Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 6 of 310
Found at i:1371246 original size:42 final size:42
Alignment explanation
Indices: 1371183--1371309 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
1371173 CTTCGTTTTC
** * *
1371183 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
1371226 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
1371267 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
1371308 TC
1 TC
1371310 TCACTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:1371371 original size:47 final size:46
Alignment explanation
Indices: 1371268--1371391 Score: 167
Period size: 47 Copynumber: 2.7 Consensus size: 46
1371258 ATTCATATAT
* * * * *
1371268 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
1371314 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
1371361 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
1371392 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:1371408 original size:7 final size:7
Alignment explanation
Indices: 1371396--1371424 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1371386 TATACGGAAA
1371396 TCACTTG
1 TCACTTG
1371403 TCACTTG
1 TCACTTG
1371410 TCACTTG
1 TCACTTG
1371417 TCACTTG
1 TCACTTG
1371424 T
1 T
1371425 AGCCAAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:1371571 original size:31 final size:31
Alignment explanation
Indices: 1371430--1371571 Score: 221
Period size: 31 Copynumber: 4.6 Consensus size: 31
1371420 CTTGTAGCCA
* *
1371430 AAGCTACCATTTTTCACCGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
* **
1371461 AAGCTACCACTTTTCACCGATCAGGTAGCCA
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
* *
1371492 AAACTACCACTTTTCACTGATCAGGTAGCAG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1371523 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1371554 AAGCTACCACTTTTCACT
1 AAGCTACCACTTTTCACT
1371572 TGTCATTTGT
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (31 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCTG
Found at i:1371653 original size:50 final size:51
Alignment explanation
Indices: 1371547--1371675 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
1371537 CACTGATCAG
* * *
1371547 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
1371598 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
1371648 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
1371676 TGCCATGGTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:1374607 original size:17 final size:17
Alignment explanation
Indices: 1374587--1374635 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1374577 AGCTATCCTC
1374587 AAAAAATAGTTGTTCTA
1 AAAAAATAGTTGTTCTA
* * *
1374604 AAAATATAATTATTCTA
1 AAAAAATAGTTGTTCTA
*
1374621 AACAAA-AGTTGTTCT
1 AAAAAATAGTTGTTCT
1374636 TTCAGAAGAG
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (17 bp):
AAAAAATAGTTGTTCTA
Found at i:1376771 original size:3 final size:3
Alignment explanation
Indices: 1376758--1376803 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
1376748 ATATTTATGA
* *
1376758 ATT AAT ATT ATT A-T ATT ATT ATT ATGT ATT ATT ATT AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
1376803 A
1 A
1376804 ACTAATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1376799 original size:19 final size:18
Alignment explanation
Indices: 1376766--1376801 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1376756 GAATTAATAT
*
1376766 TATTATATTATTATTATG
1 TATTATATTAATATTATG
1376784 TATTATTATTAATATTAT
1 TATTA-TATTAATATTAT
1376802 TAACTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTATATTAATATTATG
Found at i:1377879 original size:23 final size:23
Alignment explanation
Indices: 1377853--1377942 Score: 126
Period size: 23 Copynumber: 3.9 Consensus size: 23
1377843 CTTAGTGTCG
* *
1377853 TTCTGGTGTATTTGGGTGGATTA
1 TTCTGGTGTGTTTGGTTGGATTA
* *
1377876 TTCTGGTGTGTTTGGATGGATCA
1 TTCTGGTGTGTTTGGTTGGATTA
*
1377899 TTCTGGCGTGTTTGGTTGGATTA
1 TTCTGGTGTGTTTGGTTGGATTA
*
1377922 TTTTGGTGTGTTTGGTTGGAT
1 TTCTGGTGTGTTTGGTTGGAT
1377943 CCGTGTATCC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.10, C:0.06, G:0.36, T:0.49
Consensus pattern (23 bp):
TTCTGGTGTGTTTGGTTGGATTA
Found at i:1378615 original size:36 final size:36
Alignment explanation
Indices: 1378568--1378640 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1378558 ATAGTATCAT
*
1378568 GAATGTTGTTGATCAATTTGATAAGTCAATGTTTTA
1 GAATGTTGTTGATCAATTTGACAAGTCAATGTTTTA
1378604 GAATGTTGTTGATCAATTTGACAAGTCAATGTTTTA
1 GAATGTTGTTGATCAATTTGACAAGTCAATGTTTTA
1378640 G
1 G
1378641 GCATGATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.42
Consensus pattern (36 bp):
GAATGTTGTTGATCAATTTGACAAGTCAATGTTTTA
Found at i:1381991 original size:48 final size:49
Alignment explanation
Indices: 1381914--1382044 Score: 121
Period size: 48 Copynumber: 2.7 Consensus size: 49
1381904 TGGATATCCA
* *
1381914 GAGCTTCCCGATATATGGCT-ATC-TGGAGCTTCC-CATTAATGGCTCTT-C
1 GAGCTTACCGTTATATGGCTCA-CAT-GAGCTTCCTCATT-ATGGCTCTTAC
* * *
1381962 GAAGC-TACCTGTTAT-TGGCTCGCATGAGCTTCCTGATTATGGCTCTTAT
1 G-AGCTTACC-GTTATATGGCTCACATGAGCTTCCTCATTATGGCTCTTAC
*
1382011 GAGCTTTCCGTTATATGGCTCACATGAGCTTCCT
1 GAGCTTACCGTTATATGGCTCACATGAGCTTCCT
1382045 GTTATATGGC
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
48 35 0.51
49 33 0.49
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.35
Consensus pattern (49 bp):
GAGCTTACCGTTATATGGCTCACATGAGCTTCCTCATTATGGCTCTTAC
Found at i:1382019 original size:25 final size:25
Alignment explanation
Indices: 1381964--1382055 Score: 109
Period size: 25 Copynumber: 3.8 Consensus size: 25
1381954 GGCTCTTCGA
* *
1381964 AGCTACCTGTTAT-TGGCTCGCATG
1 AGCTTCCTGTTATATGGCTCACATG
* **
1381988 AGCTTCCTGAT-TATGGCTCTTATG
1 AGCTTCCTGTTATATGGCTCACATG
1382012 AGCTTTCC-GTTATATGGCTCACATG
1 AGC-TTCCTGTTATATGGCTCACATG
1382037 AGCTTCCTGTTATATGGCT
1 AGCTTCCTGTTATATGGCT
1382056 TGAGAGAGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.02
24 27 0.47
25 29 0.51
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (25 bp):
AGCTTCCTGTTATATGGCTCACATG
Found at i:1384244 original size:15 final size:15
Alignment explanation
Indices: 1384224--1384255 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1384214 AATTTCACTA
*
1384224 TTATATCTTTTGTAT
1 TTATATCTTTTATAT
1384239 TTATATCTTTTATAT
1 TTATATCTTTTATAT
1384254 TT
1 TT
1384256 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATATCTTTTATAT
Found at i:1385967 original size:68 final size:67
Alignment explanation
Indices: 1385870--1386067 Score: 182
Period size: 68 Copynumber: 3.0 Consensus size: 67
1385860 ATTTTAATAG
* * *
1385870 TTTAATATTAAATTTAATTTAGTACTTATCTTAATACTATTTTATTAATTTAATATTAAAGTGAT
1 TTTAATATTAAATTTAATTTAATATTTATCTTAATACTATTATATTAATTTAATATTAAAGTGAT
1385935 TA
66 TA
* * *
1385937 TCTTAATATTAAATTTAATTTAATGTTTATCTTGTAAATAAAC-ATTCTATT-ATTT--TAAT-A
1 T-TTAATATTAAATTTAATTTAATATTTATC-T-T-AAT--ACTATTATATTAATTTAATATTAA
1385997 A--GA-T-
60 AGTGATTA
* * *
1386001 TTT-ATATTAAATTTAATCTAATATTTATCTTGATATTTATTATATTAATTTAATATTAAAGTGA
1 TTTAATATTAAATTTAATTTAATATTTATCTTAATA-CTATTATATTAATTTAATATTAAAGTGA
1386065 TTA
65 TTA
1386068 ATTTTAATCA
Statistics
Matches: 104, Mismatches: 11, Indels: 32
0.71 0.07 0.22
Matches are distributed among these distances:
57 1 0.01
59 9 0.09
60 5 0.05
61 1 0.01
62 27 0.26
63 4 0.04
64 1 0.01
65 3 0.03
66 3 0.03
67 1 0.01
68 28 0.27
69 4 0.04
70 1 0.01
71 7 0.07
72 7 0.07
73 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (67 bp):
TTTAATATTAAATTTAATTTAATATTTATCTTAATACTATTATATTAATTTAATATTAAAGTGAT
TA
Found at i:1389958 original size:24 final size:25
Alignment explanation
Indices: 1389931--1389977 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1389921 AGAAGAGAGA
*
1389931 AAAATAAAG-GAGAAAAAGAAAAGG
1 AAAATAAAGAAAGAAAAAGAAAAGG
*
1389955 AAAATAAAGAAATAAAAAGAAAA
1 AAAATAAAGAAAGAAAAAGAAAA
1389978 AATTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (25 bp):
AAAATAAAGAAAGAAAAAGAAAAGG
Found at i:1390343 original size:29 final size:31
Alignment explanation
Indices: 1390267--1390343 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 31
1390257 ATTAACACTT
* *
1390267 AGTGACTAAAATGTCACAATACGATAATGTA
1 AGTGACTAAAATGTAACAATACGATAATATA
* *
1390298 AGTGACTAAAACT-TAACATTTC-A-AATATA
1 AGTGACTAAAA-TGTAACAATACGATAATATA
1390327 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
1390344 CTGAAGCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.03
29 20 0.50
30 1 0.03
31 17 0.43
32 1 0.03
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (31 bp):
AGTGACTAAAATGTAACAATACGATAATATA
Found at i:1391583 original size:31 final size:31
Alignment explanation
Indices: 1391543--1391610 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
1391533 TTAACAACCT
1391543 AGTGACTTAAATAAAAACTTTTGAATAGTTC
1 AGTGACTTAAATAAAAACTTTTGAATAGTTC
* *
1391574 AGTGGCTTAAATGAAAACTTTTGAATAGTTC
1 AGTGACTTAAATAAAAACTTTTGAATAGTTC
1391605 AGTGAC
1 AGTGAC
1391611 CATTTTGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTTGAATAGTTC
Found at i:1392782 original size:17 final size:17
Alignment explanation
Indices: 1392759--1392797 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1392749 AAATTGGGGC
*
1392759 GTGTGGGCTACATGGGT
1 GTGTGGGCCACATGGGT
*
1392776 TTGTGGGCCACATGGGT
1 GTGTGGGCCACATGGGT
1392793 GTGTG
1 GTGTG
1392798 AGCCCATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.10, C:0.13, G:0.46, T:0.31
Consensus pattern (17 bp):
GTGTGGGCCACATGGGT
Found at i:1398357 original size:18 final size:17
Alignment explanation
Indices: 1398329--1398363 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1398319 ATTATTAAGA
*
1398329 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1398346 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1398364 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1398370 original size:54 final size:54
Alignment explanation
Indices: 1398312--1398497 Score: 167
Period size: 54 Copynumber: 3.2 Consensus size: 54
1398302 TTCATATAAG
1398312 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
1 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
* * * * *
1398366 AATATTAATTATTTCA-AATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTA-TTAAGAATT-T-TATTA-A--AT--TATA-TAT--TTTAATTAAAAT-ATAT-
**
1398430 AG
53 TT
*
1398432 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTT
1 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
*
1398486 AATAATAATTAT
1 AATATTAATTAT
1398498 GTTTAAATAT
Statistics
Matches: 102, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
54 26 0.25
55 8 0.08
56 12 0.12
57 1 0.01
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 1 0.01
64 13 0.13
65 8 0.08
66 15 0.15
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (54 bp):
AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
Found at i:1398406 original size:61 final size:60
Alignment explanation
Indices: 1398234--1398406 Score: 164
Period size: 54 Copynumber: 2.9 Consensus size: 60
1398224 AACTGAGCCG
1398234 TAAAATATATTTAATATTAATTATTTCAAATTTTCTTTTATAGTATCATATATTATGATTTTAA
1 TAAAATATATTTAATATTAATTATTTCAAA-TTTCTTTTATAGTATC--ATA-TATGATTTTAA
* ** * *
1398298 TAAATTCATATAAGAATATTAATTA-TTAAGAATTT-TATTA-A--AT--TATAT-ATTTTAA
1 TAAAAT-ATAT-TTAATATTAATTATTTCA-AATTTCTTTTATAGTATCATATATGATTTTAA
1398353 TTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGTATCATATAT
1 -TAAAATATATTTAATATTAATTATTTCAAATT-TCTTTTATAGTATCATATAT
1398407 TATGATTTGA
Statistics
Matches: 87, Mismatches: 10, Indels: 27
0.70 0.08 0.22
Matches are distributed among these distances:
54 15 0.17
55 15 0.17
56 12 0.14
57 3 0.03
59 2 0.02
61 7 0.08
63 1 0.01
64 9 0.10
65 10 0.11
66 13 0.15
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (60 bp):
TAAAATATATTTAATATTAATTATTTCAAATTTCTTTTATAGTATCATATATGATTTTAA
Found at i:1398447 original size:120 final size:120
Alignment explanation
Indices: 1398234--1398497 Score: 483
Period size: 120 Copynumber: 2.2 Consensus size: 120
1398224 AACTGAGCCG
* *
1398234 TAAAATATATTTAATATTAATTATTTCAAATTTTCTTTTATAGTATCATATATTATGATTTTAAT
1 TAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAAT
1398299 AAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
66 AAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
*
1398354 TAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGT
1 TAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAAT
1398419 AAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
66 AAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
* *
1398474 TATAATATATTTAATAATAATTAT
1 TAAAATATATTTAATATTAATTAT
1398498 GTTTAAATAT
Statistics
Matches: 139, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 139 1.00
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
TAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAAT
AAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
Found at i:1398465 original size:59 final size:59
Alignment explanation
Indices: 1398282--1398465 Score: 173
Period size: 54 Copynumber: 3.1 Consensus size: 59
1398272 TATAGTATCA
*
1398282 TATATTATGATTTTAATAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTAAATAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* * ** * *
1398341 TATA-TAT--TTTAATTAAAAT-ATAT-TTAATATTAATTATTTCA-AATTATCTTTTATAGTAT
1 TATATTATGATTTAAATAAATTCATATAAGAATATTAATTA-TTAAGAATT-T-TATTA-A--AT
* *
1398400 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAATAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1398461 TATAT
1 TATAT
1398466 ATTTTAATTA
Statistics
Matches: 97, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
54 15 0.15
55 8 0.08
56 13 0.13
57 1 0.01
58 3 0.03
59 11 0.11
61 6 0.06
62 3 0.03
63 1 0.01
64 13 0.13
65 8 0.08
66 15 0.15
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (59 bp):
TATATTATGATTTAAATAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:1398483 original size:16 final size:16
Alignment explanation
Indices: 1398462--1398503 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1398452 TTATTAAATT
*
1398462 ATATATTTTAATTATA
1 ATATATTTTAATAATA
1398478 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
1398493 AT-TATGTTTAA
1 ATATAT-TTTAA
1398504 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:1398488 original size:15 final size:15
Alignment explanation
Indices: 1398453--1398494 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1398443 TTAAGAATTT
*
1398453 TATTAAATTAT-ATA
1 TATTTAATTATAATA
1398467 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
1398481 TATTTAATAATAAT
1 TATTTAATTATAAT
1398495 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:1398598 original size:157 final size:157
Alignment explanation
Indices: 1398437--1398753 Score: 557
Period size: 157 Copynumber: 2.0 Consensus size: 157
1398427 ATAAGAATAT
*
1398437 TAATTATTAAGAATTTTATTAAATTATATATT-TTAATTATAATATATTTAATAATAATTATGTT
1 TAATTA-TAAGAATTTTATTAAATTATATATTATTAATTAAAATATATTTAATAATAATTATGTT
* * *
1398501 TAAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACA
65 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
1398566 ATAATAATTTACCAAAACAAATTTT-TGC
130 ATAATAATTTACCAAAAC-AATTTTATGC
1398594 TAATTATAAGAATTTTATTAAATTATATATTATTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATAAGAATTTTATTAAATTATATATTATTAATTAAAATATATTTAATAATAATTATGTTT
1398659 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
1398724 TAATCATTTACCAAAACAATTTTATGC
131 TAATAATTTACCAAAACAATTTTATGC
1398751 TAA
1 TAA
1398754 GGGTATTCTA
Statistics
Matches: 153, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
156 31 0.20
157 122 0.80
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATAAGAATTTTATTAAATTATATATTATTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAATTTTATGC
Found at i:1398870 original size:44 final size:45
Alignment explanation
Indices: 1398805--1398895 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1398795 ACCTCTATTC
* * *
1398805 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
1398849 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
1398894 CA
1 CA
1398896 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:1398897 original size:16 final size:16
Alignment explanation
Indices: 1398876--1398944 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
1398866 GATTAGCTAT
1398876 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1398892 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
1398909 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1398925 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1398941 TACA
1 TACA
1398945 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1398918 original size:33 final size:32
Alignment explanation
Indices: 1398876--1398944 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
1398866 GATTAGCTAT
1398876 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
1398909 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
1398941 TACA
1 TACA
1398945 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:1399363 original size:26 final size:29
Alignment explanation
Indices: 1399327--1399386 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
1399317 TATATTATAT
* *
1399327 TATATTATTTTA-ATATTTAATATTTTTA
1 TATATTATTTTATATATTGAAAATTTTTA
*
1399355 TATATT-TTTTATTTATTGAAAATTTTTA
1 TATATTATTTTATATATTGAAAATTTTTA
1399383 TATA
1 TATA
1399387 GTCATCTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (29 bp):
TATATTATTTTATATATTGAAAATTTTTA
Found at i:1403438 original size:21 final size:21
Alignment explanation
Indices: 1403388--1403455 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
1403378 GGGTTTCTGA
*
1403388 TTTGAGGTTT-GTGTTCA-TGG
1 TTTGAGGTTTAGAGTTCAGT-G
1403408 TTTG-GGTTTAGAGTTCAGTG
1 TTTGAGGTTTAGAGTTCAGTG
*
1403428 TTTGAGGTTTA-AGATTTAGTG
1 TTTGAGGTTTAGAG-TTCAGTG
*
1403449 TTCGAGG
1 TTTGAGG
1403456 CTTAATGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 5 0.12
20 17 0.41
21 19 0.46
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (21 bp):
TTTGAGGTTTAGAGTTCAGTG
Found at i:1404939 original size:6 final size:6
Alignment explanation
Indices: 1404928--1404972 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1404918 AAGAAATTAA
1404928 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAA
1404973 AGAGGTACCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:1413075 original size:23 final size:24
Alignment explanation
Indices: 1413045--1413090 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1413035 ATAAAGAAAC
1413045 ATGACAAATAATTA-ACATGCCAA
1 ATGACAAATAATTAGACATGCCAA
**
1413068 ATGACAAATTCTTAGACATGCCA
1 ATGACAAATAATTAGACATGCCA
1413091 CATAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.24
Consensus pattern (24 bp):
ATGACAAATAATTAGACATGCCAA
Found at i:1413160 original size:6 final size:6
Alignment explanation
Indices: 1413149--1413174 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1413139 ATATATTAGA
1413149 TTTAAT TTTAAT TTTAAT TTTAAT TT
1 TTTAAT TTTAAT TTTAAT TTTAAT TT
1413175 CAAATTTCTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:1415943 original size:72 final size:72
Alignment explanation
Indices: 1415826--1416081 Score: 503
Period size: 72 Copynumber: 3.6 Consensus size: 72
1415816 ACAACTTGAC
*
1415826 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1415891 ACTAACA
66 ACTAACA
1415898 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1415963 ACTAACA
66 ACTAACA
1415970 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1416035 ACTAACA
66 ACTAACA
1416042 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1416082 AATAATAATA
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 183 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (72 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
ACTAACA
Found at i:1416090 original size:3 final size:3
Alignment explanation
Indices: 1416082--1416116 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1416072 ATTACATCCA
1416082 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1416117 AACATGTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1420452 original size:72 final size:72
Alignment explanation
Indices: 1420335--1420518 Score: 350
Period size: 72 Copynumber: 2.6 Consensus size: 72
1420325 ACAACTTGAC
* *
1420335 AACTTAGTTGGAATACAACTAAGTTTCATTATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1420400 ACTAACA
66 ACTAACA
1420407 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1420472 ACTAACA
66 ACTAACA
1420479 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1420519 AATAATAATA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 110 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (72 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
ACTAACA
Found at i:1420527 original size:3 final size:3
Alignment explanation
Indices: 1420519--1420556 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1420509 ATTACATCCA
1420519 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1420557 AACATGTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1423503 original size:22 final size:22
Alignment explanation
Indices: 1423478--1423543 Score: 53
Period size: 23 Copynumber: 2.9 Consensus size: 22
1423468 TTTTTGGAAT
1423478 TAAATTATAATTTTTATAATAA
1 TAAATTATAATTTTTATAATAA
* * **
1423500 TAAAAATGTAATTTTATCATTTTAA
1 T-AAATTATAATTTT-T-ATAATAA
*
1423525 TAATTTAT-ATTTTTATAAT
1 TAAATTATAATTTTTATAAT
1423544 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 9, Indels: 7
0.67 0.19 0.15
Matches are distributed among these distances:
21 3 0.09
22 2 0.06
23 16 0.50
24 5 0.16
25 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAATTATAATTTTTATAATAA
Found at i:1423542 original size:15 final size:16
Alignment explanation
Indices: 1423512--1423545 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1423502 AAAATGTAAT
1423512 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
1423528 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
1423543 TTT
1 TTT
1423546 TTAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:1430331 original size:36 final size:36
Alignment explanation
Indices: 1430260--1430331 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
1430250 TCAGAAAAGC
*
1430260 TATTTTTACATATATTAATAAATTTATATTTTAAAT
1 TATTTTTACATATATTAATAAATTTATATTATAAAT
1430296 TATTTTTACATATATTACA-ATAATTTAT-TTATAAAT
1 TATTTTTACATATATTA-ATA-AATTTATATTATAAAT
1430332 AAATAAATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 25 0.76
37 8 0.24
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (36 bp):
TATTTTTACATATATTAATAAATTTATATTATAAAT
Found at i:1433645 original size:34 final size:34
Alignment explanation
Indices: 1433605--1433712 Score: 123
Period size: 40 Copynumber: 3.1 Consensus size: 34
1433595 GACCTTGCGA
1433605 AGAGGAATGAGATTTGCCTGAGAAAGAGAGAAAG
1 AGAGGAATGAGATTTGCCTGAGAAAGAGAGAAAG
1433639 AGAGGAATGAGATTGGCCTTTGCCTGAGAAAGAGAGAAAG
1 AGAGGAATGAGA------TTTGCCTGAGAAAGAGAGAAAG
* *
1433679 GGAGGAATGAGATTTG-C--AGAAAGAGAGAGAG
1 AGAGGAATGAGATTTGCCTGAGAAAGAGAGAAAG
1433710 AGA
1 AGA
1433713 AAGAAGATGA
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
31 15 0.23
33 1 0.02
34 16 0.25
40 33 0.51
ACGTcount: A:0.42, C:0.06, G:0.37, T:0.15
Consensus pattern (34 bp):
AGAGGAATGAGATTTGCCTGAGAAAGAGAGAAAG
Found at i:1433672 original size:40 final size:40
Alignment explanation
Indices: 1433617--1433692 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
1433607 AGGAATGAGA
1433617 TTTGCCTGAGAAAGAGAGAAAGAGAGGAATGAGATTGGCC
1 TTTGCCTGAGAAAGAGAGAAAGAGAGGAATGAGATTGGCC
*
1433657 TTTGCCTGAGAAAGAGAGAAAGGGAGGAATGAGATT
1 TTTGCCTGAGAAAGAGAGAAAGAGAGGAATGAGATT
1433693 TGCAGAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.08, G:0.36, T:0.18
Consensus pattern (40 bp):
TTTGCCTGAGAAAGAGAGAAAGAGAGGAATGAGATTGGCC
Found at i:1435149 original size:52 final size:52
Alignment explanation
Indices: 1435089--1435194 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
1435079 TATTATTGAA
1435089 AATAATTTTTAATGTTTTTTTTAAAAGTTGAATTGCAAGTGGTAAATCTTTT
1 AATAATTTTTAATGTTTTTTTTAAAAGTTGAATTGCAAGTGGTAAATCTTTT
*
1435141 AATAATTTTTAATGTTTTTTTTAAAAGTTGAATTGCAAGTGGTAAATTTTTT
1 AATAATTTTTAATGTTTTTTTTAAAAGTTGAATTGCAAGTGGTAAATCTTTT
1435193 AA
1 AA
1435195 GGGATATAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (52 bp):
AATAATTTTTAATGTTTTTTTTAAAAGTTGAATTGCAAGTGGTAAATCTTTT
Found at i:1436303 original size:30 final size:30
Alignment explanation
Indices: 1436267--1436329 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
1436257 ACTTATTTTA
1436267 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
1436297 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
1436327 TTG
1 TTG
1436330 CTTCTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:1438079 original size:18 final size:19
Alignment explanation
Indices: 1438051--1438110 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 19
1438041 TTATATATAT
*
1438051 ATATT-TAAATTTTAAAAG
1 ATATTATAAATTTTAAAAA
1438069 A-ATTATAAATTTGTAAAAA
1 ATATTATAAATTT-TAAAAA
*
1438088 ATATTA-AAATTTTTAAAA
1 ATATTATAAATTTTAAAAA
*
1438106 TTATT
1 ATATT
1438111 GAATAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.08
18 17 0.47
19 12 0.33
20 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATATTATAAATTTTAAAAA
Found at i:1438134 original size:24 final size:22
Alignment explanation
Indices: 1438103--1438147 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1438093 AAAATTTTTA
*
1438103 AAATTATTGAATAAAATTCAAAAT
1 AAATTATT-AAAAAAATT-AAAAT
1438127 AAATTATTAAAAAAATTAAAA
1 AAATTATTAAAAAAATTAAAA
1438148 GTTTAAGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 8 0.40
24 8 0.40
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATTATTAAAAAAATTAAAAT
Found at i:1445198 original size:30 final size:32
Alignment explanation
Indices: 1445144--1445207 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 32
1445134 TAGTAAATAT
* *
1445144 AAAATTGTACTTTAATTTTCTTAAAAATGATA
1 AAAATTGTAATTTAATTCTCTTAAAAATGATA
*
1445176 AAAATT-TAATTTAA-TCTCTTAAAAATTATA
1 AAAATTGTAATTTAATTCTCTTAAAAATGATA
1445206 AA
1 AA
1445208 GATATAGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.55
31 7 0.24
32 6 0.21
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (32 bp):
AAAATTGTAATTTAATTCTCTTAAAAATGATA
Found at i:1455479 original size:4 final size:4
Alignment explanation
Indices: 1455470--1455502 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1455460 CAGAGGTATC
1455470 CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA C
1455503 TTTCTGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:1460797 original size:38 final size:38
Alignment explanation
Indices: 1460741--1460816 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
1460731 ACTCACCACC
* *
1460741 ATCCTCACTTGTTTCATATTTTGTAAGGATCATAACAT
1 ATCCTCACTTGTTCCATATTTTATAAGGATCATAACAT
1460779 ATCCTCACTTGTTCCATATTTTATAAGGATCATAACAT
1 ATCCTCACTTGTTCCATATTTTATAAGGATCATAACAT
1460817 GAAAAATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (38 bp):
ATCCTCACTTGTTCCATATTTTATAAGGATCATAACAT
Found at i:1468653 original size:24 final size:24
Alignment explanation
Indices: 1468621--1468690 Score: 106
Period size: 24 Copynumber: 2.9 Consensus size: 24
1468611 TTAGGATTAG
1468621 GGTTTAGTGGTTTAAGATTTTTAA
1 GGTTTAGTGGTTTAAGATTTTTAA
1468645 GGTTTAGTGGTTTAAGATTTTTAA
1 GGTTTAGTGGTTTAAGATTTTTAA
* *
1468669 GATTTAG-GGTTTTAGTATTTTT
1 GGTTTAGTGGTTTAAG-ATTTTT
1468691 TAAGAGAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.16
24 36 0.84
ACGTcount: A:0.23, C:0.00, G:0.24, T:0.53
Consensus pattern (24 bp):
GGTTTAGTGGTTTAAGATTTTTAA
Found at i:1468892 original size:153 final size:155
Alignment explanation
Indices: 1468672--1469021 Score: 503
Period size: 153 Copynumber: 2.3 Consensus size: 155
1468662 TTTTTAAGAT
* * *
1468672 TTAGGGTTTTAGTATTTTTTAAGAGAAAAATTAGTTTAATTAGAGTTAAGGGTTAATTAATTAAA
1 TTAGGGTTTTAGTATTTTTTAAGGGAAAAATTAATTTAATTAGAGTTAAGAGTTAATTAATTAAA
1468737 TTAACTATGAAATTAAAAAAAT-AATTAAAGTAGGGTTTAGGGTTTTTTAAGGTT-AGGTTTTTT
66 TTAACTATGAAATT-AAAAAATCAATTAAAGTAGGGTTTAGGG-TTTTTAAGGTTAAGG-TTTTT
* * *
1468800 ATTATTTTAGGATTAGGG-TTTAGTGGG
128 ATTATTTCAGGATTAGGGTTTTAATAGG
* * *
1468827 TTAGGGTTTTA-T-TATTTTAAGGGAAAAGTTAATTTAATTAGAGTTGAGAGTTAATTAATTAAA
1 TTAGGGTTTTAGTATTTTTTAAGGGAAAAATTAATTTAATTAGAGTTAAGAGTTAATTAATTAAA
*
1468890 TTAACTATGAAATTAAAAAATCAATTAAATTAGGGTTTAGGGTTTTTAAGGTTAAGGTTTTTATT
66 TTAACTATGAAATTAAAAAATCAATTAAAGTAGGGTTTAGGGTTTTTAAGGTTAAGGTTTTTATT
* * * *
1468955 GTTTCGGGGTTAGGGTTTTAATAGT
131 ATTTCAGGATTAGGGTTTTAATAGG
*
1468980 TTAGGGTTTTAGTATTTTTTAAGGGAAAATTTAATTTAATTA
1 TTAGGGTTTTAGTATTTTTTAAGGGAAAAATTAATTTAATTA
1469022 AAAACTCTAA
Statistics
Matches: 174, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
152 37 0.21
153 98 0.56
154 2 0.01
155 37 0.21
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.44
Consensus pattern (155 bp):
TTAGGGTTTTAGTATTTTTTAAGGGAAAAATTAATTTAATTAGAGTTAAGAGTTAATTAATTAAA
TTAACTATGAAATTAAAAAATCAATTAAAGTAGGGTTTAGGGTTTTTAAGGTTAAGGTTTTTATT
ATTTCAGGATTAGGGTTTTAATAGG
Found at i:1468986 original size:22 final size:22
Alignment explanation
Indices: 1468934--1468987 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
1468924 GTTTAGGGTT
* * *
1468934 TTTAAGGTTAAGGTTTTTATTG
1 TTTAGGGTTAAGGTTTTAATAG
* *
1468956 TTTCGGGGTTAGGGTTTTAATAG
1 TTT-AGGGTTAAGGTTTTAATAG
1468979 TTTAGGGTT
1 TTTAGGGTT
1468988 TTAGTATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.50
Consensus pattern (22 bp):
TTTAGGGTTAAGGTTTTAATAG
Found at i:1469041 original size:17 final size:17
Alignment explanation
Indices: 1469021--1469054 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1469011 TAATTTAATT
*
1469021 AAAAACTCT-AACCCTA
1 AAAAACCCTAAACCCTA
1469037 AAAAACCCTAAACCCTA
1 AAAAACCCTAAACCCTA
1469054 A
1 A
1469055 TTTAATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAACCCTAAACCCTA
Found at i:1470980 original size:31 final size:31
Alignment explanation
Indices: 1470942--1471001 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1470932 TTTAATTTGA
* *
1470942 TCAATTTTAGTCATTGTACTTTTTGAATTGG
1 TCAATTTTAGTCACTATACTTTTTGAATTGG
*
1470973 TCAATTTTAGTCCCTATACTTTTTGAATT
1 TCAATTTTAGTCACTATACTTTTTGAATT
1471002 CTAAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.13, G:0.12, T:0.52
Consensus pattern (31 bp):
TCAATTTTAGTCACTATACTTTTTGAATTGG
Found at i:1471010 original size:31 final size:31
Alignment explanation
Indices: 1470944--1471011 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
1470934 TAATTTGATC
* * * *
1470944 AATTTTAGTCATTGTACTTTTTGAATTGGTC
1 AATTTTAGTCACTATACTTTTTGAATTGCTA
*
1470975 AATTTTAGTCCCTATACTTTTTGAATT-CTAA
1 AATTTTAGTCACTATACTTTTTGAATTGCT-A
1471006 AATTTT
1 AATTTT
1471012 GGTCTTGACC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.51
Consensus pattern (31 bp):
AATTTTAGTCACTATACTTTTTGAATTGCTA
Found at i:1471299 original size:62 final size:62
Alignment explanation
Indices: 1471222--1471353 Score: 160
Period size: 62 Copynumber: 2.1 Consensus size: 62
1471212 AAAGTTTGAA
* **
1471222 GAAAGTTTTCAAAAA-TTTGAGGGGGCCTAATTAATTTTTTCTAAAAACTTCAA-GAGAGAAAT
1 GAAAATTTTCAAAAATTTTGA-GGGGCCTAATTAAAATTTTCTAAAAACTTCAATG-GAGAAAT
* * * *
1471284 GAAAATTTTCGAAAATTTTGATGGGCTTAATTAAAATTTTCTAAAAATTTCAATGGAGAAAT
1 GAAAATTTTCAAAAATTTTGAGGGGCCTAATTAAAATTTTCTAAAAACTTCAATGGAGAAAT
*
1471346 CAAAATTT
1 GAAAATTT
1471354 CCCAATTTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 54 0.90
63 6 0.10
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (62 bp):
GAAAATTTTCAAAAATTTTGAGGGGCCTAATTAAAATTTTCTAAAAACTTCAATGGAGAAAT
Found at i:1471351 original size:31 final size:31
Alignment explanation
Indices: 1471258--1471353 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 31
1471248 CTAATTAATT
* *
1471258 TTTTCTAAAAACTTCAA-GAGAGAAATGAAAA
1 TTTTCTAAAAATTTCAATG-GAGAAATCAAAA
* ** * *
1471289 TTTTC-GAAAATTTTGATGG-GCTTAATTAAAA
1 TTTTCTAAAAATTTCAATGGAG--AAATCAAAA
1471320 TTTTCTAAAAATTTCAATGGAGAAATCAAAA
1 TTTTCTAAAAATTTCAATGGAGAAATCAAAA
1471351 TTT
1 TTT
1471354 CCCAATTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
29 1 0.02
30 8 0.16
31 28 0.57
32 11 0.22
33 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (31 bp):
TTTTCTAAAAATTTCAATGGAGAAATCAAAA
Found at i:1472726 original size:9 final size:9
Alignment explanation
Indices: 1472714--1472774 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
1472704 CAATATGTTC
1472714 ATTTAATTA
1 ATTTAATTA
*
1472723 ATTT-ATAAA
1 ATTTAAT-TA
1472732 ATTTAATTA
1 ATTTAATTA
* *
1472741 ATTAAATTT
1 ATTTAATTA
1472750 ATTTAATTAAA
1 ATTTAATT--A
*
1472761 AATTAATTA
1 ATTTAATTA
1472770 ATTTA
1 ATTTA
1472775 CTTGGTTGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
8 2 0.05
9 29 0.73
10 2 0.05
11 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATTTAATTA
Found at i:1472735 original size:18 final size:17
Alignment explanation
Indices: 1472714--1472772 Score: 65
Period size: 14 Copynumber: 3.7 Consensus size: 17
1472704 CAATATGTTC
1472714 ATTTAATTAATTTATAAA
1 ATTTAATTAA-TTATAAA
1472732 ATTTAATTAA-T-T-AA
1 ATTTAATTAATTATAAA
*
1472746 ATTTATTTAATTA-AAA
1 ATTTAATTAATTATAAA
1472762 A-TTAATTAATT
1 ATTTAATTAATT
1472773 TACTTGGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 11 0.31
15 11 0.31
16 4 0.11
18 10 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAATTAATTATAAA
Found at i:1473199 original size:15 final size:15
Alignment explanation
Indices: 1473179--1473208 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1473169 AAATTTTAAT
*
1473179 TTTTTATATTTTATA
1 TTTTTATAATTTATA
1473194 TTTTTATAATTTATA
1 TTTTTATAATTTATA
1473209 AAGGATTAAA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTATAATTTATA
Found at i:1474379 original size:3 final size:3
Alignment explanation
Indices: 1474371--1474395 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1474361 TGTTTGTTCT
1474371 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1474396 GACATATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1476065 original size:14 final size:14
Alignment explanation
Indices: 1476028--1476066 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1476018 TCAGCGAACA
1476028 AAATATATAAATAT
1 AAATATATAAATAT
*
1476042 AAATAAATAAATAT
1 AAATATATAAATAT
**
1476056 TTATATATAAA
1 AAATATATAAA
1476067 GTTTTACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATATATAAATAT
Found at i:1493711 original size:5 final size:5
Alignment explanation
Indices: 1493699--1493732 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1493689 GGGAATTTAG
* *
1493699 ATAGA AGAGA AGAGA ATAGA ATAGA ATAGA ATAG
1 ATAGA ATAGA ATAGA ATAGA ATAGA ATAGA ATAG
1493733 GATTAGATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (5 bp):
ATAGA
Found at i:1500116 original size:6 final size:6
Alignment explanation
Indices: 1500107--1500136 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1500097 GCCCTTCCCC
1500107 TTCCTT TTCCTT TTCCTT TTCCTT TTCCTT
1 TTCCTT TTCCTT TTCCTT TTCCTT TTCCTT
1500137 CCATCACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCCTT
Found at i:1500122 original size:18 final size:18
Alignment explanation
Indices: 1500101--1500136 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1500091 GCCCTTGCCC
1500101 TTCCCCTTCCTTTTCCTT
1 TTCCCCTTCCTTTTCCTT
**
1500119 TTCCTTTTCCTTTTCCTT
1 TTCCCCTTCCTTTTCCTT
1500137 CCATCACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (18 bp):
TTCCCCTTCCTTTTCCTT
Found at i:1500728 original size:12 final size:12
Alignment explanation
Indices: 1500711--1500745 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1500701 TTTCTTGAAC
*
1500711 TTTTAAAGATTT
1 TTTTAAAGAATT
1500723 TTTTAAAGAATT
1 TTTTAAAGAATT
1500735 TTTTAAA-AATT
1 TTTTAAAGAATT
1500746 ATTGTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (12 bp):
TTTTAAAGAATT
Found at i:1501588 original size:305 final size:306
Alignment explanation
Indices: 1501023--1501601 Score: 772
Period size: 305 Copynumber: 1.9 Consensus size: 306
1501013 TGTATATCAT
* * * *
1501023 ATACTAGAAACTCTATCACACGCGTATGCGTGTGGAAACCATATATTTAGAACACAAATTTATGT
1 ATACTAGAAACTCCATCACACGAGTATGCATGTGGAAACCATATAGTTAGAACACAAATTTATGT
* * *
1501088 TTAAAAAAAACAACAATAAGAAATGAAATGTGTTATTTGAAACTAATTAATAATCACATGAAATA
66 TTAAAAAAAACAACAATAAGAAATGAAATGTATGATTTGAAACTAATTAATAATAACATGAAATA
* * * * * *
1501153 TGTACAATATTAAAATAAAAAAAATTGTTTTAAATTGTAAGTAAAACGATATTTAAATACATGAA
131 TGTACAATACTAAAAT-AAAAAAATAGTATTAAATTGTAAATAAAACGATATTTAAACACATAAA
* *
1501218 TACATCAAATTAAGAGGAGTAAATGAATATAATTATTTATCATGGTATTGTCATCAATTTTAAGT
195 TACATCAAATTAAAAGGAGTAAATGAATACAATTATTTATCATGGTATTGTCATCAATTTTAAGT
1501283 TGGCGTCGAGTTAACTTGTAACATCATCTCAATCAACAACTTTATTA
260 TGGCGTCGAGTTAACTTGTAACATCATCTCAATCAACAACTTTATTA
* * * * * *
1501330 ATACTAGAATCTCCATCATATGAGTATGCATGTGGAAATCATGTAGTTA-AAGCACAAATTTGTG
1 ATACTAGAAACTCCATCACACGAGTATGCATGTGGAAACCATATAGTTAGAA-CACAAATTTATG
* * *
1501394 TTTAATAATAACATACAATAA-ATAATGAAATGTATGATTTGGAACTAATTAATAATAACATGAA
65 TTTAAAAAAAACA-ACAATAAGA-AATGAAATGTATGATTTGAAACTAATTAATAATAACATGAA
** *
1501458 ATATGTATGATACTAAAAT-AAAAAATAG-ATTAAATTGTAAATAAAA-GTATTTTTAAACACAT
128 ATATGTACAATACTAAAATAAAAAAATAGTATTAAATTGTAAATAAAACG-ATATTTAAACACAT
* * * ** *
1501520 AAATACTTTAGATTAAAATTATTAAATGAATACAATTATTTATCATGGTATTGTCATCAATTTTA
192 AAATACATCAAATTAAAAGGAGTAAATGAATACAATTATTTATCATGGTATTGTCATCAATTTTA
*
1501585 AGTTGGTGTCGAGTTAA
257 AGTTGGCGTCGAGTTAA
1501602 TTTATGGTAC
Statistics
Matches: 234, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
304 1 0.00
305 100 0.43
306 10 0.04
307 63 0.27
308 60 0.26
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (306 bp):
ATACTAGAAACTCCATCACACGAGTATGCATGTGGAAACCATATAGTTAGAACACAAATTTATGT
TTAAAAAAAACAACAATAAGAAATGAAATGTATGATTTGAAACTAATTAATAATAACATGAAATA
TGTACAATACTAAAATAAAAAAATAGTATTAAATTGTAAATAAAACGATATTTAAACACATAAAT
ACATCAAATTAAAAGGAGTAAATGAATACAATTATTTATCATGGTATTGTCATCAATTTTAAGTT
GGCGTCGAGTTAACTTGTAACATCATCTCAATCAACAACTTTATTA
Found at i:1504927 original size:28 final size:28
Alignment explanation
Indices: 1504879--1504936 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1504869 ATAACAATAA
* *
1504879 TATGATATAAAAGCATATATATTTATAT
1 TATGATATAAAAGCACATATATGTATAT
*
1504907 TATGATATTAAAAG-ACGTATATGTATAT
1 TATGATA-TAAAAGCACATATATGTATAT
1504935 TA
1 TA
1504937 GGAATAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.41
Consensus pattern (28 bp):
TATGATATAAAAGCACATATATGTATAT
Found at i:1505461 original size:17 final size:17
Alignment explanation
Indices: 1505435--1505469 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1505425 GATAATAGTG
1505435 AGCCATTAATAAAGATAC
1 AGCCATTAATAAA-ATAC
1505453 AGCCA-TAATAAAATAC
1 AGCCATTAATAAAATAC
1505469 A
1 A
1505470 ATAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 7 0.41
18 5 0.29
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (17 bp):
AGCCATTAATAAAATAC
Found at i:1508800 original size:44 final size:44
Alignment explanation
Indices: 1508607--1508828 Score: 152
Period size: 43 Copynumber: 5.1 Consensus size: 44
1508597 CTTCTTTGAT
* * ** **
1508607 CTGTTTCCCTACTGCTTA-GGGTGATAAGATCTGCAAA-TTCGGC
1 CTGTTTCCCTACTGCTTAGGGGT-TTAAGCTCTATAAATTTCAAC
* * * * * *
1508650 TTGTTACCCTACTGCTTAGGGGGTTAAAGCCCTTTGAA-TTCAAC
1 CTGTTTCCCTACTGCTTA-GGGGTTTAAGCTCTATAAATTTCAAC
* *
1508694 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCTATAAATTT-AAC
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGCTCTATAAATTTCAAC
* * *
1508737 CTGTTAT-CCTACTACTTAGGGGTTTAAGACTC-AT-CATCTTCAAT
1 CTGTT-TCCCTACTGCTTAGGGGTTTAAG-CTCTATAAAT-TTCAAC
* * * *
1508781 CTGTTTCCCTACTGTTTAGGGGGTTGAGATCTATAAATCTTCAAC
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGCTCTATAAAT-TTCAAC
1508826 CTG
1 CTG
1508829 CTTCACTGCA
Statistics
Matches: 140, Mismatches: 29, Indels: 18
0.75 0.16 0.10
Matches are distributed among these distances:
42 2 0.01
43 65 0.46
44 58 0.41
45 15 0.11
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (44 bp):
CTGTTTCCCTACTGCTTAGGGGTTTAAGCTCTATAAATTTCAAC
Found at i:1509000 original size:43 final size:44
Alignment explanation
Indices: 1508919--1509023 Score: 126
Period size: 43 Copynumber: 2.4 Consensus size: 44
1508909 TTTCAGCCTA
* * *
1508919 TTACCCTACTACTTAGGGGGTTAAGGTCTGTAAATTTGGCT-TG
1 TTACCCTACTGCTTAGGGGGTTAAGCTCTGTAAATTTGGATATG
*
1508962 TTACCCTACTGCTTAGGGGGTTAATGCTCAT-T-ATTTTGGATATG
1 TTACCCTACTGCTTAGGGGGTTAA-GCTC-TGTAAATTTGGATATG
*
1509006 TTTCCCTACTGCTTAGGG
1 TTACCCTACTGCTTAGGG
1509024 TGCTAAGATC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
43 30 0.56
44 23 0.43
45 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (44 bp):
TTACCCTACTGCTTAGGGGGTTAAGCTCTGTAAATTTGGATATG
Found at i:1509101 original size:88 final size:87
Alignment explanation
Indices: 1508957--1509121 Score: 215
Period size: 88 Copynumber: 1.9 Consensus size: 87
1508947 TGTAAATTTG
* ** * * *
1508957 GCTTGTTACCCTACTGCTTAGGGGGTTAATGCTCATTATTTTGGATATGTTTCCCTACTGCTTA-
1 GCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTACCTTCGATATATTCCCCTACTGCTTAT
1509021 GGGTGCTAAGATCTCCGAACTCTA
66 GGG-G-TAAGATCTCCGAACTCTA
* * * *
1509045 GCTTGTTACCTTACTGCTTAGGGGGTTAAAGCTCGTTGCCTTCGATCTATTCCCCTACTGCTTAT
1 GCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTACCTTCGATATATTCCCCTACTGCTTAT
1509110 GGGGTAAGATCT
66 GGGGTAAGATCT
1509122 GTGAATTCAC
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
87 8 0.12
88 55 0.83
89 3 0.05
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.37
Consensus pattern (87 bp):
GCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTACCTTCGATATATTCCCCTACTGCTTAT
GGGGTAAGATCTCCGAACTCTA
Found at i:1509236 original size:219 final size:219
Alignment explanation
Indices: 1508985--1509424 Score: 853
Period size: 219 Copynumber: 2.0 Consensus size: 219
1508975 TAGGGGGTTA
* *
1508985 ATGCTCATTATTTTGGATATGTTTCCCTACTGCTTAGGGTGCTAAGATCTCCGAACTCTAGCTTG
1 ATGCTCATTATTTTGGATATGTTTCCCTACTGCTTAGGGTGATAAGATCTACGAACTCTAGCTTG
1509050 TTACCTTACTGCTTAGGGGGTTAAAGCTCGTTGCCTTCGATCTATTCCCCTACTGCTTATGGGGT
66 TTACCTTACTGCTTAGGGGGTTAAAGCTCGTTGCCTTCGATCTATTCCCCTACTGCTTATGGGGT
1509115 AAGATCTGTGAATTCACAGATTCTAGGGACATGACCTGTAGAGTCAGTTCCATGTATTTATGCTT
131 AAGATCTGTGAATTCACAGATTCTAGGGACATGACCTGTAGAGTCAGTTCCATGTATTTATGCTT
1509180 ATGTCAAAGAATTAGGATGTTATG
196 ATGTCAAAGAATTAGGATGTTATG
*
1509204 ATGCTCATTATTTTGGATATGTTTCCCTACTGCTTAGGGTGATAAGATCTACGAACTTTAGCTTG
1 ATGCTCATTATTTTGGATATGTTTCCCTACTGCTTAGGGTGATAAGATCTACGAACTCTAGCTTG
1509269 TTACCTTACTGCTTAGGGGGTTAAAGCTCGTTGCCTTCGATCTATTCCCCTACTGCTTATGGGGT
66 TTACCTTACTGCTTAGGGGGTTAAAGCTCGTTGCCTTCGATCTATTCCCCTACTGCTTATGGGGT
1509334 AAGATCTGTGAATTCACAGATTCTAGGGACATGACCTGTAGAGTCAGTTCCATGTATTTATGCTT
131 AAGATCTGTGAATTCACAGATTCTAGGGACATGACCTGTAGAGTCAGTTCCATGTATTTATGCTT
1509399 ATGTCAAAGAATTAGGATGTTATG
196 ATGTCAAAGAATTAGGATGTTATG
1509423 AT
1 AT
1509425 CAAAATGAAT
Statistics
Matches: 218, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
219 218 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (219 bp):
ATGCTCATTATTTTGGATATGTTTCCCTACTGCTTAGGGTGATAAGATCTACGAACTCTAGCTTG
TTACCTTACTGCTTAGGGGGTTAAAGCTCGTTGCCTTCGATCTATTCCCCTACTGCTTATGGGGT
AAGATCTGTGAATTCACAGATTCTAGGGACATGACCTGTAGAGTCAGTTCCATGTATTTATGCTT
ATGTCAAAGAATTAGGATGTTATG
Found at i:1517177 original size:80 final size:80
Alignment explanation
Indices: 1517083--1517241 Score: 291
Period size: 80 Copynumber: 2.0 Consensus size: 80
1517073 CTAATCCACC
*
1517083 AGCCAATAGACGCGTTAATTGATCCATCATACTCCTTTGGGACTCCAGCATCTGGTCCCTTACAT
1 AGCCAATAGACGCGTTAATTGATCCATCATACTCCTTTGGGACTCCAGCATCTGGTCCCTTAAAT
1517148 CTTGCTGGATTTTGT
66 CTTGCTGGATTTTGT
* *
1517163 AGCCAATAGACGCGTTAATTGATCCATCATACTCCTTTGGGACTCTAGCATCTGGTCCTTTAAAT
1 AGCCAATAGACGCGTTAATTGATCCATCATACTCCTTTGGGACTCCAGCATCTGGTCCCTTAAAT
1517228 CTTGCTGGATTTTG
66 CTTGCTGGATTTTG
1517242 GCCAGCTGTT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.35
Consensus pattern (80 bp):
AGCCAATAGACGCGTTAATTGATCCATCATACTCCTTTGGGACTCCAGCATCTGGTCCCTTAAAT
CTTGCTGGATTTTGT
Found at i:1523799 original size:29 final size:29
Alignment explanation
Indices: 1523750--1523821 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
1523740 TTTAATATAT
* *
1523750 TATTATATT-ATTATATAATAAAGATATTT
1 TATTGTATTAATTATATAAT-AAGATATTA
* *
1523779 TA-TGTTTTAATTATA-ATATAATATATTA
1 TATTGTATTAATTATATA-ATAAGATATTA
1523807 TATTGTATTAATTAT
1 TATTGTATTAATTAT
1523822 TTTATTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
28 14 0.40
29 21 0.60
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
TATTGTATTAATTATATAATAAGATATTA
Found at i:1524471 original size:47 final size:47
Alignment explanation
Indices: 1524420--1524520 Score: 132
Period size: 47 Copynumber: 2.1 Consensus size: 47
1524410 CTATAAGTGT
** * *
1524420 TGTACTGTTACTG-TTACTTCGGTTTAATCCGATAAGGTACTAAGTAC
1 TGTACTGTTACTGTTTACTTCGG-CAAAGCCGATAAGGCACTAAGTAC
* *
1524467 TGTACTGTTACTGTTTACTTCGGCAAAGCCGATGAGGCACTAAGTGC
1 TGTACTGTTACTGTTTACTTCGGCAAAGCCGATAAGGCACTAAGTAC
1524514 TGTACTG
1 TGTACTG
1524521 GTGTGTTGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 38 0.81
48 9 0.19
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (47 bp):
TGTACTGTTACTGTTTACTTCGGCAAAGCCGATAAGGCACTAAGTAC
Found at i:1530362 original size:19 final size:18
Alignment explanation
Indices: 1530338--1530401 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
1530328 GAATAAAGGG
1530338 TAAAAGTTGAATTATAGAT
1 TAAAAG-TGAATTATAGAT
** * *
1530357 TAAAAGAAAATAAAAAGGAT
1 TAAAAGTGAAT-TATA-GAT
1530377 TAAAAGGTGAATTATAGAT
1 TAAAA-GTGAATTATAGAT
1530396 TAAAAG
1 TAAAAG
1530402 AAAATAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
18 4 0.12
19 16 0.47
20 10 0.29
21 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (18 bp):
TAAAAGTGAATTATAGAT
Found at i:1530379 original size:20 final size:20
Alignment explanation
Indices: 1530354--1530421 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
1530344 TTGAATTATA
1530354 GATTAAAAGAAAATAAAAAG
1 GATTAAAAGAAAATAAAAAG
** * *
1530374 GATTAAAAGGTGAAT-TATA-
1 GATTAAAA-GAAAATAAAAAG
1530393 GATTAAAAGAAAATAAAAAG
1 GATTAAAAGAAAATAAAAAG
*
1530413 GACTAAAAG
1 GATTAAAAG
1530422 GACAACTATA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
18 4 0.11
19 10 0.28
20 18 0.50
21 4 0.11
ACGTcount: A:0.62, C:0.01, G:0.18, T:0.19
Consensus pattern (20 bp):
GATTAAAAGAAAATAAAAAG
Found at i:1530382 original size:39 final size:39
Alignment explanation
Indices: 1530338--1530422 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
1530328 GAATAAAGGG
* *
1530338 TAAAAGTTGAATTATAGATTAAAAGAAAATAAAAAGGAT
1 TAAAAGGTGAATTATAGATTAAAAGAAAATAAAAAGGAC
1530377 TAAAAGGTGAATTATAGATTAAAAGAAAATAAAAAGGAC
1 TAAAAGGTGAATTATAGATTAAAAGAAAATAAAAAGGAC
1530416 TAAAAGG
1 TAAAAGG
1530423 ACAACTATAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.59, C:0.01, G:0.18, T:0.22
Consensus pattern (39 bp):
TAAAAGGTGAATTATAGATTAAAAGAAAATAAAAAGGAC
Found at i:1530901 original size:22 final size:22
Alignment explanation
Indices: 1530860--1530906 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1530850 ATATTTGAGT
*
1530860 ATTGGTATTGAATTTAAATTGA
1 ATTGGTATTGAATCTAAATTGA
* * *
1530882 ATTGGTATTTAATCTGAATTTA
1 ATTGGTATTGAATCTAAATTGA
1530904 ATT
1 ATT
1530907 ATTAATTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (22 bp):
ATTGGTATTGAATCTAAATTGA
Found at i:1532716 original size:15 final size:16
Alignment explanation
Indices: 1532678--1532723 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1532668 TCTACACTTA
1532678 ATTTATCAATACTTATT
1 ATTT-TCAATACTTATT
*
1532695 ATTTTCAATATTTATT
1 ATTTTCAATACTTATT
*
1532711 -TTTTCAACACTTA
1 ATTTTCAATACTTA
1532724 ATTTTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 11 0.42
16 11 0.42
17 4 0.15
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTCAATACTTATT
Found at i:1532727 original size:16 final size:16
Alignment explanation
Indices: 1532671--1532730 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
1532661 TTAAAATTCT
*
1532671 ACACTTAA-TTTATCA
1 ACACTTAATTTTTTCA
*
1532686 ATACTT-ATTATTTTCA
1 ACACTTAATT-TTTTCA
* *
1532702 ATA-TTTATTTTTTCA
1 ACACTTAATTTTTTCA
1532717 ACACTTAATTTTTT
1 ACACTTAATTTTTT
1532731 AATCTACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.43
16 20 0.54
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (16 bp):
ACACTTAATTTTTTCA
Found at i:1532728 original size:15 final size:15
Alignment explanation
Indices: 1532671--1532729 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
1532661 TTAAAATTCT
*
1532671 ACACTTAATTTATCA
1 ACACTTAATTTTTCA
* *
1532686 ATACTTATTATTTTCA
1 ACACTTAAT-TTTTCA
* * *
1532702 ATATTTATTTTTTCA
1 ACACTTAATTTTTCA
1532717 ACACTTAATTTTT
1 ACACTTAATTTTT
1532730 TAATCTACCA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 23 0.64
16 13 0.36
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (15 bp):
ACACTTAATTTTTCA
Found at i:1535329 original size:46 final size:45
Alignment explanation
Indices: 1535273--1535446 Score: 197
Period size: 46 Copynumber: 3.8 Consensus size: 45
1535263 ATCTTGTAGT
1535273 CGATGCATGTCCCAGACATGTCTTATACTAGCTTACGTCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTATACTAGCTT-CGTCTCGAGGC
* * * **
1535319 CGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATAC
1 CGATGCATGTCCCAGACATGTCTTATACTAGC-TTCGTCTCGAGGC
* * * * *
1535365 CGATGACATGTCCCAAACATGGTCTTATACTGGCTCTCATAAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTATACTAGCT-TCGT-CTCGAGGC
1535413 CGATGCATGTCCCAGACATGTCTTATACTAGCTT
1 CGATGCATGTCCCAGACATGTCTTATACTAGCTT
1535447 ATAATAACCC
Statistics
Matches: 106, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
45 1 0.01
46 57 0.54
47 27 0.25
48 20 0.19
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTATACTAGCTTCGTCTCGAGGC
Found at i:1536444 original size:20 final size:20
Alignment explanation
Indices: 1536419--1536457 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1536409 CTCTTTGCCG
* *
1536419 AAACTTTTTCCTTTTTCTTC
1 AAACTTTTCCCTGTTTCTTC
1536439 AAACTTTTCCCTGTTTCTT
1 AAACTTTTCCCTGTTTCTT
1536458 TTATTCATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.26, G:0.03, T:0.56
Consensus pattern (20 bp):
AAACTTTTCCCTGTTTCTTC
Found at i:1539784 original size:46 final size:46
Alignment explanation
Indices: 1539717--1539896 Score: 274
Period size: 46 Copynumber: 3.9 Consensus size: 46
1539707 TGTGCTTTCT
1539717 GATATGAAAAT-TGTAAGACCATGGTTGAAAGATACCATGGCAACAG
1 GATAT-AAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACAG
*
1539763 GATATAAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACAT
1 GATATAAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACAG
* *
1539809 GATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAG
1 GATATAAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACAG
* * *
1539855 GATATAAAATGA-GTAAGACCATAGTTGAAAGACACTATGGCA
1 GATATAAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCA
1539897 TCATGTCAAA
Statistics
Matches: 123, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 5 0.04
46 118 0.96
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
GATATAAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACAG
Found at i:1539873 original size:92 final size:92
Alignment explanation
Indices: 1539716--1539901 Score: 304
Period size: 92 Copynumber: 2.0 Consensus size: 92
1539706 GTGTGCTTTC
1539716 TGATATGAAAATTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATATGTAAGA
1 TGATATGAAAATTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATATGTAAGA
* *
1539781 CCATGGTTGAAAGATACCATGGCAACA
66 CCATAGTTGAAAGACACCATGGCAACA
1539808 TGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGA-GTAA
1 TGATATGAAAAT-TGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAAT-ATGTAA
* *
1539871 GACCATAGTTGAAAGACACTATGGCATCA
64 GACCATAGTTGAAAGACACCATGGCAACA
1539900 TG
1 TG
1539902 TCAAAGATAA
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
91 4 0.05
92 83 0.94
93 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (92 bp):
TGATATGAAAATTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATATGTAAGA
CCATAGTTGAAAGACACCATGGCAACA
Found at i:1540203 original size:16 final size:17
Alignment explanation
Indices: 1540182--1540214 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1540172 ATGATGGAGC
1540182 ATGAAAT-ATTCATATA
1 ATGAAATGATTCATATA
*
1540198 ATGAAATGATTGATATA
1 ATGAAATGATTCATATA
1540215 TACTTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTCATATA
Found at i:1547339 original size:19 final size:21
Alignment explanation
Indices: 1547309--1547347 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1547299 CTCTTTGCCG
1547309 AAACTTTATCCCT-TTTCTTC
1 AAACTTTATCCCTGTTTCTTC
1547329 AAACTTT-TCCCTGTTTCTT
1 AAACTTTATCCCTGTTTCTT
1547348 TTATTCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.18, C:0.28, G:0.03, T:0.51
Consensus pattern (21 bp):
AAACTTTATCCCTGTTTCTTC
Found at i:1550977 original size:14 final size:16
Alignment explanation
Indices: 1550958--1550991 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1550948 ATATTTATTT
1550958 TATTTA-TAATTTA-A
1 TATTTAGTAATTTATA
1550972 TATTTAGTAATTTATA
1 TATTTAGTAATTTATA
1550988 TATT
1 TATT
1550992 AATTATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 7 0.39
16 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TATTTAGTAATTTATA
Found at i:1562655 original size:108 final size:105
Alignment explanation
Indices: 1562416--1562632 Score: 353
Period size: 108 Copynumber: 2.0 Consensus size: 105
1562406 GACTGAATAA
1562416 AAACAGAAGTAATGCATTTCATAATCCCCTCAACCCATTTTGTAGCAAAACCCATGCAAATCATT
1 AAACAGAAGTAATGC---TCATAATCCCCTCAACCCATTTTGTAGCAAAACCCATGCAAATCATT
1562481 ATTCCTTTATGAAACTCTATTTAACCCTATCGTAAGCTTTGCT
63 ATTCCTTTATGAAACTCTATTTAACCCTATCGTAAGCTTTGCT
* *
1562524 AAACAGAAGTAATGCATTTCATAATCCCCTTAACCCATTTTGTAGCAAAACCCATGCGAATCATT
1 AAACAGAAGTAATGC---TCATAATCCCCTCAACCCATTTTGTAGCAAAACCCATGCAAATCATT
1562589 ATTTCCTTTATGAAACTCTATTTAACCCTATCGTAAGCTTTGCT
63 A-TTCCTTTATGAAACTCTATTTAACCCTATCGTAAGCTTTGCT
1562633 CATGTCCAAT
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
108 64 0.60
109 42 0.40
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (105 bp):
AAACAGAAGTAATGCTCATAATCCCCTCAACCCATTTTGTAGCAAAACCCATGCAAATCATTATT
CCTTTATGAAACTCTATTTAACCCTATCGTAAGCTTTGCT
Found at i:1565125 original size:20 final size:20
Alignment explanation
Indices: 1565102--1565139 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1565092 AATAGATAAG
1565102 TATAATAA-AACTAAGAGAAT
1 TATAATAAGAA-TAAGAGAAT
*
1565122 TATAGTAAGAATAAGAGA
1 TATAATAAGAATAAGAGA
1565140 GAAAAGTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.58, C:0.03, G:0.16, T:0.24
Consensus pattern (20 bp):
TATAATAAGAATAAGAGAAT
Found at i:1572213 original size:21 final size:22
Alignment explanation
Indices: 1572173--1572214 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1572163 GTCAAATTGA
1572173 CCACACGGGCGTGTTGCCCCTT
1 CCACACGGGCGTGTTGCCCCTT
1572195 CCACACGGGCGTG-TGCCCCT
1 CCACACGGGCGTGTTGCCCCT
1572215 ATGTCAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.10, C:0.43, G:0.29, T:0.19
Consensus pattern (22 bp):
CCACACGGGCGTGTTGCCCCTT
Found at i:1575494 original size:30 final size:31
Alignment explanation
Indices: 1575460--1575528 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
1575450 CTTGTCACTT
* * *
1575460 GTAGCCGAAG-TATCACTATTCACTGATCAG
1 GTAGCCGAAGTTACCACTATTCACTAATCAA
* * *
1575490 GTAGCCGGAGTTACCATTTTTCACTAATCAA
1 GTAGCCGAAGTTACCACTATTCACTAATCAA
1575521 GTAGCCGA
1 GTAGCCGA
1575529 TGATCAAGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGTTACCACTATTCACTAATCAA
Found at i:1575571 original size:31 final size:31
Alignment explanation
Indices: 1575529--1575587 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1575519 AAGTAGCCGA
*
1575529 TGATCAAGTAGCCGAAGCTACCACTTTTCAT
1 TGATCAAGTAGCCGAAGCTACAACTTTTCAT
* *
1575560 TGATCAGGTAGCTGAAGCTACAACTTTT
1 TGATCAAGTAGCCGAAGCTACAACTTTT
1575588 TACTTGCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (31 bp):
TGATCAAGTAGCCGAAGCTACAACTTTTCAT
Found at i:1575656 original size:50 final size:50
Alignment explanation
Indices: 1575595--1575743 Score: 271
Period size: 50 Copynumber: 3.0 Consensus size: 50
1575585 TTTTACTTGC
1575595 CATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
*
1575645 CATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTT
1 CATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
* *
1575695 CACTTGTCATTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTT
1 CATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTT
1575744 GTTGCCATGG
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 95 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (50 bp):
CATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
Found at i:1580294 original size:21 final size:22
Alignment explanation
Indices: 1580254--1580294 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1580244 TTCCAAATAA
* *
1580254 AACATTATATCATTTCTAATTC
1 AACATTATATCAATTATAATTC
1580276 AACATT-TATCAATTATAAT
1 AACATTATATCAATTATAAT
1580295 CGGGCATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (22 bp):
AACATTATATCAATTATAATTC
Found at i:1586082 original size:46 final size:46
Alignment explanation
Indices: 1585986--1586082 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 46
1585976 CAAGTGCTAG
* * * *
1585986 TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCCAG
1 TGTAAAACATGCCTAGGACATGCATCGGCCTCGAGATGTAAGCCAA
* *
1586032 TGTAAAACATGCCTAGGACATGCGTCGG-CTACGAGATG-ATAGTCAA
1 TGTAAAACATGCCTAGGACATGCATCGGCCT-CGAGATGTA-AGCCAA
1586078 TGTAA
1 TGTAA
1586083 GACCATGTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
45 3 0.07
46 40 0.93
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
TGTAAAACATGCCTAGGACATGCATCGGCCTCGAGATGTAAGCCAA
Found at i:1593300 original size:35 final size:35
Alignment explanation
Indices: 1593249--1593319 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1593239 TGACCCGAAT
*
1593249 TCTAAGAGATTACTTGCATGTCAAGTTAAACAAAA
1 TCTAAGAGATTACTTGCAAGTCAAGTTAAACAAAA
*
1593284 TCTAAGAGATTGCTTGCAAGTCAAGTTAAACAAAA
1 TCTAAGAGATTACTTGCAAGTCAAGTTAAACAAAA
1593319 T
1 T
1593320 ATATTTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.28
Consensus pattern (35 bp):
TCTAAGAGATTACTTGCAAGTCAAGTTAAACAAAA
Found at i:1593375 original size:24 final size:24
Alignment explanation
Indices: 1593337--1593383 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1593327 CTTTCTAGAA
*
1593337 TATTTAGTAGTATAATATATTTGG
1 TATTTAGTAGCATAATATATTTGG
*
1593361 TATTTATTAGCATAATATATTTG
1 TATTTAGTAGCATAATATATTTG
1593384 ATCTACGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.51
Consensus pattern (24 bp):
TATTTAGTAGCATAATATATTTGG
Found at i:1598594 original size:8 final size:8
Alignment explanation
Indices: 1598577--1598606 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1598567 TTGCAAATAT
*
1598577 ACATTGTA
1 ACATTCTA
1598585 ACATTCTA
1 ACATTCTA
1598593 ACATTCTA
1 ACATTCTA
1598601 ACATTC
1 ACATTC
1598607 CATGGCAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (8 bp):
ACATTCTA
Found at i:1601861 original size:61 final size:58
Alignment explanation
Indices: 1601796--1601921 Score: 164
Period size: 61 Copynumber: 2.1 Consensus size: 58
1601786 TTTTAATAAG
* * *
1601796 ATTATTATTAAATATATTTTAATAAAAATAAAAATAAATAATTTAATCATATT-TTAACATA
1 ATTATTATTAAATACAATTTAAT-AAAAT---AATAAATAATTTAATAATATTCTTAACATA
* *
1601857 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAATATTCTTAATATA
1 ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAATATTCTTAACATA
1601915 ATTATTA
1 ATTATTA
1601922 ATAATATTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
57 19 0.32
58 14 0.24
60 5 0.08
61 21 0.36
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAATATTCTTAACATA
Found at i:1601912 original size:24 final size:24
Alignment explanation
Indices: 1601884--1601929 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1601874 TTTAATAAAA
1601884 TAATATATAAT-TTAATAATATTCT
1 TAATATA-AATATTAATAATATTCT
*
1601908 TAATATAATTATTAATAATATT
1 TAATATAAATATTAATAATATT
1601930 ATATAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATATAAATATTAATAATATTCT
Found at i:1602226 original size:21 final size:21
Alignment explanation
Indices: 1602200--1602240 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1602190 TTTTAGTGAA
1602200 ATAAAAA-CATTCAAATTTTAC
1 ATAAAAATCATT-AAATTTTAC
*
1602221 ATAAAAATTATTAAATTTTA
1 ATAAAAATCATTAAATTTTA
1602241 GTAACATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAAATCATTAAATTTTAC
Found at i:1602381 original size:35 final size:35
Alignment explanation
Indices: 1602334--1602405 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
1602324 ATGTTATTCA
*
1602334 AAAACTCGTAGTTCTTTATGTTATTCAAAAATTTG
1 AAAACTCATAGTTCTTTATGTTATTCAAAAATTTG
1602369 AAAACTCATAGTTCTTTATGTTATTCAAAAATTTG
1 AAAACTCATAGTTCTTTATGTTATTCAAAAATTTG
1602404 AA
1 AA
1602406 GAAAACTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.42
Consensus pattern (35 bp):
AAAACTCATAGTTCTTTATGTTATTCAAAAATTTG
Found at i:1605770 original size:5 final size:6
Alignment explanation
Indices: 1605756--1605780 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1605746 CCTATCTCTG
1605756 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
1605781 GCTCAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:1609339 original size:18 final size:19
Alignment explanation
Indices: 1609318--1609354 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1609308 TAAATAAATT
1609318 TCAA-ATATAAAATATTCA
1 TCAATATATAAAATATTCA
1609336 TCAATTATATAAAATATTC
1 TCAA-TATATAAAATATTC
1609355 TTTAATAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (19 bp):
TCAATATATAAAATATTCA
Found at i:1611010 original size:25 final size:25
Alignment explanation
Indices: 1610982--1611046 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
1610972 TCATATACAT
1610982 GTATGCTCATACGAGTTATAAATCG
1 GTATGCTCATACGAGTTATAAATCG
* * * *
1611007 GTATGCTC-TCACGAGTTGTGATTTG
1 GTATGCTCAT-ACGAGTTATAAATCG
*
1611032 GTAAGCTCATACGAG
1 GTATGCTCATACGAG
1611047 CTGGGAATAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 1 0.03
25 31 0.94
26 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (25 bp):
GTATGCTCATACGAGTTATAAATCG
Found at i:1611059 original size:25 final size:25
Alignment explanation
Indices: 1611031--1611099 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 25
1611021 GTTGTGATTT
* * **
1611031 GGTAAGCTCATACGAGCTGGGAATA
1 GGTAAACTCATACAAGCTGCAAATA
* *
1611056 GGTAAACTCTTACAAGCTGCAAATC
1 GGTAAACTCATACAAGCTGCAAATA
1611081 GGTAAACTCATACAAGCTG
1 GGTAAACTCATACAAGCTG
1611100 TGGTGTGTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (25 bp):
GGTAAACTCATACAAGCTGCAAATA
Found at i:1620058 original size:14 final size:14
Alignment explanation
Indices: 1620039--1620066 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1620029 TGGAAAAAGT
1620039 ATAATTTTGATTAA
1 ATAATTTTGATTAA
1620053 ATAATTTTGATTAA
1 ATAATTTTGATTAA
1620067 GTGTTGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAATTTTGATTAA
Found at i:1621106 original size:21 final size:21
Alignment explanation
Indices: 1621068--1621107 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1621058 AATTTACTCT
*
1621068 CCTTTTATGCTTCTCTCTCAC
1 CCTTTTATGATTCTCTCTCAC
1621089 CCTTTTA-GATTCTCCTCTC
1 CCTTTTATGATTCT-CTCTC
1621108 CTCAAACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.38, G:0.05, T:0.47
Consensus pattern (21 bp):
CCTTTTATGATTCTCTCTCAC
Found at i:1628364 original size:18 final size:19
Alignment explanation
Indices: 1628343--1628381 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1628333 AAGAATCAAG
* *
1628343 TTATTTGAGTTAA-TCGAA
1 TTATTCGAGTCAACTCGAA
1628361 TTATTCGAGTCAACTCGAA
1 TTATTCGAGTCAACTCGAA
1628380 TT
1 TT
1628382 TTTTTTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (19 bp):
TTATTCGAGTCAACTCGAA
Found at i:1639617 original size:16 final size:16
Alignment explanation
Indices: 1639598--1639643 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1639588 GAGTGTGTTA
1639598 AAATATATATTTTTAT
1 AAATATATATTTTTAT
* *
1639614 AAATATTTATATTT-T
1 AAATATATATTTTTAT
*
1639629 AAATATATAATTTTA
1 AAATATATATTTTTA
1639644 CCAAATATCC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATATATTTTTAT
Found at i:1646297 original size:23 final size:23
Alignment explanation
Indices: 1646256--1646316 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
1646246 ATCATGTAAA
* *
1646256 ATTCAAAATATTTATAAAATAT-T
1 ATTCAAAA-AATTATAAAACATAT
*
1646279 TTTCTAAAAAATTATAAAACATAT
1 ATTC-AAAAAATTATAAAACATAT
1646303 ATTCAAAAAATTAT
1 ATTCAAAAAATTAT
1646317 TTTTAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 24 0.75
24 8 0.25
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
ATTCAAAAAATTATAAAACATAT
Found at i:1648194 original size:24 final size:24
Alignment explanation
Indices: 1648167--1648222 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
1648157 AAATTACATA
*
1648167 AATATATATTGAAAATAGATAT-AT
1 AATATATATTGAAAA-ACATATAAT
*
1648191 AATA-ATATTTAAAAACATATACAT
1 AATATATATTGAAAAACATATA-AT
1648215 AATATATA
1 AATATATA
1648223 CATAACATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 9 0.33
24 10 0.37
25 3 0.11
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (24 bp):
AATATATATTGAAAAACATATAAT
Found at i:1648290 original size:15 final size:15
Alignment explanation
Indices: 1648247--1648290 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1648237 CAAAATATAC
1648247 ACATAATAT-ATTAAA
1 ACATAATATGA-TAAA
*
1648262 ACATATACATGATAAA
1 ACATA-ATATGATAAA
1648278 ACATAATATGATA
1 ACATAATATGATA
1648291 TTTACAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
16 12 0.48
17 1 0.04
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.30
Consensus pattern (15 bp):
ACATAATATGATAAA
Found at i:1650059 original size:45 final size:45
Alignment explanation
Indices: 1650010--1650113 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 45
1650000 CCTCCTGTTG
* * * *
1650010 CTTCAATCTGCTCCA-TTGTAGCTTCAGAGAAATAAGATTTGCT-A
1 CTTCAATCTGCTCCACTTGCAACTTCAAAGAAATAAGACTTG-TGA
* *
1650054 TCTTCAGTCTGCTCCACTTGCAACTTCAAAGAGATAAGACTTGTGA
1 -CTTCAATCTGCTCCACTTGCAACTTCAAAGAAATAAGACTTGTGA
*
1650100 CTTCAATCTACTCC
1 CTTCAATCTGCTCC
1650114 GTTGAAACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
45 27 0.55
46 22 0.45
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTTGCAACTTCAAAGAAATAAGACTTGTGA
Found at i:1650329 original size:43 final size:41
Alignment explanation
Indices: 1650192--1650344 Score: 110
Period size: 43 Copynumber: 3.6 Consensus size: 41
1650182 ATTTTCAGCC
* * **
1650192 TGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCATTGCT
1 TGTTACCCTACTGCTTAGGGGTTTAAGGTTTGAAAT--TTGCT
* * * * ** *
1650235 CTGTTTCCCTACTGCTGAGGGGTTT-AGATCTGTAAATTCAACC
1 -TGTTACCCTACTGCTTAGGGGTTTAAGGTTTG-AAATT-TGCT
*
1650278 TATTACCCTACTGCTTAGGGGTTTAAGGTTTGAAAATTTGGCT
1 TGTTACCCTACTGCTTAGGGGTTTAAGGTTTG-AAATTT-GCT
*
1650321 TGTTACCCTATTGCTTAGAGGGTT
1 TGTTACCCTACTGCTTAG-GGGTT
1650345 GAAGCCCATC
Statistics
Matches: 82, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
42 22 0.27
43 32 0.39
44 28 0.34
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
TGTTACCCTACTGCTTAGGGGTTTAAGGTTTGAAATTTGCT
Found at i:1650344 original size:86 final size:85
Alignment explanation
Indices: 1650185--1650344 Score: 189
Period size: 86 Copynumber: 1.9 Consensus size: 85
1650175 ACATTTGATT
* * ** *
1650185 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCATTGCTCTGTTTCCCTACTGC
1 TTCAACCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGAAAT-ATTGCTCTGTTACCCTACTGC
1650250 TGAGGGGTTTAGATCTGTAAA
65 TGAGGGGTTTAGATCTGTAAA
* * *
1650271 TTCAACCTATTACCCTACTGCTTAGGGGTTTAAGGTTTGAAA-ATTTGGCT-TGTTACCCTATTG
1 TTCAACCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGAAATA-TT-GCTCTGTTACCCTACTG
*
1650334 CTTAGAGGGTT
64 CTGAG-GGGTT
1650345 GAAGCCCATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
84 1 0.02
85 17 0.27
86 44 0.71
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (85 bp):
TTCAACCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGAAATATTGCTCTGTTACCCTACTGCT
GAGGGGTTTAGATCTGTAAA
Done.