Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 18 of 345
Found at i:6147232 original size:24 final size:24
Alignment explanation
Indices: 6147196--6147265 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
6147186 GGGTCAACAT
*
6147196 TGGCACTAAGTGTGCAGATTTGAA
1 TGGCACTATGTGTGCAGATTTGAA
* *
6147220 TGGCACTATGTGTGCGGAATTGAA
1 TGGCACTATGTGTGCAGATTTGAA
*
6147244 TGGCACTATGTGTGCTGATTTG
1 TGGCACTATGTGTGCAGATTTG
6147266 GATGTCAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (24 bp):
TGGCACTATGTGTGCAGATTTGAA
Found at i:6147972 original size:2 final size:2
Alignment explanation
Indices: 6147965--6147996 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6147955 ATTAATGAAT
6147965 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6147997 AATCTATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6149609 original size:44 final size:45
Alignment explanation
Indices: 6149519--6149647 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
6149509 GACAGAACGA
*
6149519 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
6149565 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
6149609 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
6149648 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:6155649 original size:44 final size:45
Alignment explanation
Indices: 6155559--6155687 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
6155549 GACAGAACGA
*
6155559 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
6155605 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
6155649 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
6155688 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:6162132 original size:25 final size:25
Alignment explanation
Indices: 6162104--6162182 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
6162094 ACTCTGCCCT
6162104 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * *
6162129 ATCACAT-T-GGC-CATTCGACCTT-
1 ATCACATATATACACTTTC-ACATTC
*
6162151 ATCACATATATACACTTTCACTTTC
1 ATCACATATATACACTTTCACATTC
6162176 ATCACAT
1 ATCACAT
6162183 CGGCCATTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 11 0.27
23 6 0.15
24 6 0.15
25 18 0.44
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:6162228 original size:49 final size:49
Alignment explanation
Indices: 6162054--6162513 Score: 705
Period size: 49 Copynumber: 9.7 Consensus size: 49
6162044 CCCTTCGGGA
* * * * **
6162054 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCTGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
6162101 CCTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6162148 CTTATCAC--ATATATACACTTTCACTTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6162195 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6162244 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6162293 CTTATCAC----ATAT--A--TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6162334 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6162383 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6162432 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGTC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
6162481 TTTATCACATATATATACACTTTCACATTCATC
1 CTTATCACATATATATACACTTTCACATTCATC
6162514 GCATAAAATC
Statistics
Matches: 387, Mismatches: 14, Indels: 22
0.91 0.03 0.05
Matches are distributed among these distances:
41 36 0.09
43 1 0.00
45 8 0.02
46 1 0.00
47 89 0.23
49 252 0.65
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:6162302 original size:22 final size:22
Alignment explanation
Indices: 6162274--6162343 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
6162264 TTTCACATTC
6162274 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
** *
6162296 ATCACAT---ATATTCA--CATT
1 ATCACATCGGCCATT-AGGCCTT
6162314 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
6162337 ATCACAT
1 ATCACAT
6162344 ATATATACAC
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
18 3 0.09
19 10 0.29
20 1 0.03
21 1 0.03
22 17 0.49
23 3 0.09
ACGTcount: A:0.29, C:0.30, G:0.11, T:0.30
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:6162334 original size:90 final size:90
Alignment explanation
Indices: 6162216--6162494 Score: 468
Period size: 90 Copynumber: 3.0 Consensus size: 90
6162206 TATATACACT
6162216 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACAT
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACAT
6162281 CGGCCATTAGGCCTTATCACATATA
66 CGGCCATTAGGCCTTATCACATATA
6162306 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACAT
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACAT
6162371 CGGCCATTAGGCCTTATCACATATATATACA
66 CGGCCATTAGGCCTTATCAC----ATAT--A
6162402 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCAC
1 --TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCAC
* *
6162467 ATCGGCCATTAGTCTTTATCACATATA
64 ATCGGCCATTAGGCCTTATCACATATA
6162494 T
1 T
6162495 ATACACTTTC
Statistics
Matches: 179, Mismatches: 2, Indels: 16
0.91 0.01 0.08
Matches are distributed among these distances:
90 86 0.48
92 1 0.01
94 8 0.04
96 1 0.01
98 83 0.46
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (90 bp):
TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACATATA
Found at i:6162386 original size:188 final size:186
Alignment explanation
Indices: 6162054--6162494 Score: 679
Period size: 188 Copynumber: 2.3 Consensus size: 186
6162044 CCCTTCGGGA
* * * * ** *
6162054 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCTGCCCTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATAT--
* * *
6162117 ACTTTCACATTCATCACATTGGCCATTCGACCTTATCACATATATACACTTTCACTTTCATCACA
62 A--TTCACATTCATCACATCGGCCATTAGACCTTATCACATATATACACTTTCACATTCATCACA
6162182 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
125 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6162244 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATTC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATTC
*
6162309 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGG
66 ACATTCATCACATCGGCCATTAGACCTTATCAC--ATATATACACTTTCACATTCATCACATCGG
6162374 CCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 CCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
6162432 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGTCTTTATCACATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
6162495 ATACACTTTC
Statistics
Matches: 234, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
186 33 0.14
188 149 0.64
190 14 0.06
191 1 0.00
192 37 0.16
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (186 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATTC
ACATTCATCACATCGGCCATTAGACCTTATCACATATATACACTTTCACATTCATCACATCGGCC
ATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:6162557 original size:98 final size:94
Alignment explanation
Indices: 6162332--6162538 Score: 258
Period size: 98 Copynumber: 2.2 Consensus size: 94
6162322 CGGCCATTAG
* *
6162332 GCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
1 GCCTAATCAAATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
* *
6162397 ATACACTTTCACATTCATCACATCGGCCATTAG
66 ATACACTTTCACATTCATCACAT----CATAAA
* * * *
6162430 GCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGTCTTTATCACATATAT
1 GCCTAATCAAATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
*
6162495 ATACACTTTCACATTCATCGCAT-A-AAA
66 ATACACTTTCACATTCATCACATCATAAA
*
6162522 TCCTAAATCAAA-ATATA
1 GCCT-AATCAAATATATA
6162539 AATTTTCATG
Statistics
Matches: 100, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
92 9 0.09
93 6 0.06
98 85 0.85
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (94 bp):
GCCTAATCAAATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
ATACACTTTCACATTCATCACATCATAAA
Found at i:6169154 original size:42 final size:42
Alignment explanation
Indices: 6169105--6169214 Score: 163
Period size: 42 Copynumber: 2.6 Consensus size: 42
6169095 CATAGTTCAA
*
6169105 CTATGGTCTTACACATCTTCACATAAT-GATGCCATAGCCCAG
1 CTATGGTCTTACACATATTCACAT-ATCGATGCCATAGCCCAG
*
6169147 CTATGGTCTTACACATATTCATATATCGATGCCATAGCCCAG
1 CTATGGTCTTACACATATTCACATATCGATGCCATAGCCCAG
6169189 CTATGGTCTTACACGA-A-TCACATATC
1 CTATGGTCTTACAC-ATATTCACATATC
6169215 TCACTGATGC
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
41 10 0.16
42 52 0.83
43 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
CTATGGTCTTACACATATTCACATATCGATGCCATAGCCCAG
Found at i:6169276 original size:47 final size:46
Alignment explanation
Indices: 6169173--6169296 Score: 167
Period size: 47 Copynumber: 2.7 Consensus size: 46
6169163 ATTCATATAT
* * * * *
6169173 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
6169219 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
6169266 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
6169297 GAAATCACTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 27 0.40
47 41 0.60
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:6169349 original size:31 final size:31
Alignment explanation
Indices: 6169314--6169493 Score: 297
Period size: 31 Copynumber: 5.8 Consensus size: 31
6169304 CTTGGCACTT
*
6169314 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
6169345 GTAGCCGGAGCTACCATTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
6169376 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
6169407 GTAGCCGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
6169438 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
6169469 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
6169494 TGTCATTTGT
Statistics
Matches: 138, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 138 1.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:6169574 original size:50 final size:50
Alignment explanation
Indices: 6169469--6169645 Score: 291
Period size: 50 Copynumber: 3.5 Consensus size: 50
6169459 CACTGATCAG
* * *
6169469 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAAATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
*
6169520 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
6169570 GTAGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
6169620 GTAGCCGAAGCTCTCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
6169646 GTTGCCATGG
Statistics
Matches: 118, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 94 0.80
51 24 0.20
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:6181475 original size:6 final size:6
Alignment explanation
Indices: 6181464--6181498 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
6181454 AAGAGCACCG
* *
6181464 GGTTCA GGTTCA GGTTCA GGTTCG GGTTCG GGTTC
1 GGTTCA GGTTCA GGTTCA GGTTCA GGTTCA GGTTC
6181499 TTCACTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.09, C:0.17, G:0.40, T:0.34
Consensus pattern (6 bp):
GGTTCA
Found at i:6184680 original size:6 final size:6
Alignment explanation
Indices: 6184671--6184699 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
6184661 GTTTATGACT
6184671 ATGTAC ATGTAC ATGTAC ATGTAC ATGTA
1 ATGTAC ATGTAC ATGTAC ATGTAC ATGTA
6184700 TATACTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (6 bp):
ATGTAC
Found at i:6193214 original size:23 final size:23
Alignment explanation
Indices: 6193190--6193232 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6193180 AAAATCTTTA
*
6193190 AAAT-TTAAATATTATATAAATT
1 AAATCTTAAACATTATATAAATT
*
6193212 AAATCTTTAACATTATATAAA
1 AAATCTTAAACATTATATAAA
6193233 AATCGATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATCTTAAACATTATATAAATT
Found at i:6208709 original size:19 final size:19
Alignment explanation
Indices: 6208634--6208749 Score: 103
Period size: 19 Copynumber: 5.8 Consensus size: 19
6208624 TTAGAAAATT
*
6208634 ATTATTTTAGAAAATTTTAAA
1 ATTATTTT-G-AATTTTTAAA
6208655 ATT-TTTAT-AATTTTTAAA
1 ATTATTT-TGAATTTTTAAA
*
6208673 ATATAAATTTTGGAATTTTTATA
1 AT-T--ATTTT-GAATTTTTAAA
*
6208696 ATTATTTTGAATTTTAAAA
1 ATTATTTTGAATTTTTAAA
*
6208715 ATTACTTTGAATTTTTTAAA
1 ATTATTTTGAA-TTTTTAAA
6208735 ATTATTTT-AATTTTT
1 ATTATTTTGAATTTTT
6208750 TGTAATTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
18 16 0.20
19 22 0.28
20 22 0.28
21 5 0.06
22 4 0.05
23 11 0.14
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (19 bp):
ATTATTTTGAATTTTTAAA
Found at i:6215367 original size:23 final size:23
Alignment explanation
Indices: 6215341--6215389 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
6215331 AGAGCTATGT
*
6215341 TATTTTCTGTAGTCTCATATGAA
1 TATTTTCTGTAATCTCATATGAA
6215364 TATTTTCTGTAATCTCATATGAA
1 TATTTTCTGTAATCTCATATGAA
6215387 TAT
1 TAT
6215390 GAATTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (23 bp):
TATTTTCTGTAATCTCATATGAA
Found at i:6230786 original size:16 final size:17
Alignment explanation
Indices: 6230765--6230797 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6230755 CATGCTAGAG
6230765 CATATAAATTT-AAAAC
1 CATATAAATTTGAAAAC
*
6230781 CATATATATTTGAAAAC
1 CATATAAATTTGAAAAC
6230798 TATTTCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (17 bp):
CATATAAATTTGAAAAC
Found at i:6230979 original size:18 final size:17
Alignment explanation
Indices: 6230956--6231000 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
6230946 TTTTAAAAAA
6230956 TATAAAATTTGAAATTTT
1 TATAAAATTTG-AATTTT
6230974 TATAAATATTTTGAATTTT
1 TATAAA-A-TTTGAATTTT
6230993 TA-AAAATT
1 TATAAAATT
6231001 ATTTTGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.08
17 1 0.04
18 9 0.36
19 9 0.36
20 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
TATAAAATTTGAATTTT
Found at i:6230984 original size:19 final size:18
Alignment explanation
Indices: 6230956--6231010 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
6230946 TTTTAAAAAA
6230956 TATAAA-ATTTGAAATTTT
1 TATAAATATTTG-AATTTT
6230974 TATAAATATTTTGAATTTT
1 TATAAATA-TTTGAATTTT
*
6230993 TAAAAATTATTTTGAATT
1 TATAAA-TA-TTTGAATT
6231011 ATTTTGTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 6 0.18
19 12 0.36
20 15 0.45
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
TATAAATATTTGAATTTT
Found at i:6230988 original size:20 final size:21
Alignment explanation
Indices: 6230963--6231008 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
6230953 AAATATAAAA
*
6230963 TTTGAAATTTTTATAAA-TAT
1 TTTGAAATTTTTAAAAATTAT
6230983 TTTG-AATTTTTAAAAATTAT
1 TTTGAAATTTTTAAAAATTAT
6231003 TTTGAA
1 TTTGAA
6231009 TTATTTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.48
20 11 0.48
21 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTGAAATTTTTAAAAATTAT
Found at i:6231009 original size:20 final size:19
Alignment explanation
Indices: 6230963--6231010 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
6230953 AAATATAAAA
*
6230963 TTTGAAATTTTTATAAATAT
1 TTTG-AATTTTTAAAAATAT
6230983 TTTGAATTTTTAAAAATTAT
1 TTTGAATTTTTAAAAA-TAT
6231003 TTTGAATT
1 TTTGAATT
6231011 ATTTTGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTGAATTTTTAAAAATAT
Found at i:6232710 original size:6 final size:6
Alignment explanation
Indices: 6232695--6232746 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
6232685 ATTTAGGGTT
* * * *
6232695 ATTTCG ATTTTA ATTTTG ATTTCG ATTCTG ATTTTG ATTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
6232743 ATTT
1 ATTT
6232747 CAATTTTGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.62
Consensus pattern (6 bp):
ATTTTG
Found at i:6232755 original size:18 final size:18
Alignment explanation
Indices: 6232695--6232746 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
6232685 ATTTAGGGTT
*
6232695 ATTTCGATTTTAATTTTG
1 ATTTCGATTTTGATTTTG
*
6232713 ATTTCGATTCTGATTTTG
1 ATTTCGATTTTGATTTTG
*
6232731 ATTTTGATTTTGATTT
1 ATTTCGATTTTGATTT
6232747 CAATTTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.62
Consensus pattern (18 bp):
ATTTCGATTTTGATTTTG
Found at i:6232975 original size:89 final size:89
Alignment explanation
Indices: 6232864--6233043 Score: 288
Period size: 89 Copynumber: 2.0 Consensus size: 89
6232854 TGCCATTGTA
* * * *
6232864 TGAATGCCATTATCAAACTGATGTTTGTTGTGTATATCTGCCATTGTTAGTATTCAAGCTGCTAT
1 TGAATGCCATTATCAAACTGATGTTTGCTGCGTATATCTGCCATTGTTAGTATCCAAGCTACTAT
* *
6232929 ATTGTATGTGGCAAAATTAAAATT
66 ATTGTAAGTGGCAAAATCAAAATT
* *
6232953 TGAATGCCATTATCAAATTGATGTTTGCTGCGTATATCTGCCATTGTTTGTATCCAAGCTACTAT
1 TGAATGCCATTATCAAACTGATGTTTGCTGCGTATATCTGCCATTGTTAGTATCCAAGCTACTAT
6233018 ATTGTAAGTGGCAAAATCAAAATT
66 ATTGTAAGTGGCAAAATCAAAATT
6233042 TG
1 TG
6233044 TTATTTACCT
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (89 bp):
TGAATGCCATTATCAAACTGATGTTTGCTGCGTATATCTGCCATTGTTAGTATCCAAGCTACTAT
ATTGTAAGTGGCAAAATCAAAATT
Found at i:6233278 original size:15 final size:15
Alignment explanation
Indices: 6233258--6233287 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6233248 GAAGAAGACA
*
6233258 TGTCTGGTAGTGATG
1 TGTCTGGTAGCGATG
6233273 TGTCTGGTAGCGATG
1 TGTCTGGTAGCGATG
6233288 CATCTGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.40, T:0.37
Consensus pattern (15 bp):
TGTCTGGTAGCGATG
Found at i:6235044 original size:29 final size:28
Alignment explanation
Indices: 6235005--6235064 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
6234995 GTGTTAACTA
* *
6235005 TTTTTTAATATGCATGTAGTGATTATTT
1 TTTTTTAATATACATATAGTGATTATTT
*
6235033 TTTTTATAATATACATATAGTGATTGTTT
1 TTTTT-TAATATACATATAGTGATTATTT
6235062 TTT
1 TTT
6235065 AGGGGGGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (28 bp):
TTTTTTAATATACATATAGTGATTATTT
Found at i:6237240 original size:33 final size:32
Alignment explanation
Indices: 6237198--6237316 Score: 105
Period size: 33 Copynumber: 3.7 Consensus size: 32
6237188 CCCGAGGTGC
*
6237198 ACATTCCCTTTTCAAGTGGTACACATGAAATGT
1 ACATACCCTTTTCAAGTGGTACACAT-AAATGT
* * * * *
6237231 ACATACCCTTTTCAATTTGTACATACAAAGTGC
1 ACATACCCTTTTCAAGTGGTACACATAAA-TGT
* *
6237264 ACATAACCTTTTCAAGT-GTACACATATAGTGT
1 ACATACCCTTTTCAAGTGGTACACATA-AATGT
* **
6237296 ACCTTTCCTTTTCAAGTGGTA
1 ACATACCCTTTTCAAGTGGTA
6237317 TACACAAAGT
Statistics
Matches: 68, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
32 26 0.38
33 42 0.62
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (32 bp):
ACATACCCTTTTCAAGTGGTACACATAAATGT
Found at i:6237324 original size:65 final size:66
Alignment explanation
Indices: 6237194--6237326 Score: 153
Period size: 65 Copynumber: 2.0 Consensus size: 66
6237184 TACACCCGAG
** * * *
6237194 GTGCACATTCCCTTTTCAAGTGGTACACATGAAATGTACATACCCTTTTCAATTTGTACATACAA
1 GTGCACATAACCTTTTCAAGTGGTACACATGAAATGTACATACCCTTTTCAAGTGGTACACACAA
6237259 A
66 A
* * ** *
6237260 GTGCACATAACCTTTTCAAGT-GTACACAT-ATAGTGTACCTTTCCTTTTCAAGTGGTATACACA
1 GTGCACATAACCTTTTCAAGTGGTACACATGA-AATGTACATACCCTTTTCAAGTGGTACACACA
6237323 AA
65 AA
6237325 GT
1 GT
6237327 ATACCTTTCC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
64 1 0.02
65 36 0.64
66 19 0.34
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (66 bp):
GTGCACATAACCTTTTCAAGTGGTACACATGAAATGTACATACCCTTTTCAAGTGGTACACACAA
A
Found at i:6237337 original size:33 final size:33
Alignment explanation
Indices: 6237270--6237376 Score: 137
Period size: 33 Copynumber: 3.3 Consensus size: 33
6237260 GTGCACATAA
* * * *
6237270 CCTTTTCAAGT-GTACACATATAGTGTACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
6237302 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
**
6237335 CCTTTTCATA-TGGTATACACAAAGTATACCTAA
1 CCTTTTCA-AGTGGTATACACAAAGTATACCTTT
6237368 CCTTTTCAA
1 CCTTTTCAA
6237377 ATTGTACCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.18
33 54 0.81
34 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.37
Consensus pattern (33 bp):
CCTTTTCAAGTGGTATACACAAAGTATACCTTT
Found at i:6240900 original size:18 final size:17
Alignment explanation
Indices: 6240877--6240915 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
6240867 CCATTTTTCC
6240877 TCTTCTCCTCCTTCTTCT
1 TCTTCTCCTCC-TCTTCT
6240895 TCTTCTCCTCCTCTTCT
1 TCTTCTCCTCCTCTTCT
6240912 TCTT
1 TCTT
6240916 TTTTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (17 bp):
TCTTCTCCTCCTCTTCT
Found at i:6243736 original size:8 final size:8
Alignment explanation
Indices: 6243725--6243772 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
6243715 AAAATTGTAA
6243725 ATATTTTT
1 ATATTTTT
6243733 ATATTTTT
1 ATATTTTT
*
6243741 ATGTTTTT
1 ATATTTTT
* *
6243749 GTAGTTTT
1 ATATTTTT
6243757 ATATTATTT
1 ATATT-TTT
6243766 -TATTTTT
1 ATATTTTT
6243773 TCAATATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
7 3 0.09
8 27 0.82
9 3 0.09
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (8 bp):
ATATTTTT
Found at i:6243878 original size:27 final size:27
Alignment explanation
Indices: 6243860--6243913 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
6243850 ATTTTCTATA
6243860 TCTTAAACATTTTTATAATTTTTACAT
1 TCTTAAACATTTTTATAATTTTTACAT
*
6243887 TTTTAAACATTTTTATAATTTTTACAT
1 TCTTAAACATTTTTATAATTTTTACAT
6243914 ATCATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.57
Consensus pattern (27 bp):
TCTTAAACATTTTTATAATTTTTACAT
Found at i:6243882 original size:9 final size:9
Alignment explanation
Indices: 6243868--6243953 Score: 63
Period size: 9 Copynumber: 9.7 Consensus size: 9
6243858 TATCTTAAAC
6243868 ATTTTTATA
1 ATTTTTATA
*
6243877 ATTTTTA-C
1 ATTTTTATA
*
6243885 ATTTTTAAA
1 ATTTTTATA
6243894 CATTTTTATA
1 -ATTTTTATA
*
6243904 ATTTTTA-C
1 ATTTTTATA
* *
6243912 A-TATCATA
1 ATTTTTATA
*
6243920 ATTTATAT-
1 ATTTTTATA
6243928 ATTTTTATA
1 ATTTTTATA
6243937 ATAATTTTATA
1 AT--TTTTATA
6243948 ATTTTT
1 ATTTTT
6243954 GCATATTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
7 3 0.05
8 16 0.27
9 23 0.39
10 8 0.14
11 9 0.15
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTTTATA
Found at i:6243913 original size:17 final size:18
Alignment explanation
Indices: 6243866--6243901 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
6243856 TATATCTTAA
*
6243866 ACATTTTTATA-ATTTTT
1 ACATTTTTAAACATTTTT
6243883 ACATTTTTAAACATTTTT
1 ACATTTTTAAACATTTTT
6243901 A
1 A
6243902 TAATTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (18 bp):
ACATTTTTAAACATTTTT
Found at i:6243959 original size:44 final size:43
Alignment explanation
Indices: 6243874--6243959 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 43
6243864 AAACATTTTT
* *
6243874 ATAATTTTTACATTTTTAAACATTTTTATAATTTTTACATATC
1 ATAATTTATACATTTTTAAACAATTTTATAATTTTTACATATC
* * *
6243917 ATAATTTATATATTTTTATAATAATTTTATAATTTTTGCATAT
1 ATAATTTATACATTTTTA-AACAATTTTATAATTTTTACATAT
6243960 TAATGTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 16 0.43
44 21 0.57
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (43 bp):
ATAATTTATACATTTTTAAACAATTTTATAATTTTTACATATC
Found at i:6244032 original size:12 final size:12
Alignment explanation
Indices: 6244011--6244044 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
6244001 TATTAAAAGA
6244011 TTAT-ATTTTTT
1 TTATAATTTTTT
6244022 TTATAATTTTTT
1 TTATAATTTTTT
6244034 TTATAAATTTT
1 TTAT-AATTTT
6244045 AAAGGTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 11 0.52
13 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATAATTTTTT
Found at i:6244032 original size:13 final size:13
Alignment explanation
Indices: 6244015--6244044 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
6244005 AAAAGATTAT
6244015 ATTTTTTTTAT-A
1 ATTTTTTTTATAA
6244027 ATTTTTTTTATAA
1 ATTTTTTTTATAA
6244040 ATTTT
1 ATTTT
6244045 AAAGGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTTTTTTTATAA
Found at i:6244648 original size:30 final size:32
Alignment explanation
Indices: 6244614--6244674 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 32
6244604 AATGAGTTAG
6244614 CTTTAATATTTACA-TTTTTT-ATGAATTTAT
1 CTTTAATATTTACATTTTTTTAATGAATTTAT
6244644 CTTTAATATTTACATTTTTTTAATGAATTTA
1 CTTTAATATTTACATTTTTTTAATGAATTTA
6244675 GCCATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 14 0.48
31 6 0.21
32 9 0.31
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (32 bp):
CTTTAATATTTACATTTTTTTAATGAATTTAT
Found at i:6253122 original size:4 final size:4
Alignment explanation
Indices: 6253113--6253156 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
6253103 GTCTCAATCT
* * *
6253113 TGTA TGTA TGTA TGTA TGTA TGTA TGCA TGCA TGCA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
6253157 AAGCTAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (4 bp):
TGTA
Found at i:6256494 original size:42 final size:42
Alignment explanation
Indices: 6256433--6256535 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 42
6256423 TGAGTTTTCG
** *
6256433 TCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGGTTTCCAT
1 TCAGCTCTTACGAGCTTCTGTTCAACCCTTATGGGTTTCCAT
* *
6256475 TCAGCTCTTACGAGTTTCTGTTCAACCCTTATGGGTTTCTAT
1 TCAGCTCTTACGAGCTTCTGTTCAACCCTTATGGGTTTCCAT
* * *
6256517 TTAGCTCTCATGAGCTTCT
1 TCAGCTCTTACGAGCTTCT
6256536 ATTTAGCCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.44
Consensus pattern (42 bp):
TCAGCTCTTACGAGCTTCTGTTCAACCCTTATGGGTTTCCAT
Found at i:6256505 original size:21 final size:21
Alignment explanation
Indices: 6256448--6256514 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
6256438 TCTTTTGAGC
*
6256448 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
** * * * *
6256469 TTCCATTCAGCTCTTACGAGT
1 TTCTGTTCAACCCTTATGGGT
6256490 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
6256511 TTCT
1 TTCT
6256515 ATTTAGCTCT
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.15, C:0.24, G:0.16, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAACCCTTATGGGT
Found at i:6258537 original size:25 final size:25
Alignment explanation
Indices: 6258429--6258540 Score: 125
Period size: 25 Copynumber: 4.5 Consensus size: 25
6258419 ACAAATGTGC
* * * *
6258429 TAATCGGAGAACACTGATGTGCTAA
1 TAATCAGAGAGCACTTACGTGCTAA
* *
6258454 TAATTAGAAAGCACTTACGTGCTAA
1 TAATCAGAGAGCACTTACGTGCTAA
* *
6258479 TAATCAGAGAGCACTTACATGCTAT
1 TAATCAGAGAGCACTTACGTGCTAA
* **
6258504 TATTCAGAGAGCACCAACGTGCTAA
1 TAATCAGAGAGCACTTACGTGCTAA
6258529 TAATCAGAGAGC
1 TAATCAGAGAGC
6258541 GCGCTAAGGT
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24
Consensus pattern (25 bp):
TAATCAGAGAGCACTTACGTGCTAA
Found at i:6260708 original size:44 final size:44
Alignment explanation
Indices: 6260658--6260749 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
6260648 TCGAAATAAC
** *
6260658 AGTAACAGTACGACACACATGGTGCCTTATCGACTCGAA-GTCGA
1 AGTAACAGTACGACACACATAATGCCTCATCGACTC-AAGGTCGA
**
6260702 AGTAACAGTACGACACTTATAATGCCTCATCGACTCAAGGTCGA
1 AGTAACAGTACGACACACATAATGCCTCATCGACTCAAGGTCGA
6260746 AGTA
1 AGTA
6260750 TCCCTGAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (44 bp):
AGTAACAGTACGACACACATAATGCCTCATCGACTCAAGGTCGA
Found at i:6261191 original size:16 final size:16
Alignment explanation
Indices: 6261172--6261210 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
6261162 TTTTTTCTCC
6261172 TTTCTTTTTCT-TTTCT
1 TTTCTTTTT-TATTTCT
6261188 TTTCTTTTTTATTTCT
1 TTTCTTTTTTATTTCT
*
6261204 TTACTTT
1 TTTCTTT
6261211 ATATTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTTATTTCT
Found at i:6261239 original size:18 final size:18
Alignment explanation
Indices: 6261216--6261252 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6261206 ACTTTATATT
*
6261216 ATAATAATATAATTTATA
1 ATAATAATATAATTAATA
*
6261234 ATAATAATTTAATTAATA
1 ATAATAATATAATTAATA
6261252 A
1 A
6261253 ATATCTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATAATATAATTAATA
Found at i:6261511 original size:3 final size:3
Alignment explanation
Indices: 6261489--6261546 Score: 50
Period size: 3 Copynumber: 19.3 Consensus size: 3
6261479 AATTTATTCC
*
6261489 ATA AT- ATA ATA ATGA A-A ATA ATA AT- ATAA ACA ATA ATA ATTA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA AT-A ATA ATA ATA A-TA ATA
*
6261534 ATT ATA ATA ATA A
1 ATA ATA ATA ATA A
6261547 ATATCTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
2 6 0.13
3 33 0.73
4 6 0.13
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6266563 original size:10 final size:10
Alignment explanation
Indices: 6266544--6266593 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
6266534 TTAAATTCTA
6266544 AAAGATAAAT
1 AAAGATAAAT
6266554 ACAA-ATAAAT
1 A-AAGATAAAT
*
6266564 AAAGATAATT
1 AAAGATAAAT
6266574 AAAGATAAAT
1 AAAGATAAAT
6266584 GAAA-ATAAAT
1 -AAAGATAAAT
6266594 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:6267406 original size:93 final size:93
Alignment explanation
Indices: 6267249--6267433 Score: 244
Period size: 93 Copynumber: 2.0 Consensus size: 93
6267239 ATTATTATTA
* * * * *
6267249 TTTTTACTTAGGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAACCAAGCACCCCACCCC
1 TTTTTACTTAAGAACATATCGAACCTTTTAACGCGAAGAGAAATGACAACCAAGCACCCCACCCC
*
6267314 GGTTACTCAACCCAACACACTCTTAAAT
66 GATTACTCAACCCAACACACTCTTAAAT
* * * * *
6267342 TTTTTTCTTAAGAACATATCGAACTTTTTAACGCGAAGAGAAATGACAGCCACGCACCTCACCCC
1 TTTTTACTTAAGAACATATCGAACCTTTTAACGCGAAGAGAAATGACAACCAAGCACCCCACCCC
* * *
6267407 GATTACTCAGCCTAACACATTCTTAAA
66 GATTACTCAACCCAACACACTCTTAAA
6267434 AATTAATTCC
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.26
Consensus pattern (93 bp):
TTTTTACTTAAGAACATATCGAACCTTTTAACGCGAAGAGAAATGACAACCAAGCACCCCACCCC
GATTACTCAACCCAACACACTCTTAAAT
Found at i:6268335 original size:21 final size:20
Alignment explanation
Indices: 6268311--6268387 Score: 54
Period size: 21 Copynumber: 3.8 Consensus size: 20
6268301 GAATTTTTAT
6268311 TAATATCCAAAATAAAATAAA
1 TAATAT-CAAAATAAAATAAA
*
6268332 TAAT-T-AAGATAAAAT-AA
1 TAATATCAAAATAAAATAAA
*
6268349 TAAATAACAAAAATAAAAT-AA
1 T-AATATC-AAAATAAAATAAA
*
6268370 TAAATAATAAAAATAAAA
1 T-AAT-ATCAAAATAAAA
6268388 ATAATAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
17 3 0.07
18 12 0.26
20 1 0.02
21 29 0.63
22 1 0.02
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.23
Consensus pattern (20 bp):
TAATATCAAAATAAAATAAA
Found at i:6268343 original size:18 final size:18
Alignment explanation
Indices: 6268322--6268370 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
6268312 AATATCCAAA
*
6268322 ATAAAATAAATAATTAAG
1 ATAAAATAAATAATTAAC
*
6268340 ATAAAAT-AATAAATAAC
1 ATAAAATAAATAATTAAC
6268357 A-AAAATAAAATAAT
1 ATAAAAT-AAATAAT
6268371 AAATAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.19
17 9 0.35
18 12 0.46
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
ATAAAATAAATAATTAAC
Found at i:6268355 original size:7 final size:7
Alignment explanation
Indices: 6268326--6268391 Score: 61
Period size: 7 Copynumber: 9.7 Consensus size: 7
6268316 TCCAAAATAA
6268326 AATAAAT
1 AATAAAT
6268333 AATTAAGAT
1 AA-TAA-AT
6268342 -A-AAAT
1 AATAAAT
6268347 AATAAAT
1 AATAAAT
*
6268354 AACAAA-
1 AATAAAT
6268360 AATAAAAT
1 AAT-AAAT
6268368 AATAAAT
1 AATAAAT
6268375 AATAAA-
1 AATAAAT
6268381 AATAAA-
1 AATAAAT
6268387 AATAA
1 AATAA
6268392 TAAAATAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
5 2 0.04
6 16 0.31
7 24 0.47
8 7 0.14
9 2 0.04
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (7 bp):
AATAAAT
Found at i:6268363 original size:30 final size:28
Alignment explanation
Indices: 6268320--6268400 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 28
6268310 TTAATATCCA
*
6268320 AAATAAAATAAATAATTAAGATAAAATAAT
1 AAATAAAA-AAATAA-TAAAATAAAATAAT
6268350 AAATAACAAAAATAA-AATAAT-AAATAAT
1 AAATAA-AAAAATAATAA-AATAAAATAAT
6268378 AAA-AATAAAAATAATAAAATAAA
1 AAATAA-AAAAATAATAAAATAAA
6268401 GAGAAATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
27 13 0.29
28 16 0.36
29 2 0.04
30 12 0.27
31 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (28 bp):
AAATAAAAAAATAATAAAATAAAATAAT
Found at i:6268409 original size:30 final size:29
Alignment explanation
Indices: 6268342--6268412 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 29
6268332 TAATTAAGAT
6268342 AAAATAATAAATAACAAAAATAAAATAATA
1 AAAATAA-AAATAACAAAAATAAAATAATA
6268372 AATAATAAAAATAA-AAATAATAAAATAA-A
1 AA-AATAAAAATAACAAA-AATAAAATAATA
6268401 GAGAAATAAAAA
1 -A-AAATAAAAA
6268413 ATGGGTTGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
29 4 0.11
30 27 0.73
31 6 0.16
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.18
Consensus pattern (29 bp):
AAAATAAAAATAACAAAAATAAAATAATA
Found at i:6273253 original size:93 final size:93
Alignment explanation
Indices: 6273145--6273316 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
6273135 CGCCCATAAG
* * *
6273145 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
6273210 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
6273238 CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
6273303 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
6273317 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:6273313 original size:46 final size:46
Alignment explanation
Indices: 6273138--6273313 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
6273128 TGTAACCCGC
* * *
6273138 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
6273184 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
6273234 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
6273277 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
6273314 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.57
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:6287744 original size:10 final size:10
Alignment explanation
Indices: 6287725--6287774 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
6287715 TTAAATTCTA
6287725 AAAGATAAAT
1 AAAGATAAAT
6287735 ACAA-ATAAAT
1 A-AAGATAAAT
* *
6287745 AAATATAATT
1 AAAGATAAAT
6287755 AAAGATAAAT
1 AAAGATAAAT
*
6287765 AAAAATAAAT
1 AAAGATAAAT
6287775 CCTAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 30 0.88
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:6291801 original size:23 final size:21
Alignment explanation
Indices: 6291768--6291811 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
6291758 AAAGAAAACG
6291768 AAAACAAATAAAACAAACAAA
1 AAAACAAATAAAACAAACAAA
*
6291789 AAAATCAAGATAAAACCAACAAA
1 AAAA-CAA-ATAAAACAAACAAA
6291812 CTTGATACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 3 0.15
23 13 0.65
ACGTcount: A:0.75, C:0.16, G:0.02, T:0.07
Consensus pattern (21 bp):
AAAACAAATAAAACAAACAAA
Found at i:6297408 original size:7 final size:7
Alignment explanation
Indices: 6297396--6297420 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6297386 GAATCTTTAT
6297396 TAAATTA
1 TAAATTA
6297403 TAAATTA
1 TAAATTA
6297410 TAAATTA
1 TAAATTA
6297417 TAAA
1 TAAA
6297421 AAATCATATT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATTA
Found at i:6297537 original size:14 final size:14
Alignment explanation
Indices: 6297518--6297546 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6297508 GTAATTAAAA
6297518 TGGAAAAGATACAT
1 TGGAAAAGATACAT
6297532 TGGAAAAGATACAT
1 TGGAAAAGATACAT
6297546 T
1 T
6297547 TTTATTGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (14 bp):
TGGAAAAGATACAT
Found at i:6297839 original size:5 final size:6
Alignment explanation
Indices: 6297821--6297847 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6297811 TCTCTTCATC
6297821 TTCTTT TTCTTT TTCTTT TTCTTT TTC
1 TTCTTT TTCTTT TTCTTT TTCTTT TTC
6297848 ATTGTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:6302851 original size:45 final size:45
Alignment explanation
Indices: 6302787--6302960 Score: 260
Period size: 45 Copynumber: 3.9 Consensus size: 45
6302777 TCGTACATAG
* * *
6302787 TATTCGGGCCTTTGAGCCTAGAAGGCTATAATGCCGGCGAGATAC
1 TATTCGAGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAGATAC
* *
6302832 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGAGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAGATAC
* *
6302877 TATTCCAGCCTTTGAGCCTACTAGGCTATAATGCCGGTGAGATAC
1 TATTCGAGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAGATAC
* *
6302922 TATTCGAGCCTTCGAGCCTAGTAGGCGA-AATGCCGGTGA
1 TATTCGAGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGA
6302961 ATGAATTCAG
Statistics
Matches: 119, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
44 11 0.09
45 108 0.91
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (45 bp):
TATTCGAGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAGATAC
Found at i:6309833 original size:14 final size:14
Alignment explanation
Indices: 6309810--6309839 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6309800 TTGAAAATAT
6309810 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
6309824 GTTGATTTGGATTG
1 GTTGAATTGGATTG
6309838 GT
1 GT
6309840 CTCGATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:6321327 original size:45 final size:45
Alignment explanation
Indices: 6321248--6321468 Score: 261
Period size: 45 Copynumber: 5.0 Consensus size: 45
6321238 TATCGTACAG
* * * * *
6321248 TACTATTCAGGCCTTTGAGACTAGTAGGCAATAATGTCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
* * *
6321293 TACTATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCCGATGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
* * *
6321338 TACTATTCCGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
* *
6321383 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
* * *
6321428 TAATA-TCGGG--TTTCGATCCTAGCAGGCGA-AATGCCGGTGAA
1 TACTATTCGGGCCTTT-GAGCCTAGCAGGCTATAATGCCGGTGAA
6321469 TGAATTCAGG
Statistics
Matches: 155, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
42 13 0.08
43 13 0.08
44 5 0.03
45 124 0.80
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAA
Found at i:6323360 original size:22 final size:22
Alignment explanation
Indices: 6323330--6323398 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
6323320 ATGCACAAAC
6323330 AAACAGAGAGCACTAAAGTGCT
1 AAACAGAGAGCACTAAAGTGCT
* *
6323352 ATACAGAGAGCAC-AGATGTGCT
1 AAACAGAGAGCACTA-AAGTGCT
*
6323374 AAACAGAGAGCACTTAACGTGCT
1 AAACAGAGAGCAC-TAAAGTGCT
6323397 AA
1 AA
6323399 TAATAGAACG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.75
23 8 0.20
24 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (22 bp):
AAACAGAGAGCACTAAAGTGCT
Found at i:6324576 original size:7 final size:7
Alignment explanation
Indices: 6324566--6324659 Score: 51
Period size: 7 Copynumber: 14.1 Consensus size: 7
6324556 ACTTTATGTT
6324566 TTATATA
1 TTATATA
6324573 -T-TATA
1 TTATATA
6324578 TTATATA
1 TTATATA
*
6324585 TAATATA
1 TTATATA
*
6324592 ATA-ATA
1 TTATATA
*
6324598 TAATATA
1 TTATATA
6324605 TTATATA
1 TTATATA
6324612 TTA-ATA
1 TTATATA
6324618 CTTA-A-A
1 -TTATATA
6324624 TT-TA-A
1 TTATATA
6324629 GTTAATATA
1 -TT-ATATA
*
6324638 ATATATA
1 TTATATA
*
6324645 ATATATA
1 TTATATA
*
6324652 TTTTATA
1 TTATATA
6324659 T
1 T
6324660 AAAAAATATC
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
5 8 0.12
6 12 0.17
7 45 0.65
8 3 0.04
9 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (7 bp):
TTATATA
Found at i:6324603 original size:20 final size:20
Alignment explanation
Indices: 6324575--6324617 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6324565 TTTATATATT
*
6324575 ATATTATATATAATATAATA
1 ATATAATATATAATATAATA
* *
6324595 ATATAATATATTATATATTA
1 ATATAATATATAATATAATA
6324615 ATA
1 ATA
6324618 CTTAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATAATATATAATATAATA
Found at i:6324881 original size:13 final size:13
Alignment explanation
Indices: 6324863--6324887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6324853 AATTAACTTC
6324863 ATAAATATTTATA
1 ATAAATATTTATA
6324876 ATAAATATTTAT
1 ATAAATATTTAT
6324888 GAATCCGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAAATATTTATA
Found at i:6331699 original size:28 final size:28
Alignment explanation
Indices: 6331634--6331734 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
6331624 ATAGTGAATC
*
6331634 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
6331663 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
6331691 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
6331721 CGCACACTTAGTGC
1 CGCACACTTAGTGC
6331735 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:6337272 original size:28 final size:28
Alignment explanation
Indices: 6337207--6337307 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
6337197 ATAGTGAATC
*
6337207 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
6337236 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
6337264 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
6337294 CGCACACTTAGTGC
1 CGCACACTTAGTGC
6337308 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:6345200 original size:29 final size:27
Alignment explanation
Indices: 6345167--6345266 Score: 103
Period size: 27 Copynumber: 3.5 Consensus size: 27
6345157 ATAGTGAATC
*
6345167 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA---AATCAAACT
6345196 CGCACACTTAGTGCTATAAATCAAACT
1 CGCACACTTAGTGCTATAAATCAAACT
* * *
6345223 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATA-AA--TCAAACT
6345253 CGCACACTTAGTGC
1 CGCACACTTAGTGC
6345267 CAATCTTGTC
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
26 3 0.05
27 21 0.33
28 2 0.03
29 18 0.29
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATAAATCAAACT
Found at i:6347491 original size:22 final size:22
Alignment explanation
Indices: 6347462--6347529 Score: 93
Period size: 22 Copynumber: 3.0 Consensus size: 22
6347452 TGCACAAACG
6347462 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
*
6347484 TACAGAGAGCAC-AAATGTGCTA
1 AACAGAGAGCACTAAA-GTGCTA
*
6347506 AACAGAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
6347529 A
1 A
6347530 TAATAGAACG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 3 0.08
22 28 0.70
23 7 0.17
24 2 0.05
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:6348706 original size:7 final size:7
Alignment explanation
Indices: 6348696--6348789 Score: 51
Period size: 7 Copynumber: 14.1 Consensus size: 7
6348686 ACTTTATGTT
6348696 TTATATA
1 TTATATA
6348703 TTATATA
1 TTATATA
6348710 -TA-ATA
1 TTATATA
*
6348715 TAATATA
1 TTATATA
*
6348722 ATA-ATA
1 TTATATA
*
6348728 TAATATA
1 TTATATA
6348735 TTATATA
1 TTATATA
6348742 TTA-ATA
1 TTATATA
6348748 CTTA-A-A
1 -TTATATA
6348754 TT-TA-A
1 TTATATA
6348759 GTTAATATA
1 -TT-ATATA
*
6348768 ATATATA
1 TTATATA
*
6348775 ATATATA
1 TTATATA
*
6348782 TTTTATA
1 TTATATA
6348789 T
1 T
6348790 CAAAAATATC
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
5 7 0.10
6 13 0.19
7 45 0.65
8 3 0.04
9 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (7 bp):
TTATATA
Found at i:6365988 original size:46 final size:44
Alignment explanation
Indices: 6365884--6365991 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
6365874 TGTCTTTGAC
** * * *
6365884 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
6365928 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
6365974 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
6365992 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:6368667 original size:27 final size:27
Alignment explanation
Indices: 6368602--6368798 Score: 193
Period size: 27 Copynumber: 7.3 Consensus size: 27
6368592 TTTGGTTTAC
*
6368602 AAAATTACCAAAATA-CCCTGCTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * *
6368628 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
6368655 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
6368682 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
**
6368709 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* ** **
6368736 GAAATTACTGAAATA-CCCTCGACTTGT
1 AAAATTACCAAAATACCCCT-GGTTTGT
*** *
6368763 AAAATTATTGAAATA-CCCTCGATTTGT
1 AAAATTACCAAAATACCCCT-GGTTTGT
6368790 AAAATTACC
1 AAAATTACC
6368799 GTTTTACCCT
Statistics
Matches: 148, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
26 18 0.12
27 130 0.88
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGT
Found at i:6368712 original size:54 final size:54
Alignment explanation
Indices: 6368596--6368753 Score: 214
Period size: 54 Copynumber: 2.9 Consensus size: 54
6368586 AAATACTTTG
* * *
6368596 GTTTACAAAATTACCAAAATA-CCCT-GCTTTGTAAAATTACTAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTAG-TTTGTAAAATTACTAAAATACCCCTA
6368649 GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTA-TCAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACT-AAAATACCCCTA
* * * *
6368703 GTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTACTGAAATACCC
1 GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCC
6368754 TCGACTTGTA
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
53 21 0.22
54 71 0.76
55 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.32
Consensus pattern (54 bp):
GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCCTA
Found at i:6368722 original size:81 final size:80
Alignment explanation
Indices: 6368602--6368825 Score: 227
Period size: 81 Copynumber: 2.8 Consensus size: 80
6368592 TTTGGTTTAC
* * * *
6368602 AAAATTACCAAAATACCCTGCTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAA
1 AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCAAA
*
6368667 ATACCCCTAG-TTTGT
66 ATA-CCCTAGACTTGT
* * * * **
6368682 AAAATTATCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTACTG
1 AAAATTATCAAAATA-CCCTGA-TTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCA
*
6368746 AAATACCCTCGACTTGT
64 AAATACCCTAGACTTGT
** **** *
6368763 AAAATTATTGAAATACCCTCGATTTGTAAAATTACCGTTTTACCCTTGATTTATAGAATTACC
1 AAAATTATCAAAATACCCT-GATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACC
6368826 GTTTTACCCT
Statistics
Matches: 115, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
80 23 0.20
81 91 0.79
82 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.33
Consensus pattern (80 bp):
AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCAAA
ATACCCTAGACTTGT
Found at i:6368806 original size:27 final size:27
Alignment explanation
Indices: 6368776--6369150 Score: 443
Period size: 27 Copynumber: 13.9 Consensus size: 27
6368766 ATTATTGAAA
** *
6368776 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
6368803 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** *
6368830 TACCCTC-AGTTTACAGAATTACTATGT
1 TACCCTCGA-TTTACAGAATTACCGTTT
* *
6368857 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
6368884 TACCC-CTAATTTACATAATTACCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* * *
6368911 TACCC-CTGATTTACATAATTATCATTT
1 TACCCTC-GATTTACAGAATTACCGTTT
*
6368938 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
6368965 TACCCACAATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
6368992 TACCC-CTGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
*
6369019 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
6369046 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
6369073 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
6369100 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
6369127 TACCCTCGATTTACAAAATTACCG
1 TACCCTCGATTTACAGAATTACCG
6369151 AAATACCCTC
Statistics
Matches: 303, Mismatches: 39, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.01
27 297 0.98
28 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:6369157 original size:27 final size:27
Alignment explanation
Indices: 6368737--6369202 Score: 201
Period size: 27 Copynumber: 17.3 Consensus size: 27
6368727 CTAATTTGTG
* * * **
6368737 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCGAATTACCCTCGATTTACA
** * **
6368764 AAATTATTGAAATACCCTCGATTTGTA
1 AAATTACCGAATTACCCTCGATTTACA
** * *
6368791 AAATTACCGTTTTACCCTTGATTTATA
1 AAATTACCGAATTACCCTCGATTTACA
* **
6368818 GAATTACCGTTTTACCCTC-AGTTTACA
1 AAATTACCGAATTACCCTCGA-TTTACA
* * * *
6368845 GAATTA-CTATGTTACCCTCGATTTATA
1 AAATTACCGA-ATTACCCTCGATTTACA
* * *
6368872 GAATTACC-ATTTTACCC-CTAATTTACA
1 AAATTACCGA-ATTACCCTC-GATTTACA
* **
6368899 TAATTACCGTTTTACCC-CTGATTTACA
1 AAATTACCGAATTACCCTC-GATTTACA
* * * *
6368926 TAATTATC-ATTTTACCCTCGACTTACA
1 AAATTACCGA-ATTACCCTCGATTTACA
* ** * *
6368953 GAATTACCGTTTTACCCACAATTTACA
1 AAATTACCGAATTACCCTCGATTTACA
* **
6368980 TAATTACCGTTTTACCC-CTGATTTACA
1 AAATTACCGAATTACCCTC-GATTTACA
* * ** *
6369007 TAATTATCGTTTTACCCTCGACTTACA
1 AAATTACCGAATTACCCTCGATTTACA
* **
6369034 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCGAATTACCCTCGATTTACA
* ** *
6369061 GAATTACCGTTTTACCCTCGATTTATA
1 AAATTACCGAATTACCCTCGATTTACA
* * ** *
6369088 GAATTACTGTTTTACCCTTGATTTACA
1 AAATTACCGAATTACCCTCGATTTACA
* * **
6369115 GAATTACTGTTTTACCCTCGATTTACA
1 AAATTACCGAATTACCCTCGATTTACA
* * **
6369142 AAATTACCGAAATACCCTCAATTTGTA
1 AAATTACCGAATTACCCTCGATTTACA
* *
6369169 AAATTACCAAAATACCC-CTGATTTACA
1 AAATTACCGAATTACCCTC-GATTTACA
*
6369196 AAGTTAC
1 AAATTAC
6369203 AGAAACACCC
Statistics
Matches: 371, Mismatches: 56, Indels: 24
0.82 0.12 0.05
Matches are distributed among these distances:
26 5 0.01
27 362 0.98
28 4 0.01
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.38
Consensus pattern (27 bp):
AAATTACCGAATTACCCTCGATTTACA
Found at i:6369174 original size:54 final size:54
Alignment explanation
Indices: 6368749--6369175 Score: 290
Period size: 54 Copynumber: 7.9 Consensus size: 54
6368739 ATTACTGAAA
* * ** ** * ** *
6368749 TACCCTCGACTTGTAAAATTATTGAAATACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCGATTTACCCTCAATTTACAAAATTACTGTTT
* * * * * * *
6368803 TACCCTTGATTTATAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTATGT
1 TACCCTCGATTTATAAAATTACCGATTTACCCTCAATTTACAAAATTACTGTTT
* * *
6368857 TACCCTCGATTTATAGAATTACC-ATTTTACCC-CTAATTTACATAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCGA-TTTACCCTC-AATTTACAAAATTACTGTTT
* * * * * * *
6368911 TACCC-CTGATTTACATAATTATC-ATTTTACCCTCGACTTACAGAATTACCGTTT
1 TACCCTC-GATTTATAAAATTACCGA-TTTACCCTCAATTTACAAAATTACTGTTT
* * * * * * *
6368965 TACCCACAATTTACATAATTACCGTTTTACCC-CTGATTTACATAATTA-TCGTTT
1 TACCCTCGATTTATAAAATTACCGATTTACCCTC-AATTTACAAAATTACT-GTTT
* * * * * * *
6369019 TACCCTCGACTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCGATTTACCCTCAATTTACAAAATTACTGTTT
* * * ** *
6369073 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTATAAAATTACCGATTTACCCTCAATTTACAAAATTACTGTTT
* ** **
6369127 TACCCTCGATTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTAC
1 TACCCTCGATTTATAAAATTACCGATTTACCCTCAATTTACAAAATTAC
6369176 CAAAATACCC
Statistics
Matches: 305, Mismatches: 58, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
53 3 0.01
54 299 0.98
55 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (54 bp):
TACCCTCGATTTATAAAATTACCGATTTACCCTCAATTTACAAAATTACTGTTT
Found at i:6369185 original size:81 final size:81
Alignment explanation
Indices: 6368737--6369195 Score: 231
Period size: 81 Copynumber: 5.7 Consensus size: 81
6368727 CTAATTTGTG
* * * * *** * ** *
6368737 AAATTACTGAAATACCCTCGACTTGTAAAATTATTGAAATACCCTCGATTTGTAAAATTACCGTT
1 AAATTACCGAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGATTTACAGAATTACCGTT
* *
6368802 TTACCCTTGATTTATA
66 TTACCCTCGATTTACA
* *** * * * * *** * * *
6368818 GAATTACCGTTTTACCCTCAGTTTACAGAATTACTATGTTACCCTCGATTTATAGAATTACCATT
1 AAATTACCGAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGATTTACAGAATTACCGTT
*
6368883 TTACCC-CTAATTTACA
66 TTACCCTC-GATTTACA
* *** * * * * *** * *
6368899 TAATTACCGTTTTACCC-CTGATTTACATAATTATCATTTTACCCTCGACTTACAGAATTACCGT
1 AAATTACCGAAATACCCTC-AATTTATAAAATTACCAAAATACCCTTGATTTACAGAATTACCGT
* *
6368963 TTTACCCACAATTTACA
65 TTTACCCTCGATTTACA
* *** * * * * **** * *
6368980 TAATTACCGTTTTACCC-CTGATTTACATAATTATCGTTTTACCCTCGACTTACAGAATTACCGT
1 AAATTACCGAAATACCCTC-AATTTATAAAATTACCAAAATACCCTTGATTTACAGAATTACCGT
6369044 TTTACCCTCGATTTACA
65 TTTACCCTCGATTTACA
* *** * * ***** *
6369061 GAATTACCGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTT
1 AAATTACCGAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGATTTACAGAATTACCGTT
6369126 TTACCCTCGATTTACA
66 TTACCCTCGATTTACA
* *
6369142 AAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACA
1 AAATTACCGAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGATTTACA
6369196 AAGTTACAGA
Statistics
Matches: 318, Mismatches: 56, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
80 1 0.00
81 315 0.99
82 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (81 bp):
AAATTACCGAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGATTTACAGAATTACCGTT
TTACCCTCGATTTACA
Found at i:6369254 original size:27 final size:26
Alignment explanation
Indices: 6369220--6369275 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
6369210 CCCTTGACTT
*
6369220 TTTAAAAATTA-TAGAAGTACCATTGG
1 TTTAAAAATTACT-GAAATACCATTGG
*
6369246 TTTACAAAATTACTGAAATACCTTTGG
1 TTTA-AAAATTACTGAAATACCATTGG
6369273 TTT
1 TTT
6369276 GTTGATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (26 bp):
TTTAAAAATTACTGAAATACCATTGG
Found at i:6369350 original size:27 final size:27
Alignment explanation
Indices: 6369320--6369371 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
6369310 GACTAAAATA
6369320 CCCCTAAAAGGTAAAAAGACCGTAAAG
1 CCCCTAAAAGGTAAAAAGACCGTAAAG
** * *
6369347 CCCCTGTAGGGTAAAATGACCGTAA
1 CCCCTAAAAGGTAAAAAGACCGTAA
6369372 TACCCCTGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.15
Consensus pattern (27 bp):
CCCCTAAAAGGTAAAAAGACCGTAAAG
Found at i:6369408 original size:25 final size:27
Alignment explanation
Indices: 6369329--6369393 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
6369319 ACCCCTAAAA
* *
6369329 GGTAAAAAGACCGTAA-AGCCCCTGTAG
1 GGTAAAATGACCGTAATA-CCCCTGTAT
6369356 GGTAAAATGACCGTAATACCCCTGTAT
1 GGTAAAATGACCGTAATACCCCTGTAT
6369383 GGTAAAATGAC
1 GGTAAAATGAC
6369394 GAATATGCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAATACCCCTGTAT
Found at i:6370579 original size:25 final size:25
Alignment explanation
Indices: 6370550--6370597 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
6370540 TTATAATATG
* * *
6370550 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
6370575 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
6370598 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:6370666 original size:20 final size:20
Alignment explanation
Indices: 6370641--6370699 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
6370631 TAAATATGGT
6370641 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
6370661 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
6370681 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
6370700 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:6370777 original size:24 final size:24
Alignment explanation
Indices: 6370750--6370892 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
6370740 GAGGAAGTGA
6370750 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
6370774 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
6370798 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
6370821 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
6370845 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
6370869 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
6370893 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:6370843 original size:47 final size:47
Alignment explanation
Indices: 6370750--6370892 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
6370740 GAGGAAGTGA
6370750 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
6370798 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
6370845 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
6370893 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:6370866 original size:71 final size:72
Alignment explanation
Indices: 6370750--6370893 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
6370740 GAGGAAGTGA
*
6370750 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
6370813 CCAGTTAT
65 CCAGTTAT
** * *
6370821 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
6370886 CAGTTAT
66 CAGTTAT
6370893 A
1 A
6370894 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:6371119 original size:31 final size:31
Alignment explanation
Indices: 6371084--6371178 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
6371074 CGTTTACAGT
6371084 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
6371115 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* *
6371146 AAATGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
6371177 AA
1 AA
6371179 TATGAAAAGG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:6375114 original size:20 final size:20
Alignment explanation
Indices: 6375086--6375123 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6375076 CTAGGAACTA
6375086 TGTGATCTGAGCTCATGAGT
1 TGTGATCTGAGCTCATGAGT
* *
6375106 TGTGGTCTGAGTTCATGA
1 TGTGATCTGAGCTCATGA
6375124 TATATGTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGAGT
Found at i:6380535 original size:19 final size:19
Alignment explanation
Indices: 6380472--6380535 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
6380462 GCCCCCCTCC
*
6380472 CTTTCTCTTCTCTTCCTTTCTT
1 CTTTCT-TTCT-TTCC-TCCTT
6380494 -TTTCTTTCTTT-CTCTCTT
1 CTTTCTTTCTTTCCTC-CTT
*
6380512 TTTTCTTTCTTTCCTCCTT
1 CTTTCTTTCTTTCCTCCTT
6380531 CTTTC
1 CTTTC
6380536 CTTTTCTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 1 0.03
18 4 0.11
19 20 0.54
20 7 0.19
21 5 0.14
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (19 bp):
CTTTCTTTCTTTCCTCCTT
Found at i:6384551 original size:12 final size:12
Alignment explanation
Indices: 6384529--6384559 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6384519 TAGAATCTGC
6384529 TAAAA-TAAAAA
1 TAAAAGTAAAAA
6384540 TAAAAGTAAAAA
1 TAAAAGTAAAAA
6384552 TAAAAGTA
1 TAAAAGTA
6384560 GTTTTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (12 bp):
TAAAAGTAAAAA
Found at i:6386628 original size:55 final size:55
Alignment explanation
Indices: 6386567--6386691 Score: 162
Period size: 55 Copynumber: 2.3 Consensus size: 55
6386557 TGTTAATTTA
* * *
6386567 ACAGGTTCGACCACGGGTGTTTCACACGGGCGTGTCGA-ACGCTCGTGTTGTCTTG
1 ACAGGTTCGACCACGGGTCTTCCACACGGGCGTGTC-ACACGCCCGTGTTGTCTTG
* * *
6386622 ACAGGTTCGCCCACGGTTCTTCCACACGGGCGTGTCACACGCCCGTGTTGTTTTG
1 ACAGGTTCGACCACGGGTCTTCCACACGGGCGTGTCACACGCCCGTGTTGTCTTG
* *
6386677 GCAGGCTCGACCACG
1 ACAGGTTCGACCACG
6386692 ACCATATCGC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
54 1 0.02
55 59 0.98
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.25
Consensus pattern (55 bp):
ACAGGTTCGACCACGGGTCTTCCACACGGGCGTGTCACACGCCCGTGTTGTCTTG
Found at i:6386993 original size:28 final size:28
Alignment explanation
Indices: 6386961--6387017 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
6386951 GTTTGAGGAG
* *
6386961 TTTATACTCTTCATTCCTACTATCAATC
1 TTTATACTCTTAATTCATACTATCAATC
*
6386989 TTTATACTCTTAATTCATGCTATCAATC
1 TTTATACTCTTAATTCATACTATCAATC
6387017 T
1 T
6387018 CATCAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.02, T:0.47
Consensus pattern (28 bp):
TTTATACTCTTAATTCATACTATCAATC
Found at i:6388455 original size:13 final size:14
Alignment explanation
Indices: 6388434--6388462 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6388424 TGAAAAATGG
6388434 ATTAGAAAATATTT
1 ATTAGAAAATATTT
6388448 ATTA-AAAATATTT
1 ATTAGAAAATATTT
6388461 AT
1 AT
6388463 GAAGTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:6389025 original size:31 final size:32
Alignment explanation
Indices: 6388976--6389039 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
6388966 ATATTAAATA
*
6388976 AGATATTTATTAATTAAATA-ATTATATTATG
1 AGATATTTATTAATTAAATATATTAAATTATG
*
6389007 AGATTTTTATGTAA-TAAATATATTAAATTATG
1 AGATATTTAT-TAATTAAATATATTAAATTATG
6389039 A
1 A
6389040 CAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
AGATATTTATTAATTAAATATATTAAATTATG
Found at i:6389174 original size:19 final size:19
Alignment explanation
Indices: 6389128--6389174 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
6389118 AGATTTTTAA
* * *
6389128 ATATAGATATTTTATTTTT
1 ATATATATATTTTATATAT
6389147 AT-TATTATATTTTATATAT
1 ATATA-TATATTTTATATAT
6389166 ATATATATA
1 ATATATATA
6389175 GTAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATATATATTTTATATAT
Found at i:6390001 original size:15 final size:15
Alignment explanation
Indices: 6389978--6390021 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
6389968 TATCAAATTT
6389978 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
6389993 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
6390008 ATATTGATTGAAAT
1 ATATTGATTGAAAT
6390022 ATAATATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:6390647 original size:26 final size:26
Alignment explanation
Indices: 6390610--6390745 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
6390600 TGATACAAAT
* *
6390610 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
6390636 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
6390662 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
6390688 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
6390714 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
6390740 TGATAA
1 TGATAA
6390746 GAATATCATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:6393486 original size:23 final size:23
Alignment explanation
Indices: 6393448--6393513 Score: 114
Period size: 23 Copynumber: 2.8 Consensus size: 23
6393438 AGGGTTTATA
6393448 ATATTCTGGGTGTGTTTGGGTTGG
1 ATATTCT-GGTGTGTTTGGGTTGG
6393472 ATATTCTGGTGTGTTTGGGTTGG
1 ATATTCTGGTGTGTTTGGGTTGG
*
6393495 ATATTCTAGTGTGTTTGGG
1 ATATTCTGGTGTGTTTGGG
6393514 AGGAATCCGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 34 0.83
24 7 0.17
ACGTcount: A:0.11, C:0.05, G:0.38, T:0.47
Consensus pattern (23 bp):
ATATTCTGGTGTGTTTGGGTTGG
Found at i:6393639 original size:18 final size:19
Alignment explanation
Indices: 6393618--6393658 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
6393608 AATGAAATGA
6393618 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
6393636 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
6393655 GAAA
1 GAAA
6393659 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:6402758 original size:18 final size:18
Alignment explanation
Indices: 6402737--6402800 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
6402727 TAGCAATCAG
*
6402737 TTATTCAGTAATGGTCAT
1 TTATTCAGTAATAGTCAT
*
6402755 TTATTCAGTAACAGTCAGT
1 TTATTCAGTAATAGTCA-T
* *
6402774 CT-TTCAGTAATAGTCAA
1 TTATTCAGTAATAGTCAT
6402791 TTATTCAGTA
1 TTATTCAGTA
6402801 CATTTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 1 0.03
18 35 0.92
19 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (18 bp):
TTATTCAGTAATAGTCAT
Found at i:6402759 original size:36 final size:36
Alignment explanation
Indices: 6402717--6402797 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
6402707 AATAATAATT
* * *
6402717 AATTATTTAATAGCAATCAGT-TATTCAGTAATGGTC
1 AATTATTCAATAACAATCAGTCT-TTCAGTAATAGTC
* * *
6402753 ATTTATTCAGTAACAGTCAGTCTTTCAGTAATAGTC
1 AATTATTCAATAACAATCAGTCTTTCAGTAATAGTC
6402789 AATTATTCA
1 AATTATTCA
6402798 GTACATTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
36 36 0.97
37 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (36 bp):
AATTATTCAATAACAATCAGTCTTTCAGTAATAGTC
Found at i:6403013 original size:51 final size:53
Alignment explanation
Indices: 6402915--6403033 Score: 179
Period size: 51 Copynumber: 2.3 Consensus size: 53
6402905 CCGTATCAGT
*
6402915 AACAGTAACAGTAACAGTAGCGGTACACAGAGTACCTCATCAGAATGAATCCGG
1 AACAGTAACAGTAACAGTAGAGGTA-ACAGAGTACCTCATCAGAATGAATCCGG
* * *
6402969 AACAGTAATAGTAACAGTA-AGGT-ACAGAGTACCTCTTCGGAATGAATCCGG
1 AACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTCATCAGAATGAATCCGG
6403020 AACAGTAACAGTAA
1 AACAGTAACAGTAA
6403034 GGCGACACTT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
51 39 0.65
53 3 0.05
54 18 0.30
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.18
Consensus pattern (53 bp):
AACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTCATCAGAATGAATCCGG
Found at i:6413525 original size:20 final size:22
Alignment explanation
Indices: 6413495--6413542 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
6413485 GAATATGCTG
*
6413495 TAAATTGAAA-GTTTTTGATAGA
1 TAAA-TGAAAGGTTATTGATAGA
6413517 -AAATGAAAGGTTATTGATAGA
1 TAAATGAAAGGTTATTGATAGA
6413538 TAAAT
1 TAAAT
6413543 CCCTTATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (22 bp):
TAAATGAAAGGTTATTGATAGA
Found at i:6414281 original size:32 final size:31
Alignment explanation
Indices: 6414245--6414334 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 31
6414235 AACTATGTAC
*
6414245 ACTTTGTGTGTACACTTGGAAAGGTTAGGTAT
1 ACTTTGTGTGTACACTTGGAAAGG-AAGGTAT
* *
6414277 ACTTTGTGTATAC-CATATGAAAAGGAAGGTAT
1 ACTTTGTGTGTACAC-T-TGGAAAGGAAGGTAT
6414309 ACTTTGTGTGTACCACTT-GAAAGGAA
1 ACTTTGTGTGTA-CACTTGGAAAGGAA
6414335 TGTACGCCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
31 8 0.16
32 31 0.63
33 9 0.18
34 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (31 bp):
ACTTTGTGTGTACACTTGGAAAGGAAGGTAT
Found at i:6417481 original size:50 final size:50
Alignment explanation
Indices: 6417406--6417578 Score: 265
Period size: 50 Copynumber: 3.4 Consensus size: 50
6417396 TATGGGAACT
* * * *
6417406 AGTGATAAATGATAGCTTCAGCTACACTTATCTGATCAAGGATACGTGAA
1 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAA
*
6417456 AGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAGTGAA
1 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAA
*
6417506 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGACA
1 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA-A
* *
6417557 AGTGAAAAGTGGTAGCTTCGGC
1 AGTGATAAGTGATAGCTTCGGC
6417579 AACCTGATCA
Statistics
Matches: 113, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 92 0.81
51 21 0.19
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (50 bp):
AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAA
Found at i:6417595 original size:31 final size:31
Alignment explanation
Indices: 6417557--6417674 Score: 191
Period size: 31 Copynumber: 3.8 Consensus size: 31
6417547 ACAAATGACA
*
6417557 AGTGAAAAGTGGTAGCTTCGGCAACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
6417588 AGTGAAAAGTGGTAGCTTCGGCTACCTGATT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
6417619 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
6417650 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
6417675 AAATGACAAG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:6417762 original size:47 final size:46
Alignment explanation
Indices: 6417692--6417863 Score: 164
Period size: 47 Copynumber: 3.7 Consensus size: 46
6417682 AAGTGTTTTC
* *
6417692 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * *
6417738 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * * * * * * *
6417785 CGTGTAAGACCATAGCTAGGCTATGGCATCGATATGTGATATGTGATC
1 CGTATAAGACCATATCTGGGATATGGCATCG--GTGAGATATATGATA
* * * *
6417833 CGTGTAAGACTATAGCTGGGCTATGGCATCG
1 CGTATAAGACCATATCTGGGATATGGCATCG
6417864 ATATGTGAAT
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
46 26 0.24
47 41 0.38
48 41 0.38
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
Found at i:6417841 original size:48 final size:48
Alignment explanation
Indices: 6417690--6417913 Score: 209
Period size: 48 Copynumber: 4.9 Consensus size: 48
6417680 ACAAGTGTTT
* * * * * *
6417690 TCCGTATAAGACCATATCTGGGATATGGCATCG--GTGTGATATATGC
1 TCCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGA
* * * * * *
6417736 TACTGTATAAGACCATATCTGGGATATGGCATC-A-GTGAGATATGTGA
1 T-CCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGA
* *
6417783 TTCGTGTAAGACCATAGCTAGGCTATGGCATCGATATGTGATATGTGA
1 TCCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGA
*
6417831 TCCGTGTAAGACTATAGCTGGGCTATGGCATCGATATGTGA-A--T-A
1 TCCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGA
*
6417875 T--GTGTAAGACCATAGCTGGGCTATAGCATC-ATTATGTGA
1 TCCGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATGTGA
6417914 AGATGTGTAA
Statistics
Matches: 156, Mismatches: 17, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 34 0.22
44 2 0.01
45 1 0.01
46 26 0.17
47 43 0.28
48 49 0.31
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (48 bp):
TCCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGA
Found at i:6417884 original size:42 final size:43
Alignment explanation
Indices: 6417786--6417948 Score: 179
Period size: 42 Copynumber: 3.7 Consensus size: 43
6417776 TATGTGATTC
*
6417786 GTGTAAGACCATAGCTAGGCTATGGCATCGA-TATGTGATATGTGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATGTGA-A---GAT
* *
6417832 CCGTGTAAGACTATAGCTGGGCTATGGCATCGA-TATGTGAATAT
1 --GTGTAAGACCATAGCTGGGCTATGGCATCGATTATGTGAAGAT
*
6417876 GTGTAAGACCATAGCTGGGCTATAGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATGTGAAGAT
* * **
6417918 GTGTAAAACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
6417949 GAAACGAAGT
Statistics
Matches: 102, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 61 0.60
43 1 0.01
44 2 0.02
47 1 0.01
48 36 0.35
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATGTGAAGAT
Found at i:6422495 original size:6 final size:6
Alignment explanation
Indices: 6422484--6422649 Score: 135
Period size: 6 Copynumber: 26.8 Consensus size: 6
6422474 TATCATAACT
* * *
6422484 AGAATC AGAATC AGAATC AG-GTGAC AGAATC AAAATC AGAACC AGAATC
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC
* *
6422533 AGAATT AGGTAA-C AGAATC AGAATC AGTATC AGGTAA-C AGAATC AGAATC
1 AGAATC A-G-AATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
* * *
6422583 AGAACC AGAATC AGAATT AGGTAAT- AGAATC AGAATC AGTATC AGGTAA-C
1 AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAATC A-G-AATC
6422633 AGAATC AGAATC AGAAT
1 AGAATC AGAATC AGAAT
6422650 GTGAATGCAA
Statistics
Matches: 130, Mismatches: 15, Indels: 30
0.74 0.09 0.17
Matches are distributed among these distances:
5 10 0.08
6 99 0.76
7 13 0.10
8 8 0.06
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:6422531 original size:37 final size:37
Alignment explanation
Indices: 6422484--6422559 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
6422474 TATCATAACT
* *
6422484 AGAATCAGAATCAGAATCAGGTGACAGAATCAAAATC
1 AGAACCAGAATCAGAATCAGGTAACAGAATCAAAATC
* *
6422521 AGAACCAGAATCAGAATTAGGTAACAGAATCAGAATC
1 AGAACCAGAATCAGAATCAGGTAACAGAATCAAAATC
6422558 AG
1 AG
6422560 TATCAGGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.16
Consensus pattern (37 bp):
AGAACCAGAATCAGAATCAGGTAACAGAATCAAAATC
Found at i:6422554 original size:62 final size:62
Alignment explanation
Indices: 6422479--6422648 Score: 295
Period size: 62 Copynumber: 2.7 Consensus size: 62
6422469 AACATTATCA
* * *
6422479 TAACTAGAATCAGAATCAGAATCAGGTGACAGAATCAAAATCAGAACCAGAATCAGAATTAGG
1 TAAC-AGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCAGAACCAGAATCAGAATTAGG
6422542 TAACAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCAGAACCAGAATCAGAATTAGG
1 TAACAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCAGAACCAGAATCAGAATTAGG
*
6422604 TAATAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCAGAA
1 TAACAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCAGAA
6422649 TGTGAATGCA
Statistics
Matches: 103, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
62 99 0.96
63 4 0.04
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (62 bp):
TAACAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCAGAACCAGAATCAGAATTAGG
Found at i:6422586 original size:37 final size:37
Alignment explanation
Indices: 6422545--6422640 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
6422535 AATTAGGTAA
*
6422545 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAAT
1 CAGAATCAGAATCAGAATCAGGTAACAGAATCAGAAT
* * *
6422582 CAGAACCAGAATCAGAATTAGGTAATAGAATCAGAAT
1 CAGAATCAGAATCAGAATCAGGTAACAGAATCAGAAT
*
6422619 CAGTATCAGGTAA-CAGAATCAG
1 CAGAATCA-G-AATCAGAATCAG
6422641 AATCAGAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 39 0.78
38 9 0.18
39 2 0.04
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19
Consensus pattern (37 bp):
CAGAATCAGAATCAGAATCAGGTAACAGAATCAGAAT
Found at i:6422616 original size:25 final size:25
Alignment explanation
Indices: 6422479--6422649 Score: 133
Period size: 25 Copynumber: 6.8 Consensus size: 25
6422469 AACATTATCA
6422479 TAACTAGAATCAGAATCAGAATCAGG
1 TAAC-AGAATCAGAATCAGAATCAGG
* * *
6422505 TGACAGAATCAAAATCAGAACCA-G
1 TAACAGAATCAGAATCAGAATCAGG
*
6422529 -AATCAGAATTAGGTAA-CAGAATCA-G
1 TAA-CAGAATCA-G-AATCAGAATCAGG
*
6422554 -AATCAGTATCAGGTAA-CAGAATCA-G
1 TAA-CAGAATCA-G-AATCAGAATCAGG
* *
6422579 -AATCAGAACCAGAATCAGAATTAGG
1 TAA-CAGAATCAGAATCAGAATCAGG
* *
6422604 TAATAGAATCAGAATCAGTATCAGG
1 TAACAGAATCAGAATCAGAATCAGG
6422629 TAACAGAATCAGAATCAGAAT
1 TAACAGAATCAGAATCAGAAT
6422650 GTGAATGCAA
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
23 3 0.02
24 16 0.13
25 95 0.79
26 7 0.06
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (25 bp):
TAACAGAATCAGAATCAGAATCAGG
Found at i:6422816 original size:27 final size:26
Alignment explanation
Indices: 6422768--6422819 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
6422758 GCGAGGCTGC
*
6422768 CAGATATTGTGACAAAGTCACCAGAA
1 CAGATATTGTGACAAAGCCACCAGAA
* *
6422794 CAGATATATGTGGCGAAGCCACCAGA
1 CAGATAT-TGTGACAAAGCCACCAGA
6422820 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACAAAGCCACCAGAA
Done.