i:2400363 original size:84 final size:84
Alignment explanation
Indices: 2399685--2400319 Score: 801
Period size: 84 Copynumber: 7.6 Consensus size: 84
2399675 CCTATCATCC
* * *
2399685 ATTTATGTCATGTTGTCACTGAAAGTTAGGCTTTGTATAAGCTGCATTTGTTAATCCGAGTTCGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTG-TAATCCGAGTTCGG
2399750 GTTCAGCTCTCATATAATAG
65 GTTCAGCTCTCATATAATAG
* **
2399770 A-TT-TGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGTATTTGTAATCCGAGTTCAAG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
*
2399833 TTCAGCTCTTATATAATAG
66 TTCAGCTCTCATATAATAG
* * * * *
2399852 ATTTATGTTATGGTGTCATTGAAAGTTAAGACTTTGTTTAAGCTGTATTTGTGATCCGAGTTCTG
1 ATTTATGTTATGGTGTCACTGAAAGTT-AGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGG
* * * * *
2399917 GTTTAGCCCTCGTTTGATAG
65 GTTCAGCTCTCATATAATAG
* * * * * *
2399937 ATTTATGTTATTGTATCGCTGAAAGTTAGACATTGTAGAAGCTGCATTTGTAATCTGAGTTCGGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
** *
2400002 TTTGGCTCTCATATAATAT
66 TTCAGCTCTCATATAATAG
* * * *
2400021 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGTTGTATTTGTAACCCAAGTTCGGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
2400086 TTCAGCTCTC--ATAATAG
66 TTCAGCTCTCATATAATAG
* * *
2400103 ATTTATGTTATGATGTCACTGAAAGTTAGACTTTGCACAAGCTGCATTTGTAATCCGAGTTCGGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
*
2400168 TTCAGCTCTCATATAATAT
66 TTCAGCTCTCATATAATAG
* * * *
2400187 ATTTATGTTGTGGTGTCACTGAAAGTTAGACTTTGTATAAGTTGCATTTGTAATCCAAGTTCAGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * * * *
2400252 TTTAGCCCTCGTTTGATAG
66 TTCAGCTCTCATATAATAG
* * * *
2400271 ATTTATGTTATTGTGTCGCTGAAAGTTAGACTTTGCATGAGCTGCATTT
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTT
2400320 ATAACCCAAA
Statistics
Matches: 470, Mismatches: 75, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
82 106 0.23
83 43 0.09
84 250 0.53
85 71 0.15
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (84 bp):
ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
TTCAGCTCTCATATAATAG
Found at i:2400409 original size:68 final size:68
Alignment explanation
Indices: 2400300--2400431 Score: 264
Period size: 68 Copynumber: 1.9 Consensus size: 68
2400290 TGAAAGTTAG
2400300 ACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTG
1 ACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTG
2400365 TGA
66 TGA
2400368 ACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTT
1 ACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTT
2400432 ATTGTGTCAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (68 bp):
ACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTG
TGA
Found at i:2400507 original size:152 final size:152
Alignment explanation
Indices: 2400229--2400512 Score: 435
Period size: 152 Copynumber: 1.9 Consensus size: 152
2400219 TTGTATAAGT
* * * *
2400229 TGCATTTGTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAA
1 TGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAA
* * * *
2400294 AGTTAGACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTT
66 AGTTAAACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGCTTAGCCCTCATTTAATAGATTT
2400359 ATGTTGTGAACTTTGCATGAGC
131 ATGTTGTGAACTTTGCATGAGC
2400381 TGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAA
1 TGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAA
** * * *
2400446 AGTTAAACTTTGCATGAGCTGCATTTATAACCTGAGTTCGGGCTTAGCTCT-ATTGTAATAGATT
66 AGTTAAACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGCTTAGCCCTCATT-TAATAGATT
2400510 TAT
130 TAT
2400513 ATATGGTTTT
Statistics
Matches: 118, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
151 2 0.02
152 116 0.98
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (152 bp):
TGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAA
AGTTAAACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGCTTAGCCCTCATTTAATAGATTT
ATGTTGTGAACTTTGCATGAGC
Found at i:2400640 original size:85 final size:83
Alignment explanation
Indices: 2400368--2400883 Score: 345
Period size: 84 Copynumber: 6.2 Consensus size: 83
2400358 TATGTTGTGA
* * * * * * * *
2400368 ACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTA
1 ACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGGTTTAGCTCTTGATT-ATAGATTTATGTTA
* ** *
2400433 TTGTGTCACTGAAAGTTAA
65 TGGTGTTGCTGAAAGTTAG
* * * * * *
2400452 ACTTTGCATGAGCTGCATTTATAA-CCTGAGTTCGGGCTTAGCTCTATTG-TAATAGATTTAT-A
1 ACTTTGTATGAGCTGCATTTGTAATCC-GAGTTCAGGTTTAGCTC--TTGATTATAGATTTATGT
* *
2400514 TATGGTTTTGCTGAATGTTAG
63 TATGGTGTTGCTGAAAGTTAG
* * *
2400535 ACTTTTTATGAGTTGTATTTGTAATCCGAGTTCAGGTTTAGCTCTTGAATTATAGATTTTATGTT
1 ACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGGTTTAGCTCTTG-ATTATAGA-TTTATGTT
*
2400600 ACGGTGTTGCTGAAAGTTAG
64 ATGGTGTTGCTGAAAGTTAG
* * * ** * *
2400620 ACTTTGTGTGAGCTGCATTTGCAATCCGATTTTTGGATTAGCTCTTGAATCATAGATTTATGTTA
1 ACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGGTTTAGCTCTTG-ATTATAGATTTATGTTA
2400685 ---TG--G-TG-AAGTTAG
65 TGGTGTTGCTGAAAGTTAG
* ** * * ** * *
2400697 ACTTTGTATGAGCTGCATTTGTAATCTGAGTTTGGGTTCAGCCCTCATG-CCATAGATTTGTCTT
1 ACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGGTTTAG--CTCTTGATTATAGATTTATGTT
** ** * *
2400761 ATGGTGTCACTGCCACTTGG
64 ATGGTGTTGCTGAAAGTTAG
* * * ** * * *
2400781 ACTTTGTATGAGCTGCATTTCTAA-CCTCAGTTCGGGTTTAGCTCTCAAATCATAGGTTTATATT
1 ACTTTGTATGAGCTGCATTTGTAATCC-GAGTTCAGGTTTAGCTCT-TGATTATAGATTTATGTT
*
2400845 ATGTTGTTGCTGAAAGTTAG
64 ATGGTGTTGCTGAAAGTTAG
*
2400865 ACTTTGTATGTGCTGCATT
1 ACTTTGTATGAGCTGCATT
2400884 CGTACTAAGA
Statistics
Matches: 341, Mismatches: 71, Indels: 40
0.75 0.16 0.09
Matches are distributed among these distances:
77 54 0.16
78 2 0.01
79 6 0.02
80 2 0.01
81 5 0.01
82 3 0.01
83 60 0.18
84 142 0.42
85 65 0.19
86 2 0.01
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.41
Consensus pattern (83 bp):
ACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGGTTTAGCTCTTGATTATAGATTTATGTTAT
GGTGTTGCTGAAAGTTAG
Found at i:2400681 original size:320 final size:320
Alignment explanation
Indices: 2400099--2400683 Score: 741
Period size: 320 Copynumber: 1.8 Consensus size: 320
2400089 AGCTCTCATA
* *
2400099 ATAGATTTATGTTATGATGTCACTGAAAGTTAGACTTTGCACAAGCTGCATTTGTAATCCGAGTT
1 ATAGATTTATGTTATGATGTCACTGAAAGTTAAACTTTGCACAAGCTGCATTTATAATCCGAGTT
* * *
2400164 CGGGTTCAGCTCTCATATAATATATTTATGTTGTGGTGTCACTGAAAGTTAGACTTTGTATAAGT
66 CGGGTTCAGCTCTCATATAATAGATTTATGATATGGTGTCACTGAAAGTTAGACTTTGTATAAGT
* **
2400229 TGCATTTGTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAA
131 TGCATTTGTAATCCAAGTTCAGGTTTAGCCCTCGATTGATAGATTTATGTTACGGTGTCGCTGAA
* * ** *
2400294 AGTTAGACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTT
196 AGTTAGACTTTGCATGAGCTGCATTTACAACCCAAATTCAGGATTAGCCCTCGAATCATAGATTT
2400359 ATGTTGTGAACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTG
261 ATGTTGTGAACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTG
**
2400419 ATAGATTTATGTTATTG-TGTCACTGAAAGTTAAACTTTGCATGAGCTGCATTTATAA-CCTGAG
1 ATAGATTTATGTTA-TGATGTCACTGAAAGTTAAACTTTGCACAAGCTGCATTTATAATCC-GAG
* * ** * *
2400482 TTCGGGCTT-AGCTCT-ATTGTAATAGATTTAT-ATATGGTTTTGCTGAATGTTAGACTTTTTAT
64 TTCGGG-TTCAGCTCTCA-TATAATAGATTTATGATATGGTGTCACTGAAAGTTAGACTTTGTAT
* * * * * *
2400544 GAGTTGTATTTGTAATCCGAGTTCAGGTTTAGCTCTTGAATT-ATAGATTTTATGTTACGGTGTT
127 AAGTTGCATTTGTAATCCAAGTTCAGGTTTAGCCCTCG-ATTGATAGA-TTTATGTTACGGTGTC
** * * * * ** * *
2400608 GCTGAAAGTTAGACTTTGTGTGAGCTGCATTTGCAATCCGATTTTTGGATTAGCTCTTGAATCAT
190 GCTGAAAGTTAGACTTTGCATGAGCTGCATTTACAACCCAAATTCAGGATTAGCCCTCGAATCAT
2400673 AGATTTATGTT
255 AGATTTATGTT
2400684 ATGGTGAAGT
Statistics
Matches: 222, Mismatches: 37, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
319 65 0.29
320 153 0.69
321 4 0.02
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.41
Consensus pattern (320 bp):
ATAGATTTATGTTATGATGTCACTGAAAGTTAAACTTTGCACAAGCTGCATTTATAATCCGAGTT
CGGGTTCAGCTCTCATATAATAGATTTATGATATGGTGTCACTGAAAGTTAGACTTTGTATAAGT
TGCATTTGTAATCCAAGTTCAGGTTTAGCCCTCGATTGATAGATTTATGTTACGGTGTCGCTGAA
AGTTAGACTTTGCATGAGCTGCATTTACAACCCAAATTCAGGATTAGCCCTCGAATCATAGATTT
ATGTTGTGAACTTTGCATGAGCTGCATTTATAACCCAAATTCAGGTTTAGCCCTCGTTTG
Found at i:2400751 original size:77 final size:76
Alignment explanation
Indices: 2400613--2400766 Score: 177
Period size: 77 Copynumber: 2.0 Consensus size: 76
2400603 GTGTTGCTGA
* * * *
2400613 AAGTTAGACTTTGTGTGAGCTGCATTTGCAATCCGATTTTTGGATTAGCTCTTGAATCATAGATT
1 AAGTTAGACTTTGTATGAGCTGCATTTGCAATCCGATGTTTGGATTAGCTCATG-ACCATAGATT
*
2400678 TATGTTATGGTG
65 TATCTTATGGTG
* * *
2400690 AAGTTAGACTTTGTATGAGCTGCATTTGTAATCTGA-GTTTGGGTTCAGCCCTCATG-CCATAGA
1 AAGTTAGACTTTGTATGAGCTGCATTTGCAATCCGATGTTTGGATT-AG--CTCATGACCATAGA
*
2400753 TTTGTCTTATGGTG
63 TTTATCTTATGGTG
2400767 TCACTGCCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
76 7 0.11
77 53 0.82
79 5 0.08
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (76 bp):
AAGTTAGACTTTGTATGAGCTGCATTTGCAATCCGATGTTTGGATTAGCTCATGACCATAGATTT
ATCTTATGGTG
Found at i:2403786 original size:21 final size:21
Alignment explanation
Indices: 2403760--2403840 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
2403750 ATAAAAATTT
* *
2403760 TAAAAAATATAAAAACATAAA
1 TAAAAATTATAAAAACATATA
**
2403781 TAAAAATTTATAAATCCAATATA
1 TAAAAA-TTATAAAAAC-ATATA
*
2403804 TAAAAATTAAAAAAACATATA
1 TAAAAATTATAAAAACATATA
*
2403825 TAAAAATT-TCAAAACA
1 TAAAAATTATAAAAACA
2403841 AAAACTACCT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.12
21 19 0.39
22 14 0.29
23 10 0.20
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAAATTATAAAAACATATA
Found at i:2403810 original size:23 final size:22
Alignment explanation
Indices: 2403770--2403838 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
2403760 TAAAAAATAT
* *
2403770 AAAAACATAAATAAAAATTTAT
1 AAAAACATATATAAAAATTTAA
**
2403792 AAATCCAATATATAAAAA-TTAA
1 AAAAAC-ATATATAAAAATTTAA
*
2403814 AAAAACATATATAAAAATTTCA
1 AAAAACATATATAAAAATTTAA
2403836 AAA
1 AAA
2403839 CAAAAACTAC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 11 0.29
22 17 0.45
23 10 0.26
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAACATATATAAAAATTTAA
Found at i:2404107 original size:22 final size:23
Alignment explanation
Indices: 2404051--2404108 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
2404041 CGACCCGTTT
* * *
2404051 TTAATTAAAATTAAAATTATTTTT
1 TTAA-TAAAATTAAAACTATATTG
2404075 TTAATAAAATTAAAACTA-ATTG
1 TTAATAAAATTAAAACTATATTG
*
2404097 TTAGTAAAATTA
1 TTAATAAAATTA
2404109 TCAAATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 13 0.43
23 13 0.43
24 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
TTAATAAAATTAAAACTATATTG
Found at i:2404193 original size:9 final size:9
Alignment explanation
Indices: 2404181--2404217 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
2404171 TTTATCAAAT
2404181 TATTAATTG
1 TATTAATTG
2404190 TATTAATTG
1 TATTAATTG
2404199 TATTAATTG
1 TATTAATTG
2404208 TATTAATTG
1 TATTAATTG
2404217 T
1 T
2404218 TGTAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:2404354 original size:22 final size:24
Alignment explanation
Indices: 2404314--2404357 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2404304 AAATAAACTT
2404314 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
2404338 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
2404358 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:2404797 original size:26 final size:27
Alignment explanation
Indices: 2404768--2404830 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
2404758 TCAATTTTTA
2404768 ATAAAACTTTTAA-TTTTTATATATTT
1 ATAAAACTTTTAACTTTTTATATATTT
*
2404794 AT--AATTTTCTAACTTTTTATATATTT
1 ATAAAACTTT-TAACTTTTTATATATTT
* *
2404820 TTAAAAGTTTT
1 ATAAAACTTTT
2404831 GTGCATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
24 5 0.17
25 3 0.10
26 16 0.53
27 1 0.03
28 5 0.17
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (27 bp):
ATAAAACTTTTAACTTTTTATATATTT
Found at i:2405902 original size:23 final size:22
Alignment explanation
Indices: 2405872--2405914 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
2405862 GAAAAAAAAT
2405872 AAAAAAACTCA-TAAACTACTTG
1 AAAAAAACTCATTAAA-TACTTG
2405894 AAAACAAACTCATTAAATACT
1 AAAA-AAACTCATTAAATACT
2405915 CGAGAGCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.56, C:0.19, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAAAAACTCATTAAATACTTG
Found at i:2439295 original size:30 final size:29
Alignment explanation
Indices: 2439220--2439275 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2439210 TTTGACTCTT
*
2439220 TTTAATAGTATAGGGACTAAATTGATCGA
1 TTTAATAATATAGGGACTAAATTGATCGA
*
2439249 TTTAATAAT-TGAGGGACTAATTTGATC
1 TTTAATAATAT-AGGGACTAAATTGATC
2439276 TGTCTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (29 bp):
TTTAATAATATAGGGACTAAATTGATCGA
Found at i:2442775 original size:12 final size:11
Alignment explanation
Indices: 2442752--2442784 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
2442742 TGTATTTTCA
2442752 ATTTTT-TTAT
1 ATTTTTATTAT
2442762 ATTTTTAATTAT
1 ATTTTT-ATTAT
2442774 ATTTTTATTAT
1 ATTTTTATTAT
2442785 TGTTTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 5 0.24
12 10 0.48
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTTATTAT
Found at i:2444530 original size:20 final size:19
Alignment explanation
Indices: 2444501--2444544 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2444491 AAATTGTGAA
*
2444501 AAATTCAAAATTGAGGAGTT
1 AAATTCAAAATAG-GGAGTT
* *
2444521 TAATTGAAAATAGGGAGTT
1 AAATTCAAAATAGGGAGTT
2444540 AAATT
1 AAATT
2444545 TATTTTAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.32
Consensus pattern (19 bp):
AAATTCAAAATAGGGAGTT
Found at i:2448865 original size:23 final size:24
Alignment explanation
Indices: 2448839--2448892 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
2448829 ACCTTAGCGC
2448839 GCTCT-GATCATTAGCACATTAGT
1 GCTCTCGATCATTAGCACATTAGT
* *
2448862 GCTCTCCGATTATTAGCATATTAGT
1 GCTCT-CGATCATTAGCACATTAGT
2448887 GCTCTC
1 GCTCTC
2448893 TGTATAGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 1 0.04
25 21 0.78
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (24 bp):
GCTCTCGATCATTAGCACATTAGT
Found at i:2450199 original size:44 final size:42
Alignment explanation
Indices: 2450151--2450307 Score: 142
Period size: 43 Copynumber: 3.6 Consensus size: 42
2450141 TATGTTTTCA
*
2450151 TGTAAGACCATATCTGGGACGGTGGCATCGATTTGAGATTTACG
1 TGTAAGACCATGTCTGGGAC-GTGGCATCGATTT-AGATTTACG
* *
2450195 TGTAAGACCATGTCTGGGACATCGGCATC-ATATATGATTT-CG
1 TGTAAGACCATGTCTGGGACGT-GGCATCGATTTA-GATTTACG
* * * *
2450237 TGTAAGACCCTGTCTGGGATAGTGGCATCGATATTTGA-TTACA
1 TGTAAGACCATGTCTGGGA-CGTGGCATCGAT-TTAGATTTACG
*
2450280 TGTAAGACCACG-CATGGGACGTTGGCAT
1 TGTAAGACCATGTC-TGGGACG-TGGCAT
2450308 TGTACGACCT
Statistics
Matches: 93, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
42 31 0.33
43 36 0.39
44 26 0.28
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACGTGGCATCGATTTAGATTTACG
Found at i:2450251 original size:42 final size:43
Alignment explanation
Indices: 2450140--2450289 Score: 162
Period size: 43 Copynumber: 3.5 Consensus size: 43
2450130 GGATTCCGAG
* * * *
2450140 ATATGTTTTCATGTAAGACCATATCTGGGACGGTGGCATCGAT
1 ATATGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
*
2450183 TTGA-GATTTACGTGTAAGACCATGTCTGGGACA-TCGGCATC-AT
1 AT-ATGATTT-CGTGTAAGACCATGTCTGGGACAGT-GGCATCGAT
* *
2450226 ATATGATTTCGTGTAAGACCCTGTCTGGGATAGTGGCATCGAT
1 ATATGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
* * *
2450269 ATTTGATTACATGTAAGACCA
1 ATATGATTTCGTGTAAGACCA
2450290 CGCATGGGAC
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
42 28 0.31
43 34 0.38
44 27 0.30
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (43 bp):
ATATGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
Found at i:2450298 original size:43 final size:42
Alignment explanation
Indices: 2450140--2450288 Score: 122
Period size: 42 Copynumber: 3.5 Consensus size: 42
2450130 GGATTCCGAG
* * * * **
2450140 ATATGTTTTCATGTAAGACCATATCTGGGACGGTGGCATCGAT
1 ATATGATTACATGTAAGACCCTGTCTGGGATAGTGGCATC-AT
* * * *
2450183 TTGA-GATTTACGTGTAAGACCATGTCTGGGACA-TCGGCATCAT
1 AT-ATGA-TTACATGTAAGACCCTGTCTGGGATAGT-GGCATCAT
* *
2450226 ATATGATTTCGTGTAAGACCCTGTCTGGGATAGTGGCATCGAT
1 ATATGATTACATGTAAGACCCTGTCTGGGATAGTGGCATC-AT
*
2450269 ATTTGATTACATGTAAGACC
1 ATATGATTACATGTAAGACC
2450289 ACGCATGGGA
Statistics
Matches: 87, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
42 30 0.34
43 28 0.32
44 29 0.33
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (42 bp):
ATATGATTACATGTAAGACCCTGTCTGGGATAGTGGCATCAT
Found at i:2450777 original size:2 final size:2
Alignment explanation
Indices: 2450770--2450834 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
2450760 TTTGAAATGC
2450770 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
2450812 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
2450835 GCCATGCGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2452024 original size:15 final size:15
Alignment explanation
Indices: 2452004--2452040 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
2451994 CCAACTAGCA
2452004 AAACCCGAATAGCCC
1 AAACCCGAATAGCCC
2452019 AAACCCGAATAGCCC
1 AAACCCGAATAGCCC
2452034 AATACCC
1 AA-ACCC
2452041 TTCAGCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.41, G:0.11, T:0.08
Consensus pattern (15 bp):
AAACCCGAATAGCCC
Found at i:2465960 original size:46 final size:44
Alignment explanation
Indices: 2465776--2466162 Score: 239
Period size: 44 Copynumber: 8.9 Consensus size: 44
2465766 TTGAAGCCAG
* *
2465776 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATCGAAG-A-C
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATC
* * * * ** * *
2465818 ACTATCATATCTCCCTGAGTTTACAGCGGAGCGGAT-TAA-AATAA
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAAT-C
* * * *
2465862 AGGATCTCATCTCTCTGAAGTTACAGTGGAGTAGATC---GCATC
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATC
* *
2465904 AGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAA--TC
* * *
2465950 AGATCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAA--
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAG--AATC
* *
2465994 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATCGAAG-A-C
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATC
* * * * ** * *
2466036 ACTATCCTATCTCCCTGAGTTTACAGTGGGGCGGAT-TAA-AATAA
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAAT-C
* * * *
2466080 AGGATCTCATCTCTCTGAAGTTACAGTGGAGTAGATC---GCATC
1 A-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATC
* * * *
2466122 AGGTCTTATCTCCCTGAAGTCACAGTGGAGTAGACCGAAGA
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGA
2466163 TACAAGTATT
Statistics
Matches: 260, Mismatches: 62, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
41 61 0.23
42 10 0.04
43 60 0.23
44 90 0.35
46 37 0.14
48 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAATC
Found at i:2465999 original size:131 final size:128
Alignment explanation
Indices: 2465779--2466030 Score: 294
Period size: 131 Copynumber: 1.9 Consensus size: 128
2465769 AAGCCAGAGA
* * * *
2465779 TCTTATCTCCCTGAGATTACAGCGGAGTAGATCGAAGACACTATCATATCTCCCTGAGTTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGTAGACCGAAGACACGATCATATCTCCCTAAGGTTACAG
* * * *
2465844 CGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGA-AGTTACAGTGGAGTAGATCGCATCAGG
66 CGGAGCAGATTAAAACAAAGGATCTCATCTCCCTGAGA-TTACAGCGGAGTAGATCGCATCAGG
* * *
2465907 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTTCAGATCTTATCTCCCTAAGGTT
1 TCTTATCTCCCTGAGATTACAGCGGAGTAGACCGAAGACA---C-GATCATATCTCCCTAAGGTT
* ** *
2465971 ACAGTGGAGCAGATTGAAGCCAAA-GATCTTATCTCCCTGAGATTACAGCGGAGTAGATCG
62 ACAGCGGAGCAGATT-AAAACAAAGGATCTCATCTCCCTGAGATTACAGCGGAGTAGATCG
2466031 AAGACACTAT
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
127 1 0.01
128 35 0.34
130 1 0.01
131 60 0.58
132 6 0.06
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (128 bp):
TCTTATCTCCCTGAGATTACAGCGGAGTAGACCGAAGACACGATCATATCTCCCTAAGGTTACAG
CGGAGCAGATTAAAACAAAGGATCTCATCTCCCTGAGATTACAGCGGAGTAGATCGCATCAGG
Found at i:2466129 original size:218 final size:218
Alignment explanation
Indices: 2465751--2466162 Score: 752
Period size: 218 Copynumber: 1.9 Consensus size: 218
2465741 CCTTCATCGA
* * *
2465751 TTACAGTGGAGCTGGTTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATCGAAG
1 TTACAGTGGAGCAGATTGAAGCCAAAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATCGAAG
2465816 ACACTATCATATCTCCCTGAGTTTACAGCGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAA
66 ACACTATCATATCTCCCTGAGTTTACAGCGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAA
* *
2465881 GTTACAGTGGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAA
131 GTTACAGTGGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTCACAGTGGAGTAGACCGAAGAA
2465946 TTTCAGATCTTATCTCCCTAAGG
196 TTTCAGATCTTATCTCCCTAAGG
2465969 TTACAGTGGAGCAGATTGAAGCCAAAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATCGAAG
1 TTACAGTGGAGCAGATTGAAGCCAAAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATCGAAG
* * *
2466034 ACACTATCCTATCTCCCTGAGTTTACAGTGGGGCGGATTAAAATAAAGGATCTCATCTCTCTGAA
66 ACACTATCATATCTCCCTGAGTTTACAGCGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAA
2466099 GTTACAGTGGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTCACAGTGGAGTAGACCGAAGA
131 GTTACAGTGGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTCACAGTGGAGTAGACCGAAGA
2466163 TACAAGTATT
Statistics
Matches: 186, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
218 186 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (218 bp):
TTACAGTGGAGCAGATTGAAGCCAAAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATCGAAG
ACACTATCATATCTCCCTGAGTTTACAGCGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAA
GTTACAGTGGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTCACAGTGGAGTAGACCGAAGAA
TTTCAGATCTTATCTCCCTAAGG
Found at i:2466596 original size:15 final size:15
Alignment explanation
Indices: 2466576--2466612 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
2466566 CCAACTAGCA
2466576 AAACCCGAATAGCCC
1 AAACCCGAATAGCCC
2466591 AAACCCGAATAGCCC
1 AAACCCGAATAGCCC
2466606 AATACCC
1 AA-ACCC
2466613 TTCAGCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.41, G:0.11, T:0.08
Consensus pattern (15 bp):
AAACCCGAATAGCCC
Found at i:2473114 original size:23 final size:23
Alignment explanation
Indices: 2473088--2473141 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
2473078 TACTAAATAA
* *
2473088 ATTAATAACAAT-AAAATAATAT
1 ATTAATAAAAATCAAAATAAAAT
*
2473110 CATTAA-AAAAATCAAATTAAAAT
1 -ATTAATAAAAATCAAAATAAAAT
2473133 ATTAATAAA
1 ATTAATAAA
2473142 CGTGGTTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTAATAAAAATCAAAATAAAAT
Found at i:2476926 original size:21 final size:21
Alignment explanation
Indices: 2476902--2476943 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2476892 AGTTCTTTTT
2476902 AATTAGTT-AACGAAACGTTAA
1 AATT-GTTCAACGAAACGTTAA
* *
2476923 AATTTTTCAACGAAACTTTAA
1 AATTGTTCAACGAAACGTTAA
2476944 TAACACCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (21 bp):
AATTGTTCAACGAAACGTTAA
Found at i:2483270 original size:16 final size:16
Alignment explanation
Indices: 2483242--2483275 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2483232 AGTAAAAATG
2483242 GAAGTAACTTTTAGTA
1 GAAGTAACTTTTAGTA
2483258 GAAG-AACTATTTAGTA
1 GAAGTAACT-TTTAGTA
2483274 GA
1 GA
2483276 GGGAGCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (16 bp):
GAAGTAACTTTTAGTA
Found at i:2485817 original size:70 final size:70
Alignment explanation
Indices: 2485704--2485834 Score: 253
Period size: 70 Copynumber: 1.9 Consensus size: 70
2485694 ATAAAATAAC
*
2485704 TAATGTATAATGCTTCATCAAACTGATATAGGCTTTCGCAAGTTATAAAGAAGATTACATCAAAC
1 TAATGTATAATGCTTCATCAAACTGATATAGGCTTTCCCAAGTTATAAAGAAGATTACATCAAAC
2485769 TGATA
66 TGATA
2485774 TAATGTATAATGCTTCATCAAACTGATATAGGCTTTCCCAAGTTATAAAGAAGATTACATC
1 TAATGTATAATGCTTCATCAAACTGATATAGGCTTTCCCAAGTTATAAAGAAGATTACATC
2485835 CTTTTACAAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (70 bp):
TAATGTATAATGCTTCATCAAACTGATATAGGCTTTCCCAAGTTATAAAGAAGATTACATCAAAC
TGATA
Found at i:2488230 original size:6 final size:6
Alignment explanation
Indices: 2488216--2488254 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
2488206 CTTCTTCCTT
* *
2488216 TTCTTC TTCTGC TTCTGC TTCTGC TTCTGC TTCTTC TTC
1 TTCTGC TTCTGC TTCTGC TTCTGC TTCTGC TTCTGC TTC
2488255 CTCTTCGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.33, G:0.10, T:0.56
Consensus pattern (6 bp):
TTCTGC
Found at i:2488230 original size:18 final size:19
Alignment explanation
Indices: 2488221--2488260 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2488211 TCCTTTTCTT
2488221 CTTCTGCTTCTGCTT-CTG
1 CTTCTGCTTCTGCTTCCTG
*
2488239 CTTCTGCTTCTTCTTCCT-
1 CTTCTGCTTCTGCTTCCTG
2488257 CTTC
1 CTTC
2488261 GGATTCTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.00, C:0.38, G:0.10, T:0.53
Consensus pattern (19 bp):
CTTCTGCTTCTGCTTCCTG
Found at i:2497169 original size:212 final size:216
Alignment explanation
Indices: 2496830--2497315 Score: 581
Period size: 212 Copynumber: 2.3 Consensus size: 216
2496820 ATGGCATGTT
* * * *
2496830 CCAGTATACGAAAAAAGTAAAAAAAAA--TTGGTAGTGGTCTGCCAATGGCAGGCATCACCTATT
1 CCAGTATACGAAAAAAGTAAAAAAAAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTATT
* * * *
2496893 TCCAAAAAAAAAATATTTTTGGTCTGTTAATTGCCGGCATCAGTATACGAAAAAAGT-AAAAAAA
66 TCCAAAAAAAAAATACTTTTGGTCTGTCAATAGCCGGCACCAGTATACGAAAAAAGTAAAAAAAA
* ** *
2496957 AATTTTGTGGTGGCTTGCCAATGGTCGGCACCACCTTT-T-TTCCAA-TTT-TTTTTTTTTACTT
131 AATTTGGTGGTGGCTTGCCAATGGTCGGCACCACCTTTATGGGCAAATTTTATTTTTTTTTACTT
* *
2497018 TTCGTCTCTCAATGGTCGACA
196 TTCGTCTCTCAAAGGCCGACA
* *
2497039 CCAGTATACGAAAAAAGTAAAAAAATAATTTTGGTGGTGGCCTGCCAATGGCCGGTACCACCTTT
1 CCAGTATACGAAAAAAGTAAAAAAA-AATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTAT
******** *
2497104 TTCCAATTTTTTTTTACTTTTGGTCTGTCAATAGCCGGCACCAGTATACGAAAAAAGTTAAAAAA
65 TTCCAAAAAAAAAATACTTTTGGTCTGTCAATAGCCGGCACCAGTATACGAAAAAAGTAAAAAAA
* ** *
2497169 AAATTTGGTGGTGGCTTGCCTATGGTCGGTGCCACCTTTATGGGGAAATTTTTATTTTTTTTTAC
130 AAATTTGGTGGTGGCTTGCCAATGGTCGGCACCACCTTTATGGGCAAA-TTTTATTTTTTTTTAC
* * *
2497234 TTTTGGTCTGTCAAAGGCCGGCA
194 TTTTCGTCTCTCAAAGGCCGACA
*** *
2497257 CCAGTATACGAAAAAAGTTTTAAAAAATTTTGGTGGTGGCCGGCCAATGGCCGGCACCA
1 CCAGTATACGAAAAAAGTAAAAAAAAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCA
2497316 AATTTATCAA
Statistics
Matches: 232, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
209 25 0.11
210 2 0.01
212 75 0.32
213 41 0.18
214 1 0.00
215 2 0.01
217 35 0.15
218 51 0.22
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (216 bp):
CCAGTATACGAAAAAAGTAAAAAAAAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTATT
TCCAAAAAAAAAATACTTTTGGTCTGTCAATAGCCGGCACCAGTATACGAAAAAAGTAAAAAAAA
AATTTGGTGGTGGCTTGCCAATGGTCGGCACCACCTTTATGGGCAAATTTTATTTTTTTTTACTT
TTCGTCTCTCAAAGGCCGACA
Found at i:2497322 original size:113 final size:113
Alignment explanation
Indices: 2497109--2497322 Score: 313
Period size: 113 Copynumber: 1.9 Consensus size: 113
2497099 CCTTTTTCCA
2497109 ATTTTTTTTTACTTTTGGTCTGTCAATAGCCGGCACCAGTATACGAAAAAAGTTAAAAAAAAATT
1 ATTTTTTTTTACTTTTGGTCTGTCAATAGCCGGCACCAGTATACGAAAAAAGTTAAAAAAAAATT
** * * ** **
2497174 TGGTGGTGGCTTGCCTATGGTCGGTGCCACCTTTATGGGGAAATTTTT
66 TGGTGGTGGCCGGCCAATGGCCGGCACCAAATTTATGGGGAAATTTTT
** *
2497222 ATTTTTTTTTACTTTTGGTCTGTCAA-AGGCCGGCACCAGTATACGAAAAAAGTTTTAAAAAATT
1 ATTTTTTTTTACTTTTGGTCTGTCAATA-GCCGGCACCAGTATACGAAAAAAGTTAAAAAAAAAT
2497286 TTGGTGGTGGCCGGCCAATGGCCGGCACCAAATTTAT
65 TTGGTGGTGGCCGGCCAATGGCCGGCACCAAATTTAT
2497323 CAAATATATA
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
112 1 0.01
113 88 0.99
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (113 bp):
ATTTTTTTTTACTTTTGGTCTGTCAATAGCCGGCACCAGTATACGAAAAAAGTTAAAAAAAAATT
TGGTGGTGGCCGGCCAATGGCCGGCACCAAATTTATGGGGAAATTTTT
Found at i:2498849 original size:107 final size:106
Alignment explanation
Indices: 2498659--2499235 Score: 564
Period size: 103 Copynumber: 5.4 Consensus size: 106
2498649 AAAAAGAAAA
* * * *
2498659 TTTTAACTTTTTTCGTATACTGGTGCCCGCCATTGACAGACCGAAAGTAAAAAAAAAATTGGGAA
1 TTTTTACTTTTTTCGTATACTGGTGCCGGCCATTGACAGACCAAAAGTAAAAAAAAAATTGGTAA
* * *
2498724 AAAAAGTGATGCCGGCCATTGGCAAGCCACCACCAATTTTT
66 ATAAAGTGGTGCCGGCCATTGGCAGGCCACCACCAATTTTT
* * *
2498765 TTTTTACTTTTTTCGTATACTGGTGCCGGTCATTGATAGACCAAAAGTAAAAAAAAAATTGGGGA
1 TTTTTACTTTTTTCGTATACTGGTGCCGGCCATTGACAGACCAAAAGTAAAAAAAAAATT-GGTA
* *
2498830 AAAAAAGTGGTGCCGGCCATTGGCAAGCCACCACCAAAAATTATTT
65 AATAAAGTGGTGCCGGCCATTGGCAGGCCACCACC---AATT-TTT
** * * * **
2498876 TTTTTACTTTTTTCGTATACTGGTGCCTACTATTGACACA-AAAAAAAAAAATAAAAATATTTTT
1 TTTTTACTTTTTTCGTATACTGGTGCCGGCCATTGACAGACCAAAAGTAAAA-AAAAA-A---TT
** *
2498940 TTTCAATAAAGATGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTT
61 GGTAAATAAAG-TGGTGCCGGCCATTGGCAGGCCACCACC-AATTTTT
* * * ** *
2498988 TTTTTACTTTTTTCGTATACTGGTGTCTGCTATTGAC--A-CAAAA--AAATAAAAAAATTACTT
1 TTTTTACTTTTTTCGTATACTGGTGCCGGCCATTGACAGACCAAAAGTAAA-AAAAAAATTGGTA
** * * * *
2499048 TTTAAGGTGTTGCTGGCCATTGGCAGGCCACCA-CAAATTTT
65 AATAAAGTGGTGCCGGCCATTGGCAGGCCACCACCAATTTTT
* * *
2499089 TTTTTACTTTTTTCGTATACTGGTGCCTGCCATTGACACGA-AAAAAGTAAAAAAAAAATT-GTT
1 TTTTTACTTTTTTCGTATACTGGTGCCGGCCATTGACA-GACCAAAAGTAAAAAAAAAATTGGTA
** * *
2499152 TTTAAGGTGGTGCCGGCCATTGGCAGGCCACTACCAA--TTT
65 AATAAAGTGGTGCCGGCCATTGGCAGGCCACCACCAATTTTT
* *
2499192 TTTTTACTTTTTTCGTATTCTGGTGCCGACCATTGACAGACCAA
1 TTTTTACTTTTTTCGTATACTGGTGCCGGCCATTGACAGACCAA
2499236 TACCTGGAAT
Statistics
Matches: 408, Mismatches: 44, Indels: 41
0.83 0.09 0.08
Matches are distributed among these distances:
101 41 0.10
102 3 0.01
103 64 0.16
104 44 0.11
105 12 0.03
106 58 0.14
107 39 0.10
108 8 0.02
109 1 0.00
110 17 0.04
111 42 0.10
112 39 0.10
113 5 0.01
114 6 0.01
115 29 0.07
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (106 bp):
TTTTTACTTTTTTCGTATACTGGTGCCGGCCATTGACAGACCAAAAGTAAAAAAAAAATTGGTAA
ATAAAGTGGTGCCGGCCATTGGCAGGCCACCACCAATTTTT
Found at i:2501847 original size:20 final size:21
Alignment explanation
Indices: 2501818--2501857 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2501808 ACCCAAAACC
2501818 AACAGCAAAAAAAAAAAAGAT
1 AACAGCAAAAAAAAAAAAGAT
*
2501839 AACAG-AAAAAGAAAAAAGA
1 AACAGCAAAAAAAAAAAAGA
2501858 AAACCCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.03
Consensus pattern (21 bp):
AACAGCAAAAAAAAAAAAGAT
Found at i:2503917 original size:36 final size:36
Alignment explanation
Indices: 2503870--2503988 Score: 220
Period size: 36 Copynumber: 3.3 Consensus size: 36
2503860 CCCTGACCAA
*
2503870 ATAAGTGTAGCACTTATCACTTTTTCACTTGATCAG
1 ATAAGTATAGCACTTATCACTTTTTCACTTGATCAG
2503906 ATAAGTATAGCACTTATCACTTTTTCACTTGATCAG
1 ATAAGTATAGCACTTATCACTTTTTCACTTGATCAG
2503942 ATAAGTATAGCACTTATCACTTTTTCACTTGATCAG
1 ATAAGTATAGCACTTATCACTTTTTCACTTGATCAG
*
2503978 ATAAGTGTAGC
1 ATAAGTATAGC
2503989 TAAAGCTACC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 81 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (36 bp):
ATAAGTATAGCACTTATCACTTTTTCACTTGATCAG
Found at i:2505084 original size:16 final size:17
Alignment explanation
Indices: 2505045--2505085 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2505035 TCTAAAAATA
*
2505045 AACTCATAAAAGATTCT
1 AACTCATAAAAGATTAT
*
2505062 AAC-CATATAA-ATTAT
1 AACTCATAAAAGATTAT
2505077 AACTCATAA
1 AACTCATAA
2505086 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 7 0.35
16 10 0.50
17 3 0.15
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.29
Consensus pattern (17 bp):
AACTCATAAAAGATTAT
Found at i:2515074 original size:147 final size:147
Alignment explanation
Indices: 2514715--2515141 Score: 767
Period size: 147 Copynumber: 2.9 Consensus size: 147
2514705 GTTAAACTAC
*
2514715 CATCTCCACTTGAACTAACCTCATCTCCATTGCTAATAATCCTGTAAACATTCCCATTTTCAGCA
1 CATCTCCACTTGAACTAACCTCATCTCCATTGCTAATAATCCTATAAACATTCCCATTTTCAGCA
2514780 AAGCTTACAGTTTTCTTCACTTTTGGTTGAATCCCTTGCCTTTTCAACAAAAGCTCACC------
66 AAGCTTACAGTTTTCTTCACTTTTGGTTGAATCCCTTGCCTTTTCAACAAAAGCTCACCATTTTT
*
2514839 ATTTTTGTTCTCTGCTT
131 ATTTTTATTCTCTGCTT
*
2514856 CATCTCCACTTGAAGTAACCTCATCTCCATTGCTAATAATCCTATAAACATTCCCATTTTCAGCA
1 CATCTCCACTTGAACTAACCTCATCTCCATTGCTAATAATCCTATAAACATTCCCATTTTCAGCA
2514921 AAGCTTACAGTTTTCTTCACTTTTGGTTGAATCCCTTGCCTTTTCAACAAAAGCTCACCATTTTT
66 AAGCTTACAGTTTTCTTCACTTTTGGTTGAATCCCTTGCCTTTTCAACAAAAGCTCACCATTTTT
2514986 ATTTTTATTCTCTGCTT
131 ATTTTTATTCTCTGCTT
*
2515003 CATCTCCACTTGAACTAACCTCATCTCCATTGCTAATAATCCTATAAACATTCCCATTTTCAGTA
1 CATCTCCACTTGAACTAACCTCATCTCCATTGCTAATAATCCTATAAACATTCCCATTTTCAGCA
*
2515068 AAGCTTACAGCTTTCTTCACTTTTGGTTGAATCCCTTGCCTTTTCAACAAAAGCTCACCATTTTT
66 AAGCTTACAGTTTTCTTCACTTTTGGTTGAATCCCTTGCCTTTTCAACAAAAGCTCACCATTTTT
2515133 ATTTTTATT
131 ATTTTTATT
2515142 TTTATTCTCT
Statistics
Matches: 274, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
141 122 0.45
147 152 0.55
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.39
Consensus pattern (147 bp):
CATCTCCACTTGAACTAACCTCATCTCCATTGCTAATAATCCTATAAACATTCCCATTTTCAGCA
AAGCTTACAGTTTTCTTCACTTTTGGTTGAATCCCTTGCCTTTTCAACAAAAGCTCACCATTTTT
ATTTTTATTCTCTGCTT
Found at i:2525695 original size:67 final size:66
Alignment explanation
Indices: 2525557--2525695 Score: 163
Period size: 67 Copynumber: 2.1 Consensus size: 66
2525547 TTGGCTTTTG
* * *
2525557 ATCAACATTTAGGCCCTTTCATGAACCATTCAACAGCTCTCTGCATAGGCAAGGCATATCTCCAA
1 ATCAACATTTAGGCCCTTCCATGAACCATTCAACAACTCTCT-CATAGGCAAGGCATATCTACAA
**
2525622 CC
65 AA
* * **
2525624 ATCAACATTTGGGCTCTTCCATGAACCATTCAACAACTCTCT-ATTGAGGTGAGGCATATCTACA
1 ATCAACATTTAGGCCCTTCCATGAACCATTCAACAACTCTCTCA-T-AGGCAAGGCATATCTACA
2525688 AAA
64 AAA
2525691 ATCAA
1 ATCAA
2525696 AATTCGAGCC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
65 1 0.02
66 1 0.02
67 59 0.97
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (66 bp):
ATCAACATTTAGGCCCTTCCATGAACCATTCAACAACTCTCTCATAGGCAAGGCATATCTACAAA
A
Found at i:2525951 original size:32 final size:31
Alignment explanation
Indices: 2525915--2525999 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 31
2525905 GTGCATAAGA
*
2525915 TATTTGGAAAAGTATAAATATTAATATGAATT
1 TATTTGGAAAAG-ATAAATATTAATATAAATT
*
2525947 TATTT---AGAGATAAATATTAATATAAATT
1 TATTTGGAAAAGATAAATATTAATATAAATT
*
2525975 TATTTGGAGAAACGATTAA-ATTAAT
1 TATTTGGA-AAA-GATAAATATTAAT
2526000 CGAAAGCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
28 23 0.52
29 3 0.07
32 13 0.30
33 5 0.11
ACGTcount: A:0.47, C:0.01, G:0.12, T:0.40
Consensus pattern (31 bp):
TATTTGGAAAAGATAAATATTAATATAAATT
Found at i:2525960 original size:28 final size:28
Alignment explanation
Indices: 2525928--2525984 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
2525918 TTGGAAAAGT
*
2525928 ATAAATATTAATATGAATTTATTTAGAG
1 ATAAATATTAATATAAATTTATTTAGAG
*
2525956 ATAAATATTAATATAAATTTATTTGGAG
1 ATAAATATTAATATAAATTTATTTAGAG
2525984 A
1 A
2525985 AACGATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (28 bp):
ATAAATATTAATATAAATTTATTTAGAG
Found at i:2527206 original size:5 final size:5
Alignment explanation
Indices: 2527183--2527218 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
2527173 CTTACATTGC
2527183 TATTT TA-TT TATTT CTATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT -TATTT TATTT TATTT TATTT T
2527219 TTGTTTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:2527959 original size:3 final size:3
Alignment explanation
Indices: 2527951--2527994 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2527941 GAATTAGTCC
2527951 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2527995 CCTATTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2530251 original size:25 final size:25
Alignment explanation
Indices: 2530201--2530262 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
2530191 ACCCTAGCGC
* *
2530201 GCTCTCTGGTTATTAGAACGTTAGT
1 GCTCTCTGATTATTAGAACGTCAGT
* *
2530226 GCTCTCTGATTATTAGTATGTCAGT
1 GCTCTCTGATTATTAGAACGTCAGT
2530251 GCTCAT-TGATTA
1 GCTC-TCTGATTA
2530263 GCACATTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (25 bp):
GCTCTCTGATTATTAGAACGTCAGT
Found at i:2532936 original size:3 final size:3
Alignment explanation
Indices: 2532928--2532959 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2532918 ATGCATTAGT
2532928 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2532960 TATTATTATA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2533132 original size:14 final size:14
Alignment explanation
Indices: 2533088--2533123 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2533078 TAAAATATAA
*
2533088 TAATAATAATAATT
1 TAATAATACTAATT
2533102 TAATAATACTAATT
1 TAATAATACTAATT
2533116 TAATAATA
1 TAATAATA
2533124 TATTTTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATAATACTAATT
Found at i:2533513 original size:29 final size:29
Alignment explanation
Indices: 2533478--2533535 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2533468 AAGGGGTAAA
2533478 GTATGAATTTCTGTTGTTTCAATAAATGG
1 GTATGAATTTCTGTTGTTTCAATAAATGG
2533507 GTATGAATTTCTGTTGTTTCAATAAATGG
1 GTATGAATTTCTGTTGTTTCAATAAATGG
2533536 CATGTACCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (29 bp):
GTATGAATTTCTGTTGTTTCAATAAATGG
Found at i:2534098 original size:26 final size:28
Alignment explanation
Indices: 2534037--2534100 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 28
2534027 GGGGTGTTAC
2534037 AAGTACCCTT-CCACGATACCTTCCCAT
1 AAGTACCCTTCCCACGATACCTTCCCAT
*
2534064 GAGTA-CCTTCCCACGATTA-C-TCCCA-
1 AAGTACCCTTCCCACGA-TACCTTCCCAT
2534089 AAGTACCCTTCC
1 AAGTACCCTTCC
2534101 ACGGAACCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
25 4 0.12
26 15 0.47
27 11 0.34
28 2 0.06
ACGTcount: A:0.25, C:0.41, G:0.09, T:0.25
Consensus pattern (28 bp):
AAGTACCCTTCCCACGATACCTTCCCAT
Found at i:2536682 original size:43 final size:42
Alignment explanation
Indices: 2536527--2536683 Score: 149
Period size: 43 Copynumber: 3.7 Consensus size: 42
2536517 TATGTGTTTT
* * *
2536527 CGTGTAAGACCACGTCTGGGACGTCGGCATCGACT-TGTGTTTA
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCGA-TATGTG-ATA
* * * *
2536570 CGTGTAAGACCATGTCTAGGACATTGGCATCG-TATTTGATT
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCGATATGTGATA
* * * *
2536611 CGTGTAAGACCCTGTCAGGGAAAG-TGGCATCGATATGAGATA
1 CGTGTAAGACCATGTCTGGG-ACGTTGGCATCGATATGTGATA
*
2536653 GCATGTAAGACCATGTCTGGGACGTTGGCAT
1 -CGTGTAAGACCATGTCTGGGACGTTGGCAT
2536684 TGTTCGATAT
Statistics
Matches: 90, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
41 27 0.30
42 12 0.13
43 51 0.57
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.27
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACGTTGGCATCGATATGTGATA
Found at i:2538596 original size:14 final size:14
Alignment explanation
Indices: 2538577--2538606 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2538567 ATAGAAGTTA
2538577 ATTTGCATGACCGG
1 ATTTGCATGACCGG
2538591 ATTTGCATGACCGG
1 ATTTGCATGACCGG
2538605 AT
1 AT
2538607 ATATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (14 bp):
ATTTGCATGACCGG
Found at i:2547266 original size:21 final size:21
Alignment explanation
Indices: 2547241--2547286 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2547231 ACAATAAGAT
*
2547241 AAAATCATTTTGAAAGC-TTTA
1 AAAAT-ATTTTAAAAGCATTTA
*
2547262 AAAATATTTTAAAATCATTTA
1 AAAATATTTTAAAAGCATTTA
2547283 AAAA
1 AAAA
2547287 CTTTTCGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (21 bp):
AAAATATTTTAAAAGCATTTA
Found at i:2552181 original size:22 final size:22
Alignment explanation
Indices: 2552146--2552201 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
2552136 ATTTCCTCTC
2552146 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
*
2552169 AATTCTCTTAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
2552191 AATTCTCTCAA
1 AATTCTCTCAA
2552202 ATCCATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.29, C:0.30, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:2552227 original size:29 final size:29
Alignment explanation
Indices: 2552195--2552281 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
2552185 TTCCAAAATT
2552195 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTCAATTTC
* * *
2552224 CTCTCAATTTCC---TTCAA----AAATT-
1 CTCTCAA-ATCCATATTTAATTTCAATTTC
2552246 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTCAATTTC
2552275 CTCTCAA
1 CTCTCAA
2552282 TTTCATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 18
0.64 0.09 0.27
Matches are distributed among these distances:
21 3 0.07
22 7 0.16
23 4 0.09
24 4 0.09
27 4 0.09
28 4 0.09
29 14 0.33
30 3 0.07
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (29 bp):
CTCTCAAATCCATATTTAATTTCAATTTC
Found at i:2552235 original size:51 final size:51
Alignment explanation
Indices: 2552173--2552285 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
2552163 TTCCAAAATT
* *
2552173 CTCTTAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
2552224 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
2552275 CTCTCAATTTC
1 CTCTCAATTTC
2552286 ATTTTTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:2553436 original size:7 final size:7
Alignment explanation
Indices: 2553426--2553450 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2553416 ATTCGATTAA
2553426 TATTTAG
1 TATTTAG
2553433 TATTTAG
1 TATTTAG
2553440 TATTTAG
1 TATTTAG
2553447 TATT
1 TATT
2553451 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:2554112 original size:18 final size:18
Alignment explanation
Indices: 2554086--2554120 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2554076 AGGTGCGTTT
*
2554086 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
2554104 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
2554121 TTGTTTTCCA
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:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:2554583 original size:43 final size:43
Alignment explanation
Indices: 2554531--2554629 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 43
2554521 TTATTTGTAC
* *
2554531 AAATATTTTGA-ATATTTTGATATTATTTTATGTAAAAAAATA
1 AAATTTTTTGAGATATTTTGATATTATTTAATGTAAAAAAATA
* *
2554573 GAAATTTTTTGAGTTATTTTGATATTATTTAATGTAATAAAATA
1 -AAATTTTTTGAGATATTTTGATATTATTTAATGTAAAAAAATA
2554617 AAAGTTTATTTGA
1 AAA-TTT-TTTGA
2554630 TGTAATAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
43 13 0.27
44 31 0.63
45 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (43 bp):
AAATTTTTTGAGATATTTTGATATTATTTAATGTAAAAAAATA
Done.