Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold407
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: 4418299
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 127125 characters in sequence are not A, C, G, or T
File 9 of 28
Found at i:1262852 original size:5 final size:5
Alignment explanation
Indices: 1262842--1262912 Score: 58
Period size: 5 Copynumber: 14.6 Consensus size: 5
1262832 GCATCCTCCG
* * * *
1262842 CAAAA CAAAA C-AAA -AAAA CAAAA AAATAA AAAAA CCAAA -AAAA TAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAA-AA CAAAA CAAAA CAAAA CAAAA
* *
1262890 CAAAA CAAAA GAAAA AAAAA CAA
1 CAAAA CAAAA CAAAA CAAAA CAA
1262913 CAAAAAGGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
4 9 0.17
5 40 0.74
6 5 0.09
ACGTcount: A:0.83, C:0.13, G:0.01, T:0.03
Consensus pattern (5 bp):
CAAAA
Found at i:1262861 original size:8 final size:8
Alignment explanation
Indices: 1262848--1262918 Score: 72
Period size: 8 Copynumber: 8.5 Consensus size: 8
1262838 TCCGCAAAAC
1262848 AAAACAAA
1 AAAACAAA
1262856 AAAACAAA
1 AAAACAAA
*
1262864 AAAATAAA
1 AAAACAAA
1262872 AAAACCAAA
1 AAAA-CAAA
*
1262881 AAAATAAAA
1 AAAA-CAAA
1262890 CAAAACAAA
1 -AAAACAAA
*
1262899 AGAA-AAA
1 AAAACAAA
1262906 AAAACAACA
1 AAAACAA-A
1262915 AAAA
1 AAAA
1262919 GGGTCCGAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
7 6 0.12
8 24 0.46
9 18 0.35
10 4 0.08
ACGTcount: A:0.85, C:0.11, G:0.01, T:0.03
Consensus pattern (8 bp):
AAAACAAA
Found at i:1264352 original size:28 final size:27
Alignment explanation
Indices: 1264306--1264381 Score: 98
Period size: 28 Copynumber: 2.8 Consensus size: 27
1264296 AAACACTCCT
*
1264306 CACCCTTTTAAGCCTATGACTCCGTAG
1 CACCCTTTTAAGCCCATGACTCCGTAG
* * *
1264333 CAACCTTTTTAAGCCCATGACTCTGTGG
1 C-ACCCTTTTAAGCCCATGACTCCGTAG
*
1264361 CGCCCTTTTAAGCCCATGACT
1 CACCCTTTTAAGCCCATGACT
1264382 TTGTGGCATC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 19 0.45
28 23 0.55
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30
Consensus pattern (27 bp):
CACCCTTTTAAGCCCATGACTCCGTAG
Found at i:1264396 original size:27 final size:27
Alignment explanation
Indices: 1264306--1264399 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
1264296 AAACACTCCT
* * * *
1264306 CACCCTTTTAAGCCTATGACTCCGTAG
1 CACCTTTTTAAGCCCATGACTCTGTGG
1264333 CAACCTTTTTAAGCCCATGACTCTGTGG
1 C-ACCTTTTTAAGCCCATGACTCTGTGG
* * *
1264361 CGCCCTTTTAAGCCCATGACTTTGTGG
1 CACCTTTTTAAGCCCATGACTCTGTGG
*
1264388 CATCTTTTTAAG
1 CACCTTTTTAAG
1264400 TCCACAACTT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 33 0.59
28 23 0.41
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (27 bp):
CACCTTTTTAAGCCCATGACTCTGTGG
Found at i:1264423 original size:27 final size:27
Alignment explanation
Indices: 1264306--1264423 Score: 76
Period size: 27 Copynumber: 4.3 Consensus size: 27
1264296 AAACACTCCT
* ** * *
1264306 CACCCTTTTAAGCCTATGACTCCGTAG
1 CACCCTTTTAAGCCCACAACTTCGTGG
* **
1264333 CAACCTTTTTAAGCCCATGAC-TCTGTGG
1 C-ACCCTTTTAAGCCCACAACTTC-GTGG
* ** *
1264361 CGCCCTTTTAAGCCCATGACTTTGTGG
1 CACCCTTTTAAGCCCACAACTTCGTGG
* * *
1264388 CATCTTTTTAAGTCCACAACTTCGTGG
1 CACCCTTTTAAGCCCACAACTTCGTGG
1264415 CACCCTTTT
1 CACCCTTTT
1264424 TCCTTTTAAG
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
27 50 0.69
28 22 0.31
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (27 bp):
CACCCTTTTAAGCCCACAACTTCGTGG
Found at i:1264463 original size:32 final size:32
Alignment explanation
Indices: 1264393--1264508 Score: 160
Period size: 32 Copynumber: 3.6 Consensus size: 32
1264383 TGTGGCATCT
* *
1264393 TTTTAAGTCCACAACTTCGTGGCACCCTTTTTCC
1 TTTTAAGTCCACAACTCCATGGCA-CC-TTTTCC
* * *
1264427 TTTTAAGTCTATAACTCCATGGCACCTTTTCT
1 TTTTAAGTCCACAACTCCATGGCACCTTTTCC
*
1264459 TTTTAAGTCCACAACTCCATGGCACATTTTCC
1 TTTTAAGTCCACAACTCCATGGCACCTTTTCC
1264491 TTTTAAGTCCACAACTCC
1 TTTTAAGTCCACAACTCC
1264509 GTGGTACCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
32 51 0.70
33 2 0.03
34 20 0.27
ACGTcount: A:0.22, C:0.30, G:0.09, T:0.38
Consensus pattern (32 bp):
TTTTAAGTCCACAACTCCATGGCACCTTTTCC
Found at i:1264683 original size:49 final size:51
Alignment explanation
Indices: 1264616--1264740 Score: 164
Period size: 49 Copynumber: 2.5 Consensus size: 51
1264606 CATCTACTTC
* *
1264616 TAAGCCCAATATCACTGGCCTTGAATCAACATATTGGCA-CCT-TCATCTT
1 TAAGACCAATGTCACTGGCCTTGAATCAACATATTGGCATCCTCTCATCTT
* *
1264665 TAAGACCAATGTCGCTGGCCTTGAATCAACATATTGGCATTCTTCTCATCTT
1 TAAGACCAATGTCACTGGCCTTGAATCAACATATTGGCA-TCCTCTCATCTT
* * *
1264717 CAAGTCCAATGTCACTAGCCTTGA
1 TAAGACCAATGTCACTGGCCTTGA
1264741 GTCAGTACAT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
49 36 0.55
51 2 0.03
52 27 0.42
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (51 bp):
TAAGACCAATGTCACTGGCCTTGAATCAACATATTGGCATCCTCTCATCTT
Found at i:1264753 original size:52 final size:52
Alignment explanation
Indices: 1264612--1264756 Score: 143
Period size: 52 Copynumber: 2.8 Consensus size: 52
1264602 ATGGCATCTA
* * * * *
1264612 CTTCTAAGCCCAATATCACTGGCCTTGAATCAACATATTGGCA--CCT-TCAT
1 CTTC-AAGACCAATGTCACTAGCCTTGAATCAACACATTGGCATTCTTCTCAT
* * * *
1264662 CTTTAAGACCAATGTCGCTGGCCTTGAATCAACATATTGGCATTCTTCTCAT
1 CTTCAAGACCAATGTCACTAGCCTTGAATCAACACATTGGCATTCTTCTCAT
* * **
1264714 CTTCAAGTCCAATGTCACTAGCCTTGAGTCAGTACATTGGCAT
1 CTTCAAGACCAATGTCACTAGCCTTGAATCAACACATTGGCAT
1264757 AAGCCCAATA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 35 0.44
50 3 0.04
51 2 0.03
52 39 0.49
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (52 bp):
CTTCAAGACCAATGTCACTAGCCTTGAATCAACACATTGGCATTCTTCTCAT
Found at i:1264825 original size:91 final size:90
Alignment explanation
Indices: 1264665--1264847 Score: 235
Period size: 91 Copynumber: 2.0 Consensus size: 90
1264655 CCTTCATCTT
* * * *
1264665 TAAGACCAATGTCGCTGGCCTTGAATCAACATATTGGCATTCTTCTCATCTTCAAGTCCAATGTC
1 TAAGACCAATATCGCTGGCCTTGAATCAACACATTGGCATTCTTCT-ATCTTCAAGCCCAATATC
* **
1264730 ACTAGCCTTGAGTCAGTACATTGGCA
65 ACTAGCCTTGAATCAACACATTGGCA
* *
1264756 TAAGCCCAATATCGCTGGCCTTGAAT-AAGCACATTGGCACCTTCTTCT-TTTTCAAGCCCAATA
1 TAAGACCAATATCGCTGGCCTTGAATCAA-CACATTGGCA--TTCTTCTATCTTCAAGCCCAATA
1264819 TCACTAGCCTTGAATCAACACATTGGCA
63 TCACTAGCCTTGAATCAACACATTGGCA
1264847 T
1 T
1264848 TTTTCTCATC
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
90 2 0.03
91 71 0.89
93 7 0.09
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (90 bp):
TAAGACCAATATCGCTGGCCTTGAATCAACACATTGGCATTCTTCTATCTTCAAGCCCAATATCA
CTAGCCTTGAATCAACACATTGGCA
Found at i:1264841 original size:52 final size:52
Alignment explanation
Indices: 1264757--1264887 Score: 160
Period size: 52 Copynumber: 2.5 Consensus size: 52
1264747 ACATTGGCAT
* *
1264757 AAGCCCAATATCGCTGGCCTTGAAT-AAGCACATTGGCACCTTCTTCT-TTTTC
1 AAGCCCAATATCGCTAGCCTTGAATCAAGCACATTGGCA--TTCTTCTATCTTC
* *
1264809 AAGCCCAATATCACTAGCCTTGAATCAA-CACATTGGCATTTTTCTCATCTTC
1 AAGCCCAATATCGCTAGCCTTGAATCAAGCACATTGGCATTCTTCT-ATCTTC
* *
1264861 AAGTCCAATGTCGCTAGCCTTGAATCA
1 AAGCCCAATATCGCTAGCCTTGAATCA
1264888 GTATATTGGC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 6 0.09
52 61 0.88
53 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (52 bp):
AAGCCCAATATCGCTAGCCTTGAATCAAGCACATTGGCATTCTTCTATCTTC
Found at i:1264871 original size:143 final size:141
Alignment explanation
Indices: 1264616--1265015 Score: 475
Period size: 143 Copynumber: 2.8 Consensus size: 141
1264606 CATCTACTTC
* * * * *
1264616 TAAGCCCAATATCACTGGCCTTGAATCAA-CATATTGGCACCTTCATCTTT-AAGACCAATGTCG
1 TAAGCCCAATATCGCTGGCCTTGAAT-AAGCATATTGGCACCTTCTTCTTTCAAGCCCAATATCA
* *
1264679 CTGGCCTTGAATCAACATATTGGCATTCTTCTCATCTTCAAGTCCAATGTCACTAGCCTTGAGTC
65 CTGGCCTTGAATCAACACATTGGCATTCTTCTCATCTTCAAGTCCAATGTCACTAGCCTTGAATC
1264744 AGTACATTGGCA
130 AGTACATTGGCA
*
1264756 TAAGCCCAATATCGCTGGCCTTGAATAAGCACATTGGCACCTTCTTCTTTTTCAAGCCCAATATC
1 TAAGCCCAATATCGCTGGCCTTGAATAAGCATATTGGCACCTTCTTC--TTTCAAGCCCAATATC
* * *
1264821 ACTAGCCTTGAATCAACACATTGGCATTTTTCTCATCTTCAAGTCCAATGTCGCTAGCCTTGAAT
64 ACTGGCCTTGAATCAACACATTGGCATTCTTCTCATCTTCAAGTCCAATGTCACTAGCCTTGAAT
*
1264886 CAGTATATTGGCA
129 CAGTACATTGGCA
* * ** * * * * * * *
1264899 CAAACTTAATATCGCTAGTCTTGAATCAGCATATTGGCATCTT-TAACATTCCTAAGCCCAATTT
1 TAAGCCCAATATCGCTGGCCTTGAATAAGCATATTGGCACCTTCT-TC-TTTC-AAGCCCAA-TA
* * *
1264963 TGA-TGGCCTTGAATCAACACATTGGCATTCTTCTCATCTTTAAGTCTAATGTC
62 TCACTGGCCTTGAATCAACACATTGGCATTCTTCTCATCTTCAAGTCCAATGTC
1265016 GCTGACTGTG
Statistics
Matches: 223, Mismatches: 30, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
139 2 0.01
140 41 0.18
142 7 0.03
143 170 0.76
144 3 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (141 bp):
TAAGCCCAATATCGCTGGCCTTGAATAAGCATATTGGCACCTTCTTCTTTCAAGCCCAATATCAC
TGGCCTTGAATCAACACATTGGCATTCTTCTCATCTTCAAGTCCAATGTCACTAGCCTTGAATCA
GTACATTGGCA
Found at i:1265837 original size:19 final size:19
Alignment explanation
Indices: 1265789--1265840 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
1265779 TAAAAAATAA
1265789 ATGTATCGATACACAAGCC
1 ATGTATCGATACACAAGCC
* **
1265808 ATGTAATCGATACATAAGTT
1 ATGT-ATCGATACACAAGCC
*
1265828 TTGTATCGATACA
1 ATGTATCGATACA
1265841 AAGATGCCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACACAAGCC
Found at i:1270345 original size:61 final size:59
Alignment explanation
Indices: 1270217--1270709 Score: 373
Period size: 61 Copynumber: 8.5 Consensus size: 59
1270207 AGTTCAAATG
* * * *
1270217 TGCTGATTTAAGGCTAGTGACATTGGACTTAAAAGATGAAAAGGATGA-AAAGAGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGATGAAAA--ATGATAAAG-GTGCCAATA
* *
1270279 TGCTGATTCAAGGTCAACGATATTGGACTTAAAGAGATGAAAAATGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-AGATGAAAAATGATAAAGGTGCCAATA
* * * *
1270340 TGCTGATTCACGACCAGCGATATTGGGCTTGAAGATGAGAAAAATGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAAAATGATAAAGGTGCCAATA
* * * * *
1270401 TACTGATTCAAGGCTAGCGATATTGGGCTTAAAGATGACAAA-G----A--TGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAATGATAAAGGTGCCAATA
* * * * *
1270453 TGTTGACTCAAGGCCAGCGACATTGGACTTGAAGATGAAAAGAATGATAAAGGTGCCGATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG-AAA-AATGATAAAGGTGCCAATA
* ** * * *
1270514 TTCTGATTCAAAACTAACGATATTGGGCTT-AA-A-G----ATGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAATGATAAAGGTGCCAATA
* * * * * *
1270566 TGCTAATTTAAGGCCAACGATATTGGACTTGAAGATAAGAAGAATGATAAAGGTGCCGATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAAAATGATAAAGGTGCCAATA
* * * *
1270627 TGCTAATTCAAGGCCAGCGATATTAGACTTAAAGA--AAGAA--AT--A-GTGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAATGATAAAGGTGCCAATA
* * *
1270679 TGTTGATTCAAGGCCAGCAACATTGGACTTA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTA
1270710 GAAAGAAATA
Statistics
Matches: 351, Mismatches: 58, Indels: 54
0.76 0.13 0.12
Matches are distributed among these distances:
52 110 0.31
53 5 0.01
54 4 0.01
55 3 0.01
57 6 0.02
58 2 0.01
59 11 0.03
60 3 0.01
61 167 0.48
62 31 0.09
63 9 0.03
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (59 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAATGATAAAGGTGCCAATA
Found at i:1270489 original size:113 final size:111
Alignment explanation
Indices: 1270322--1270708 Score: 443
Period size: 113 Copynumber: 3.4 Consensus size: 111
1270312 GAGATGAAAA
* * * * * *
1270322 ATGATAAAGGTGCCAATATGCTGATTCACGACCAGCGATATTGGGCTTGAAGATGAGAAAAATGA
1 ATGA-AAA-GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTTGAAGATGAGAAAAATGA
*
1270387 TAAAGGTGCCAATATACTGATTCAAGGCTAGCGATATTGGGCTTAAAG
64 TAAAGGTGCCGATATACTGATTCAAGGCTAGCGATATTGGGCTTAAAG
*
1270435 ATGACAAAGATGCCAATGTGTTGACTCAAGGCCAGCGACATTGGACTTGAAGATGA-AAAGAATG
1 ATGA-AAAG-TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTTGAAGATGAGAAA-AATG
* ** *
1270499 ATAAAGGTGCCGATATTCTGATTCAAAACTAACGATATTGGGCTTAAAG
63 ATAAAGGTGCCGATATACTGATTCAAGGCTAGCGATATTGGGCTTAAAG
* * * * * * * *
1270548 ATGATAAAGGTGCCAATATGCTAATTTAAGGCCAACGATATTGGACTTGAAGATAAGAAGAATGA
1 ATGA-AAA-GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTTGAAGATGAGAAAAATGA
* * * * *
1270613 TAAAGGTGCCGATATGCTAATTCAAGGCCAGCGATATTAGACTTAAAG
64 TAAAGGTGCCGATATACTGATTCAAGGCTAGCGATATTGGGCTTAAAG
* *
1270661 AAAGAAATAGTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGACTT
1 -ATGAAA-AGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTT
1270709 AGAAAGAAAT
Statistics
Matches: 229, Mismatches: 39, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
112 4 0.02
113 218 0.95
114 7 0.03
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (111 bp):
ATGAAAAGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTTGAAGATGAGAAAAATGATA
AAGGTGCCGATATACTGATTCAAGGCTAGCGATATTGGGCTTAAAG
Found at i:1270845 original size:31 final size:31
Alignment explanation
Indices: 1270766--1270920 Score: 134
Period size: 31 Copynumber: 4.9 Consensus size: 31
1270756 TATACAAGGC
* * *
1270766 TTAGAAGCAGATGCCA-TCAACTGGTGTAGGCT
1 TTAGAAG-AGTTGCCACT-AACTTGTGTGGGCT
* * *
1270798 TTTGAAAGGGTTGCCACTGACTTGTGTGGGCT
1 TTAG-AAGAGTTGCCACTAACTTGTGTGGGCT
*
1270830 TTAGAAGAGTTGCCACTAATTTGTGTGGGCT
1 TTAGAAGAGTTGCCACTAACTTGTGTGGGCT
* *
1270861 TTAGAA-AGGTGGCCACTAACTTGTGTGAGCT
1 TTAGAAGA-GTTGCCACTAACTTGTGTGGGCT
* **
1270892 TTAGAGAAGGGTTGCCACCGACTTGTGTG
1 TT--AGAAGAGTTGCCACTAACTTGTGTG
1270921 AACTTAAAAA
Statistics
Matches: 100, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
30 1 0.01
31 52 0.52
32 23 0.23
33 24 0.24
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (31 bp):
TTAGAAGAGTTGCCACTAACTTGTGTGGGCT
Found at i:1270916 original size:33 final size:32
Alignment explanation
Indices: 1270795--1270921 Score: 150
Period size: 31 Copynumber: 4.0 Consensus size: 32
1270785 ACTGGTGTAG
* * *
1270795 GCTTTTGAAAGGGTTGCCACTGACTTGTGTGG
1 GCTTTAGAAAGGGTTGCCACTAACTTGTGTGA
* * *
1270827 GCTTTAG-AAGAGTTGCCACTAATTTGTGTGG
1 GCTTTAGAAAGGGTTGCCACTAACTTGTGTGA
*
1270858 GCTTTAGAAA-GGTGGCCACTAACTTGTGTGA
1 GCTTTAGAAAGGGTTGCCACTAACTTGTGTGA
**
1270889 GCTTTAGAGAAGGGTTGCCACCGACTTGTGTGA
1 GCTTTAGA-AAGGGTTGCCACTAACTTGTGTGA
1270922 ACTTAAAAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
31 53 0.65
32 10 0.12
33 18 0.22
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.31
Consensus pattern (32 bp):
GCTTTAGAAAGGGTTGCCACTAACTTGTGTGA
Found at i:1270964 original size:33 final size:33
Alignment explanation
Indices: 1270904--1271069 Score: 188
Period size: 33 Copynumber: 4.9 Consensus size: 33
1270894 AGAGAAGGGT
*
1270904 TGCCACCGACTTGTGTGAACTTAAAAAGAAAAAGG
1 TGCCACCGAGTTGTG-G-ACTTAAAAAGAAAAAGG
* *
1270939 TGCCACCAACTTGTGGACTTAAAAAGAAAAAGG
1 TGCCACCGAGTTGTGGACTTAAAAAGAAAAAGG
** ** **
1270972 TGCCATGGAGTCATGGACTTTGAAAGAAAAAGGG
1 TGCCACCGAGTTGTGGACTTAAAAAGAAAAA-GG
* * *
1271006 TGCCACAGAGTTATCGACTTAAAAAGAAAAAGG
1 TGCCACCGAGTTGTGGACTTAAAAAGAAAAAGG
*
1271039 TGCCACGGAGTTGTGGACTTAAAAAGAAAAA
1 TGCCACCGAGTTGTGGACTTAAAAAGAAAAA
1271070 AAAAAGCCAT
Statistics
Matches: 112, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
33 70 0.62
34 28 0.25
35 14 0.12
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.19
Consensus pattern (33 bp):
TGCCACCGAGTTGTGGACTTAAAAAGAAAAAGG
Found at i:1271025 original size:67 final size:66
Alignment explanation
Indices: 1270922--1271069 Score: 199
Period size: 67 Copynumber: 2.2 Consensus size: 66
1270912 ACTTGTGTGA
* * *
1270922 ACTTAAAAAGAAAAAGGTGCCACCAACTTGTGGACTTAAAAAGAAAAAGGTGCCATGGAGTCATG
1 ACTTAAAAAGAAAAAGGTGCCACCAACTTATCGACTTAAAAAGAAAAAGGTGCCACGGAGTCATG
1270987 G
66 G
** * **
1270988 ACTTTGAAAGAAAAAGGGTGCCA-CAGAGTTATCGACTTAAAAAGAAAAAGGTGCCACGGAGTTG
1 ACTTAAAAAGAAAAA-GGTGCCACCA-ACTTATCGACTTAAAAAGAAAAAGGTGCCACGGAGTCA
1271052 TGG
64 TGG
1271055 ACTTAAAAAGAAAAA
1 ACTTAAAAAGAAAAA
1271070 AAAAAGCCAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
66 15 0.21
67 55 0.79
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (66 bp):
ACTTAAAAAGAAAAAGGTGCCACCAACTTATCGACTTAAAAAGAAAAAGGTGCCACGGAGTCATG
G
Found at i:1271070 original size:34 final size:33
Alignment explanation
Indices: 1270917--1271215 Score: 235
Period size: 34 Copynumber: 9.3 Consensus size: 33
1270907 CACCGACTTG
* *** *
1270917 TGTGAACTTAAAAAGAAAAAGGTGCCACCAACT
1 TGTGGACTTAAAAAGAAAAAGGTGCCATGGAGT
1270950 TGTGGACTTAAAAAGAAAAAGGTGCCATGGAGT
1 TGTGGACTTAAAAAGAAAAAGGTGCCATGGAGT
** ** **
1270983 CATGGACTTTGAAAGAAAAAGGGTGCCACAGAGT
1 TGTGGACTTAAAAAGAAAAA-GGTGCCATGGAGT
* * *
1271017 TATCGACTTAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGACTTAAAAAGAAAAAGGTGCCATGGAGT
*** *
1271050 TGTGGACTTAAAAAGAAAAAAAAAAGCCATGAAGT
1 TGTGGACTTAAAAAG--AAAAAGGTGCCATGGAGT
1271085 TGTGGAC-TAAAAAG-----GGTGCCATGGAGT
1 TGTGGACTTAAAAAGAAAAAGGTGCCATGGAGT
1271112 TGTGGAC-T----A-AAAAAGGTGCCATGGAGT
1 TGTGGACTTAAAAAGAAAAAGGTGCCATGGAGT
* * * *
1271139 TGTGGACTTTTAAAAGGAAAATGTGGCATGGAGT
1 TGTGGAC-TTAAAAAGAAAAAGGTGCCATGGAGT
* * * *
1271173 TGTGGACTTTTAAAAGGAAAATGTGCCACGGAGT
1 TGTGGAC-TTAAAAAGAAAAAGGTGCCATGGAGT
1271207 TGTGGACTT
1 TGTGGACTT
1271216 TGACAGATGC
Statistics
Matches: 219, Mismatches: 32, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.00
27 37 0.17
29 1 0.00
33 72 0.33
34 88 0.40
35 20 0.09
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (33 bp):
TGTGGACTTAAAAAGAAAAAGGTGCCATGGAGT
Found at i:1271096 original size:67 final size:67
Alignment explanation
Indices: 1270949--1271126 Score: 172
Period size: 67 Copynumber: 2.7 Consensus size: 67
1270939 TGCCACCAAC
** ** ****
1270949 TTGTGGACTTAAAAAGAAAAAGGTGCCATGGAGTCATGGACTTTGAAAGAAAAAGGGTGCCACAG
1 TTGTGGACTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAGAAAAAAAAAGCCACAG
1271014 AG
66 AG
* * * *
1271016 TTATCGACTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAGAAAAAAAAAAGCCA-T
1 TTGTGGACTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAG-AAAAAAAAAGCCACA
1271080 GAAG
65 G-AG
*
1271084 TTGTGGAC-TAAAAAG-----GGTGCCATGGAGTTGTGGACTAAAAAAG
1 TTGTGGACTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAG
1271127 GTGCCATGGA
Statistics
Matches: 93, Mismatches: 16, Indels: 9
0.79 0.14 0.08
Matches are distributed among these distances:
62 26 0.28
67 50 0.54
68 17 0.18
ACGTcount: A:0.42, C:0.11, G:0.28, T:0.20
Consensus pattern (67 bp):
TTGTGGACTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAGAAAAAAAAAGCCACAG
AG
Found at i:1271105 original size:27 final size:27
Alignment explanation
Indices: 1271075--1271146 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
1271065 AAAAAAAAAA
* *
1271075 GCCATGAAGTTGTGGACTAAAAAGGGT
1 GCCATGGAGTTGTGGACTAAAAAAGGT
1271102 GCCATGGAGTTGTGGACTAAAAAAGGT
1 GCCATGGAGTTGTGGACTAAAAAAGGT
1271129 GCCATGGAGTTGTGGACT
1 GCCATGGAGTTGTGGACT
1271147 TTTAAAAGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.29, C:0.12, G:0.35, T:0.24
Consensus pattern (27 bp):
GCCATGGAGTTGTGGACTAAAAAAGGT
Found at i:1271267 original size:34 final size:33
Alignment explanation
Indices: 1271220--1271310 Score: 119
Period size: 34 Copynumber: 2.7 Consensus size: 33
1271210 GGACTTTGAC
*
1271220 AGATGCCACTGAGTCATGGACTTAAAGAAAAAA
1 AGATGCCACTGAGTCGTGGACTTAAAGAAAAAA
* * *
1271253 AGGATGCTAGTGAGTCGTGGACTTTGAAGAAAAAA
1 A-GATGCCACTGAGTCGTGGAC-TTAAAGAAAAAA
*
1271288 ATATGCCACTGAGTCGTGGACTT
1 AGATGCCACTGAGTCGTGGACTT
1271311 GGAAAAGAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
33 3 0.06
34 34 0.69
35 12 0.24
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.23
Consensus pattern (33 bp):
AGATGCCACTGAGTCGTGGACTTAAAGAAAAAA
Found at i:1271324 original size:30 final size:30
Alignment explanation
Indices: 1271220--1271430 Score: 174
Period size: 30 Copynumber: 6.8 Consensus size: 30
1271210 GGACTTTGAC
* * *
1271220 AGATGCCACTGAGTCATGGACTTAAAGAAAAAA
1 AGATGCCACTGAGTCGTGGACTT---GGAAAAG
* * *
1271253 AGGATGCTAGTGAGTCGTGGACTTTGAAGAAAAAA
1 A-GATGCCACTGAGTCGTGGAC-TTG--G-AAAAG
*
1271288 ATATGCCACTGAGTCGTGGACTTGGAAAAG
1 AGATGCCACTGAGTCGTGGACTTGGAAAAG
* * *
1271318 AGATGCCA-TTATGTCATGGACTTTGAAGAAG
1 AGATGCCACTGA-GTCGTGGACTTGGAA-AAG
* *
1271349 -GATGCCACTAAGTCGTGGACTTGGAGAAG
1 AGATGCCACTGAGTCGTGGACTTGGAAAAG
* ** *
1271378 AGATGCCACTAAGTTATGGACTTGGAGAAG
1 AGATGCCACTGAGTCGTGGACTTGGAAAAG
1271408 AGATGCCACTGAGTCGTGGACTT
1 AGATGCCACTGAGTCGTGGACTT
1271431 TGAAGAAGGA
Statistics
Matches: 148, Mismatches: 21, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
29 5 0.03
30 90 0.61
31 6 0.04
32 1 0.01
33 4 0.03
34 34 0.23
35 8 0.05
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (30 bp):
AGATGCCACTGAGTCGTGGACTTGGAAAAG
Found at i:1271369 original size:60 final size:60
Alignment explanation
Indices: 1271290--1271430 Score: 212
Period size: 60 Copynumber: 2.4 Consensus size: 60
1271280 AGAAAAAAAT
* *
1271290 ATGCCACTGAGTCGTGGACTTGGAAAAGAGATGCCATTATGTCATGGACTTTGAAGAAG-G
1 ATGCCACTGAGTCGTGGACTTGGAAAAGAGATGCCACTAAGTCATGGAC-TTGAAGAAGAG
* * * *
1271350 ATGCCACTAAGTCGTGGACTTGGAGAAGAGATGCCACTAAGTTATGGACTTGGAGAAGAG
1 ATGCCACTGAGTCGTGGACTTGGAAAAGAGATGCCACTAAGTCATGGACTTGAAGAAGAG
1271410 ATGCCACTGAGTCGTGGACTT
1 ATGCCACTGAGTCGTGGACTT
1271431 TGAAGAAGGA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 8 0.11
60 65 0.89
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.24
Consensus pattern (60 bp):
ATGCCACTGAGTCGTGGACTTGGAAAAGAGATGCCACTAAGTCATGGACTTGAAGAAGAG
Found at i:1277758 original size:13 final size:13
Alignment explanation
Indices: 1277740--1277765 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1277730 CATTTTGGGA
1277740 TGTATCGATACAT
1 TGTATCGATACAT
1277753 TGTATCGATACAT
1 TGTATCGATACAT
1277766 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1277762 original size:33 final size:32
Alignment explanation
Indices: 1277720--1277783 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1277710 TACAAGCCAA
*
1277720 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
1277753 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
1277784 AATAGTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:1277872 original size:20 final size:21
Alignment explanation
Indices: 1277825--1277877 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1277815 GCCAATCACC
*
1277825 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
1277846 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
1277866 TGTATCGATACA
1 TGTATCGATACA
1277878 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:1277883 original size:13 final size:13
Alignment explanation
Indices: 1277865--1277889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1277855 ACATTTGGTC
1277865 ATGTATCGATACA
1 ATGTATCGATACA
1277878 ATGTATCGATAC
1 ATGTATCGATAC
1277890 TGTGCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1280351 original size:13 final size:13
Alignment explanation
Indices: 1280333--1280370 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
1280323 ATAAACCCTT
1280333 TGTATCGATACAA
1 TGTATCGATACAA
1280346 TGTATCGATACAA
1 TGTATCGATACAA
1280359 TGTATCGATACA
1 TGTATCGATACA
1280371 TCTCAGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1286530 original size:19 final size:20
Alignment explanation
Indices: 1286485--1286536 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1286475 TTACAAGCCA
* *
1286485 ATGTATAGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
1286505 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
1286525 -TGTATCGATACA
1 ATGTATCGATACA
1286537 AACACTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:1286675 original size:20 final size:19
Alignment explanation
Indices: 1286652--1286690 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1286642 CTGTGCATTA
1286652 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTT-AAGG
1286672 TGTATCGATACATTTAAGG
1 TGTATCGATACATTTAAGG
1286691 GTTTTGATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATTTAAGG
Found at i:1287694 original size:20 final size:21
Alignment explanation
Indices: 1287666--1287704 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1287656 GATACAAAGT
1287666 AAATGGTATCAATACATTTGG
1 AAATGGTATCAATACATTTGG
**
1287687 AAAT-GTATTGATACATTT
1 AAATGGTATCAATACATTT
1287705 ACTTATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (21 bp):
AAATGGTATCAATACATTTGG
Found at i:1287795 original size:20 final size:20
Alignment explanation
Indices: 1287770--1287823 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1287760 CATTTGAGAC
*
1287770 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTA
*
1287790 ATGTATCGACACATTCACTA
1 ATGTATCGATACATTCACTA
1287810 ATTGTATCGATACA
1 A-TGTATCGATACA
1287824 AATCATAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:1289150 original size:18 final size:18
Alignment explanation
Indices: 1289107--1289153 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1289097 TCAGTTTTAA
1289107 AAAATTTCTTTTTTCATG
1 AAAATTTCTTTTTTCATG
** * *
1289125 AATTTTTCTTTTTTCCTT
1 AAAATTTCTTTTTTCATG
1289143 AAAATTTCTTT
1 AAAATTTCTTT
1289154 ATTTTCGAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.62
Consensus pattern (18 bp):
AAAATTTCTTTTTTCATG
Found at i:1289433 original size:164 final size:164
Alignment explanation
Indices: 1289117--1289466 Score: 408
Period size: 164 Copynumber: 2.1 Consensus size: 164
1289107 AAAATTTCTT
* * *
1289117 TTTTCATGAATTTTTCTTTTTTCCTTAAAATTTCTTTATTTTCGAAAAATAAGTTTTCTATTCCA
1 TTTTCATGAATTTTTATTTTTTCCTTAAAATTTCTTTAGTTTCGAAAAACAAGTTTTCTATTCCA
** * *
1289182 TAAATGTTGTCGAAGGGTCTTTTTCTTAGTTTAAAATTTTAAACTTCATCTAACATTGTCATTAA
66 TAAATGTTGTC-AAGGGGATTTTTCTTAGTTTAAAATTTTAAAATTCATCTAACATTATCATTAA
* * *
1289247 ATTCAGACTAAATTATTTTTGAAAAATTC-ATTTA
130 ATTCACACTAAATCAATTTTGAAAAATTCAATTTA
* * *
1289281 TTTTCATGAGTTTTTTATTTTTTCTTTAAAATTT-TCTTAGTTT-GAAGAACCAAGTTTTCTATT
1 TTTTCATGA-ATTTTTATTTTTTCCTTAAAATTTCT-TTAGTTTCGAA-AAACAAGTTTTCTATT
* * * *
1289344 CTATAAATGTTTTC-AGGGAGATTTTT-TTGGTTTAAAATTTTTAAAATTCATCTAATATTATCA
63 CCATAAATGTTGTCAAGGG-GATTTTTCTTAGTTTAAAA-TTTTAAAATTCATCTAACATTATCA
*
1289407 TTAAATTTACA-TGAAATCAATTTTGAAAAATTCAATTTA
126 TTAAATTCACACT-AAATCAATTTTGAAAAATTCAATTTA
**
1289446 -TTTCATGAATTTGGATTTTTT
1 TTTTCATGAATTTTTATTTTTT
1289467 TATATATGTT
Statistics
Matches: 158, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
163 25 0.16
164 75 0.47
165 58 0.37
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (164 bp):
TTTTCATGAATTTTTATTTTTTCCTTAAAATTTCTTTAGTTTCGAAAAACAAGTTTTCTATTCCA
TAAATGTTGTCAAGGGGATTTTTCTTAGTTTAAAATTTTAAAATTCATCTAACATTATCATTAAA
TTCACACTAAATCAATTTTGAAAAATTCAATTTA
Found at i:1289994 original size:17 final size:17
Alignment explanation
Indices: 1289974--1290024 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 17
1289964 AAAACAAGAG
1289974 AGAAAAAAAAAGAAAAC
1 AGAAAAAAAAAGAAAAC
1289991 AGAAAAAAAAAGAGAAAAC
1 AG-AAAAAAAA-AGAAAAC
1290010 AGAAAAAAAAA-AAAA
1 AGAAAAAAAAAGAAAA
1290025 GCTAAACTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 16 0.50
19 9 0.28
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAGAAAAC
Found at i:1290000 original size:19 final size:19
Alignment explanation
Indices: 1289962--1290022 Score: 86
Period size: 19 Copynumber: 3.1 Consensus size: 19
1289952 GAAAGTGGAG
1289962 AGAAAACAAGAGAGAAAAAAAA
1 AGAAAAC-AGA-A-AAAAAAAA
*
1289984 AGAAAACAGAAAAAAAAAG
1 AGAAAACAGAAAAAAAAAA
1290003 AGAAAACAGAAAAAAAAAA
1 AGAAAACAGAAAAAAAAAA
1290022 A
1 A
1290023 AAGCTAAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 26 0.70
20 1 0.03
21 3 0.08
22 7 0.19
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (19 bp):
AGAAAACAGAAAAAAAAAA
Found at i:1290635 original size:19 final size:19
Alignment explanation
Indices: 1290597--1290635 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1290587 GCCTAATATT
* **
1290597 TCATATGATATATTTTAGG
1 TCATATGATAAATTGGAGG
1290616 TCATATGATAAATTGGAGG
1 TCATATGATAAATTGGAGG
1290635 T
1 T
1290636 GTTTGTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (19 bp):
TCATATGATAAATTGGAGG
Found at i:1294428 original size:13 final size:13
Alignment explanation
Indices: 1294410--1294435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1294400 CAATTTTTTG
1294410 TGTATCGATACAT
1 TGTATCGATACAT
1294423 TGTATCGATACAT
1 TGTATCGATACAT
1294436 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1294500 original size:21 final size:21
Alignment explanation
Indices: 1294474--1294549 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1294464 CTGCCAAGAA
*
1294474 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1294495 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1294515 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1294536 ATGTATCGATACAT
1 ATGTATCGATACAT
1294550 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1294520 original size:20 final size:20
Alignment explanation
Indices: 1294495--1294567 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1294485 CATCTTTTTT
1294495 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1294515 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1294536 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1294556 ATGTATCGATAC
1 ATGTATCGATAC
1294568 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1294531 original size:41 final size:41
Alignment explanation
Indices: 1294474--1294567 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1294464 CTGCCAAGAA
*
1294474 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1294515 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1294556 ATGTATCGATAC
1 ATGTATCGATAC
1294568 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1297039 original size:13 final size:13
Alignment explanation
Indices: 1297021--1297058 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1297011 ATAAACACCC
1297021 TGTATCGATACAG
1 TGTATCGATACAG
*
1297034 TGTATCGATACAT
1 TGTATCGATACAG
1297047 TGTATCGATACA
1 TGTATCGATACA
1297059 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1299158 original size:15 final size:15
Alignment explanation
Indices: 1299138--1299168 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1299128 ATTTCGTTTG
*
1299138 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1299153 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1299168 G
1 G
1299169 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1303247 original size:13 final size:13
Alignment explanation
Indices: 1303229--1303254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1303219 CAATTTTTTG
1303229 TGTATCGATACAT
1 TGTATCGATACAT
1303242 TGTATCGATACAT
1 TGTATCGATACAT
1303255 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1303319 original size:21 final size:21
Alignment explanation
Indices: 1303293--1303368 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1303283 CTGCCAAGAA
*
1303293 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1303314 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1303334 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1303355 ATGTATCGATACAT
1 ATGTATCGATACAT
1303369 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1303339 original size:20 final size:20
Alignment explanation
Indices: 1303314--1303386 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1303304 CATCTTTTTT
1303314 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1303334 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1303355 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1303375 ATGTATCGATAC
1 ATGTATCGATAC
1303387 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1303350 original size:41 final size:41
Alignment explanation
Indices: 1303293--1303386 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1303283 CTGCCAAGAA
*
1303293 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1303334 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1303375 ATGTATCGATAC
1 ATGTATCGATAC
1303387 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1304511 original size:13 final size:13
Alignment explanation
Indices: 1304493--1304522 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1304483 ACAATTCATC
1304493 ATGTATCGATATA
1 ATGTATCGATATA
*
1304506 ATGTATGGATATA
1 ATGTATCGATATA
1304519 ATGT
1 ATGT
1304523 GCCATGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:1304593 original size:20 final size:19
Alignment explanation
Indices: 1304568--1304605 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1304558 CTGCTAGTTT
*
1304568 CATGTATCGATACAATTGTC
1 CATGTATCCATAC-ATTGTC
1304588 CATGTATCCATACATTGT
1 CATGTATCCATACATTGT
1304606 ATTGATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (19 bp):
CATGTATCCATACATTGTC
Found at i:1306654 original size:22 final size:20
Alignment explanation
Indices: 1306609--1306682 Score: 51
Period size: 21 Copynumber: 3.6 Consensus size: 20
1306599 TTTGTTGATG
*
1306609 ATTTTGATGAAAAATGAAGT
1 ATTTTGATGAAAAATGAAGA
1306629 ATTTTGAAGTGAAAAAT-AAGA
1 ATTTTG-A-TGAAAAATGAAGA
* * * ** *
1306650 AATTTAAAGAAGATTTGATGA
1 ATTTTGATGAA-AAATGAAGA
1306671 ATTTTGATGAAA
1 ATTTTGATGAAA
1306683 TGATGTTAGG
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
19 3 0.08
20 10 0.25
21 19 0.47
22 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (20 bp):
ATTTTGATGAAAAATGAAGA
Found at i:1306947 original size:18 final size:20
Alignment explanation
Indices: 1306906--1306958 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
1306896 CTATATACCC
1306906 TAATTCACATCAAACAATTA
1 TAATTCACATCAAACAATTA
1306926 TAATTCA-AT-AACACAA-TA
1 TAATTCACATCAA-ACAATTA
*
1306944 TAATTAAACATCAAA
1 TAATT-CACATCAAA
1306959 TTCATCCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 10 0.36
21 2 0.07
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (20 bp):
TAATTCACATCAAACAATTA
Found at i:1315823 original size:13 final size:13
Alignment explanation
Indices: 1315805--1315829 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1315795 AAAATTCAGA
1315805 TGTATCGATACAG
1 TGTATCGATACAG
1315818 TGTATCGATACA
1 TGTATCGATACA
1315830 AAGGGTTTAT
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1318121 original size:19 final size:20
Alignment explanation
Indices: 1318097--1318148 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1318087 CTTAACTGTT
1318097 TGTATCGATACAT-A-CAAGA
1 TGTATCGATACATGACCAA-A
1318116 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
1318136 TGTATCGATACAT
1 TGTATCGATACAT
1318149 TGGCTTGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.42
20 15 0.48
21 3 0.10
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:1318547 original size:14 final size:14
Alignment explanation
Indices: 1318528--1318564 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1318518 TAAAACATCT
1318528 TTGTGTTCATAAAG
1 TTGTGTTCATAAAG
*
1318542 TTGTGTTCATAAGG
1 TTGTGTTCATAAAG
1318556 TTGTGTTCA
1 TTGTGTTCA
1318565 ACCTTGAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (14 bp):
TTGTGTTCATAAAG
Found at i:1322551 original size:13 final size:13
Alignment explanation
Indices: 1322535--1322564 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1322525 ACAATTCATC
*
1322535 ATGTATTGATATA
1 ATGTATCGATATA
1322548 ATGTATCGATATA
1 ATGTATCGATATA
1322561 ATGT
1 ATGT
1322565 GCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:1324871 original size:20 final size:20
Alignment explanation
Indices: 1324846--1324883 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1324836 TATATATGAT
1324846 AAAATCAAAATCATATCACA
1 AAAATCAAAATCATATCACA
*
1324866 AAAATCAACATCATATCA
1 AAAATCAAAATCATATCA
1324884 AAAGCAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATCAAAATCATATCACA
Found at i:1326589 original size:40 final size:40
Alignment explanation
Indices: 1326552--1326632 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
1326542 AGAGTTGAGT
* * *
1326552 AGGACAAAACGGGCAAGTCAATGATTGAGAAGGGTTGACC
1 AGGACAAAACCGACAAGTCAATGATTGAAAAGGGTTGACC
* *
1326592 AGGACAAAACCTACAAGTTAATGATTGAAAA-GGTCTGACC
1 AGGACAAAACCGACAAGTCAATGATTGAAAAGGGT-TGACC
1326632 A
1 A
1326633 AAATGAAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.09
40 32 0.91
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.17
Consensus pattern (40 bp):
AGGACAAAACCGACAAGTCAATGATTGAAAAGGGTTGACC
Found at i:1327233 original size:76 final size:76
Alignment explanation
Indices: 1327074--1327406 Score: 268
Period size: 76 Copynumber: 4.4 Consensus size: 76
1327064 CTAGGAGCTA
* * * * * * *
1327074 AAAAAGAAGAACTTGATTGGGAATATATGGTTCTTAAAATTTCCATCAATAGTA-GAAACAAACT
1 AAAAAGAAGAACATGATAGGGACTATGTGGTTTTTACAATTTCCATCAATAG-ACAAAACAAACT
* **
1327138 GATAACGAGTT-
65 AATAATAAGTTG
* * * * *
1327149 AAAGAAGAAGAACATGATAGGGACTATGTGGTTTCTACAATTTCCCATCACA-A-TCGAAATAAG
1 AAA-AAGAAGAACATGATAGGGACTATGTGGTTTTTACAATTT-CCATCA-ATAGACAAAACAAA
1327212 CTAATAATAAGTTG
63 CTAATAATAAGTTG
* * * *
1327226 AAAAAGAAGATCATGTTGGGGACTATGTGGTTTTTACAAATTTTCATCAATAGACAAAACAAACT
1 AAAAAGAAGAACATGATAGGGACTATGTGGTTTTTAC-AATTTCCATCAATAGACAAAACAAACT
* *
1327291 GATAATAAATTG
65 AATAATAAGTTG
* * * * * * *
1327303 AAGAAA-AAGAACTTGATAGGGAATATATGGTTTTTGCAATTTCCATCAATAGCCAAAATAAATT
1 AA-AAAGAAGAACATGATAGGGACTATGTGGTTTTTACAATTTCCATCAATAGACAAAACAAACT
*
1327367 AATAACAAGCTCT-
65 AATAATAAG-T-TG
*
1327380 AAAAA-AA-AACATGATAGGGAATATGTG
1 AAAAAGAAGAACATGATAGGGACTATGTG
1327407 AATTCTAAAA
Statistics
Matches: 207, Mismatches: 40, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
75 22 0.11
76 118 0.57
77 62 0.30
78 5 0.02
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.27
Consensus pattern (76 bp):
AAAAAGAAGAACATGATAGGGACTATGTGGTTTTTACAATTTCCATCAATAGACAAAACAAACTA
ATAATAAGTTG
Found at i:1327362 original size:153 final size:152
Alignment explanation
Indices: 1327074--1327426 Score: 344
Period size: 153 Copynumber: 2.3 Consensus size: 152
1327064 CTAGGAGCTA
* *
1327074 AAAAAGAAGAACTTGATTGGGAATATATGGTTCTTAAAATTTCCATCAATAGTAGAAACAAACTG
1 AAAAAGAAGAACATGATTGGGAATATATGGTTCTTAAAATTTCCATCAATAGTAAAAACAAACTG
* * * * * *
1327139 ATAACGAGTTAAAGAAGAAGAACATGATAGGGACTATGTGGTTTCTACAATTTCCCATCACAATC
66 ATAACAAATTAAAGAAAAAGAACATGATAGGGAATATATGGTTTCTACAATTTCCCATCACAACC
*
1327204 GAAATAAGCTAATAATAAGTTG
131 AAAATAAGCTAATAATAAGTTG
* * * * *
1327226 AAAAAGAAGATCATG-TTGGGGACTATGTGGTTTTTACAAATTTTCATCAATAG-ACAAAACAAA
1 AAAAAGAAGAACATGATT-GGGAATATATGGTTCTTA-AAATTTCCATCAATAGTA-AAAACAAA
* * * * *
1327289 CTGATAATAAATTGAAGAAAAAGAACTTGATAGGGAATATATGGTTTTTGCAATTT-CCATCA-A
63 CTGATAACAAATTAAAGAAAAAGAACATGATAGGGAATATATGGTTTCTACAATTTCCCATCACA
** *
1327352 TAGCCAAAATAAATTAATAACAAGCTCT-
128 -A-CCAAAATAAGCTAATAATAAG-T-TG
* * * *
1327380 AAAAA-AA-AACATGATAGGGAATATGTGAATTC-TAAAATTTTCATCAA
1 AAAAAGAAGAACATGATTGGGAATATATG-GTTCTTAAAATTTCCATCAA
1327427 CAACCAAAAC
Statistics
Matches: 165, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
151 16 0.10
152 53 0.32
153 89 0.54
154 6 0.04
155 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (152 bp):
AAAAAGAAGAACATGATTGGGAATATATGGTTCTTAAAATTTCCATCAATAGTAAAAACAAACTG
ATAACAAATTAAAGAAAAAGAACATGATAGGGAATATATGGTTTCTACAATTTCCCATCACAACC
AAAATAAGCTAATAATAAGTTG
Found at i:1330255 original size:7 final size:7
Alignment explanation
Indices: 1330243--1330278 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
1330233 TATAAAAAAG
1330243 ATATTTT
1 ATATTTT
1330250 ATATTTT
1 ATATTTT
1330257 ATATTTT
1 ATATTTT
*
1330264 AATATTTA
1 -ATATTTT
1330272 ATATTTT
1 ATATTTT
1330279 TTCATTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
ATATTTT
Found at i:1330270 original size:15 final size:14
Alignment explanation
Indices: 1330243--1330278 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1330233 TATAAAAAAG
*
1330243 ATATTTTATATTTT
1 ATATTTTATATTTA
1330257 ATATTTTAATATTTA
1 ATATTTT-ATATTTA
1330272 ATATTTT
1 ATATTTT
1330279 TTCATTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATATTTTATATTTA
Found at i:1333662 original size:18 final size:18
Alignment explanation
Indices: 1333635--1333669 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1333625 ATATTAATCA
1333635 TTATAATTTTTTATTTTT
1 TTATAATTTTTTATTTTT
*
1333653 TTATATTTTTTTATTTT
1 TTATAATTTTTTATTTT
1333670 GATTTTAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTATAATTTTTTATTTTT
Found at i:1334181 original size:22 final size:21
Alignment explanation
Indices: 1334153--1334196 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
1334143 AAATATTAAA
1334153 ATATATTTT-TATATTAATATTT
1 ATATATTTTATA-ATTAA-ATTT
1334175 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1334196 A
1 A
1334197 AATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 14 0.67
23 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1334646 original size:23 final size:25
Alignment explanation
Indices: 1334597--1334674 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 25
1334587 ATTTAAAAAA
* *
1334597 TTAATTTGAAAGTAAATATAATTTAAT
1 TTAATTT-AAAATTAATA-AATTTAAT
*
1334624 TTAATTT-AATTTAA-AAATTTAA-
1 TTAATTTAAAATTAATAAATTTAAT
1334646 -TAATTTAAAATTAATAAATTTAAAT
1 TTAATTTAAAATTAATAAATTT-AAT
1334671 TTAA
1 TTAA
1334675 AATAATTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
21 6 0.14
22 6 0.14
23 13 0.30
24 3 0.07
25 5 0.12
26 3 0.07
27 7 0.16
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (25 bp):
TTAATTTAAAATTAATAAATTTAAT
Found at i:1334655 original size:15 final size:15
Alignment explanation
Indices: 1334630--1334674 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
1334620 TAATTTAATT
1334630 TAATTTAAAAATTTAA
1 TAATTT-AAAATTTAA
1334646 TAATTTAAAA-TTAA
1 TAATTTAAAATTTAA
1334660 TAAATTT-AAATTTAA
1 T-AATTTAAAATTTAA
1334675 AATAATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.30
15 13 0.48
16 6 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATTTAAAATTTAA
Found at i:1334671 original size:21 final size:20
Alignment explanation
Indices: 1334621--1334677 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
1334611 AATATAATTT
*
1334621 AATTT-AATTT-AATTTAAA
1 AATTTAAATTTAAAATTAAA
1334639 AATTTAATAATTTAAAATTAATA
1 AATTT-A-AATTTAAAATTAA-A
1334662 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
1334678 AATTTGAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 5 0.15
21 15 0.45
22 7 0.21
23 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTAAATTTAAAATTAAA
Found at i:1334707 original size:14 final size:16
Alignment explanation
Indices: 1334583--1334707 Score: 64
Period size: 16 Copynumber: 7.8 Consensus size: 16
1334573 CATTTTACTC
1334583 TTGAATTTAAAAAATTAAT
1 TTGAATTT--AAAA-TAAT
**
1334602 TTGAAAGTAAATATAAT
1 TTGAATTTAAA-ATAAT
**
1334619 TT-AATTTAATTTAAT
1 TTGAATTTAAAATAAT
*
1334634 TTAAAAATTT--AATAAT
1 TT--GAATTTAAAATAAT
* * *
1334650 TTAAAATTAATA-AAT
1 TTGAATTTAAAATAAT
*
1334665 TTAAATTTAAAATAAT
1 TTGAATTTAAAATAAT
*
1334681 TTGAATCTAAAATAA-
1 TTGAATTTAAAATAAT
1334696 TT-AATTTAAAAT
1 TTGAATTTAAAAT
1334708 TACTCAAATA
Statistics
Matches: 84, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
14 14 0.17
15 21 0.25
16 28 0.33
17 9 0.11
18 6 0.07
19 6 0.07
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (16 bp):
TTGAATTTAAAATAAT
Found at i:1334899 original size:2 final size:2
Alignment explanation
Indices: 1334886--1334917 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1334876 TTTGTTGTCT
*
1334886 TA TA TT 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
1334918 ATAAGATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1335019 original size:4 final size:4
Alignment explanation
Indices: 1335006--1335037 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
1334996 AAAATATATC
1335006 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1335038 GAGGCACGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:1335142 original size:17 final size:17
Alignment explanation
Indices: 1335120--1335155 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1335110 CATAGCCTTT
*
1335120 ATAATTATACTATTATG
1 ATAATTATAATATTATG
1335137 ATAATTATAATATTATG
1 ATAATTATAATATTATG
1335154 AT
1 AT
1335156 TAGTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (17 bp):
ATAATTATAATATTATG
Found at i:1335567 original size:15 final size:16
Alignment explanation
Indices: 1335547--1335605 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
1335537 TTTAATAAAA
1335547 ATTT-AATTTAATCTG
1 ATTTAAATTTAATCTG
* * *
1335562 ATTT-AATCTAATAATT
1 ATTTAAATTTAAT-CTG
* *
1335578 TTTTAAATTTGATCTG
1 ATTTAAATTTAATCTG
1335594 ATTTAAATTTAA
1 ATTTAAATTTAA
1335606 AATTAATAAA
Statistics
Matches: 32, Mismatches: 10, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
15 11 0.34
16 15 0.47
17 6 0.19
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTAAATTTAATCTG
Found at i:1335721 original size:8 final size:8
Alignment explanation
Indices: 1335708--1335732 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1335698 ATTCGAAATT
1335708 AAATTAAA
1 AAATTAAA
1335716 AAATTAAA
1 AAATTAAA
1335724 AAATTAAA
1 AAATTAAA
1335732 A
1 A
1335733 TTAATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATTAAA
Found at i:1336988 original size:2 final size:2
Alignment explanation
Indices: 1336956--1336980 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1336946 AAAATTCTAG
1336956 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1336981 GTTATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1339086 original size:16 final size:16
Alignment explanation
Indices: 1339067--1339111 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1339057 CCTGAACTCG
1339067 AAATGACCTGAAACTA
1 AAATGACCTGAAACTA
* * *
1339083 AAATAACTTGAATCTA
1 AAATGACCTGAAACTA
1339099 AAATGACCTGAAA
1 AAATGACCTGAAA
1339112 TTGAAACAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.22
Consensus pattern (16 bp):
AAATGACCTGAAACTA
Found at i:1339674 original size:17 final size:18
Alignment explanation
Indices: 1339644--1339677 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1339634 ATACACTTTG
1339644 AAAAATAAAATAATATTC
1 AAAAATAAAATAATATTC
*
1339662 AAAAA-AAATTAATATT
1 AAAAATAAAATAATATT
1339678 AGCATTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATAAAATAATATTC
Found at i:1341318 original size:21 final size:22
Alignment explanation
Indices: 1341293--1341338 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1341283 GATACTTTGG
1341293 ATTATTGTTT-TACTTG-AAAAC
1 ATTATT-TTTATACTTGAAAAAC
*
1341314 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTTTATACTTGAAAAAC
1341336 ATT
1 ATT
1341339 TATACTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 11 0.50
22 8 0.36
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (22 bp):
ATTATTTTTATACTTGAAAAAC
Found at i:1344300 original size:4 final size:4
Alignment explanation
Indices: 1344291--1344315 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1344281 TTTTGTTTCA
1344291 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
1344316 GCTTTGCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1345356 original size:28 final size:28
Alignment explanation
Indices: 1345323--1345383 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
1345313 TCGATACAAT
*
1345323 TGCTTGTTTCTTCATGTGTCCATGTAGC
1 TGCTTGTTTCTTCATATGTCCATGTAGC
* *
1345351 TGCTTGTTTCTTCATATGTCCTTGTGGC
1 TGCTTGTTTCTTCATATGTCCATGTAGC
1345379 TGCTT
1 TGCTT
1345384 TAGATTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.08, C:0.21, G:0.21, T:0.49
Consensus pattern (28 bp):
TGCTTGTTTCTTCATATGTCCATGTAGC
Found at i:1345695 original size:8 final size:8
Alignment explanation
Indices: 1345674--1345773 Score: 53
Period size: 8 Copynumber: 12.1 Consensus size: 8
1345664 GGCCATTATT
1345674 TTTTTTTA
1 TTTTTTTA
1345682 TGTTTTTT-
1 T-TTTTTTA
*
1345690 TATTTTTA
1 TTTTTTTA
*
1345698 TTTTTGATAAA
1 TTTTT--T-TA
1345709 TTTTTTTTGA
1 -TTTTTTT-A
1345719 TTTTTTTA
1 TTTTTTTA
**
1345727 TTAATTTA
1 TTTTTTTA
*
1345735 -TTATTTA
1 TTTTTTTA
**
1345742 TTAATTTA
1 TTTTTTTA
1345750 -TTTTTTA
1 TTTTTTTA
*
1345757 TATTTTTA
1 TTTTTTTA
1345765 TTTTTTTA
1 TTTTTTTA
1345773 T
1 T
1345774 GTTGAAAATC
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
7 16 0.23
8 33 0.46
9 13 0.18
10 3 0.04
11 1 0.01
12 5 0.07
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1345702 original size:15 final size:15
Alignment explanation
Indices: 1345673--1345771 Score: 53
Period size: 15 Copynumber: 6.5 Consensus size: 15
1345663 CGGCCATTAT
1345673 TTTTTTTTATGTTTT-
1 TTTTTTTTAT-TTTTA
1345688 TTTATTTTTATTTTTGA
1 TTT-TTTTTATTTTT-A
*** *
1345705 TAAATTTT-TTTTGA
1 TTTTTTTTATTTTTA
1345719 -TTTTTTTATTAATTTA
1 TTTTTTTTATT--TTTA
* *
1345735 TTATTTATTA-ATTTA
1 TT-TTTTTTATTTTTA
*
1345750 TTTTTTATATTTTTA
1 TTTTTTTTATTTTTA
1345765 TTTTTTT
1 TTTTTTT
1345772 ATGTTGAAAA
Statistics
Matches: 61, Mismatches: 14, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
13 4 0.07
14 8 0.13
15 27 0.44
16 14 0.23
17 2 0.03
18 6 0.10
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTTTTTATTTTTA
Found at i:1345773 original size:38 final size:37
Alignment explanation
Indices: 1345671--1345773 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 37
1345661 GCCGGCCATT
*
1345671 ATTTTTTTTTATGTTTTT-TTATTTTTATTTTTGATAA
1 ATTTTTTTTTATATTTTTATT-TTTTTATTTTTGATAA
* * ** *
1345708 ATTTTTTTTGATTTTTTTATTAATTTATTATTT-ATTA
1 ATTTTTTTTTATATTTTTATTTTTTTATT-TTTGATAA
1345745 ATTTATTTTTTATATTTTTATTTTTTTAT
1 ATTT-TTTTTTATATTTTTATTTTTTTAT
1345774 GTTGAAAATC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
37 29 0.54
38 25 0.46
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (37 bp):
ATTTTTTTTTATATTTTTATTTTTTTATTTTTGATAA
Found at i:1364730 original size:28 final size:28
Alignment explanation
Indices: 1364690--1364750 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
1364680 TTGATGCAAT
**
1364690 TGCTTGTTTCTTCATGTGTCCATGTAGC
1 TGCTTGTTTCTTCACCTGTCCATGTAGC
*
1364718 TGCTTGTTTCTTCACCTGTCCATGTGGC
1 TGCTTGTTTCTTCACCTGTCCATGTAGC
1364746 TGCTT
1 TGCTT
1364751 TAGATTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.08, C:0.25, G:0.21, T:0.46
Consensus pattern (28 bp):
TGCTTGTTTCTTCACCTGTCCATGTAGC
Found at i:1365087 original size:15 final size:15
Alignment explanation
Indices: 1365058--1365108 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1365048 TTTTATTTGA
*
1365058 TTTTT-TTAATTTAT
1 TTTTTATTATTTTAT
*
1365072 TATTTATTATTTTAT
1 TTTTTATTATTTTAT
1365087 TTTTTA-TATTATTAT
1 TTTTTATTATT-TTAT
1365102 TTTTTAT
1 TTTTTAT
1365109 GTTGAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATTATTTTAT
Found at i:1365089 original size:27 final size:28
Alignment explanation
Indices: 1365050--1365113 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
1365040 TTGGTGTGTT
1365050 TTATTTGATTTTTTTA-ATTTATTATTTA
1 TTATTTGATTTTTTTATA-TTATTATTTA
* *
1365078 TTATTTTA-TTTTTTATATTATTATTTT
1 TTATTTGATTTTTTTATATTATTATTTA
1365105 TTATGTTGA
1 TTAT-TTGA
1365114 AAATCGAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (28 bp):
TTATTTGATTTTTTTATATTATTATTTA
Found at i:1365098 original size:20 final size:20
Alignment explanation
Indices: 1365048--1365104 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1365038 TTTTGGTGTG
*
1365048 TTTTATTTGATTTTTTTAATT
1 TTTTATTT-ATTATTTTAATT
*
1365069 TATTATTTATTATTTT-ATT
1 TTTTATTTATTATTTTAATT
1365088 TTTTATATTATTATTTT
1 TTTTAT-TTATTATTTT
1365105 TTATGTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.25
20 17 0.53
21 7 0.22
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTATTTATTATTTTAATT
Found at i:1367081 original size:12 final size:12
Alignment explanation
Indices: 1367064--1367088 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1367054 AGTGAAAAAC
1367064 AGATTTTGATGA
1 AGATTTTGATGA
1367076 AGATTTTGATGA
1 AGATTTTGATGA
1367088 A
1 A
1367089 AAATGAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AGATTTTGATGA
Found at i:1368954 original size:19 final size:20
Alignment explanation
Indices: 1368930--1368983 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
1368920 ATCGATAAAA
**
1368930 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGGACAAT
*
1368949 TGTATCGATATATGGACAAAT
1 TGTATCGATACATGGAC-AAT
1368970 TGTATCGATACATG
1 TGTATCGATACATG
1368984 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.48
21 15 0.52
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATGGACAAT
Found at i:1369049 original size:13 final size:13
Alignment explanation
Indices: 1369028--1369058 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1369018 CGATACATGG
*
1369028 TACAATGTATCGA
1 TACATTGTATCGA
1369041 TACATTGTATCGA
1 TACATTGTATCGA
1369054 TACAT
1 TACAT
1369059 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1369054 original size:33 final size:32
Alignment explanation
Indices: 1369012--1369078 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
1369002 CTATCACTAT
1369012 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
1369045 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
1369078 T
1 T
1369079 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:1374488 original size:98 final size:98
Alignment explanation
Indices: 1374319--1374514 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
1374309 TAACGAATTT
1374319 GTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATA
1 GTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATA
1374384 AATCTCCCCCTTAATCAAGTAATTCATATCAAA
66 AATCTCCCCCTTAATCAAGTAATTCATATCAAA
1374417 GTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATA
1 GTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATA
1374482 AATCTCCCCCTTAATCAAGTAATTCATATCAAA
66 AATCTCCCCCTTAATCAAGTAATTCATATCAAA
1374515 AATTTATTTG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.29, C:0.30, G:0.06, T:0.36
Consensus pattern (98 bp):
GTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATA
AATCTCCCCCTTAATCAAGTAATTCATATCAAA
Found at i:1378222 original size:15 final size:15
Alignment explanation
Indices: 1378202--1378232 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1378192 ATTTCGTTTG
*
1378202 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1378217 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1378232 G
1 G
1378233 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1382440 original size:19 final size:20
Alignment explanation
Indices: 1382380--1382449 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 20
1382370 TTCTTACATA
1382380 AAGGGGGAGAAGATAATTGTTT
1 AAGGGGGAG-A-ATAATTGTTT
1382402 AAGGGGGAG-ATAATTGTTT
1 AAGGGGGAGAATAATTGTTT
* *
1382421 AAGGGGGAGAAT-TTTTTTT
1 AAGGGGGAGAATAATTGTTT
1382440 AA-GGGGAGAA
1 AAGGGGGAGAA
1382450 AAATGAAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.18
19 26 0.58
20 2 0.04
22 9 0.20
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (20 bp):
AAGGGGGAGAATAATTGTTT
Found at i:1383028 original size:32 final size:33
Alignment explanation
Indices: 1382967--1383031 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1382957 ACACACCCAG
*
1382967 ATGTATCGATACATGCTGCTTTGTATCGATACA
1 ATGTATCGATACATGCTGCATTGTATCGATACA
* *
1383000 ATGTATTGATACATG-TTCATTGTATCGATACA
1 ATGTATCGATACATGCTGCATTGTATCGATACA
1383032 TGGACAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (33 bp):
ATGTATCGATACATGCTGCATTGTATCGATACA
Found at i:1383029 original size:19 final size:20
Alignment explanation
Indices: 1382997--1383054 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
1382987 TTGTATCGAT
* *
1382997 ACAA-TGTATTGATACATGT
1 ACAATTGTATCGATACATGG
*
1383016 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
1383035 ACAAATTGTATCGATACATG
1 AC-AATTGTATCGATACATG
1383055 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 15 0.47
21 16 0.50
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:1383120 original size:13 final size:13
Alignment explanation
Indices: 1383099--1383129 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1383089 CGATACATGG
*
1383099 TACAATGTATCGA
1 TACATTGTATCGA
1383112 TACATTGTATCGA
1 TACATTGTATCGA
1383125 TACAT
1 TACAT
1383130 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1383128 original size:33 final size:32
Alignment explanation
Indices: 1383086--1383149 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 32
1383076 TCACTATTTA
1383086 TATCGATACATG-GTACAATGTATCGATACATTG
1 TATCGATACATGAG-A-AATGTATCGATACATTG
1383119 TATCGATACATGAAGAAATGTATCGATACAT
1 TATCGATACATG-AGAAATGTATCGATACAT
1383150 AGATTGTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (32 bp):
TATCGATACATGAGAAATGTATCGATACATTG
Found at i:1386685 original size:3 final size:3
Alignment explanation
Indices: 1386677--1386716 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1386667 CAAGTCAACT
*
1386677 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1386717 ATTTGGTGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:1387880 original size:22 final size:24
Alignment explanation
Indices: 1387850--1387894 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1387840 CCTCTCAATC
*
1387850 TCTTCAAGA-ATTATACCCCAAGT
1 TCTTCAAGAGATTATAACCCAAGT
*
1387873 TCTT-AAGAGATTGTAACCCAAG
1 TCTTCAAGAGATTATAACCCAAG
1387895 GTTGGATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (24 bp):
TCTTCAAGAGATTATAACCCAAGT
Found at i:1388397 original size:19 final size:20
Alignment explanation
Indices: 1388352--1388399 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1388342 CTACCAGTTT
* *
1388352 CATGTATCGATACTTTTCAA
1 CATGTATCGATACTTATAAA
*
1388372 GATGTATCGATAC-TATAAA
1 CATGTATCGATACTTATAAA
1388391 CATGTATCG
1 CATGTATCG
1388400 CTACAATGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACTTATAAA
Found at i:1390006 original size:22 final size:24
Alignment explanation
Indices: 1389976--1390019 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1389966 CCTCTCAATC
*
1389976 TCTTCAAGA-ATTATACCCCAAAT
1 TCTTCAAGAGATTATAACCCAAAT
1389999 TCTT-AAGAGATTATAACCCAA
1 TCTTCAAGAGATTATAACCCAA
1390020 GGTTGAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (24 bp):
TCTTCAAGAGATTATAACCCAAAT
Found at i:1390526 original size:19 final size:20
Alignment explanation
Indices: 1390502--1390551 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1390492 CAATTCACTG
1390502 TGTATCGATACCAAG-AACA
1 TGTATCGATACCAAGCAACA
* *
1390521 TGTATCGATACTAAGCAATA
1 TGTATCGATACCAAGCAACA
*
1390541 TGTATCAATAC
1 TGTATCGATAC
1390552 ATCTGGGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (20 bp):
TGTATCGATACCAAGCAACA
Found at i:1390689 original size:22 final size:21
Alignment explanation
Indices: 1390648--1390688 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1390638 GATACTTTGG
*
1390648 ATTATTTTTTTACTTGAAAAC
1 ATTATTTTTATACTTGAAAAC
*
1390669 ATTATTTTTATGCTTGAAAA
1 ATTATTTTTATACTTGAAAA
1390689 ATATTTATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (21 bp):
ATTATTTTTATACTTGAAAAC
Found at i:1392560 original size:13 final size:13
Alignment explanation
Indices: 1392542--1392566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1392532 AGATTGCACA
1392542 GTATCGATACATT
1 GTATCGATACATT
1392555 GTATCGATACAT
1 GTATCGATACAT
1392567 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1392598 original size:21 final size:20
Alignment explanation
Indices: 1392554--1392606 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1392544 ATCGATACAT
**
1392554 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
1392574 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
*
1392595 TGTATCAATACA
1 TGTATCGATACA
1392607 GGTCATTGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:1392683 original size:20 final size:20
Alignment explanation
Indices: 1392640--1392691 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1392630 TAGCCAAATT
*
1392640 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
1392659 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
1392679 TGTATCGATACAT
1 TGTATCGATACAT
1392692 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:1396605 original size:15 final size:15
Alignment explanation
Indices: 1396585--1396616 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1396575 ATAAAAGTGT
*
1396585 TCAAAATGAGGAAGC
1 TCAAAATGAAGAAGC
1396600 TCAAAATGAAGAAGC
1 TCAAAATGAAGAAGC
1396615 TC
1 TC
1396617 CAAACGAAAT
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:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (15 bp):
TCAAAATGAAGAAGC
Found at i:1401290 original size:32 final size:33
Alignment explanation
Indices: 1401249--1401310 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
1401239 TAGCCAAACT
**
1401249 TGTATCGATACACAAAGTA-TGTATCGATATAA
1 TGTATCGATACACAAAAAATTGTATCGATATAA
1401281 TGTATCGATACACAAAAAATTGTATCGATA
1 TGTATCGATACACAAAAAATTGTATCGATA
1401311 CATTGGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATATAA
Found at i:1401432 original size:13 final size:13
Alignment explanation
Indices: 1401414--1401439 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1401404 TACATAAAGT
1401414 ATGTATCGATACA
1 ATGTATCGATACA
1401427 ATGTATCGATACA
1 ATGTATCGATACA
1401440 CAAAAAATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1401437 original size:32 final size:33
Alignment explanation
Indices: 1401396--1401459 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1401386 TAGCCAAACT
* **
1401396 TGTATCGATACATAAAGTAT-GTATCGATACAA
1 TGTATCGATACACAAAAAATCGTATCGATACAA
1401428 TGTATCGATACACAAAAAATCGTATCGATACA
1 TGTATCGATACACAAAAAATCGTATCGATACA
1401460 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATCGTATCGATACAA
Found at i:1401471 original size:147 final size:147
Alignment explanation
Indices: 1401204--1401511 Score: 571
Period size: 147 Copynumber: 2.1 Consensus size: 147
1401194 CATGAAAAAG
1401204 ATGTATCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACAAAGTAT
1 ATGTATCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACAAAGTAT
* * *
1401269 GTATCGATATAATGTATCGATACACAAAAAATTGTATCGATACATTGGCTTGTAACGGCTAGAAA
66 GTATCGATACAATGTATCGATACACAAAAAATCGTATCGATACATTGGCTTGTAACGGCGAGAAA
*
1401334 CGGCTATATTTTCAAAT
131 CGGCTACATTTTCAAAT
*
1401351 ATGTATCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACATAAAGTAT
1 ATGTATCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACAAAGTAT
1401416 GTATCGATACAATGTATCGATACACAAAAAATCGTATCGATACATTGGCTTGTAACGGCGAGAAA
66 GTATCGATACAATGTATCGATACACAAAAAATCGTATCGATACATTGGCTTGTAACGGCGAGAAA
1401481 CGGCTACATTTTCAAAT
131 CGGCTACATTTTCAAAT
1401498 ATGTATCGATACAT
1 ATGTATCGATACAT
1401512 CAAAAATTGT
Statistics
Matches: 156, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 156 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (147 bp):
ATGTATCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACAAAGTAT
GTATCGATACAATGTATCGATACACAAAAAATCGTATCGATACATTGGCTTGTAACGGCGAGAAA
CGGCTACATTTTCAAAT
Found at i:1404302 original size:13 final size:13
Alignment explanation
Indices: 1404284--1404308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1404274 AACATTCCTT
1404284 GTATCGATACATC
1 GTATCGATACATC
1404297 GTATCGATACAT
1 GTATCGATACAT
1404309 TGGGTACTAT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
GTATCGATACATC
Found at i:1406017 original size:21 final size:21
Alignment explanation
Indices: 1405993--1406041 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1405983 GTAATTTGAA
1405993 TTTATGAAATGCAATGTTTGT
1 TTTATGAAATGCAATGTTTGT
1406014 TTTATGAAATGCAATGTTTGT
1 TTTATGAAATGCAATGTTTGT
1406035 TTTATGA
1 TTTATGA
1406042 TTGTGTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (21 bp):
TTTATGAAATGCAATGTTTGT
Found at i:1406188 original size:26 final size:28
Alignment explanation
Indices: 1406152--1406208 Score: 100
Period size: 26 Copynumber: 2.1 Consensus size: 28
1406142 GAAAATAAAT
1406152 AAATTTTTTAATA-TTGACAAAGGGG-G
1 AAATTTTTTAATATTTGACAAAGGGGAG
1406178 AAATTTTTTAATATTTGACAAAGGGGAG
1 AAATTTTTTAATATTTGACAAAGGGGAG
1406206 AAA
1 AAA
1406209 AGCTTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 13 0.45
27 12 0.41
28 4 0.14
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (28 bp):
AAATTTTTTAATATTTGACAAAGGGGAG
Found at i:1406862 original size:19 final size:20
Alignment explanation
Indices: 1406838--1406890 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1406828 ATCGATATAA
*
1406838 TGTATCGATACATGCTC-AT
1 TGTATCGATACATGCACAAT
*
1406857 TGTATCGATACATGGACAAT
1 TGTATCGATACATGCACAAT
1406877 TGTATCGATACATG
1 TGTATCGATACATG
1406891 AGATTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGCACAAT
Found at i:1406961 original size:33 final size:33
Alignment explanation
Indices: 1406919--1406987 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1406909 CTACCATTGT
* *
1406919 TTGTATCGATACATGGT-ACAATGTATTGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
1406952 TTGTATCGATACATGATGAAATGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
1406985 TTG
1 TTG
1406988 CTTGTAACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:1407043 original size:72 final size:72
Alignment explanation
Indices: 1406953--1407129 Score: 300
Period size: 72 Copynumber: 2.5 Consensus size: 72
1406943 ATTGATACAT
1406953 TGTATCGATACATGATGAAATGTATCGATACATTGCTTGTAACGACTATAAACAGCTATAATTTC
1 TGTATCGATACATGATGAAATGTATCGATACATTGCTTGTAACGACTATAAACAGCTATAATTTC
1407018 AAATCAA
66 AAATCAA
* * *
1407025 TGTATCAACACATGATGAAATGTATCGATACATTGCTTGTAACGGCTATAAACAGCTATAATTTC
1 TGTATCGATACATGATGAAATGTATCGATACATTGCTTGTAACGACTATAAACAGCTATAATTTC
1407090 AAATCAA
66 AAATCAA
* * *
1407097 TGTATCGATACATTATGAATTGTATCCATACAT
1 TGTATCGATACATGATGAAATGTATCGATACAT
1407130 GGCTATGGGA
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 97 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (72 bp):
TGTATCGATACATGATGAAATGTATCGATACATTGCTTGTAACGACTATAAACAGCTATAATTTC
AAATCAA
Found at i:1416266 original size:49 final size:49
Alignment explanation
Indices: 1416194--1416828 Score: 690
Period size: 49 Copynumber: 12.8 Consensus size: 49
1416184 ATGAGAAGAA
* * *
1416194 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTAAAGATGAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
*** *
1416243 TGCCAATGTGCTGATTTTTGGCCAGCGACATTGGTCTTAAAGATGAAGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGAT---GAAGG
* * * * * * *
1416295 TGCCAATATGCTAATTCAAGGCCAGCAATACTGGTCTTAAAGATAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
* * * *
1416344 TGCCAATGTGCTGAGTCAAGGCCAACGACATTGGACTTAAAGAAGAA--
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
* * * *
1416391 TGCCAATGTGTTGATT-AAGGCCAACAACATTGGGTTTTAAAGATGACAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGG-CTTAAAGATG---AAGG
* * * * *
1416443 CGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
* * *
1416492 TGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGACTTAACGATGATAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAA--A-GATGAAGG
* * * *
1416544 CGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
*
1416593 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
* **
1416642 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC-T---GACAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
* * * *
1416687 CGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
*
1416736 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATG---AAGG
* * *
1416788 CGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAA
1416829 AGAAGATGCC
Statistics
Matches: 492, Mismatches: 74, Indels: 37
0.82 0.12 0.06
Matches are distributed among these distances:
45 39 0.08
46 17 0.03
47 22 0.04
48 1 0.00
49 252 0.51
50 3 0.01
51 1 0.00
52 144 0.29
53 13 0.03
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (49 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAAGG
Found at i:1416335 original size:101 final size:100
Alignment explanation
Indices: 1416144--1416828 Score: 718
Period size: 101 Copynumber: 6.9 Consensus size: 100
1416134 AAAAGGCTGT
** ** * * *
1416144 CAATGTGCTGATTCACTGTTAGCGACATTTAGACTTGAAGATGAGAAGAATGCCAATGTGCTGAT
1 CAATGTGCTGATTCAAGGCCAGCGACA-TTGGACTTAAAGATGAGAAG-GTGCCAATGTGCTGAT
* ** *
1416209 TCAAGGCCAACGACATTGGGTTTAAAGATGAAGATGC
64 TCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
*** * * *
1416246 CAATGTGCTGATTTTTGGCCAGCGACATTGGTCTTAAAGATGAAGAAGGTGCCAATATGCTAATT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-AGAAGGTGCCAATGTGCTGATT
* * * * *
1416311 CAAGGCCAGCAATACTGGTCTTAAAGATAAAGGTGC
65 CAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * *
1416347 CAATGTGCTGAGTCAAGGCCAACGACATTGGACTTAAAGA--AGAA--TGCCAATGTGTTGATT-
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTGCCAATGTGCTGATTC
* * ** *
1416407 AAGGCCAACAACATTGGGTTTTAAAGATGACAAAGGCGC
66 AAGGCCAGCGACATT-GGACTTAAAGATG---AAGGTGC
* * * *
1416446 CAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGAT--GAAGGTGCCAATGTGCTGAGTC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTGCCAATGTGCTGATTC
* *
1416509 AAGGCCAGCGACATTGGACTTAACGATGATAAAGGCGC
66 AAGGCCAGCGACATTGGACTTAA--A-GATGAAGGTGC
* *
1416547 CAATATGCTGATTCAAGGCCAGCGATATTAGG-CTTAAAGAT--GAAGGTGCCAATGTGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGAGAAGGTGCCAATGTGCTGATT
1416609 CAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
65 CAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * *
1416645 CAATGTGCTGATTCAAGGCCAGCGACATTGGAC-T---GA-CA-AAGGCGCCAATATGCTGATTC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTGCCAATGTGCTGATTC
*
1416704 AAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
66 AAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * *
1416739 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGGTGCCAATGTGCTGATT
* *
1416804 CAAGGCCAGCGATATTGGGCTTAAA
65 CAAGGCCAGCGACATTGGACTTAAA
1416829 AGAAGATGCC
Statistics
Matches: 501, Mismatches: 59, Indels: 47
0.83 0.10 0.08
Matches are distributed among these distances:
94 87 0.17
95 13 0.03
96 24 0.05
97 3 0.01
98 43 0.09
99 46 0.09
101 241 0.48
102 40 0.08
103 1 0.00
104 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (100 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTGCCAATGTGCTGATTC
AAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
Found at i:1416624 original size:249 final size:241
Alignment explanation
Indices: 1416195--1416828 Score: 894
Period size: 249 Copynumber: 2.6 Consensus size: 241
1416185 TGAGAAGAAT
* * * ** * *
1416195 GCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTAAAGATGAAGATGCCAATGTGCTGATTT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTC
** * * *
1416260 TTGGCCAGCGACATTGGTCTTAAAGATGAAGAAGGTGCCAATATGCTAATTCAAGGCCAGCAATA
66 AAGGCCAGCGACATTGGTCTTAAAGATGAA-AAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
*
1416325 CTGGTCTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAACGACATTGGACTTAAAGAAGA
130 TTGG-CTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAACGACATTGGACTTAAAGAAGA
*
1416390 A-TGCCAATGTGTTGATT-AAGGCCAACAACATTGGGTTTTAAAGATGACAAAGGC
194 AGTGCCAATGTGCTGATTCAAGGCCAACAACATT-GG------A-ATGACAAAGGC
* *
1416444 GCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGAAGGTGCCAATGTGCTGAGTC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTC
* *
1416509 AAGGCCAGCGACATTGGACTTAACGATGATAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
66 AAGGCCAGCGACATTGGTCTTAAAGATGA-AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
* * * *
1416574 TTAGGCTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
130 TT-GGCTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAACGACATTGGACTTAAAGAAGA
* * *
1416639 AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTGACAAAGGC
194 A-GTGCCAATGTGCTGATTCAAGGCCAACAACATTGGAATGACAAAGGC
1416688 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTC
1416753 AAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
66 AAGGCCAGCGACATTGGTCTTAAAGATGA-AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
1416818 TTGGGCTTAAA
130 TT-GGCTTAAA
1416829 AGAAGATGCC
Statistics
Matches: 349, Mismatches: 31, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
244 145 0.42
245 1 0.00
249 170 0.49
250 3 0.01
251 17 0.05
252 13 0.04
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (241 bp):
GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTC
AAGGCCAGCGACATTGGTCTTAAAGATGAAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATAT
TGGCTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAACGACATTGGACTTAAAGAAGAAG
TGCCAATGTGCTGATTCAAGGCCAACAACATTGGAATGACAAAGGC
Done.